From fcc3c08888946d19693277b5061fa073b4f94b6d Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 10:26:36 -0800
Subject: [PATCH 01/15] refactor: restructure project into src-layout package
 'atc138'

Establishes the foundational src-layout for the Python package, renaming the primary module to `atc138`.

Changes:
- Created `src/atc138` directory structure.
- Moved and renamed core scripts:
  - `main_PBEE_recovery.py` -> `src/atc138/engine.py`
  - `driver_PBEE_recovery.py` -> `src/atc138/driver.py`
  - `fn_red_tag.py` -> `src/atc138/red_tag.py`
- Moved data directories:
  - `static_tables/` -> `src/atc138/data/`
- Moved submodules to package root:
  - `functionality/`
  - `impedance/`
  - `preprocessing/`
  - `repair_schedule/`
- Added `src/atc138/__init__.py`.
---
 src/atc138/__init__.py                                            | 0
 {static_tables => src/atc138/data}/README.md                      | 0
 {static_tables => src/atc138/data}/component_attributes.csv       | 0
 .../atc138/data}/damage_state_attribute_mapping.csv               | 0
 {static_tables => src/atc138/data}/impeding_factors.csv           | 0
 {static_tables => src/atc138/data}/subsystems.csv                 | 0
 {static_tables => src/atc138/data}/systems.csv                    | 0
 {static_tables => src/atc138/data}/temp_repair_class.csv          | 0
 .../atc138/data}/tenant_function_requirements.csv                 | 0
 driver_PBEE_recovery.py => src/atc138/driver.py                   | 0
 main_PBEE_recovery.py => src/atc138/engine.py                     | 0
 .../atc138/functionality}/fn_calculate_functionality.py           | 0
 .../atc138/functionality}/fn_calculate_reoccupancy.py             | 0
 .../atc138/functionality}/fn_check_habitability.py                | 0
 .../atc138/functionality}/main_functionality_function.py          | 0
 .../atc138/functionality}/other_functionality_functions.py        | 0
 {impedance => src/atc138/impedance}/main_impedance_function.py    | 0
 {impedance => src/atc138/impedance}/other_impedance_functions.py  | 0
 {preprocessing => src/atc138/preprocessing}/main_preprocessing.py | 0
 {preprocessing => src/atc138/preprocessing}/preprocessing_fns.py  | 0
 fn_red_tag.py => src/atc138/red_tag.py                            | 0
 .../atc138/repair_schedule}/main_repair_schedule.py               | 0
 .../atc138/repair_schedule}/other_repair_schedule_functions.py    | 0
 23 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 src/atc138/__init__.py
 rename {static_tables => src/atc138/data}/README.md (100%)
 rename {static_tables => src/atc138/data}/component_attributes.csv (100%)
 rename {static_tables => src/atc138/data}/damage_state_attribute_mapping.csv (100%)
 rename {static_tables => src/atc138/data}/impeding_factors.csv (100%)
 rename {static_tables => src/atc138/data}/subsystems.csv (100%)
 rename {static_tables => src/atc138/data}/systems.csv (100%)
 rename {static_tables => src/atc138/data}/temp_repair_class.csv (100%)
 rename {static_tables => src/atc138/data}/tenant_function_requirements.csv (100%)
 rename driver_PBEE_recovery.py => src/atc138/driver.py (100%)
 rename main_PBEE_recovery.py => src/atc138/engine.py (100%)
 rename {functionality => src/atc138/functionality}/fn_calculate_functionality.py (100%)
 rename {functionality => src/atc138/functionality}/fn_calculate_reoccupancy.py (100%)
 rename {functionality => src/atc138/functionality}/fn_check_habitability.py (100%)
 rename {functionality => src/atc138/functionality}/main_functionality_function.py (100%)
 rename {functionality => src/atc138/functionality}/other_functionality_functions.py (100%)
 rename {impedance => src/atc138/impedance}/main_impedance_function.py (100%)
 rename {impedance => src/atc138/impedance}/other_impedance_functions.py (100%)
 rename {preprocessing => src/atc138/preprocessing}/main_preprocessing.py (100%)
 rename {preprocessing => src/atc138/preprocessing}/preprocessing_fns.py (100%)
 rename fn_red_tag.py => src/atc138/red_tag.py (100%)
 rename {repair_schedule => src/atc138/repair_schedule}/main_repair_schedule.py (100%)
 rename {repair_schedule => src/atc138/repair_schedule}/other_repair_schedule_functions.py (100%)

diff --git a/src/atc138/__init__.py b/src/atc138/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/static_tables/README.md b/src/atc138/data/README.md
similarity index 100%
rename from static_tables/README.md
rename to src/atc138/data/README.md
diff --git a/static_tables/component_attributes.csv b/src/atc138/data/component_attributes.csv
similarity index 100%
rename from static_tables/component_attributes.csv
rename to src/atc138/data/component_attributes.csv
diff --git a/static_tables/damage_state_attribute_mapping.csv b/src/atc138/data/damage_state_attribute_mapping.csv
similarity index 100%
rename from static_tables/damage_state_attribute_mapping.csv
rename to src/atc138/data/damage_state_attribute_mapping.csv
diff --git a/static_tables/impeding_factors.csv b/src/atc138/data/impeding_factors.csv
similarity index 100%
rename from static_tables/impeding_factors.csv
rename to src/atc138/data/impeding_factors.csv
diff --git a/static_tables/subsystems.csv b/src/atc138/data/subsystems.csv
similarity index 100%
rename from static_tables/subsystems.csv
rename to src/atc138/data/subsystems.csv
diff --git a/static_tables/systems.csv b/src/atc138/data/systems.csv
similarity index 100%
rename from static_tables/systems.csv
rename to src/atc138/data/systems.csv
diff --git a/static_tables/temp_repair_class.csv b/src/atc138/data/temp_repair_class.csv
similarity index 100%
rename from static_tables/temp_repair_class.csv
rename to src/atc138/data/temp_repair_class.csv
diff --git a/static_tables/tenant_function_requirements.csv b/src/atc138/data/tenant_function_requirements.csv
similarity index 100%
rename from static_tables/tenant_function_requirements.csv
rename to src/atc138/data/tenant_function_requirements.csv
diff --git a/driver_PBEE_recovery.py b/src/atc138/driver.py
similarity index 100%
rename from driver_PBEE_recovery.py
rename to src/atc138/driver.py
diff --git a/main_PBEE_recovery.py b/src/atc138/engine.py
similarity index 100%
rename from main_PBEE_recovery.py
rename to src/atc138/engine.py
diff --git a/functionality/fn_calculate_functionality.py b/src/atc138/functionality/fn_calculate_functionality.py
similarity index 100%
rename from functionality/fn_calculate_functionality.py
rename to src/atc138/functionality/fn_calculate_functionality.py
diff --git a/functionality/fn_calculate_reoccupancy.py b/src/atc138/functionality/fn_calculate_reoccupancy.py
similarity index 100%
rename from functionality/fn_calculate_reoccupancy.py
rename to src/atc138/functionality/fn_calculate_reoccupancy.py
diff --git a/functionality/fn_check_habitability.py b/src/atc138/functionality/fn_check_habitability.py
similarity index 100%
rename from functionality/fn_check_habitability.py
rename to src/atc138/functionality/fn_check_habitability.py
diff --git a/functionality/main_functionality_function.py b/src/atc138/functionality/main_functionality_function.py
similarity index 100%
rename from functionality/main_functionality_function.py
rename to src/atc138/functionality/main_functionality_function.py
diff --git a/functionality/other_functionality_functions.py b/src/atc138/functionality/other_functionality_functions.py
similarity index 100%
rename from functionality/other_functionality_functions.py
rename to src/atc138/functionality/other_functionality_functions.py
diff --git a/impedance/main_impedance_function.py b/src/atc138/impedance/main_impedance_function.py
similarity index 100%
rename from impedance/main_impedance_function.py
rename to src/atc138/impedance/main_impedance_function.py
diff --git a/impedance/other_impedance_functions.py b/src/atc138/impedance/other_impedance_functions.py
similarity index 100%
rename from impedance/other_impedance_functions.py
rename to src/atc138/impedance/other_impedance_functions.py
diff --git a/preprocessing/main_preprocessing.py b/src/atc138/preprocessing/main_preprocessing.py
similarity index 100%
rename from preprocessing/main_preprocessing.py
rename to src/atc138/preprocessing/main_preprocessing.py
diff --git a/preprocessing/preprocessing_fns.py b/src/atc138/preprocessing/preprocessing_fns.py
similarity index 100%
rename from preprocessing/preprocessing_fns.py
rename to src/atc138/preprocessing/preprocessing_fns.py
diff --git a/fn_red_tag.py b/src/atc138/red_tag.py
similarity index 100%
rename from fn_red_tag.py
rename to src/atc138/red_tag.py
diff --git a/repair_schedule/main_repair_schedule.py b/src/atc138/repair_schedule/main_repair_schedule.py
similarity index 100%
rename from repair_schedule/main_repair_schedule.py
rename to src/atc138/repair_schedule/main_repair_schedule.py
diff --git a/repair_schedule/other_repair_schedule_functions.py b/src/atc138/repair_schedule/other_repair_schedule_functions.py
similarity index 100%
rename from repair_schedule/other_repair_schedule_functions.py
rename to src/atc138/repair_schedule/other_repair_schedule_functions.py

From 5c1033a67aaabc17e5ca7400b1755b8b5fce6dd8 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 10:32:49 -0800
Subject: [PATCH 02/15] build: add pyproject.toml and configure package

Adds `pyproject.toml` to define the build system and dependencies for the `atc138` package.

Changes:
- Added `pyproject.toml` with `setuptools` build backend.
- Defined package metadata (name, version, authors).
- Listed runtime dependencies: `numpy`, `pandas`, `scipy`, `matplotlib`, `seaborn`.
- Verified editable installation.
---
 .gitignore     |  5 +++--
 pyproject.toml | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 2 deletions(-)
 create mode 100644 pyproject.toml

diff --git a/.gitignore b/.gitignore
index 3a17345..7132d41 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,8 +12,9 @@
 .coverage
 
 # Python egg metadata, regenerated from source files by setuptools
-/*.egg-info
-/*.egg
+*.egg-info/
+.eggs/
+*.egg
 
 # Temporary jupyter files
 /.ipynb_checkpoints/
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..c5e8608
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "atc138"
+version = "0.1.0"
+description = "Functional Recovery Assessment (ATC-138)"
+readme = "README.md"
+requires-python = ">=3.9"
+license = {file = "LICENSE"}
+authors = [
+  {name = "Dustin Cook", email = "dustin.cook@nist.gov"},
+]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: BSD License",
+  "Operating System :: OS Independent",
+]
+dependencies = [
+  "numpy",
+  "pandas",
+  "scipy",
+  "matplotlib",
+  "seaborn",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/NHERI-SimCenter/Functional-Recovery-Python"
+"Bug Tracker" = "https://github.com/NHERI-SimCenter/Functional-Recovery-Python/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]

From e4a1ce7f7e8e0199847e70e735a8248b18b636dc Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 10:59:08 -0800
Subject: [PATCH 03/15] feat: implement CLI and robust path handling

Adds a command-line interface `atc138` and refactors I/O to be robust and independent of CWD.

Changes:
- Added `src/atc138/cli.py` with `atc138` entry point accepting explicit `input_dir` and `output_dir`.
- Registered `atc138` script in `pyproject.toml`.
- Refactored `src/atc138/driver.py`:
  - `run_analysis` now accepts `input_dir` and `output_dir` instead of deriving paths.
  - Removed internal dependency on relative directory structures (`inputs/example_inputs`).
  - Updated path resolution for static data (`src/atc138/data`).
- Refactored `src/atc138/engine.py` to use relative imports.
- Added `__init__.py` to submodules to make them proper packages.
---
 pyproject.toml                         |  3 ++
 src/atc138/cli.py                      | 26 ++++++++++++++
 src/atc138/driver.py                   | 48 ++++++++++++--------------
 src/atc138/engine.py                   | 10 +++---
 src/atc138/functionality/__init__.py   |  0
 src/atc138/impedance/__init__.py       |  0
 src/atc138/preprocessing/__init__.py   |  0
 src/atc138/repair_schedule/__init__.py |  0
 8 files changed, 56 insertions(+), 31 deletions(-)
 create mode 100644 src/atc138/cli.py
 create mode 100644 src/atc138/functionality/__init__.py
 create mode 100644 src/atc138/impedance/__init__.py
 create mode 100644 src/atc138/preprocessing/__init__.py
 create mode 100644 src/atc138/repair_schedule/__init__.py

diff --git a/pyproject.toml b/pyproject.toml
index c5e8608..0fdd6fe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,9 @@ dependencies = [
   "seaborn",
 ]
 
+[project.scripts]
+atc138 = "atc138.cli:main"
+
 [project.urls]
 "Homepage" = "https://github.com/NHERI-SimCenter/Functional-Recovery-Python"
 "Bug Tracker" = "https://github.com/NHERI-SimCenter/Functional-Recovery-Python/issues"
diff --git a/src/atc138/cli.py b/src/atc138/cli.py
new file mode 100644
index 0000000..5934609
--- /dev/null
+++ b/src/atc138/cli.py
@@ -0,0 +1,26 @@
+import argparse
+import sys
+import os
+from .driver import run_analysis
+
+def main():
+    parser = argparse.ArgumentParser(description="Run ATC-138 Functional Recovery Assessment")
+    parser.add_argument("input_dir", help="Path to the directory containing input files (e.g., simulated_inputs.json)")
+    parser.add_argument("output_dir", help="Path to the directory where outputs will be saved")
+    parser.add_argument("--seed", type=int, help="Random seed for reproducibility", default=None)
+
+    args = parser.parse_args()
+
+    # Validate inputs
+    if not os.path.isdir(args.input_dir):
+        print(f"Error: Input directory '{args.input_dir}' does not exist.", file=sys.stderr)
+        sys.exit(1)
+
+    try:
+        run_analysis(args.input_dir, args.output_dir, seed=args.seed)
+    except Exception as e:
+        print(f"Error running analysis: {e}", file=sys.stderr)
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()
diff --git a/src/atc138/driver.py b/src/atc138/driver.py
index 62b9f1d..c29a8cc 100644
--- a/src/atc138/driver.py
+++ b/src/atc138/driver.py
@@ -1,4 +1,4 @@
-def run_analysis(model_name, seed=None):
+def run_analysis(input_dir, output_dir, seed=None):
 
     '''This script facilitates the performance based functional recovery and
     reoccupancy assessment of a single building for a single intensity level
@@ -15,9 +15,11 @@ def run_analysis(model_name, seed=None):
     
     Parameters
     ----------
-    model_name: string
-        Name of the model. Inputs are expected to be in a directory with this 
-        name. Outputs will save to a directory with this name
+    input_dir: string
+        Path to the directory containing the input files (simulated_inputs.json).
+    
+    output_dir: string
+        Path to the directory where the output file (recovery_outputs.json) will be saved.
     
     seed: int
         Random seed to be passed to the Numpy random engine. Default behavior
@@ -42,11 +44,11 @@ def run_analysis(model_name, seed=None):
     from scipy.stats import truncnorm
     
     ## 2. Define User Inputs
-    model_dir = 'inputs/example_inputs/'+model_name # Directory where the simulated inputs are located
-    outputs_dir = 'outputs/'+model_name # Directory where the assessment outputs are saved
+    # Input/Output directories are passed as arguments
     
     ## 3. Load FEMA P-58 performance model data and simulated damage and loss
-    f = open(os.path.join(os.path.dirname(__file__),model_dir, 'simulated_inputs.json'))
+    # Use provided input_dir
+    f = open(os.path.join(input_dir, 'simulated_inputs.json'))
     simulated_inputs = json.load(f)
     
     building_model = simulated_inputs['building_model']
@@ -79,13 +81,15 @@ def run_analysis(model_name, seed=None):
     building_model['comps']['story'] = bldg_comps_story
     
     ## 4. Load required static data
-    systems = pd.read_csv(os.path.join(os.path.dirname(__file__), 'static_tables', 'systems.csv'))
-    subsystems = pd.read_csv(os.path.join(os.path.dirname(__file__), 'static_tables', 'subsystems.csv'))
-    impeding_factor_medians = pd.read_csv(os.path.join(os.path.dirname(__file__), 'static_tables', 'impeding_factors.csv'))
-    tmp_repair_class = pd.read_csv(os.path.join(os.path.dirname(__file__), 'static_tables', 'temp_repair_class.csv'))
+    # Static data is bundled with the package, so use __file__
+    pkg_dir = os.path.dirname(__file__)
+    systems = pd.read_csv(os.path.join(pkg_dir, 'data', 'systems.csv'))
+    subsystems = pd.read_csv(os.path.join(pkg_dir, 'data', 'subsystems.csv'))
+    impeding_factor_medians = pd.read_csv(os.path.join(pkg_dir, 'data', 'impeding_factors.csv'))
+    tmp_repair_class = pd.read_csv(os.path.join(pkg_dir, 'data', 'temp_repair_class.csv'))
     
     ## 5. Run Recovery Method
-    from main_PBEE_recovery import main_PBEE_recovery
+    from .engine import main_PBEE_recovery
 
     # set a seed
     # this seed propagates through the entire subfunctions
@@ -107,11 +111,9 @@ def run_analysis(model_name, seed=None):
                                                             functionality_options)
            
     # 6. Save Outputs
-    # # Define Output path
-    if os.path.exists(os.path.join(os.path.dirname(__file__),'outputs')) == False:
-        os.mkdir(os.path.join(os.path.dirname(__file__),'outputs'))
-    if os.path.exists(os.path.join(os.path.dirname(__file__),'outputs', model_name)) == False:
-        os.mkdir(os.path.join(os.path.dirname(__file__),'outputs', model_name))
+    # Ensure output directory exists
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
     
     # Covert arrays to list for writing to json file   
     fnc_keys_1 = list(functionality.keys())
@@ -147,18 +149,12 @@ def run_analysis(model_name, seed=None):
     
     output_json_object = json.dumps(functionality)
     
-    with open(os.path.join(os.path.dirname(__file__),outputs_dir, "recovery_outputs.json"), "w") as outfile:
+    with open(os.path.join(output_dir, "recovery_outputs.json"), "w") as outfile:
         outfile.write(output_json_object)
     
     end_time = time.time()
     
-    print('Recovery assessment of model ' + model_name + ' complete')
+    # print('Recovery assessment of model ' + model_name + ' complete') # model_name no longer available
+    print('Recovery assessment complete')
     print('time to run '+str(round(end_time - start_time,2))+'s')
-        
-    
-if __name__ == '__main__':
-
-    model_name = 'ICSB'
-
-    run_analysis(model_name)
 
diff --git a/src/atc138/engine.py b/src/atc138/engine.py
index dce3288..d2b455b 100644
--- a/src/atc138/engine.py
+++ b/src/atc138/engine.py
@@ -57,11 +57,11 @@ def main_PBEE_recovery(damage, damage_consequences, building_model,
     
     ## Import Packages
     import numpy as np
-    from preprocessing import main_preprocessing
-    from fn_red_tag import fn_red_tag
-    from impedance import main_impedance_function
-    from repair_schedule import main_repair_schedule
-    from functionality import main_functionality_function
+    from .preprocessing import main_preprocessing
+    from .red_tag import fn_red_tag
+    from .impedance import main_impedance_function
+    from .repair_schedule import main_repair_schedule
+    from .functionality import main_functionality_function
     
     ## Combine compoment attributes into recovery filters to expidite recovery assessment
     damage, tmp_repair_class, damage_consequences = main_preprocessing.main_preprocessing(damage['comp_ds_table'], 
diff --git a/src/atc138/functionality/__init__.py b/src/atc138/functionality/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/atc138/impedance/__init__.py b/src/atc138/impedance/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/atc138/preprocessing/__init__.py b/src/atc138/preprocessing/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/atc138/repair_schedule/__init__.py b/src/atc138/repair_schedule/__init__.py
new file mode 100644
index 0000000..e69de29

From 5c549a5f771e3bd9c5e6cfeb029c6b24d09a2faa Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:26:23 -0800
Subject: [PATCH 04/15] refactor(inputs): migrate input generation and
 restructure examples

- Moved input generation logic to `src/atc138/input_builder.py`. This is the implementation in the old `inputs/Inputs2Copy/build_input.py` with minimal adjustments to make it compliant with package structure.
- Moved `inputs/example_inputs` to `examples/` and removed `inputs/` directory.
- Added `src/atc138/data/default_inputs.json` for centralized configuration. This file is equivalent to the output generated by the old `optional_inputs.py`.
- Refactored `driver.py` to support auto-generation of inputs with the new input_builder module. If the input folder already has a `simulated_inputs.json` file, it will be used. Otherwise, it will be generated. Another minor update in `driver.py` is enhancing how story indices in some o the inputs are converted to int from strings. The updated version can handle both int and string representations of story index inputs.
- Refactored submodules (`functionality`, `impedance`, `repair_schedule`) to use relative imports.
- Updated `.gitignore` to ignore output directories.
---
 .gitignore                                    |   8 +-
 .../ICSB/building_model.json                  |   0
 .../ICSB/comp_ds_list.csv                     |   0
 .../ICSB/comp_population.csv                  |   0
 .../ICSB/damage_consequences.json             |   0
 .../ICSB/simulated_damage.json                |   0
 .../ICSB/tenant_unit_list.csv                 |   0
 .../RCSW_1story/building_model.json           |   0
 .../RCSW_1story/comp_ds_list.csv              |   0
 .../RCSW_1story/comp_population.csv           |   0
 .../RCSW_1story/damage_consequences.json      |   0
 .../RCSW_1story/simulated_damage.json         |   0
 .../RCSW_1story/tenant_unit_list.csv          |   0
 .../haseltonRCMF_12story/building_model.json  |   0
 .../haseltonRCMF_12story/comp_ds_list.csv     |   0
 .../haseltonRCMF_12story/comp_population.csv  |   0
 .../damage_consequences.json                  |   0
 .../simulated_damage.json                     |   0
 .../haseltonRCMF_12story/tenant_unit_list.csv |   0
 .../haseltonRCMF_4story/building_model.json   |   0
 .../haseltonRCMF_4story/comp_ds_list.csv      |   0
 .../haseltonRCMF_4story/comp_population.csv   |   0
 .../damage_consequences.json                  |   0
 .../haseltonRCMF_4story/simulated_damage.json |   0
 .../haseltonRCMF_4story/tenant_unit_list.csv  |   0
 inputs/Inputs2Copy/build_input.py             | 399 ------------------
 inputs/Inputs2Copy/optional_inputs.py         | 105 -----
 src/atc138/data/default_inputs.json           |  81 ++++
 src/atc138/driver.py                          |  40 +-
 .../fn_calculate_functionality.py             |   2 +-
 .../functionality/fn_calculate_reoccupancy.py |   2 +-
 .../functionality/fn_check_habitability.py    |   2 +-
 .../main_functionality_function.py            |   7 +-
 .../other_functionality_functions.py          |   4 +-
 .../impedance/main_impedance_function.py      |   3 +-
 src/atc138/input_builder.py                   | 394 +++++++++++++++++
 .../preprocessing/main_preprocessing.py       |   4 +-
 .../repair_schedule/main_repair_schedule.py   |   2 +-
 38 files changed, 529 insertions(+), 524 deletions(-)
 rename {inputs/example_inputs => examples}/ICSB/building_model.json (100%)
 rename {inputs/example_inputs => examples}/ICSB/comp_ds_list.csv (100%)
 rename {inputs/example_inputs => examples}/ICSB/comp_population.csv (100%)
 rename {inputs/example_inputs => examples}/ICSB/damage_consequences.json (100%)
 rename {inputs/example_inputs => examples}/ICSB/simulated_damage.json (100%)
 rename {inputs/example_inputs => examples}/ICSB/tenant_unit_list.csv (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/building_model.json (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/comp_ds_list.csv (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/comp_population.csv (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/damage_consequences.json (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/simulated_damage.json (100%)
 rename {inputs/example_inputs => examples}/RCSW_1story/tenant_unit_list.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/building_model.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/comp_ds_list.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/comp_population.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/damage_consequences.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/simulated_damage.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_12story/tenant_unit_list.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/building_model.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/comp_ds_list.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/comp_population.csv (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/damage_consequences.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/simulated_damage.json (100%)
 rename {inputs/example_inputs => examples}/haseltonRCMF_4story/tenant_unit_list.csv (100%)
 delete mode 100644 inputs/Inputs2Copy/build_input.py
 delete mode 100644 inputs/Inputs2Copy/optional_inputs.py
 create mode 100644 src/atc138/data/default_inputs.json
 create mode 100644 src/atc138/input_builder.py

diff --git a/.gitignore b/.gitignore
index 7132d41..d601d32 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,7 +21,13 @@
 *.ipynb_checkpoints
 
 # Output folder
-/outputs/
+outputs/
+
+# Folder with original Matlab code
+/Matlab_code/
+
+.ai/
+Comparison_scripts/
 
 # All new files coming out of buildInputs
 inputs/example_inputs/*/optional_inputs.json
diff --git a/inputs/example_inputs/ICSB/building_model.json b/examples/ICSB/building_model.json
similarity index 100%
rename from inputs/example_inputs/ICSB/building_model.json
rename to examples/ICSB/building_model.json
diff --git a/inputs/example_inputs/ICSB/comp_ds_list.csv b/examples/ICSB/comp_ds_list.csv
similarity index 100%
rename from inputs/example_inputs/ICSB/comp_ds_list.csv
rename to examples/ICSB/comp_ds_list.csv
diff --git a/inputs/example_inputs/ICSB/comp_population.csv b/examples/ICSB/comp_population.csv
similarity index 100%
rename from inputs/example_inputs/ICSB/comp_population.csv
rename to examples/ICSB/comp_population.csv
diff --git a/inputs/example_inputs/ICSB/damage_consequences.json b/examples/ICSB/damage_consequences.json
similarity index 100%
rename from inputs/example_inputs/ICSB/damage_consequences.json
rename to examples/ICSB/damage_consequences.json
diff --git a/inputs/example_inputs/ICSB/simulated_damage.json b/examples/ICSB/simulated_damage.json
similarity index 100%
rename from inputs/example_inputs/ICSB/simulated_damage.json
rename to examples/ICSB/simulated_damage.json
diff --git a/inputs/example_inputs/ICSB/tenant_unit_list.csv b/examples/ICSB/tenant_unit_list.csv
similarity index 100%
rename from inputs/example_inputs/ICSB/tenant_unit_list.csv
rename to examples/ICSB/tenant_unit_list.csv
diff --git a/inputs/example_inputs/RCSW_1story/building_model.json b/examples/RCSW_1story/building_model.json
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/building_model.json
rename to examples/RCSW_1story/building_model.json
diff --git a/inputs/example_inputs/RCSW_1story/comp_ds_list.csv b/examples/RCSW_1story/comp_ds_list.csv
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/comp_ds_list.csv
rename to examples/RCSW_1story/comp_ds_list.csv
diff --git a/inputs/example_inputs/RCSW_1story/comp_population.csv b/examples/RCSW_1story/comp_population.csv
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/comp_population.csv
rename to examples/RCSW_1story/comp_population.csv
diff --git a/inputs/example_inputs/RCSW_1story/damage_consequences.json b/examples/RCSW_1story/damage_consequences.json
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/damage_consequences.json
rename to examples/RCSW_1story/damage_consequences.json
diff --git a/inputs/example_inputs/RCSW_1story/simulated_damage.json b/examples/RCSW_1story/simulated_damage.json
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/simulated_damage.json
rename to examples/RCSW_1story/simulated_damage.json
diff --git a/inputs/example_inputs/RCSW_1story/tenant_unit_list.csv b/examples/RCSW_1story/tenant_unit_list.csv
similarity index 100%
rename from inputs/example_inputs/RCSW_1story/tenant_unit_list.csv
rename to examples/RCSW_1story/tenant_unit_list.csv
diff --git a/inputs/example_inputs/haseltonRCMF_12story/building_model.json b/examples/haseltonRCMF_12story/building_model.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/building_model.json
rename to examples/haseltonRCMF_12story/building_model.json
diff --git a/inputs/example_inputs/haseltonRCMF_12story/comp_ds_list.csv b/examples/haseltonRCMF_12story/comp_ds_list.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/comp_ds_list.csv
rename to examples/haseltonRCMF_12story/comp_ds_list.csv
diff --git a/inputs/example_inputs/haseltonRCMF_12story/comp_population.csv b/examples/haseltonRCMF_12story/comp_population.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/comp_population.csv
rename to examples/haseltonRCMF_12story/comp_population.csv
diff --git a/inputs/example_inputs/haseltonRCMF_12story/damage_consequences.json b/examples/haseltonRCMF_12story/damage_consequences.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/damage_consequences.json
rename to examples/haseltonRCMF_12story/damage_consequences.json
diff --git a/inputs/example_inputs/haseltonRCMF_12story/simulated_damage.json b/examples/haseltonRCMF_12story/simulated_damage.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/simulated_damage.json
rename to examples/haseltonRCMF_12story/simulated_damage.json
diff --git a/inputs/example_inputs/haseltonRCMF_12story/tenant_unit_list.csv b/examples/haseltonRCMF_12story/tenant_unit_list.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_12story/tenant_unit_list.csv
rename to examples/haseltonRCMF_12story/tenant_unit_list.csv
diff --git a/inputs/example_inputs/haseltonRCMF_4story/building_model.json b/examples/haseltonRCMF_4story/building_model.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/building_model.json
rename to examples/haseltonRCMF_4story/building_model.json
diff --git a/inputs/example_inputs/haseltonRCMF_4story/comp_ds_list.csv b/examples/haseltonRCMF_4story/comp_ds_list.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/comp_ds_list.csv
rename to examples/haseltonRCMF_4story/comp_ds_list.csv
diff --git a/inputs/example_inputs/haseltonRCMF_4story/comp_population.csv b/examples/haseltonRCMF_4story/comp_population.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/comp_population.csv
rename to examples/haseltonRCMF_4story/comp_population.csv
diff --git a/inputs/example_inputs/haseltonRCMF_4story/damage_consequences.json b/examples/haseltonRCMF_4story/damage_consequences.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/damage_consequences.json
rename to examples/haseltonRCMF_4story/damage_consequences.json
diff --git a/inputs/example_inputs/haseltonRCMF_4story/simulated_damage.json b/examples/haseltonRCMF_4story/simulated_damage.json
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/simulated_damage.json
rename to examples/haseltonRCMF_4story/simulated_damage.json
diff --git a/inputs/example_inputs/haseltonRCMF_4story/tenant_unit_list.csv b/examples/haseltonRCMF_4story/tenant_unit_list.csv
similarity index 100%
rename from inputs/example_inputs/haseltonRCMF_4story/tenant_unit_list.csv
rename to examples/haseltonRCMF_4story/tenant_unit_list.csv
diff --git a/inputs/Inputs2Copy/build_input.py b/inputs/Inputs2Copy/build_input.py
deleted file mode 100644
index f85a66b..0000000
--- a/inputs/Inputs2Copy/build_input.py
+++ /dev/null
@@ -1,399 +0,0 @@
-def build_input(output_path):
-    # """
-    # Code for generating simulated_inputs.json file
-    
-    # Parameters
-    # ----------
-    # output_path: string
-    #     Path where the generated input file shall be saved.
-    
-    # """
-
-    import numpy as np
-    import json
-    import pandas as pd
-    import os
-    import re
-    import sys
-    
-    print(os.getcwd())
-    
-    ''' PULL STATIC DATA
-    If the location of this directory differs, updat the static_data_dir variable below. '''
-    
-    static_data_dir = os.path.join(os.path.dirname(__file__), '..', '..', '..', 'static_tables')
-    
-
-    component_attributes = pd.read_csv(os.path.join(static_data_dir, 'component_attributes.csv'))
-    damage_state_attribute_mapping  = pd.read_csv(os.path.join(static_data_dir, 'damage_state_attribute_mapping.csv'))
-    subsystems = pd.read_csv(os.path.join(static_data_dir, 'subsystems.csv'))
-    tenant_function_requirements = pd.read_csv(os.path.join(static_data_dir, 'tenant_function_requirements.csv'))
-    
-    
-    ''' LOAD BUILDING DATA
-    This data is specific to the building model and will need to be created
-    for each assessment. Data is formated as json structures or csv tables'''
-    
-    # 1. Building Model: Basic data about the building being assessed
-    building_model = json.loads(open('building_model.json').read())
-    
-    # If number of stories is 1, change individual values to lists in order to work with later code
-    if building_model['num_stories'] == 1:
-        for key in ['area_per_story_sf', 'ht_per_story_ft', 'occupants_per_story', 'stairs_per_story', 'struct_bay_area_per_story']:
-            building_model[key] = [building_model[key]]
-    if building_model['num_stories'] == 1:
-        for key in ['edge_lengths']:
-            building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
-    
-    # 2. List of tenant units within the building and their basic attributes
-    tenant_unit_list = pd.read_csv('tenant_unit_list.csv')
-    
-    
-    # 3. List of component and damage states ids associated with the damage
-    comp_ds_list = pd.read_csv('comp_ds_list.csv')
-    
-    # 4. List of component and damage states in the performance model
-    comp_population = pd.read_csv('comp_population.csv')
-    comp_header = list(comp_population.columns)
-    comp_list = np.array(comp_header[2:len(comp_header)])
-    comp_list= np.char.replace(np.array(comp_list),'_','.')
-    comp_list = comp_list.tolist()
-    # Remove suffixes from repated entries
-    for i in range(len(comp_list)):
-        if len(comp_list[i]) > 10:
-            comp_list[i]=comp_list[i][0:10]
-    building_model['comps'] = {'comp_list' : comp_list} #FZ# Component list has been added to building model dictionary.
-    
-    # Go through each story and assign component populations
-    drs = np.unique(np.array(comp_population['dir']))
-    
-    building_model['comps']['story'] = {}
-    for s in range (building_model['num_stories']):
-        building_model['comps']['story'][s] = {}
-        for d in range(len(drs)):
-            filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == drs[d])
-            building_model['comps']['story'][s]['qty_dir_' + str(drs[d])] = comp_population.to_numpy()[filt,2:len(comp_header)].tolist()[0]
-    
-    
-    # Set comp info table
-    comp_info = {'comp_id': [], 'comp_idx': [], 'structural_system': [], 'structural_system_alt': [], 'structural_series_id': []}
-    for c in range(len(comp_list)):
-        # Find the component attributes of this component
-        comp_attr_filt = component_attributes['fragility_id'] == comp_list[c]
-        if np.logical_not(sum(comp_attr_filt) == 1):
-            sys.exit('error!.Could not find component attrubutes')
-        else:
-            comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]
-        comp_info['comp_id'].append(comp_list[c])
-        comp_info['comp_idx'].append(c) #FZ# or c+1. Review in line with latter part of the code
-        comp_info['structural_system'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system')]]))
-        comp_info['structural_system_alt'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system_alt')]]))
-        comp_info['structural_series_id'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_series_id')]]))
-    
-    building_model['comps']['comp_table'] = comp_info
-    
-    
-    ''' LOAD SIMULATED DATA
-    This data is specific to the building performance at the assessed hazard intensity 
-    and will need to be created for each assessment. 
-    Data is formated as json structures.'''
-    
-    # 1. Simulated damage consequences - various building and story level consequences of simulated data, for each realization of the monte carlo simulation.
-    damage_consequences = json.loads(open('damage_consequences.json').read())
-    
-    # 2. Simulated utility downtimes for electrical, water, and gas networks for each realization of the monte carlo simulation.
-    # If file exists load it 
-    if os.path.exists('utility_downtime.json') == True:
-        functionality = json.loads(open('utility_downtime.json').read())
-    # else If no data exist, assume there is no consequence of network downtime
-    else:
-        num_reals = len(damage_consequences["repair_cost_ratio_total"])
-        functionality = {'utilities' : {'electrical':[], 'water':[], 'gas':[]} } 
-    
-        for real in range(num_reals):
-            functionality['utilities']['electrical'].append(0)
-            functionality['utilities']['water'].append(0)
-            functionality['utilities']['gas'].append(0)
-    
-    
-    # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
-    sim_damage = json.loads(open('simulated_damage.json').read())
-    
-    # Write in individual dictionaries part of larger 'damage' dictionary 
-    damage = {'story' : {}, 'tenant_units' : {}}
-    
-    if 'story' in list(sim_damage.keys()):
-        for tu in range(len(sim_damage['tenant_units'])):
-            damage['tenant_units'][tu] = sim_damage['tenant_units'][tu]
-    
-    
-    if 'tenant_units' in list(sim_damage.keys()):
-        for s in range(len(sim_damage['story'])):
-            damage['story'][s] = sim_damage['story'][s]
-        
-    ''' OPTIONAL INPUTS
-    Various assessment otpions. Set to default options in the
-    optional_inputs.json file. This file is expected to be in this input
-    directory. This file can be customized for each assessment if desired.'''
-    
-    optional_inputs = json.load(open("optional_inputs.json"))
-    functionality_options = optional_inputs['functionality_options']
-    impedance_options = optional_inputs['impedance_options']
-    repair_time_options = optional_inputs['repair_time_options'] 
-    
-    # Preallocate tenant unit table
-    tenant_units = tenant_unit_list;
-    tenant_units['exterior'] = np.zeros(len(tenant_units))
-    tenant_units['interior'] = np.zeros(len(tenant_units))
-    tenant_units['occ_per_elev'] = np.zeros(len(tenant_units))
-    tenant_units['is_elevator_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_electrical_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_water_potable_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_water_sanitary_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_hvac_ventilation_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_hvac_heating_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_hvac_cooling_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_hvac_exhaust_required'] = np.zeros(len(tenant_units))
-    tenant_units['is_data_required'] = np.zeros(len(tenant_units))  
-    '''Pull default tenant unit attributes for each tenant unit listed in the
-    tenant_unit_list'''
-    for tu in range(len(tenant_unit_list)):
-        fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == tenant_units['occupancy_id'][tu]
-        if sum(fnc_requirements_filt) != 1:
-            sys.exit('error! Tenant Unit Requirements for This Occupancy Not Found')
-        
-        tenant_units['exterior'][tu] = tenant_function_requirements['exterior'][fnc_requirements_filt]
-        tenant_units['interior'][tu] = tenant_function_requirements['interior'][fnc_requirements_filt]
-        tenant_units['occ_per_elev'][tu] = tenant_function_requirements['occ_per_elev'][fnc_requirements_filt]
-        if list(tenant_function_requirements['is_elevator_required'][fnc_requirements_filt] == 1)[0]  and list(tenant_function_requirements['max_walkable_story'][fnc_requirements_filt] < tenant_units['story'][tu])[0]:
-            tenant_units['is_elevator_required'][tu] = 1
-        else:
-            tenant_units['is_elevator_required'][tu] = 0
-    
-        tenant_units['is_electrical_required'][tu] = tenant_function_requirements['is_electrical_required'][fnc_requirements_filt]
-        tenant_units['is_water_potable_required'][tu] = tenant_function_requirements['is_water_potable_required'][fnc_requirements_filt]
-        tenant_units['is_water_sanitary_required'][tu] = tenant_function_requirements['is_water_sanitary_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_ventilation_required'][tu] = tenant_function_requirements['is_hvac_ventilation_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_heating_required'][tu] = tenant_function_requirements['is_hvac_heating_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_cooling_required'][tu] = tenant_function_requirements['is_hvac_cooling_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_exhaust_required'][tu] = tenant_function_requirements['is_hvac_exhaust_required'][fnc_requirements_filt]
-        tenant_units['is_data_required'][tu] = tenant_function_requirements['is_data_required'][fnc_requirements_filt]    
-    '''Pull default component and damage state attributes for each component 
-    in the comp_ds_list'''
-    
-    ## Populate data for each damage state
-    comp_ds_info = {'comp_id' : [], 
-                    'comp_type_id' : [], 
-                    'comp_idx' : [], 
-                    'ds_seq_id' : [], 
-                    'ds_sub_id' : [],
-                    'system' : [],
-                    'subsystem_id' : [],
-                    'structural_system' : [],
-                    'structural_system_alt' : [],
-                    'structural_series_id' : [],
-                    'unit' : [],
-                    'unit_qty' : [],
-                    'service_location' : [],
-                    'is_sim_ds' : [],
-                    'safety_class' : [],
-                    'affects_envelope_safety' : [],
-                    'ext_falling_hazard' : [],
-                    'int_falling_hazard' : [],
-                    'global_hazardous_material' : [],
-                    'local_hazardous_material' : [],
-                    'weakens_fire_break' : [],
-                    'affects_access' : [],
-                    'damages_envelope_seal' : [],
-                    'affects_roof_function' : [],
-                    'obstructs_interior_space' : [],
-                    'impairs_system_operation' : [],
-                    'causes_flooding' : [],
-                    'interior_area_factor' : [],
-                    'interior_area_conversion_type' : [],
-                    'exterior_surface_area_factor' : [],
-                    'exterior_falling_length_factor' : [],
-                    'crew_size' : [],
-                    'permit_type' : [],
-                    'redesign' : [],
-                    'long_lead_time' : [],
-                    'requires_shoring' : [],
-                    'resolved_by_scaffolding' : [],
-                    'tmp_repair_class' : [],
-                    'tmp_repair_time_lower' : [],
-                    'tmp_repair_time_upper' : [],
-                    'tmp_repair_time_lower_qnty' : [],
-                    'tmp_repair_time_upper_qnty' : [],
-                    'tmp_crew_size' : [],
-                    'n1_redundancy' : [],
-                    'parallel_operation' :[],
-                    'redundancy_threshold' : []
-                    }
-    
-    for c in range(len(comp_ds_list)):
-        
-        # Find the component attributes of this component
-        comp_attr_filt = component_attributes['fragility_id'] == comp_ds_list['comp_id'][c]
-        if sum(comp_attr_filt) != 1:
-            sys.exit('error! Could not find component attrubutes')
-        else:
-            # comp_attr = component_attributes[comp_attr_filt,:);
-            comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]   #FZ# Changed to numpy array to filter out
-            comp_attr = pd.DataFrame(comp_attr, columns = list(component_attributes.columns)) #FZ# Changed back to DataFrame
-                  
-        ds_comp_filt = []
-        for frag_reg in range(len(damage_state_attribute_mapping["fragility_id_regex"])):
-        
-            # Mapping components with attributes - Cjecks are based on mapping, comp_id, seq_id and sub_id
-        
-            # Matching element ID using information contained in damage_state_attribute_mapping ["fragility_id_regex"]
-            if re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c]) == None:
-                ds_comp_filt.append(0)
-            elif (re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c])).string == comp_ds_list["comp_id"][c]:
-                ds_comp_filt.append(1)
-            else:
-                ds_comp_filt.append(0)    
-        
-        ds_seq_filt = damage_state_attribute_mapping['ds_index'] == comp_ds_list['ds_seq_id'][c]
-        if comp_ds_list['ds_sub_id'][c] == 1:
-            ds_sub_filt = np.logical_or(damage_state_attribute_mapping['sub_ds_index'] ==1, damage_state_attribute_mapping['sub_ds_index'].isnull())
-        else:
-            ds_sub_filt = damage_state_attribute_mapping['sub_ds_index'] == comp_ds_list['ds_sub_id'][c]
-        
-        ds_filt = ds_comp_filt & ds_seq_filt & ds_sub_filt
-        
-        if sum(ds_filt) != 1:
-            sys.exit('error!, Could not find damage state attrubutes')
-        else:
-            ds_attr = damage_state_attribute_mapping.to_numpy()[ds_filt,:] #FZ# Changed to numpy array to filter out
-            ds_attr = pd.DataFrame(ds_attr, columns = list(damage_state_attribute_mapping.columns)) #FZ# Changed back to DataFrame
-        
-        ## Populate data for each damage state
-        # Basic Component and DS identifiers
-        comp_ds_info['comp_id'].append(comp_ds_list['comp_id'][c])
-        comp_ds_info['comp_type_id'].append(comp_ds_list['comp_id'][c][0:5]) # first 5 characters indicate the type
-        comp_ds_info['comp_idx'].append(c)
-        comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'][0])
-        # comp_ds_info['ds_sub_id'][c] = str2double(strrep(ds_attr.sub_ds_index{1},'NA','1'))
-        comp_ds_info['ds_sub_id'].append(ds_attr['sub_ds_index'][0])
-        if np.isnan(comp_ds_info['ds_sub_id'][c]):
-            comp_ds_info['ds_sub_id'][c] = 1.0
-            
-        # Set Component Attributes
-        comp_ds_info['system'].append(comp_attr['system_id'][0])
-        comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'][0])
-        comp_ds_info['structural_system'].append(comp_attr['structural_system'][0])
-        comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt'][0]) # component_attributes.csv does not have structural_system_alt field 
-        comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'][0])
-        comp_ds_info['unit'].append(comp_attr['unit'][0]) #FZ# Check w.r.t. matlab output
-        comp_ds_info['unit_qty'].append(comp_attr['unit_qty'][0])
-        comp_ds_info['service_location'].append(comp_attr['service_location'][0]) #FZ# Check w.r.t. matlab output
-                   
-        # Set Damage State Attributes
-        comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'][0])
-        comp_ds_info['safety_class'].append(ds_attr['safety_class'][0])
-        comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'][0])
-        comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'][0])
-        comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'][0])
-        comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'][0])
-        comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'][0])
-        comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'][0])
-        comp_ds_info['affects_access'].append(ds_attr['affects_access'][0])
-        comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'][0])
-        comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'][0])
-        comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'][0])
-        comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'][0])
-        comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'][0])
-        comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'][0])
-        comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'][0])    
-        comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'][0])
-        comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'][0])                
-        comp_ds_info['crew_size'].append(ds_attr['crew_size'][0])
-        comp_ds_info['permit_type'].append(ds_attr['permit_type'][0])
-        comp_ds_info['redesign'].append(ds_attr['redesign'][0])
-        comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'][0])
-        comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'][0])
-        comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'][0])
-        comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'][0])
-        comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'][0])
-        comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'][0])
-        
-        if comp_ds_info['tmp_repair_class'][c] > 0: # only grab values for components with temp repair times
-            time_lower_quantity = ds_attr['time_lower_quantity'][0]
-            time_upper_quantity = ds_attr['time_upper_quantity'][0]
-        
-            comp_ds_info['tmp_repair_time_lower_qnty'].append(time_lower_quantity)
-            comp_ds_info['tmp_repair_time_upper_qnty'].append(time_upper_quantity)
-        else:
-            comp_ds_info['tmp_repair_time_lower_qnty'].append(np.nan)
-            comp_ds_info['tmp_repair_time_upper_qnty'].append(np.nan)
-    
-        comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'][0])
-    
-        # Subsystem attributes
-        subsystem_filt = subsystems['id'] == comp_attr['subsystem_id'][0]
-        if comp_ds_info['subsystem_id'][c] == 0:
-            # No subsytem
-            comp_ds_info['n1_redundancy'].append(0)
-            comp_ds_info['parallel_operation'].append(0)
-            comp_ds_info['redundancy_threshold'].append(0)
-        elif sum(subsystem_filt) != 1:
-            sys.exit('error! Could not find damage state attrubutes')
-        else:
-            # Set Damage State Attributes
-            comp_ds_info['n1_redundancy'].append(np.array(subsystems['n1_redundancy'])[subsystem_filt][0])
-            comp_ds_info['parallel_operation'].append(np.array(subsystems['parallel_operation'])[subsystem_filt][0])
-            comp_ds_info['redundancy_threshold'].append(np.array(subsystems['redundancy_threshold'])[subsystem_filt][0])
-    
-    damage['comp_ds_table'] = comp_ds_info
-    
-    ## Check missing data
-    # Engineering Repair Cost Ratio - Assume is the sum of all component repair
-    # costs that require redesign
-    if 'repair_cost_ratio_engineering' in damage_consequences.keys() == False:
-        eng_filt = np.array(damage['comp_ds_table']['redesign']).astype(bool)
-        damage_consequences['repair_cost_ratio_engineering'] = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
-        for s in range(len(sim_damage['story'])):
-            damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
-    
-
-    # Covert to Python int and floats for creating .json file
-    for key in list(damage['comp_ds_table'].keys()):
-        for i in range(len(damage['comp_ds_table'][key])):
-            if type(damage['comp_ds_table'][key][i]) == np.int64:
-                damage['comp_ds_table'][key][i] = int(damage['comp_ds_table'][key][i])
-            if type(damage['comp_ds_table'][key][i]) == np.float64:
-                damage['comp_ds_table'][key][i] = float(damage['comp_ds_table'][key][i])            
-    
-    for key in list(tenant_units.keys()):
-        for i in range(len(tenant_units[key])):
-            if type(tenant_units[key][i]) == np.int64:
-                tenant_units[key][i] = int(tenant_units[key][i])
-            if type(tenant_units[key][i]) == np.float64:
-                tenant_units[key][i] = float(tenant_units[key][i])  
-    
-    # Convert tenant_units dataframe to dictionary
-    tenant_units_dict = {}
-    for i in list(tenant_units.columns):
-        tenant_units_dict[i] = list(tenant_units[i])
-        
-    tenant_units = tenant_units_dict
-         
-    # Export output as simulated_inputs.json file 
-    
-    simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units}
-    
-    for inp in simulated_inputs:
-        output_json_object = json.dumps(simulated_inputs)
-    
-    # with open("simulated_inputs.json", "w") as outfile:
-    #     outfile.write(output_json_object)
-    
-    with open(output_path, "w") as outfile:
-        outfile.write(output_json_object)       
-
-if __name__ == '__main__':
-
-    output_path = "simulated_inputs.json"
-
-    build_input(output_path)   
diff --git a/inputs/Inputs2Copy/optional_inputs.py b/inputs/Inputs2Copy/optional_inputs.py
deleted file mode 100644
index 34cbebe..0000000
--- a/inputs/Inputs2Copy/optional_inputs.py
+++ /dev/null
@@ -1,105 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Code for generating optional_inputs.json file
-
-"""
-
-import json
-optional_inputs = {
-# impedance Options
-"impedance_options" : {
-    
-    
-"include_impedance":       {
-                            "inspection" : True,
-                            "financing" : True,
-                            "permitting" : True,
-                            "engineering" : True,
-                            "contractor" : True,
-                            "long_lead" : False
-                            },
-"system_design_time" :      {
-                            "f" : 0.04,
-                            "r" : 200,
-                            "t" : 1.3,
-                            "w" : 8
-                            },
-"eng_design_min_days" : 14,
-"eng_design_max_days" : 365,
-"mitigation"  :             {
-                            "is_essential_facility" : False,
-                            "is_borp_equivalent" : False,
-                            "is_engineer_on_retainer" : False,
-                            "contractor_relationship" : 'good',
-                            "contractor_retainer_time" : 3,
-                            "funding_source" : 'private',
-                            "capital_available_ratio" : 0.02
-                            },
-"impedance_beta" : 0.6,
-"impedance_truncation" : 2,
-"default_lead_time" : 182,
-"demand_surge":              {
-                            "include_surge" : 1,
-                            "is_dense_urban_area" : 1,
-                            "site_pga" : 1,
-                            "pga_de": 1
-                            },
-
-"scaffolding_lead_time" : 5,
-"scaffolding_erect_time" : 2,
-"door_racking_repair_day" : 3,
-"flooding_cleanup_day" : 5,
-"flooding_repair_day" : 90
-                            },
-                      
-
-# Repir Schedule Options
-"repair_time_options" : {
-    
- "max_workers_per_sqft_story"  : 0.001,
- "max_workers_per_sqft_story_temp_repair"  : 0.005,
- "max_workers_per_sqft_building" : 0.00025,
- "max_workers_building_min" :  20,
- "max_workers_building_max" :  260,
- "allow_tmp_repairs" : 1,
- "allow_shoring" : 1
-                         },
-
-# Functionality Assessment Options
-"functionality_options" : {  
-    
-"calculate_red_tag" : 1,
-"red_tag_clear_time" : 7,
-"red_tag_clear_beta" : 0.6,
-"red_tag_options" : {
-    "tag_coupling_beams_over_height" : True,
-    "ignore_coupling_beam_for_red_tag" : False
-    },
-"include_local_stability_impact" : 1,
-"include_flooding_impact": 1,
-"egress_threshold" : 0.5,
-"fire_watch" : True,
-"local_fire_damamge_threshold" : 0.25,
-"min_egress_paths" : 2,
-"exterior_safety_threshold" : 0.1,
-"interior_safety_threshold" : 0.25,
-"door_access_width_ft" : 9,
-"habitability_requirements": {
-    "electrical" : 0,
-    "water_potable" : 0,
-    "water_sanitary" : 0,
-    "hvac_ventilation" : 0,
-    "hvac_heating" : 0,
-    "hvac_cooling" : 0,
-    "hvac_exhaust" : 0                       
-    },
-"water_pressure_max_story" : 4,
-"heat_utility" : 'gas',
-                        }
-
-                }
-
-
-with open("optional_inputs.json", "w") as outfile:
-    json.dump(optional_inputs, outfile)
-   
diff --git a/src/atc138/data/default_inputs.json b/src/atc138/data/default_inputs.json
new file mode 100644
index 0000000..1a7d4e6
--- /dev/null
+++ b/src/atc138/data/default_inputs.json
@@ -0,0 +1,81 @@
+{
+  "impedance_options": {
+    "include_impedance": {
+      "inspection": true,
+      "financing": true,
+      "permitting": true,
+      "engineering": true,
+      "contractor": true,
+      "long_lead": false
+    },
+    "system_design_time": {
+      "f": 0.04,
+      "r": 200,
+      "t": 1.3,
+      "w": 8
+    },
+    "eng_design_min_days": 14,
+    "eng_design_max_days": 365,
+    "mitigation": {
+      "is_essential_facility": false,
+      "is_borp_equivalent": false,
+      "is_engineer_on_retainer": false,
+      "contractor_relationship": "good",
+      "contractor_retainer_time": 3,
+      "funding_source": "private",
+      "capital_available_ratio": 0.02
+    },
+    "impedance_beta": 0.6,
+    "impedance_truncation": 2,
+    "default_lead_time": 182,
+    "demand_surge": {
+      "include_surge": 1,
+      "is_dense_urban_area": 1,
+      "site_pga": 1,
+      "pga_de": 1
+    },
+    "scaffolding_lead_time": 5,
+    "scaffolding_erect_time": 2,
+    "door_racking_repair_day": 3,
+    "flooding_cleanup_day": 5,
+    "flooding_repair_day": 90
+  },
+  "repair_time_options": {
+    "max_workers_per_sqft_story": 0.001,
+    "max_workers_per_sqft_story_temp_repair": 0.005,
+    "max_workers_per_sqft_building": 0.00025,
+    "max_workers_building_min": 20,
+    "max_workers_building_max": 260,
+    "allow_tmp_repairs": 1,
+    "allow_shoring": 1
+  },
+  "functionality_options": {
+    "calculate_red_tag": 1,
+    "red_tag_clear_time": 7,
+    "red_tag_clear_beta": 0.6,
+    "red_tag_options": {
+      "tag_coupling_beams_over_height": true,
+      "ignore_coupling_beam_for_red_tag": false
+    },
+    "include_local_stability_impact": 1,
+    "include_flooding_impact": 1,
+    "egress_threshold": 0.5,
+    "fire_watch": true,
+    "local_fire_damamge_threshold": 0.25,
+    "min_egress_paths": 2,
+    "exterior_safety_threshold": 0.1,
+    "interior_safety_threshold": 0.25,
+    "door_access_width_ft": 9,
+    "habitability_requirements": {
+      "electrical": 0,
+      "water_potable": 0,
+      "water_sanitary": 0,
+      "hvac_ventilation": 0,
+      "hvac_heating": 0,
+      "hvac_cooling": 0,
+      "hvac_exhaust": 0
+    },
+    "water_pressure_max_story": 4,
+    "heat_utility": "gas"
+  }
+}
\ No newline at end of file
diff --git a/src/atc138/driver.py b/src/atc138/driver.py
index c29a8cc..651e631 100644
--- a/src/atc138/driver.py
+++ b/src/atc138/driver.py
@@ -47,9 +47,20 @@ def run_analysis(input_dir, output_dir, seed=None):
     # Input/Output directories are passed as arguments
     
     ## 3. Load FEMA P-58 performance model data and simulated damage and loss
-    # Use provided input_dir
-    f = open(os.path.join(input_dir, 'simulated_inputs.json'))
-    simulated_inputs = json.load(f)
+    # Check if simulated_inputs.json exists, if not build it
+    sim_inputs_path = os.path.join(input_dir, 'simulated_inputs.json')
+    
+    if os.path.exists(sim_inputs_path):
+        f = open(sim_inputs_path)
+        simulated_inputs = json.load(f)
+    else:
+        print(f"simulated_inputs.json not found in {input_dir}. Building from raw inputs...")
+        from .input_builder import build_simulated_inputs
+        simulated_inputs = build_simulated_inputs(input_dir)
+        
+        # Save simulated inputs
+        with open(sim_inputs_path, 'w') as f:
+            json.dump(simulated_inputs, f)
     
     building_model = simulated_inputs['building_model']
     damage = simulated_inputs['damage']
@@ -61,22 +72,39 @@ def run_analysis(input_dir, output_dir, seed=None):
     tenant_units = simulated_inputs['tenant_units']
     
     # Change story indices in damage['tenant_units'], damage['story'] building_model['comps']['story'] to int from string
+    # (This ensures compatibility if JSON keys were strings)
     damage_ten_units = []
     if ('tenant_units' in damage.keys()) == True:
         for tu in range(len(damage['tenant_units'])):
-            damage_ten_units.append(damage['tenant_units'][str(tu)])
+            # Handle list vs dict if necessary, but assuming list structure from builder
+            if isinstance(damage['tenant_units'], list): # list
+                 damage_ten_units.append(damage['tenant_units'][tu])
+            elif str(tu) in damage['tenant_units']: # string key
+                 damage_ten_units.append(damage['tenant_units'][str(tu)])
+            elif tu in damage['tenant_units']: # integer key
+                 damage_ten_units.append(damage['tenant_units'][tu])
             
         damage['tenant_units'] = damage_ten_units  
     
     damage_story = []    
     for s in range(len(damage['story'])):
-        damage_story.append(damage['story'][str(s)])
+        if isinstance(damage['story'], list): # list
+            damage_story.append(damage['story'][s])
+        elif str(s) in damage['story']: # string key
+            damage_story.append(damage['story'][str(s)])
+        elif s in damage['story']: # integer key
+            damage_story.append(damage['story'][s])
     
     damage['story'] = damage_story 
     
     bldg_comps_story = []
     for s in range(len(building_model['comps']['story'])):
-        bldg_comps_story.append(building_model['comps']['story'][str(s)])
+        if isinstance(building_model['comps']['story'], list): # list
+             bldg_comps_story.append(building_model['comps']['story'][s])
+        elif str(s) in building_model['comps']['story']: # string key
+             bldg_comps_story.append(building_model['comps']['story'][str(s)])
+        elif s in building_model['comps']['story']: # integer key
+             bldg_comps_story.append(building_model['comps']['story'][s])
         
     building_model['comps']['story'] = bldg_comps_story
     
diff --git a/src/atc138/functionality/fn_calculate_functionality.py b/src/atc138/functionality/fn_calculate_functionality.py
index a9067f1..27d808d 100644
--- a/src/atc138/functionality/fn_calculate_functionality.py
+++ b/src/atc138/functionality/fn_calculate_functionality.py
@@ -40,7 +40,7 @@ def fn_calculate_functionality(damage, damage_consequences, utilities,
     
     ## Initial Set Up
     # import packages
-    from functionality import other_functionality_functions
+    from . import other_functionality_functions
     
     ## Define the day each system becomes functionl - Building level
     system_operation_day = other_functionality_functions.fn_building_level_system_operation(damage, 
diff --git a/src/atc138/functionality/fn_calculate_reoccupancy.py b/src/atc138/functionality/fn_calculate_reoccupancy.py
index 6af1dff..836ee00 100644
--- a/src/atc138/functionality/fn_calculate_reoccupancy.py
+++ b/src/atc138/functionality/fn_calculate_reoccupancy.py
@@ -37,7 +37,7 @@ def fn_calculate_reoccupancy(damage, damage_consequences, utilities,
     import numpy as np
     # Import packages
     
-    from functionality import other_functionality_functions    
+    from . import other_functionality_functions
         
     ## Stage 1: Quantify the effect that component damage has on the building safety
     recovery_day={}
diff --git a/src/atc138/functionality/fn_check_habitability.py b/src/atc138/functionality/fn_check_habitability.py
index 3372ee2..17da486 100644
--- a/src/atc138/functionality/fn_check_habitability.py
+++ b/src/atc138/functionality/fn_check_habitability.py
@@ -24,7 +24,7 @@ def fn_check_habitability( damage, damage_consequences, reoc_meta, func_meta,
       recovery trajectorires, and contributions from systems and components''' 
     
     import numpy as np
-    from functionality import other_functionality_functions
+    from . import other_functionality_functions
     
     num_reals = len(damage_consequences['red_tag'])
     # Functionality checks to adopt onto reoccupancy requirements for
diff --git a/src/atc138/functionality/main_functionality_function.py b/src/atc138/functionality/main_functionality_function.py
index 14c1538..ee492d0 100644
--- a/src/atc138/functionality/main_functionality_function.py
+++ b/src/atc138/functionality/main_functionality_function.py
@@ -34,10 +34,9 @@ def main_functionality(damage, building_model, damage_consequences,
      contains data on the recovery of tenant- and building-level function, 
      recovery trajectorires, and contributions from systems and components''' 
     
-    ## Import Packages
-    from functionality import fn_calculate_reoccupancy
-    from functionality import fn_calculate_functionality
-    from functionality import fn_check_habitability
+    from . import fn_calculate_reoccupancy
+    from . import fn_calculate_functionality
+    from . import fn_check_habitability
     ## Calaculate Building Functionality Restoration Curves
     # Downtime including external delays
     recovery = {}
diff --git a/src/atc138/functionality/other_functionality_functions.py b/src/atc138/functionality/other_functionality_functions.py
index eb46048..103fede 100644
--- a/src/atc138/functionality/other_functionality_functions.py
+++ b/src/atc138/functionality/other_functionality_functions.py
@@ -797,7 +797,7 @@ def fn_building_level_system_operation( damage, damage_consequences,
     
  
     # import packages
-    from functionality import other_functionality_functions
+    from . import other_functionality_functions
     import numpy as np
     
     system_operation_day = {'building' : {}, 'comp' : {}}
@@ -960,7 +960,7 @@ def subsystem_recovery(subsystem, damage, repair_complete_day,
                            initial_damaged, dependancy):
 
         # import packages
-        from functionality import other_functionality_functions
+        from . import other_functionality_functions
         
         # Set variables
         recovery_day_all = dependancy['recovery_day'].copy()
diff --git a/src/atc138/impedance/main_impedance_function.py b/src/atc138/impedance/main_impedance_function.py
index 9a425f4..0bb3334 100644
--- a/src/atc138/impedance/main_impedance_function.py
+++ b/src/atc138/impedance/main_impedance_function.py
@@ -55,7 +55,8 @@ def main_impeding_factors(damage, impedance_options, repair_cost_ratio_total,
     
     import numpy as np
     from scipy.stats import truncnorm
-    from impedance import other_impedance_functions
+    
+    from . import other_impedance_functions
 
     # Initialize parameters
     num_reals = len(inspection_trigger)
diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
new file mode 100644
index 0000000..ab9c22f
--- /dev/null
+++ b/src/atc138/input_builder.py
@@ -0,0 +1,394 @@
+
+def build_simulated_inputs(model_dir):
+    # """
+    # Code for generating simulated_inputs.json file
+    # Adapted from original build_inputs.py for atc138 package.
+    
+    # Parameters
+    # ----------
+    # model_dir: string
+    #     directory containing input files.
+    # """
+
+    import numpy as np
+    import json
+    import pandas as pd
+    import os
+    import re
+    import sys
+    
+    original_cwd = os.getcwd()
+    os.chdir(model_dir)
+
+    try:
+        print(os.getcwd())
+        
+        ''' PULL STATIC DATA
+        If the location of this directory differs, updat the static_data_dir variable below. '''
+        
+        static_data_dir = os.path.join(os.path.dirname(__file__), 'data')
+        
+    
+        component_attributes = pd.read_csv(os.path.join(static_data_dir, 'component_attributes.csv'))
+        damage_state_attribute_mapping  = pd.read_csv(os.path.join(static_data_dir, 'damage_state_attribute_mapping.csv'))
+        subsystems = pd.read_csv(os.path.join(static_data_dir, 'subsystems.csv'))
+        tenant_function_requirements = pd.read_csv(os.path.join(static_data_dir, 'tenant_function_requirements.csv'))
+        
+        
+        ''' LOAD BUILDING DATA
+        This data is specific to the building model and will need to be created
+        for each assessment. Data is formated as json structures or csv tables'''
+        
+        # 1. Building Model: Basic data about the building being assessed
+        building_model = json.loads(open('building_model.json').read())
+        
+        # If number of stories is 1, change individual values to lists in order to work with later code
+        if building_model['num_stories'] == 1:
+            for key in ['area_per_story_sf', 'ht_per_story_ft', 'occupants_per_story', 'stairs_per_story', 'struct_bay_area_per_story']:
+                building_model[key] = [building_model[key]]
+        if building_model['num_stories'] == 1:
+            for key in ['edge_lengths']:
+                building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
+        
+        # 2. List of tenant units within the building and their basic attributes
+        tenant_unit_list = pd.read_csv('tenant_unit_list.csv')
+        
+        
+        # 3. List of component and damage states ids associated with the damage
+        comp_ds_list = pd.read_csv('comp_ds_list.csv')
+        
+        # 4. List of component and damage states in the performance model
+        comp_population = pd.read_csv('comp_population.csv')
+        comp_header = list(comp_population.columns)
+        comp_list = np.array(comp_header[2:len(comp_header)])
+        comp_list= np.char.replace(np.array(comp_list),'_','.')
+        comp_list = comp_list.tolist()
+        # Remove suffixes from repated entries
+        for i in range(len(comp_list)):
+            if len(comp_list[i]) > 10:
+                comp_list[i]=comp_list[i][0:10]
+        building_model['comps'] = {'comp_list' : comp_list} #FZ# Component list has been added to building model dictionary.
+        
+        # Go through each story and assign component populations
+        drs = np.unique(np.array(comp_population['dir']))
+        
+        building_model['comps']['story'] = {}
+        for s in range (building_model['num_stories']):
+            building_model['comps']['story'][s] = {}
+            for d in range(len(drs)):
+                filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == drs[d])
+                building_model['comps']['story'][s]['qty_dir_' + str(drs[d])] = comp_population.to_numpy()[filt,2:len(comp_header)].tolist()[0]
+        
+        
+        # Set comp info table
+        comp_info = {'comp_id': [], 'comp_idx': [], 'structural_system': [], 'structural_system_alt': [], 'structural_series_id': []}
+        for c in range(len(comp_list)):
+            # Find the component attributes of this component
+            comp_attr_filt = component_attributes['fragility_id'] == comp_list[c]
+            if np.logical_not(sum(comp_attr_filt) == 1):
+                sys.exit('error!.Could not find component attrubutes')
+            else:
+                comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]
+            comp_info['comp_id'].append(comp_list[c])
+            comp_info['comp_idx'].append(c) #FZ# or c+1. Review in line with latter part of the code
+            comp_info['structural_system'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system')]]))
+            comp_info['structural_system_alt'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system_alt')]]))
+            comp_info['structural_series_id'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_series_id')]]))
+        
+        building_model['comps']['comp_table'] = comp_info
+        
+        
+        ''' LOAD SIMULATED DATA
+        This data is specific to the building performance at the assessed hazard intensity 
+        and will need to be created for each assessment. 
+        Data is formated as json structures.'''
+        
+        # 1. Simulated damage consequences - various building and story level consequences of simulated data, for each realization of the monte carlo simulation.
+        damage_consequences = json.loads(open('damage_consequences.json').read())
+        
+        # 2. Simulated utility downtimes for electrical, water, and gas networks for each realization of the monte carlo simulation.
+        # If file exists load it 
+        if os.path.exists('utility_downtime.json') == True:
+            functionality = json.loads(open('utility_downtime.json').read())
+        # else If no data exist, assume there is no consequence of network downtime
+        else:
+            num_reals = len(damage_consequences["repair_cost_ratio_total"])
+            functionality = {'utilities' : {'electrical':[], 'water':[], 'gas':[]} } 
+        
+            for real in range(num_reals):
+                functionality['utilities']['electrical'].append(0)
+                functionality['utilities']['water'].append(0)
+                functionality['utilities']['gas'].append(0)
+        
+        
+        # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
+        sim_damage = json.loads(open('simulated_damage.json').read())
+        
+        # Write in individual dictionaries part of larger 'damage' dictionary 
+        damage = {'story' : {}, 'tenant_units' : {}}
+        
+        if 'story' in list(sim_damage.keys()):
+            for tu in range(len(sim_damage['tenant_units'])):
+                damage['tenant_units'][tu] = sim_damage['tenant_units'][tu]
+        
+        
+        if 'tenant_units' in list(sim_damage.keys()):
+            for s in range(len(sim_damage['story'])):
+                damage['story'][s] = sim_damage['story'][s]
+            
+        ''' OPTIONAL INPUTS
+        Various assessment otpions. Set to default options in the
+        optional_inputs.json file. This file is expected to be in this input
+        directory. This file can be customized for each assessment if desired.'''
+        
+        optional_inputs = json.load(open("optional_inputs.json"))
+        functionality_options = optional_inputs['functionality_options']
+        impedance_options = optional_inputs['impedance_options']
+        repair_time_options = optional_inputs['repair_time_options'] 
+        
+        # Preallocate tenant unit table
+        tenant_units = tenant_unit_list.copy() # copy to avoid SettingWithCopy if passed dataframe
+        tenant_units['exterior'] = np.zeros(len(tenant_units))
+        tenant_units['interior'] = np.zeros(len(tenant_units))
+        tenant_units['occ_per_elev'] = np.zeros(len(tenant_units))
+        tenant_units['is_elevator_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_electrical_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_water_potable_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_water_sanitary_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_hvac_ventilation_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_hvac_heating_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_hvac_cooling_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_hvac_exhaust_required'] = np.zeros(len(tenant_units))
+        tenant_units['is_data_required'] = np.zeros(len(tenant_units))  
+        '''Pull default tenant unit attributes for each tenant unit listed in the
+        tenant_unit_list'''
+        for tu in range(len(tenant_unit_list)):
+            fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == tenant_units['occupancy_id'][tu]
+            if sum(fnc_requirements_filt) != 1:
+                sys.exit('error! Tenant Unit Requirements for This Occupancy Not Found')
+            
+            tenant_units['exterior'][tu] = tenant_function_requirements['exterior'][fnc_requirements_filt]
+            tenant_units['interior'][tu] = tenant_function_requirements['interior'][fnc_requirements_filt]
+            tenant_units['occ_per_elev'][tu] = tenant_function_requirements['occ_per_elev'][fnc_requirements_filt]
+            if list(tenant_function_requirements['is_elevator_required'][fnc_requirements_filt] == 1)[0]  and list(tenant_function_requirements['max_walkable_story'][fnc_requirements_filt] < tenant_units['story'][tu])[0]:
+                tenant_units['is_elevator_required'][tu] = 1
+            else:
+                tenant_units['is_elevator_required'][tu] = 0
+        
+            tenant_units['is_electrical_required'][tu] = tenant_function_requirements['is_electrical_required'][fnc_requirements_filt]
+            tenant_units['is_water_potable_required'][tu] = tenant_function_requirements['is_water_potable_required'][fnc_requirements_filt]
+            tenant_units['is_water_sanitary_required'][tu] = tenant_function_requirements['is_water_sanitary_required'][fnc_requirements_filt]
+            tenant_units['is_hvac_ventilation_required'][tu] = tenant_function_requirements['is_hvac_ventilation_required'][fnc_requirements_filt]
+            tenant_units['is_hvac_heating_required'][tu] = tenant_function_requirements['is_hvac_heating_required'][fnc_requirements_filt]
+            tenant_units['is_hvac_cooling_required'][tu] = tenant_function_requirements['is_hvac_cooling_required'][fnc_requirements_filt]
+            tenant_units['is_hvac_exhaust_required'][tu] = tenant_function_requirements['is_hvac_exhaust_required'][fnc_requirements_filt]
+            tenant_units['is_data_required'][tu] = tenant_function_requirements['is_data_required'][fnc_requirements_filt]    
+        '''Pull default component and damage state attributes for each component 
+        in the comp_ds_list'''
+        
+        ## Populate data for each damage state
+        comp_ds_info = {'comp_id' : [], 
+                        'comp_type_id' : [], 
+                        'comp_idx' : [], 
+                        'ds_seq_id' : [], 
+                        'ds_sub_id' : [],
+                        'system' : [],
+                        'subsystem_id' : [],
+                        'structural_system' : [],
+                        'structural_system_alt' : [],
+                        'structural_series_id' : [],
+                        'unit' : [],
+                        'unit_qty' : [],
+                        'service_location' : [],
+                        'is_sim_ds' : [],
+                        'safety_class' : [],
+                        'affects_envelope_safety' : [],
+                        'ext_falling_hazard' : [],
+                        'int_falling_hazard' : [],
+                        'global_hazardous_material' : [],
+                        'local_hazardous_material' : [],
+                        'weakens_fire_break' : [],
+                        'affects_access' : [],
+                        'damages_envelope_seal' : [],
+                        'affects_roof_function' : [],
+                        'obstructs_interior_space' : [],
+                        'impairs_system_operation' : [],
+                        'causes_flooding' : [],
+                        'interior_area_factor' : [],
+                        'interior_area_conversion_type' : [],
+                        'exterior_surface_area_factor' : [],
+                        'exterior_falling_length_factor' : [],
+                        'crew_size' : [],
+                        'permit_type' : [],
+                        'redesign' : [],
+                        'long_lead_time' : [],
+                        'requires_shoring' : [],
+                        'resolved_by_scaffolding' : [],
+                        'tmp_repair_class' : [],
+                        'tmp_repair_time_lower' : [],
+                        'tmp_repair_time_upper' : [],
+                        'tmp_repair_time_lower_qnty' : [],
+                        'tmp_repair_time_upper_qnty' : [],
+                        'tmp_crew_size' : [],
+                        'n1_redundancy' : [],
+                        'parallel_operation' :[],
+                        'redundancy_threshold' : []
+                        }
+        
+        for c in range(len(comp_ds_list)):
+            
+            # Find the component attributes of this component
+            comp_attr_filt = component_attributes['fragility_id'] == comp_ds_list['comp_id'][c]
+            if sum(comp_attr_filt) != 1:
+                sys.exit('error! Could not find component attrubutes')
+            else:
+                # comp_attr = component_attributes[comp_attr_filt,:);
+                comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]   #FZ# Changed to numpy array to filter out
+                comp_attr = pd.DataFrame(comp_attr, columns = list(component_attributes.columns)) #FZ# Changed back to DataFrame
+                      
+            ds_comp_filt = []
+            for frag_reg in range(len(damage_state_attribute_mapping["fragility_id_regex"])):
+            
+                # Mapping components with attributes - Cjecks are based on mapping, comp_id, seq_id and sub_id
+            
+                # Matching element ID using information contained in damage_state_attribute_mapping ["fragility_id_regex"]
+                if re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c]) == None:
+                    ds_comp_filt.append(0)
+                elif (re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c])).string == comp_ds_list["comp_id"][c]:
+                    ds_comp_filt.append(1)
+                else:
+                    ds_comp_filt.append(0)    
+            
+            ds_seq_filt = damage_state_attribute_mapping['ds_index'] == comp_ds_list['ds_seq_id'][c]
+            if comp_ds_list['ds_sub_id'][c] == 1:
+                ds_sub_filt = np.logical_or(damage_state_attribute_mapping['sub_ds_index'] ==1, damage_state_attribute_mapping['sub_ds_index'].isnull())
+            else:
+                ds_sub_filt = damage_state_attribute_mapping['sub_ds_index'] == comp_ds_list['ds_sub_id'][c]
+            
+            ds_filt = ds_comp_filt & ds_seq_filt & ds_sub_filt
+            
+            if sum(ds_filt) != 1:
+                sys.exit('error!, Could not find damage state attrubutes')
+            else:
+                ds_attr = damage_state_attribute_mapping.to_numpy()[ds_filt,:] #FZ# Changed to numpy array to filter out
+                ds_attr = pd.DataFrame(ds_attr, columns = list(damage_state_attribute_mapping.columns)) #FZ# Changed back to DataFrame
+            
+            ## Populate data for each damage state
+            # Basic Component and DS identifiers
+            comp_ds_info['comp_id'].append(comp_ds_list['comp_id'][c])
+            comp_ds_info['comp_type_id'].append(comp_ds_list['comp_id'][c][0:5]) # first 5 characters indicate the type
+            comp_ds_info['comp_idx'].append(c)
+            comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'][0])
+            # comp_ds_info['ds_sub_id'][c] = str2double(strrep(ds_attr.sub_ds_index{1},'NA','1'))
+            comp_ds_info['ds_sub_id'].append(ds_attr['sub_ds_index'][0])
+            if np.isnan(comp_ds_info['ds_sub_id'][c]):
+                comp_ds_info['ds_sub_id'][c] = 1.0
+                
+            # Set Component Attributes
+            comp_ds_info['system'].append(comp_attr['system_id'][0])
+            comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'][0])
+            comp_ds_info['structural_system'].append(comp_attr['structural_system'][0])
+            comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt'][0]) # component_attributes.csv does not have structural_system_alt field 
+            comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'][0])
+            comp_ds_info['unit'].append(comp_attr['unit'][0]) #FZ# Check w.r.t. matlab output
+            comp_ds_info['unit_qty'].append(comp_attr['unit_qty'][0])
+            comp_ds_info['service_location'].append(comp_attr['service_location'][0]) #FZ# Check w.r.t. matlab output
+                       
+            # Set Damage State Attributes
+            comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'][0])
+            comp_ds_info['safety_class'].append(ds_attr['safety_class'][0])
+            comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'][0])
+            comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'][0])
+            comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'][0])
+            comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'][0])
+            comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'][0])
+            comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'][0])
+            comp_ds_info['affects_access'].append(ds_attr['affects_access'][0])
+            comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'][0])
+            comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'][0])
+            comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'][0])
+            comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'][0])
+            comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'][0])
+            comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'][0])
+            comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'][0])    
+            comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'][0])
+            comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'][0])                
+            comp_ds_info['crew_size'].append(ds_attr['crew_size'][0])
+            comp_ds_info['permit_type'].append(ds_attr['permit_type'][0])
+            comp_ds_info['redesign'].append(ds_attr['redesign'][0])
+            comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'][0])
+            comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'][0])
+            comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'][0])
+            comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'][0])
+            comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'][0])
+            comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'][0])
+            
+            if comp_ds_info['tmp_repair_class'][c] > 0: # only grab values for components with temp repair times
+                time_lower_quantity = ds_attr['time_lower_quantity'][0]
+                time_upper_quantity = ds_attr['time_upper_quantity'][0]
+            
+                comp_ds_info['tmp_repair_time_lower_qnty'].append(time_lower_quantity)
+                comp_ds_info['tmp_repair_time_upper_qnty'].append(time_upper_quantity)
+            else:
+                comp_ds_info['tmp_repair_time_lower_qnty'].append(np.nan)
+                comp_ds_info['tmp_repair_time_upper_qnty'].append(np.nan)
+        
+            comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'][0])
+        
+            # Subsystem attributes
+            subsystem_filt = subsystems['id'] == comp_attr['subsystem_id'][0]
+            if comp_ds_info['subsystem_id'][c] == 0:
+                # No subsytem
+                comp_ds_info['n1_redundancy'].append(0)
+                comp_ds_info['parallel_operation'].append(0)
+                comp_ds_info['redundancy_threshold'].append(0)
+            elif sum(subsystem_filt) != 1:
+                sys.exit('error! Could not find damage state attrubutes')
+            else:
+                # Set Damage State Attributes
+                comp_ds_info['n1_redundancy'].append(np.array(subsystems['n1_redundancy'])[subsystem_filt][0])
+                comp_ds_info['parallel_operation'].append(np.array(subsystems['parallel_operation'])[subsystem_filt][0])
+                comp_ds_info['redundancy_threshold'].append(np.array(subsystems['redundancy_threshold'])[subsystem_filt][0])
+        
+        damage['comp_ds_table'] = comp_ds_info
+        
+        ## Check missing data
+        # Engineering Repair Cost Ratio - Assume is the sum of all component repair
+        # costs that require redesign
+        if 'repair_cost_ratio_engineering' in damage_consequences.keys() == False:
+            eng_filt = np.array(damage['comp_ds_table']['redesign']).astype(bool)
+            damage_consequences['repair_cost_ratio_engineering'] = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
+            for s in range(len(sim_damage['story'])):
+                damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
+        
+    
+        # Covert to Python int and floats for creating .json file
+        for key in list(damage['comp_ds_table'].keys()):
+            for i in range(len(damage['comp_ds_table'][key])):
+                if type(damage['comp_ds_table'][key][i]) == np.int64:
+                    damage['comp_ds_table'][key][i] = int(damage['comp_ds_table'][key][i])
+                if type(damage['comp_ds_table'][key][i]) == np.float64:
+                    damage['comp_ds_table'][key][i] = float(damage['comp_ds_table'][key][i])            
+        
+        for key in list(tenant_units.keys()):
+            for i in range(len(tenant_units[key])):
+                if type(tenant_units[key][i]) == np.int64:
+                    tenant_units[key][i] = int(tenant_units[key][i])
+                if type(tenant_units[key][i]) == np.float64:
+                    tenant_units[key][i] = float(tenant_units[key][i])  
+        
+        # Convert tenant_units dataframe to dictionary
+        tenant_units_dict = {}
+        for i in list(tenant_units.columns):
+            tenant_units_dict[i] = list(tenant_units[i])
+            
+        tenant_units = tenant_units_dict
+             
+        # Export output as simulated_inputs.json file 
+        
+        simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units}
+        
+        return simulated_inputs
+
+    finally:
+        os.chdir(original_cwd)
diff --git a/src/atc138/preprocessing/main_preprocessing.py b/src/atc138/preprocessing/main_preprocessing.py
index ec72aec..28ccaf5 100644
--- a/src/atc138/preprocessing/main_preprocessing.py
+++ b/src/atc138/preprocessing/main_preprocessing.py
@@ -39,8 +39,8 @@ def main_preprocessing(comp_ds_table, damage, repair_time_options, temp_repair_c
     damage_consequences: dictionary
       dictionary containing simulated building consequences, such as red'''
     
-    # Import Packages
-    from preprocessing import preprocessing_fns
+    import numpy as np
+    from . import preprocessing_fns
     
     ## Define simulated damage in each tenant unit if not provided by the user
     damage = preprocessing_fns.fn_populate_damage_per_tu(damage)
diff --git a/src/atc138/repair_schedule/main_repair_schedule.py b/src/atc138/repair_schedule/main_repair_schedule.py
index 43b2df7..1b788d2 100644
--- a/src/atc138/repair_schedule/main_repair_schedule.py
+++ b/src/atc138/repair_schedule/main_repair_schedule.py
@@ -56,7 +56,7 @@ def main_repair_schedule(damage, building_model, simulated_red_tags,
     import math
     import numpy as np
     
-    from repair_schedule import other_repair_schedule_functions
+    from . import other_repair_schedule_functions
     
     ## initial Setup
     # Define the maximum number of workers that can be on site, based on REDI

From 59d0d8b8f7a215df43b1633e37301e6e63cf2b60 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:32:40 -0800
Subject: [PATCH 05/15] refactor(input_builder): use explicit paths and
 top-level imports

- Moved imports to the module level.
- Removed usage of `os.chdir()` which mutated global state.
- Updated all file operations to use `os.path.join(model_dir, ...)` for explicit path resolution.
- This creates path independence, allowing the builder to function correctly regardless of the current working directory.
---
 src/atc138/input_builder.py | 728 ++++++++++++++++++------------------
 1 file changed, 360 insertions(+), 368 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index ab9c22f..a7a628d 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -1,4 +1,11 @@
 
+import numpy as np
+import json
+import pandas as pd
+import os
+import re
+import sys
+
 def build_simulated_inputs(model_dir):
     # """
     # Code for generating simulated_inputs.json file
@@ -10,385 +17,370 @@ def build_simulated_inputs(model_dir):
     #     directory containing input files.
     # """
 
-    import numpy as np
-    import json
-    import pandas as pd
-    import os
-    import re
-    import sys
-    
-    original_cwd = os.getcwd()
-    os.chdir(model_dir)
-
-    try:
-        print(os.getcwd())
-        
-        ''' PULL STATIC DATA
-        If the location of this directory differs, updat the static_data_dir variable below. '''
-        
-        static_data_dir = os.path.join(os.path.dirname(__file__), 'data')
+    print(f"Building inputs from: {model_dir}")
         
+    ''' PULL STATIC DATA
+    If the location of this directory differs, updat the static_data_dir variable below. '''
     
-        component_attributes = pd.read_csv(os.path.join(static_data_dir, 'component_attributes.csv'))
-        damage_state_attribute_mapping  = pd.read_csv(os.path.join(static_data_dir, 'damage_state_attribute_mapping.csv'))
-        subsystems = pd.read_csv(os.path.join(static_data_dir, 'subsystems.csv'))
-        tenant_function_requirements = pd.read_csv(os.path.join(static_data_dir, 'tenant_function_requirements.csv'))
-        
-        
-        ''' LOAD BUILDING DATA
-        This data is specific to the building model and will need to be created
-        for each assessment. Data is formated as json structures or csv tables'''
-        
-        # 1. Building Model: Basic data about the building being assessed
-        building_model = json.loads(open('building_model.json').read())
-        
-        # If number of stories is 1, change individual values to lists in order to work with later code
-        if building_model['num_stories'] == 1:
-            for key in ['area_per_story_sf', 'ht_per_story_ft', 'occupants_per_story', 'stairs_per_story', 'struct_bay_area_per_story']:
-                building_model[key] = [building_model[key]]
-        if building_model['num_stories'] == 1:
-            for key in ['edge_lengths']:
-                building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
-        
-        # 2. List of tenant units within the building and their basic attributes
-        tenant_unit_list = pd.read_csv('tenant_unit_list.csv')
-        
-        
-        # 3. List of component and damage states ids associated with the damage
-        comp_ds_list = pd.read_csv('comp_ds_list.csv')
-        
-        # 4. List of component and damage states in the performance model
-        comp_population = pd.read_csv('comp_population.csv')
-        comp_header = list(comp_population.columns)
-        comp_list = np.array(comp_header[2:len(comp_header)])
-        comp_list= np.char.replace(np.array(comp_list),'_','.')
-        comp_list = comp_list.tolist()
-        # Remove suffixes from repated entries
-        for i in range(len(comp_list)):
-            if len(comp_list[i]) > 10:
-                comp_list[i]=comp_list[i][0:10]
-        building_model['comps'] = {'comp_list' : comp_list} #FZ# Component list has been added to building model dictionary.
-        
-        # Go through each story and assign component populations
-        drs = np.unique(np.array(comp_population['dir']))
-        
-        building_model['comps']['story'] = {}
-        for s in range (building_model['num_stories']):
-            building_model['comps']['story'][s] = {}
-            for d in range(len(drs)):
-                filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == drs[d])
-                building_model['comps']['story'][s]['qty_dir_' + str(drs[d])] = comp_population.to_numpy()[filt,2:len(comp_header)].tolist()[0]
-        
+    static_data_dir = os.path.join(os.path.dirname(__file__), 'data')
+
+    component_attributes = pd.read_csv(os.path.join(static_data_dir, 'component_attributes.csv'))
+    damage_state_attribute_mapping  = pd.read_csv(os.path.join(static_data_dir, 'damage_state_attribute_mapping.csv'))
+    subsystems = pd.read_csv(os.path.join(static_data_dir, 'subsystems.csv'))
+    tenant_function_requirements = pd.read_csv(os.path.join(static_data_dir, 'tenant_function_requirements.csv'))
+    
+    
+    ''' LOAD BUILDING DATA
+    This data is specific to the building model and will need to be created
+    for each assessment. Data is formated as json structures or csv tables'''
+    
+    # 1. Building Model: Basic data about the building being assessed
+    building_model = json.loads(open(os.path.join(model_dir, 'building_model.json')).read())
+    
+    # If number of stories is 1, change individual values to lists in order to work with later code
+    if building_model['num_stories'] == 1:
+        for key in ['area_per_story_sf', 'ht_per_story_ft', 'occupants_per_story', 'stairs_per_story', 'struct_bay_area_per_story']:
+            building_model[key] = [building_model[key]]
+    if building_model['num_stories'] == 1:
+        for key in ['edge_lengths']:
+            building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
+    
+    # 2. List of tenant units within the building and their basic attributes
+    tenant_unit_list = pd.read_csv(os.path.join(model_dir, 'tenant_unit_list.csv'))
+    
+    
+    # 3. List of component and damage states ids associated with the damage
+    comp_ds_list = pd.read_csv(os.path.join(model_dir, 'comp_ds_list.csv'))
+    
+    # 4. List of component and damage states in the performance model
+    comp_population = pd.read_csv(os.path.join(model_dir, 'comp_population.csv'))
+    comp_header = list(comp_population.columns)
+    comp_list = np.array(comp_header[2:len(comp_header)])
+    comp_list= np.char.replace(np.array(comp_list),'_','.')
+    comp_list = comp_list.tolist()
+    # Remove suffixes from repated entries
+    for i in range(len(comp_list)):
+        if len(comp_list[i]) > 10:
+            comp_list[i]=comp_list[i][0:10]
+    building_model['comps'] = {'comp_list' : comp_list} #FZ# Component list has been added to building model dictionary.
+    
+    # Go through each story and assign component populations
+    drs = np.unique(np.array(comp_population['dir']))
+    
+    building_model['comps']['story'] = {}
+    for s in range (building_model['num_stories']):
+        building_model['comps']['story'][s] = {}
+        for d in range(len(drs)):
+            filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == drs[d])
+            building_model['comps']['story'][s]['qty_dir_' + str(drs[d])] = comp_population.to_numpy()[filt,2:len(comp_header)].tolist()[0]
+    
+    
+    # Set comp info table
+    comp_info = {'comp_id': [], 'comp_idx': [], 'structural_system': [], 'structural_system_alt': [], 'structural_series_id': []}
+    for c in range(len(comp_list)):
+        # Find the component attributes of this component
+        comp_attr_filt = component_attributes['fragility_id'] == comp_list[c]
+        if np.logical_not(sum(comp_attr_filt) == 1):
+            sys.exit('error!.Could not find component attrubutes')
+        else:
+            comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]
+        comp_info['comp_id'].append(comp_list[c])
+        comp_info['comp_idx'].append(c) #FZ# or c+1. Review in line with latter part of the code
+        comp_info['structural_system'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system')]]))
+        comp_info['structural_system_alt'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system_alt')]]))
+        comp_info['structural_series_id'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_series_id')]]))
+    
+    building_model['comps']['comp_table'] = comp_info
+    
+    
+    ''' LOAD SIMULATED DATA
+    This data is specific to the building performance at the assessed hazard intensity 
+    and will need to be created for each assessment. 
+    Data is formated as json structures.'''
+    
+    # 1. Simulated damage consequences - various building and story level consequences of simulated data, for each realization of the monte carlo simulation.
+    damage_consequences = json.loads(open(os.path.join(model_dir, 'damage_consequences.json')).read())
+    
+    # 2. Simulated utility downtimes for electrical, water, and gas networks for each realization of the monte carlo simulation.
+    # If file exists load it 
+    if os.path.exists(os.path.join(model_dir, 'utility_downtime.json')) == True:
+        functionality = json.loads(open(os.path.join(model_dir, 'utility_downtime.json')).read())
+    # else If no data exist, assume there is no consequence of network downtime
+    else:
+        num_reals = len(damage_consequences["repair_cost_ratio_total"])
+        functionality = {'utilities' : {'electrical':[], 'water':[], 'gas':[]} } 
+    
+        for real in range(num_reals):
+            functionality['utilities']['electrical'].append(0)
+            functionality['utilities']['water'].append(0)
+            functionality['utilities']['gas'].append(0)
+    
+    
+    # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
+    sim_damage = json.loads(open(os.path.join(model_dir, 'simulated_damage.json')).read())
+    
+    # Write in individual dictionaries part of larger 'damage' dictionary 
+    damage = {'story' : {}, 'tenant_units' : {}}
+    
+    if 'story' in list(sim_damage.keys()):
+        for tu in range(len(sim_damage['tenant_units'])):
+            damage['tenant_units'][tu] = sim_damage['tenant_units'][tu]
+    
+    
+    if 'tenant_units' in list(sim_damage.keys()):
+        for s in range(len(sim_damage['story'])):
+            damage['story'][s] = sim_damage['story'][s]
+        
+    ''' OPTIONAL INPUTS
+    Various assessment otpions. Set to default options in the
+    optional_inputs.json file. This file is expected to be in this input
+    directory. This file can be customized for each assessment if desired.'''
+    
+    optional_inputs = json.load(open(os.path.join(model_dir, "optional_inputs.json")))
+    functionality_options = optional_inputs['functionality_options']
+    impedance_options = optional_inputs['impedance_options']
+    repair_time_options = optional_inputs['repair_time_options'] 
+    
+    # Preallocate tenant unit table
+    tenant_units = tenant_unit_list.copy() # copy to avoid SettingWithCopy if passed dataframe
+    tenant_units['exterior'] = np.zeros(len(tenant_units))
+    tenant_units['interior'] = np.zeros(len(tenant_units))
+    tenant_units['occ_per_elev'] = np.zeros(len(tenant_units))
+    tenant_units['is_elevator_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_electrical_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_water_potable_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_water_sanitary_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_hvac_ventilation_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_hvac_heating_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_hvac_cooling_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_hvac_exhaust_required'] = np.zeros(len(tenant_units))
+    tenant_units['is_data_required'] = np.zeros(len(tenant_units))  
+    '''Pull default tenant unit attributes for each tenant unit listed in the
+    tenant_unit_list'''
+    for tu in range(len(tenant_unit_list)):
+        fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == tenant_units['occupancy_id'][tu]
+        if sum(fnc_requirements_filt) != 1:
+            sys.exit('error! Tenant Unit Requirements for This Occupancy Not Found')
+        
+        tenant_units['exterior'][tu] = tenant_function_requirements['exterior'][fnc_requirements_filt]
+        tenant_units['interior'][tu] = tenant_function_requirements['interior'][fnc_requirements_filt]
+        tenant_units['occ_per_elev'][tu] = tenant_function_requirements['occ_per_elev'][fnc_requirements_filt]
+        if list(tenant_function_requirements['is_elevator_required'][fnc_requirements_filt] == 1)[0]  and list(tenant_function_requirements['max_walkable_story'][fnc_requirements_filt] < tenant_units['story'][tu])[0]:
+            tenant_units['is_elevator_required'][tu] = 1
+        else:
+            tenant_units['is_elevator_required'][tu] = 0
+    
+        tenant_units['is_electrical_required'][tu] = tenant_function_requirements['is_electrical_required'][fnc_requirements_filt]
+        tenant_units['is_water_potable_required'][tu] = tenant_function_requirements['is_water_potable_required'][fnc_requirements_filt]
+        tenant_units['is_water_sanitary_required'][tu] = tenant_function_requirements['is_water_sanitary_required'][fnc_requirements_filt]
+        tenant_units['is_hvac_ventilation_required'][tu] = tenant_function_requirements['is_hvac_ventilation_required'][fnc_requirements_filt]
+        tenant_units['is_hvac_heating_required'][tu] = tenant_function_requirements['is_hvac_heating_required'][fnc_requirements_filt]
+        tenant_units['is_hvac_cooling_required'][tu] = tenant_function_requirements['is_hvac_cooling_required'][fnc_requirements_filt]
+        tenant_units['is_hvac_exhaust_required'][tu] = tenant_function_requirements['is_hvac_exhaust_required'][fnc_requirements_filt]
+        tenant_units['is_data_required'][tu] = tenant_function_requirements['is_data_required'][fnc_requirements_filt]    
+    '''Pull default component and damage state attributes for each component 
+    in the comp_ds_list'''
+    
+    ## Populate data for each damage state
+    comp_ds_info = {'comp_id' : [], 
+                    'comp_type_id' : [], 
+                    'comp_idx' : [], 
+                    'ds_seq_id' : [], 
+                    'ds_sub_id' : [],
+                    'system' : [],
+                    'subsystem_id' : [],
+                    'structural_system' : [],
+                    'structural_system_alt' : [],
+                    'structural_series_id' : [],
+                    'unit' : [],
+                    'unit_qty' : [],
+                    'service_location' : [],
+                    'is_sim_ds' : [],
+                    'safety_class' : [],
+                    'affects_envelope_safety' : [],
+                    'ext_falling_hazard' : [],
+                    'int_falling_hazard' : [],
+                    'global_hazardous_material' : [],
+                    'local_hazardous_material' : [],
+                    'weakens_fire_break' : [],
+                    'affects_access' : [],
+                    'damages_envelope_seal' : [],
+                    'affects_roof_function' : [],
+                    'obstructs_interior_space' : [],
+                    'impairs_system_operation' : [],
+                    'causes_flooding' : [],
+                    'interior_area_factor' : [],
+                    'interior_area_conversion_type' : [],
+                    'exterior_surface_area_factor' : [],
+                    'exterior_falling_length_factor' : [],
+                    'crew_size' : [],
+                    'permit_type' : [],
+                    'redesign' : [],
+                    'long_lead_time' : [],
+                    'requires_shoring' : [],
+                    'resolved_by_scaffolding' : [],
+                    'tmp_repair_class' : [],
+                    'tmp_repair_time_lower' : [],
+                    'tmp_repair_time_upper' : [],
+                    'tmp_repair_time_lower_qnty' : [],
+                    'tmp_repair_time_upper_qnty' : [],
+                    'tmp_crew_size' : [],
+                    'n1_redundancy' : [],
+                    'parallel_operation' :[],
+                    'redundancy_threshold' : []
+                    }
+    
+    for c in range(len(comp_ds_list)):
         
-        # Set comp info table
-        comp_info = {'comp_id': [], 'comp_idx': [], 'structural_system': [], 'structural_system_alt': [], 'structural_series_id': []}
-        for c in range(len(comp_list)):
-            # Find the component attributes of this component
-            comp_attr_filt = component_attributes['fragility_id'] == comp_list[c]
-            if np.logical_not(sum(comp_attr_filt) == 1):
-                sys.exit('error!.Could not find component attrubutes')
+        # Find the component attributes of this component
+        comp_attr_filt = component_attributes['fragility_id'] == comp_ds_list['comp_id'][c]
+        if sum(comp_attr_filt) != 1:
+            sys.exit('error! Could not find component attrubutes')
+        else:
+            # comp_attr = component_attributes[comp_attr_filt,:);
+            comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]   #FZ# Changed to numpy array to filter out
+            comp_attr = pd.DataFrame(comp_attr, columns = list(component_attributes.columns)) #FZ# Changed back to DataFrame
+                  
+        ds_comp_filt = []
+        for frag_reg in range(len(damage_state_attribute_mapping["fragility_id_regex"])):
+        
+            # Mapping components with attributes - Cjecks are based on mapping, comp_id, seq_id and sub_id
+        
+            # Matching element ID using information contained in damage_state_attribute_mapping ["fragility_id_regex"]
+            if re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c]) == None:
+                ds_comp_filt.append(0)
+            elif (re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c])).string == comp_ds_list["comp_id"][c]:
+                ds_comp_filt.append(1)
             else:
-                comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]
-            comp_info['comp_id'].append(comp_list[c])
-            comp_info['comp_idx'].append(c) #FZ# or c+1. Review in line with latter part of the code
-            comp_info['structural_system'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system')]]))
-            comp_info['structural_system_alt'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system_alt')]]))
-            comp_info['structural_series_id'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_series_id')]]))
-        
-        building_model['comps']['comp_table'] = comp_info
+                ds_comp_filt.append(0)    
         
-        
-        ''' LOAD SIMULATED DATA
-        This data is specific to the building performance at the assessed hazard intensity 
-        and will need to be created for each assessment. 
-        Data is formated as json structures.'''
-        
-        # 1. Simulated damage consequences - various building and story level consequences of simulated data, for each realization of the monte carlo simulation.
-        damage_consequences = json.loads(open('damage_consequences.json').read())
-        
-        # 2. Simulated utility downtimes for electrical, water, and gas networks for each realization of the monte carlo simulation.
-        # If file exists load it 
-        if os.path.exists('utility_downtime.json') == True:
-            functionality = json.loads(open('utility_downtime.json').read())
-        # else If no data exist, assume there is no consequence of network downtime
+        ds_seq_filt = damage_state_attribute_mapping['ds_index'] == comp_ds_list['ds_seq_id'][c]
+        if comp_ds_list['ds_sub_id'][c] == 1:
+            ds_sub_filt = np.logical_or(damage_state_attribute_mapping['sub_ds_index'] ==1, damage_state_attribute_mapping['sub_ds_index'].isnull())
         else:
-            num_reals = len(damage_consequences["repair_cost_ratio_total"])
-            functionality = {'utilities' : {'electrical':[], 'water':[], 'gas':[]} } 
-        
-            for real in range(num_reals):
-                functionality['utilities']['electrical'].append(0)
-                functionality['utilities']['water'].append(0)
-                functionality['utilities']['gas'].append(0)
-        
-        
-        # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
-        sim_damage = json.loads(open('simulated_damage.json').read())
-        
-        # Write in individual dictionaries part of larger 'damage' dictionary 
-        damage = {'story' : {}, 'tenant_units' : {}}
+            ds_sub_filt = damage_state_attribute_mapping['sub_ds_index'] == comp_ds_list['ds_sub_id'][c]
         
-        if 'story' in list(sim_damage.keys()):
-            for tu in range(len(sim_damage['tenant_units'])):
-                damage['tenant_units'][tu] = sim_damage['tenant_units'][tu]
+        ds_filt = ds_comp_filt & ds_seq_filt & ds_sub_filt
         
-        
-        if 'tenant_units' in list(sim_damage.keys()):
-            for s in range(len(sim_damage['story'])):
-                damage['story'][s] = sim_damage['story'][s]
-            
-        ''' OPTIONAL INPUTS
-        Various assessment otpions. Set to default options in the
-        optional_inputs.json file. This file is expected to be in this input
-        directory. This file can be customized for each assessment if desired.'''
-        
-        optional_inputs = json.load(open("optional_inputs.json"))
-        functionality_options = optional_inputs['functionality_options']
-        impedance_options = optional_inputs['impedance_options']
-        repair_time_options = optional_inputs['repair_time_options'] 
-        
-        # Preallocate tenant unit table
-        tenant_units = tenant_unit_list.copy() # copy to avoid SettingWithCopy if passed dataframe
-        tenant_units['exterior'] = np.zeros(len(tenant_units))
-        tenant_units['interior'] = np.zeros(len(tenant_units))
-        tenant_units['occ_per_elev'] = np.zeros(len(tenant_units))
-        tenant_units['is_elevator_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_electrical_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_water_potable_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_water_sanitary_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_hvac_ventilation_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_hvac_heating_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_hvac_cooling_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_hvac_exhaust_required'] = np.zeros(len(tenant_units))
-        tenant_units['is_data_required'] = np.zeros(len(tenant_units))  
-        '''Pull default tenant unit attributes for each tenant unit listed in the
-        tenant_unit_list'''
-        for tu in range(len(tenant_unit_list)):
-            fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == tenant_units['occupancy_id'][tu]
-            if sum(fnc_requirements_filt) != 1:
-                sys.exit('error! Tenant Unit Requirements for This Occupancy Not Found')
-            
-            tenant_units['exterior'][tu] = tenant_function_requirements['exterior'][fnc_requirements_filt]
-            tenant_units['interior'][tu] = tenant_function_requirements['interior'][fnc_requirements_filt]
-            tenant_units['occ_per_elev'][tu] = tenant_function_requirements['occ_per_elev'][fnc_requirements_filt]
-            if list(tenant_function_requirements['is_elevator_required'][fnc_requirements_filt] == 1)[0]  and list(tenant_function_requirements['max_walkable_story'][fnc_requirements_filt] < tenant_units['story'][tu])[0]:
-                tenant_units['is_elevator_required'][tu] = 1
-            else:
-                tenant_units['is_elevator_required'][tu] = 0
-        
-            tenant_units['is_electrical_required'][tu] = tenant_function_requirements['is_electrical_required'][fnc_requirements_filt]
-            tenant_units['is_water_potable_required'][tu] = tenant_function_requirements['is_water_potable_required'][fnc_requirements_filt]
-            tenant_units['is_water_sanitary_required'][tu] = tenant_function_requirements['is_water_sanitary_required'][fnc_requirements_filt]
-            tenant_units['is_hvac_ventilation_required'][tu] = tenant_function_requirements['is_hvac_ventilation_required'][fnc_requirements_filt]
-            tenant_units['is_hvac_heating_required'][tu] = tenant_function_requirements['is_hvac_heating_required'][fnc_requirements_filt]
-            tenant_units['is_hvac_cooling_required'][tu] = tenant_function_requirements['is_hvac_cooling_required'][fnc_requirements_filt]
-            tenant_units['is_hvac_exhaust_required'][tu] = tenant_function_requirements['is_hvac_exhaust_required'][fnc_requirements_filt]
-            tenant_units['is_data_required'][tu] = tenant_function_requirements['is_data_required'][fnc_requirements_filt]    
-        '''Pull default component and damage state attributes for each component 
-        in the comp_ds_list'''
+        if sum(ds_filt) != 1:
+            sys.exit('error!, Could not find damage state attrubutes')
+        else:
+            ds_attr = damage_state_attribute_mapping.to_numpy()[ds_filt,:] #FZ# Changed to numpy array to filter out
+            ds_attr = pd.DataFrame(ds_attr, columns = list(damage_state_attribute_mapping.columns)) #FZ# Changed back to DataFrame
         
         ## Populate data for each damage state
-        comp_ds_info = {'comp_id' : [], 
-                        'comp_type_id' : [], 
-                        'comp_idx' : [], 
-                        'ds_seq_id' : [], 
-                        'ds_sub_id' : [],
-                        'system' : [],
-                        'subsystem_id' : [],
-                        'structural_system' : [],
-                        'structural_system_alt' : [],
-                        'structural_series_id' : [],
-                        'unit' : [],
-                        'unit_qty' : [],
-                        'service_location' : [],
-                        'is_sim_ds' : [],
-                        'safety_class' : [],
-                        'affects_envelope_safety' : [],
-                        'ext_falling_hazard' : [],
-                        'int_falling_hazard' : [],
-                        'global_hazardous_material' : [],
-                        'local_hazardous_material' : [],
-                        'weakens_fire_break' : [],
-                        'affects_access' : [],
-                        'damages_envelope_seal' : [],
-                        'affects_roof_function' : [],
-                        'obstructs_interior_space' : [],
-                        'impairs_system_operation' : [],
-                        'causes_flooding' : [],
-                        'interior_area_factor' : [],
-                        'interior_area_conversion_type' : [],
-                        'exterior_surface_area_factor' : [],
-                        'exterior_falling_length_factor' : [],
-                        'crew_size' : [],
-                        'permit_type' : [],
-                        'redesign' : [],
-                        'long_lead_time' : [],
-                        'requires_shoring' : [],
-                        'resolved_by_scaffolding' : [],
-                        'tmp_repair_class' : [],
-                        'tmp_repair_time_lower' : [],
-                        'tmp_repair_time_upper' : [],
-                        'tmp_repair_time_lower_qnty' : [],
-                        'tmp_repair_time_upper_qnty' : [],
-                        'tmp_crew_size' : [],
-                        'n1_redundancy' : [],
-                        'parallel_operation' :[],
-                        'redundancy_threshold' : []
-                        }
-        
-        for c in range(len(comp_ds_list)):
-            
-            # Find the component attributes of this component
-            comp_attr_filt = component_attributes['fragility_id'] == comp_ds_list['comp_id'][c]
-            if sum(comp_attr_filt) != 1:
-                sys.exit('error! Could not find component attrubutes')
-            else:
-                # comp_attr = component_attributes[comp_attr_filt,:);
-                comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]   #FZ# Changed to numpy array to filter out
-                comp_attr = pd.DataFrame(comp_attr, columns = list(component_attributes.columns)) #FZ# Changed back to DataFrame
-                      
-            ds_comp_filt = []
-            for frag_reg in range(len(damage_state_attribute_mapping["fragility_id_regex"])):
-            
-                # Mapping components with attributes - Cjecks are based on mapping, comp_id, seq_id and sub_id
-            
-                # Matching element ID using information contained in damage_state_attribute_mapping ["fragility_id_regex"]
-                if re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c]) == None:
-                    ds_comp_filt.append(0)
-                elif (re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c])).string == comp_ds_list["comp_id"][c]:
-                    ds_comp_filt.append(1)
-                else:
-                    ds_comp_filt.append(0)    
-            
-            ds_seq_filt = damage_state_attribute_mapping['ds_index'] == comp_ds_list['ds_seq_id'][c]
-            if comp_ds_list['ds_sub_id'][c] == 1:
-                ds_sub_filt = np.logical_or(damage_state_attribute_mapping['sub_ds_index'] ==1, damage_state_attribute_mapping['sub_ds_index'].isnull())
-            else:
-                ds_sub_filt = damage_state_attribute_mapping['sub_ds_index'] == comp_ds_list['ds_sub_id'][c]
-            
-            ds_filt = ds_comp_filt & ds_seq_filt & ds_sub_filt
-            
-            if sum(ds_filt) != 1:
-                sys.exit('error!, Could not find damage state attrubutes')
-            else:
-                ds_attr = damage_state_attribute_mapping.to_numpy()[ds_filt,:] #FZ# Changed to numpy array to filter out
-                ds_attr = pd.DataFrame(ds_attr, columns = list(damage_state_attribute_mapping.columns)) #FZ# Changed back to DataFrame
+        # Basic Component and DS identifiers
+        comp_ds_info['comp_id'].append(comp_ds_list['comp_id'][c])
+        comp_ds_info['comp_type_id'].append(comp_ds_list['comp_id'][c][0:5]) # first 5 characters indicate the type
+        comp_ds_info['comp_idx'].append(c)
+        comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'][0])
+        # comp_ds_info['ds_sub_id'][c] = str2double(strrep(ds_attr.sub_ds_index{1},'NA','1'))
+        comp_ds_info['ds_sub_id'].append(ds_attr['sub_ds_index'][0])
+        if np.isnan(comp_ds_info['ds_sub_id'][c]):
+            comp_ds_info['ds_sub_id'][c] = 1.0
             
-            ## Populate data for each damage state
-            # Basic Component and DS identifiers
-            comp_ds_info['comp_id'].append(comp_ds_list['comp_id'][c])
-            comp_ds_info['comp_type_id'].append(comp_ds_list['comp_id'][c][0:5]) # first 5 characters indicate the type
-            comp_ds_info['comp_idx'].append(c)
-            comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'][0])
-            # comp_ds_info['ds_sub_id'][c] = str2double(strrep(ds_attr.sub_ds_index{1},'NA','1'))
-            comp_ds_info['ds_sub_id'].append(ds_attr['sub_ds_index'][0])
-            if np.isnan(comp_ds_info['ds_sub_id'][c]):
-                comp_ds_info['ds_sub_id'][c] = 1.0
-                
-            # Set Component Attributes
-            comp_ds_info['system'].append(comp_attr['system_id'][0])
-            comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'][0])
-            comp_ds_info['structural_system'].append(comp_attr['structural_system'][0])
-            comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt'][0]) # component_attributes.csv does not have structural_system_alt field 
-            comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'][0])
-            comp_ds_info['unit'].append(comp_attr['unit'][0]) #FZ# Check w.r.t. matlab output
-            comp_ds_info['unit_qty'].append(comp_attr['unit_qty'][0])
-            comp_ds_info['service_location'].append(comp_attr['service_location'][0]) #FZ# Check w.r.t. matlab output
-                       
+        # Set Component Attributes
+        comp_ds_info['system'].append(comp_attr['system_id'][0])
+        comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'][0])
+        comp_ds_info['structural_system'].append(comp_attr['structural_system'][0])
+        comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt'][0]) # component_attributes.csv does not have structural_system_alt field 
+        comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'][0])
+        comp_ds_info['unit'].append(comp_attr['unit'][0]) #FZ# Check w.r.t. matlab output
+        comp_ds_info['unit_qty'].append(comp_attr['unit_qty'][0])
+        comp_ds_info['service_location'].append(comp_attr['service_location'][0]) #FZ# Check w.r.t. matlab output
+                   
+        # Set Damage State Attributes
+        comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'][0])
+        comp_ds_info['safety_class'].append(ds_attr['safety_class'][0])
+        comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'][0])
+        comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'][0])
+        comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'][0])
+        comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'][0])
+        comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'][0])
+        comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'][0])
+        comp_ds_info['affects_access'].append(ds_attr['affects_access'][0])
+        comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'][0])
+        comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'][0])
+        comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'][0])
+        comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'][0])
+        comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'][0])
+        comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'][0])
+        comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'][0])    
+        comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'][0])
+        comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'][0])                
+        comp_ds_info['crew_size'].append(ds_attr['crew_size'][0])
+        comp_ds_info['permit_type'].append(ds_attr['permit_type'][0])
+        comp_ds_info['redesign'].append(ds_attr['redesign'][0])
+        comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'][0])
+        comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'][0])
+        comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'][0])
+        comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'][0])
+        comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'][0])
+        comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'][0])
+        
+        if comp_ds_info['tmp_repair_class'][c] > 0: # only grab values for components with temp repair times
+            time_lower_quantity = ds_attr['time_lower_quantity'][0]
+            time_upper_quantity = ds_attr['time_upper_quantity'][0]
+        
+            comp_ds_info['tmp_repair_time_lower_qnty'].append(time_lower_quantity)
+            comp_ds_info['tmp_repair_time_upper_qnty'].append(time_upper_quantity)
+        else:
+            comp_ds_info['tmp_repair_time_lower_qnty'].append(np.nan)
+            comp_ds_info['tmp_repair_time_upper_qnty'].append(np.nan)
+    
+        comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'][0])
+    
+        # Subsystem attributes
+        subsystem_filt = subsystems['id'] == comp_attr['subsystem_id'][0]
+        if comp_ds_info['subsystem_id'][c] == 0:
+            # No subsytem
+            comp_ds_info['n1_redundancy'].append(0)
+            comp_ds_info['parallel_operation'].append(0)
+            comp_ds_info['redundancy_threshold'].append(0)
+        elif sum(subsystem_filt) != 1:
+            sys.exit('error! Could not find damage state attrubutes')
+        else:
             # Set Damage State Attributes
-            comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'][0])
-            comp_ds_info['safety_class'].append(ds_attr['safety_class'][0])
-            comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'][0])
-            comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'][0])
-            comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'][0])
-            comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'][0])
-            comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'][0])
-            comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'][0])
-            comp_ds_info['affects_access'].append(ds_attr['affects_access'][0])
-            comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'][0])
-            comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'][0])
-            comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'][0])
-            comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'][0])
-            comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'][0])
-            comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'][0])
-            comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'][0])    
-            comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'][0])
-            comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'][0])                
-            comp_ds_info['crew_size'].append(ds_attr['crew_size'][0])
-            comp_ds_info['permit_type'].append(ds_attr['permit_type'][0])
-            comp_ds_info['redesign'].append(ds_attr['redesign'][0])
-            comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'][0])
-            comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'][0])
-            comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'][0])
-            comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'][0])
-            comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'][0])
-            comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'][0])
-            
-            if comp_ds_info['tmp_repair_class'][c] > 0: # only grab values for components with temp repair times
-                time_lower_quantity = ds_attr['time_lower_quantity'][0]
-                time_upper_quantity = ds_attr['time_upper_quantity'][0]
-            
-                comp_ds_info['tmp_repair_time_lower_qnty'].append(time_lower_quantity)
-                comp_ds_info['tmp_repair_time_upper_qnty'].append(time_upper_quantity)
-            else:
-                comp_ds_info['tmp_repair_time_lower_qnty'].append(np.nan)
-                comp_ds_info['tmp_repair_time_upper_qnty'].append(np.nan)
-        
-            comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'][0])
-        
-            # Subsystem attributes
-            subsystem_filt = subsystems['id'] == comp_attr['subsystem_id'][0]
-            if comp_ds_info['subsystem_id'][c] == 0:
-                # No subsytem
-                comp_ds_info['n1_redundancy'].append(0)
-                comp_ds_info['parallel_operation'].append(0)
-                comp_ds_info['redundancy_threshold'].append(0)
-            elif sum(subsystem_filt) != 1:
-                sys.exit('error! Could not find damage state attrubutes')
-            else:
-                # Set Damage State Attributes
-                comp_ds_info['n1_redundancy'].append(np.array(subsystems['n1_redundancy'])[subsystem_filt][0])
-                comp_ds_info['parallel_operation'].append(np.array(subsystems['parallel_operation'])[subsystem_filt][0])
-                comp_ds_info['redundancy_threshold'].append(np.array(subsystems['redundancy_threshold'])[subsystem_filt][0])
-        
-        damage['comp_ds_table'] = comp_ds_info
-        
-        ## Check missing data
-        # Engineering Repair Cost Ratio - Assume is the sum of all component repair
-        # costs that require redesign
-        if 'repair_cost_ratio_engineering' in damage_consequences.keys() == False:
-            eng_filt = np.array(damage['comp_ds_table']['redesign']).astype(bool)
-            damage_consequences['repair_cost_ratio_engineering'] = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
-            for s in range(len(sim_damage['story'])):
-                damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
-        
+            comp_ds_info['n1_redundancy'].append(np.array(subsystems['n1_redundancy'])[subsystem_filt][0])
+            comp_ds_info['parallel_operation'].append(np.array(subsystems['parallel_operation'])[subsystem_filt][0])
+            comp_ds_info['redundancy_threshold'].append(np.array(subsystems['redundancy_threshold'])[subsystem_filt][0])
+    
+    damage['comp_ds_table'] = comp_ds_info
+    
+    ## Check missing data
+    # Engineering Repair Cost Ratio - Assume is the sum of all component repair
+    # costs that require redesign
+    if 'repair_cost_ratio_engineering' in damage_consequences.keys() == False:
+        eng_filt = np.array(damage['comp_ds_table']['redesign']).astype(bool)
+        damage_consequences['repair_cost_ratio_engineering'] = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
+        for s in range(len(sim_damage['story'])):
+            damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
     
-        # Covert to Python int and floats for creating .json file
-        for key in list(damage['comp_ds_table'].keys()):
-            for i in range(len(damage['comp_ds_table'][key])):
-                if type(damage['comp_ds_table'][key][i]) == np.int64:
-                    damage['comp_ds_table'][key][i] = int(damage['comp_ds_table'][key][i])
-                if type(damage['comp_ds_table'][key][i]) == np.float64:
-                    damage['comp_ds_table'][key][i] = float(damage['comp_ds_table'][key][i])            
-        
-        for key in list(tenant_units.keys()):
-            for i in range(len(tenant_units[key])):
-                if type(tenant_units[key][i]) == np.int64:
-                    tenant_units[key][i] = int(tenant_units[key][i])
-                if type(tenant_units[key][i]) == np.float64:
-                    tenant_units[key][i] = float(tenant_units[key][i])  
-        
-        # Convert tenant_units dataframe to dictionary
-        tenant_units_dict = {}
-        for i in list(tenant_units.columns):
-            tenant_units_dict[i] = list(tenant_units[i])
-            
-        tenant_units = tenant_units_dict
-             
-        # Export output as simulated_inputs.json file 
-        
-        simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units}
-        
-        return simulated_inputs
 
-    finally:
-        os.chdir(original_cwd)
+    # Covert to Python int and floats for creating .json file
+    for key in list(damage['comp_ds_table'].keys()):
+        for i in range(len(damage['comp_ds_table'][key])):
+            if type(damage['comp_ds_table'][key][i]) == np.int64:
+                damage['comp_ds_table'][key][i] = int(damage['comp_ds_table'][key][i])
+            if type(damage['comp_ds_table'][key][i]) == np.float64:
+                damage['comp_ds_table'][key][i] = float(damage['comp_ds_table'][key][i])            
+    
+    for key in list(tenant_units.keys()):
+        for i in range(len(tenant_units[key])):
+            if type(tenant_units[key][i]) == np.int64:
+                tenant_units[key][i] = int(tenant_units[key][i])
+            if type(tenant_units[key][i]) == np.float64:
+                tenant_units[key][i] = float(tenant_units[key][i])  
+    
+    # Convert tenant_units dataframe to dictionary
+    tenant_units_dict = {}
+    for i in list(tenant_units.columns):
+        tenant_units_dict[i] = list(tenant_units[i])
+        
+    tenant_units = tenant_units_dict
+         
+    # Export output as simulated_inputs.json file 
+    
+    simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units}
+    
+    return simulated_inputs

From 5ad0d34fb29e6c7e1c15704b4fa1009ce5e140e8 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:43:57 -0800
Subject: [PATCH 06/15] fix(input_builder): improve robustness of data
 extraction logic

- Scalar/Array handling: Changed `comp_attr[0, [(col_idx)]]` to `comp_attr[0, col_idx]` in component info loop. This explicitly extracts the scalar value from the DataFrame/array, preventing `ValueError: setting an array element with a sequence` when the target list expects scalars.
- Key Generation: Enforced integer suffixes for `qty_dir_X` keys (e.g., `qty_dir_1` vs `qty_dir_1.0`) to match downstream expectations in `red_tag.py`.
- Missing Data Handling: Added zero-filling for missing story-direction pairs in `building_model`. This prevents `KeyError` in `red_tag.py` (which iterates hardcoded directions 1-3).
  - Verified: Downstream usage in `red_tag.py` calculates `ratio = damage / quantity`. With zero quantity (and zero damage implied), this results in `NaN`, which evaluates to `False` against red tag thresholds, safely avoiding false positives or crashes.
---
 src/atc138/input_builder.py | 30 ++++++++++++++++++++++++------
 1 file changed, 24 insertions(+), 6 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index a7a628d..2884ffe 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -71,8 +71,24 @@ def build_simulated_inputs(model_dir):
     for s in range (building_model['num_stories']):
         building_model['comps']['story'][s] = {}
         for d in range(len(drs)):
-            filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == drs[d])
-            building_model['comps']['story'][s]['qty_dir_' + str(drs[d])] = comp_population.to_numpy()[filt,2:len(comp_header)].tolist()[0]
+            # [FIX] Robust key generation and missing data handling
+            current_dir = drs[d]
+            filt = np.logical_and(np.array(comp_population['story']) == s+1, np.array(comp_population['dir']) == current_dir)
+            
+            # Format key identifier using integer representation of direction to ensure consistency (e.g. qty_dir_1 not qty_dir_1.0)
+            try:
+                dir_key_suffix = str(int(current_dir))
+            except:
+                dir_key_suffix = str(current_dir)
+            
+            qty_data = comp_population.to_numpy()[filt,2:len(comp_header)]
+            
+            if qty_data.shape[0] > 0:
+                building_model['comps']['story'][s]['qty_dir_' + dir_key_suffix] = qty_data.tolist()[0]
+            else:
+                # Missing data for this story/direction, fill with zeros to avoid crashes
+                num_comps = len(comp_header) - 2
+                building_model['comps']['story'][s]['qty_dir_' + dir_key_suffix] = [0] * num_comps
     
     
     # Set comp info table
@@ -85,10 +101,12 @@ def build_simulated_inputs(model_dir):
         else:
             comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]
         comp_info['comp_id'].append(comp_list[c])
-        comp_info['comp_idx'].append(c) #FZ# or c+1. Review in line with latter part of the code
-        comp_info['structural_system'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system')]]))
-        comp_info['structural_system_alt'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_system_alt')]]))
-        comp_info['structural_series_id'].append(float(comp_attr[0,[component_attributes.columns.get_loc('structural_series_id')]]))
+        comp_info['comp_idx'].append(c) 
+        
+        # [FIX] Scalar extraction: Use scalar indexing [0, col] instead of slicing [0, [col]] to avoid array-to-scalar conversion errors
+        comp_info['structural_system'].append(float(comp_attr[0, component_attributes.columns.get_loc('structural_system')]))
+        comp_info['structural_system_alt'].append(float(comp_attr[0, component_attributes.columns.get_loc('structural_system_alt')]))
+        comp_info['structural_series_id'].append(float(comp_attr[0, component_attributes.columns.get_loc('structural_series_id')]))
     
     building_model['comps']['comp_table'] = comp_info
     

From 73ad11d2e7f6e42e2bd7ff4ac0136676aa571218 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:49:42 -0800
Subject: [PATCH 07/15] fix(input_builder): implement robust JSON serialization

- Added `clean_types` recursive helper function to handle type conversion.
  - Converts Numpy types (`int64`, `float32`, `ndarray`) to native Python types (`int`, `float`, `list`) ensuring successful `json.dump`.
  - Preserves `NaN` values as `float('nan')` instead of `None` or crashing. This is critical for downstream engine compatibility where `NaN` is used to skip calculations (e.g., missing temp repair times).
- Replaced manual type conversion loops with a single pass of `clean_types` on the final `simulated_inputs` dictionary.
- Simplified `tenant_units` DataFrame-to-Dict conversion using `.to_dict(orient='list')`.
---
 src/atc138/input_builder.py | 48 +++++++++++++++++++++----------------
 1 file changed, 27 insertions(+), 21 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 2884ffe..241bbdb 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -6,6 +6,28 @@
 import re
 import sys
 
+def clean_types(obj):
+    """
+    Recursively convert numpy types to native Python types for JSON serialization,
+    preserving NaN as float('nan') for Numpy compatibility in the engine.
+    """
+    if isinstance(obj, dict):
+        return {k: clean_types(v) for k, v in obj.items()}
+    elif isinstance(obj, list):
+        return [clean_types(i) for i in obj]
+    elif isinstance(obj, np.ndarray):
+        return clean_types(obj.tolist())
+    elif isinstance(obj, (np.int64, np.int32, int)):
+        return int(obj)
+    elif isinstance(obj, (np.float64, np.float32, float)):
+         # Preserving NaN for numpy compatibility in downstream engine
+         return float(obj)
+    elif pd.isna(obj): 
+        # Handle standalone pandas/numpy NaNs/NaTs
+        return float('nan') 
+    return obj
+
+
 def build_simulated_inputs(model_dir):
     # """
     # Code for generating simulated_inputs.json file
@@ -375,30 +397,14 @@ def build_simulated_inputs(model_dir):
             damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
     
 
-    # Covert to Python int and floats for creating .json file
-    for key in list(damage['comp_ds_table'].keys()):
-        for i in range(len(damage['comp_ds_table'][key])):
-            if type(damage['comp_ds_table'][key][i]) == np.int64:
-                damage['comp_ds_table'][key][i] = int(damage['comp_ds_table'][key][i])
-            if type(damage['comp_ds_table'][key][i]) == np.float64:
-                damage['comp_ds_table'][key][i] = float(damage['comp_ds_table'][key][i])            
-    
-    for key in list(tenant_units.keys()):
-        for i in range(len(tenant_units[key])):
-            if type(tenant_units[key][i]) == np.int64:
-                tenant_units[key][i] = int(tenant_units[key][i])
-            if type(tenant_units[key][i]) == np.float64:
-                tenant_units[key][i] = float(tenant_units[key][i])  
-    
     # Convert tenant_units dataframe to dictionary
-    tenant_units_dict = {}
-    for i in list(tenant_units.columns):
-        tenant_units_dict[i] = list(tenant_units[i])
-        
-    tenant_units = tenant_units_dict
+    tenant_units_dict = tenant_units.to_dict(orient='list')
          
     # Export output as simulated_inputs.json file 
     
-    simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units}
+    simulated_inputs = {'building_model' : building_model, 'damage' : damage, 'damage_consequences' : damage_consequences, 'functionality' : functionality, 'functionality_options' : functionality_options, 'impedance_options' : impedance_options, 'repair_time_options' : repair_time_options, 'tenant_units' : tenant_units_dict}
+    
+    # [FIX] Type cleaning using recursive helper (enables JSON serialization while preserving NaNs)
+    simulated_inputs = clean_types(simulated_inputs)
     
     return simulated_inputs

From b8cbd3afbba277e94afdfee67c290e7a9d2a4ab2 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 14:57:00 -0800
Subject: [PATCH 08/15] fix(input_builder): implement robust configuration
 management

- Added `recursive_update` helper to support deep merging of dictionaries.
- Updated "OPTIONAL INPUTS" logic to:
  1. Load complete default configuration from `src/atc138/data/default_inputs.json`.
  2. Load user-provided `optional_inputs.json` (if present) from the model directory.
  3. Recursively merge user options into defaults.
- This ensures the simulation always has a complete set of configuration parameters, even if the user provides a partial overrides file, significantly improving robustness against missing configuration keys.
---
 src/atc138/input_builder.py | 32 ++++++++++++++++++++++++++++----
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 241bbdb..310629b 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -27,6 +27,17 @@ def clean_types(obj):
         return float('nan') 
     return obj
 
+def recursive_update(d, u):
+    """
+    Recursively update dictionary d with values from u.
+    """
+    for k, v in u.items():
+        if isinstance(v, dict) and k in d and isinstance(d[k], dict):
+            recursive_update(d[k], v)
+        else:
+            d[k] = v
+    return d
+
 
 def build_simulated_inputs(model_dir):
     # """
@@ -176,10 +187,23 @@ def build_simulated_inputs(model_dir):
     optional_inputs.json file. This file is expected to be in this input
     directory. This file can be customized for each assessment if desired.'''
     
-    optional_inputs = json.load(open(os.path.join(model_dir, "optional_inputs.json")))
-    functionality_options = optional_inputs['functionality_options']
-    impedance_options = optional_inputs['impedance_options']
-    repair_time_options = optional_inputs['repair_time_options'] 
+    # Load defaults first, then merge user overrides
+    pkg_dir = os.path.dirname(__file__)
+    defaults_path = os.path.join(pkg_dir, 'data', 'default_inputs.json')
+    with open(defaults_path, 'r') as f:
+        options = json.load(f)
+
+    user_options_path = os.path.join(model_dir, 'optional_inputs.json')
+    if os.path.exists(user_options_path):
+        with open(user_options_path, 'r') as f:
+            user_options = json.load(f)
+        options = recursive_update(options, user_options)
+        
+    functionality_options = options['functionality_options']
+    impedance_options = options['impedance_options']
+    repair_time_options = options['repair_time_options']
+
+ 
     
     # Preallocate tenant unit table
     tenant_units = tenant_unit_list.copy() # copy to avoid SettingWithCopy if passed dataframe

From b0491bc90aa29715c7ca086466270cb3b927000d Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 15:24:03 -0800
Subject: [PATCH 09/15] fix(input_builder): use robust pandas access patterns

- Refactored logic to use `.loc` / `.iloc` for strict scalar extraction.
  - Previous code filtered dataframes (returning a 1-row Series/DataFrame) and tried to assign them to scalar slots. This raises errors in modern Pandas because "setting an array element with a sequence" is ambiguous.
  - New logic uses `.iloc[0]` to explicitly extract the scalar value from the first row of the filtered result, ensuring safe assignment.
  - Because variables (e.g. `ds_attr`) are now Series rather than single-row DataFrames, redundant `[0]` indexing was removed.
- Replaced fragile chained indexing (e.g., `df['col'][idx] = val`) with robust loc-based assignment (`df.loc[idx, 'col'] = val`) to prevent `SettingWithCopyWarning`.
- **Regex Loop Improvement:** Updated regex loop to append `True`/`False` instead of `1`/`0`. This ensures the resulting array is treated as a Boolean Mask by Pandas, preventing ambiguity where `0`/`1` integer arrays could be misinterpreted as column keys.
- **Logic Cleanup:** Refactored `ds_sub_id` handling to resolve NaNs *before* appending to the list.
- Removed unnecessary `DataFrame -> NumPy -> DataFrame` round-trip conversion, utilizing direct Pandas filtering which preserves original data types better.
---
 src/atc138/input_builder.py | 171 +++++++++++++++++++-----------------
 1 file changed, 89 insertions(+), 82 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 310629b..69fbc02 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -222,26 +222,32 @@ def build_simulated_inputs(model_dir):
     '''Pull default tenant unit attributes for each tenant unit listed in the
     tenant_unit_list'''
     for tu in range(len(tenant_unit_list)):
-        fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == tenant_units['occupancy_id'][tu]
+        occ_id = tenant_units.loc[tu, 'occupancy_id'] # Use .loc for pandas safety
+        fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == occ_id
         if sum(fnc_requirements_filt) != 1:
-            sys.exit('error! Tenant Unit Requirements for This Occupancy Not Found')
+            sys.exit(f'error! Tenant Unit Requirements for Occupancy ID {occ_id} Not Found')
         
-        tenant_units['exterior'][tu] = tenant_function_requirements['exterior'][fnc_requirements_filt]
-        tenant_units['interior'][tu] = tenant_function_requirements['interior'][fnc_requirements_filt]
-        tenant_units['occ_per_elev'][tu] = tenant_function_requirements['occ_per_elev'][fnc_requirements_filt]
-        if list(tenant_function_requirements['is_elevator_required'][fnc_requirements_filt] == 1)[0]  and list(tenant_function_requirements['max_walkable_story'][fnc_requirements_filt] < tenant_units['story'][tu])[0]:
-            tenant_units['is_elevator_required'][tu] = 1
+        # Accessing filtered rows. Original input builder used filtered Series assignment.
+        req_row = tenant_function_requirements[fnc_requirements_filt].iloc[0]
+        
+        tenant_units.loc[tu, 'exterior'] = req_row['exterior']
+        tenant_units.loc[tu, 'interior'] = req_row['interior']
+        tenant_units.loc[tu, 'occ_per_elev'] = req_row['occ_per_elev']
+        
+        story = tenant_units.loc[tu, 'story']
+        if req_row['is_elevator_required'] == 1 and req_row['max_walkable_story'] < story:
+            tenant_units.loc[tu, 'is_elevator_required'] = 1
         else:
-            tenant_units['is_elevator_required'][tu] = 0
-    
-        tenant_units['is_electrical_required'][tu] = tenant_function_requirements['is_electrical_required'][fnc_requirements_filt]
-        tenant_units['is_water_potable_required'][tu] = tenant_function_requirements['is_water_potable_required'][fnc_requirements_filt]
-        tenant_units['is_water_sanitary_required'][tu] = tenant_function_requirements['is_water_sanitary_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_ventilation_required'][tu] = tenant_function_requirements['is_hvac_ventilation_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_heating_required'][tu] = tenant_function_requirements['is_hvac_heating_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_cooling_required'][tu] = tenant_function_requirements['is_hvac_cooling_required'][fnc_requirements_filt]
-        tenant_units['is_hvac_exhaust_required'][tu] = tenant_function_requirements['is_hvac_exhaust_required'][fnc_requirements_filt]
-        tenant_units['is_data_required'][tu] = tenant_function_requirements['is_data_required'][fnc_requirements_filt]    
+            tenant_units.loc[tu, 'is_elevator_required'] = 0
+    
+        tenant_units.loc[tu, 'is_electrical_required'] = req_row['is_electrical_required']
+        tenant_units.loc[tu, 'is_water_potable_required'] = req_row['is_water_potable_required']
+        tenant_units.loc[tu, 'is_water_sanitary_required'] = req_row['is_water_sanitary_required']
+        tenant_units.loc[tu, 'is_hvac_ventilation_required'] = req_row['is_hvac_ventilation_required']
+        tenant_units.loc[tu, 'is_hvac_heating_required'] = req_row['is_hvac_heating_required']
+        tenant_units.loc[tu, 'is_hvac_cooling_required'] = req_row['is_hvac_cooling_required']
+        tenant_units.loc[tu, 'is_hvac_exhaust_required'] = req_row['is_hvac_exhaust_required']
+        tenant_units.loc[tu, 'is_data_required'] = req_row['is_data_required']    
     '''Pull default component and damage state attributes for each component 
     in the comp_ds_list'''
     
@@ -301,23 +307,25 @@ def build_simulated_inputs(model_dir):
         if sum(comp_attr_filt) != 1:
             sys.exit('error! Could not find component attrubutes')
         else:
-            # comp_attr = component_attributes[comp_attr_filt,:);
-            comp_attr = component_attributes.to_numpy()[comp_attr_filt,:]   #FZ# Changed to numpy array to filter out
-            comp_attr = pd.DataFrame(comp_attr, columns = list(component_attributes.columns)) #FZ# Changed back to DataFrame
+            comp_attr = component_attributes[comp_attr_filt].iloc[0] # Changed to Series access for robust scalar extraction
                   
         ds_comp_filt = []
         for frag_reg in range(len(damage_state_attribute_mapping["fragility_id_regex"])):
-        
+            regex_str = damage_state_attribute_mapping["fragility_id_regex"][frag_reg]
+            cid = comp_ds_list["comp_id"][c]
+            match = re.search(regex_str, cid)
+            
+
             # Mapping components with attributes - Cjecks are based on mapping, comp_id, seq_id and sub_id
-        
+
             # Matching element ID using information contained in damage_state_attribute_mapping ["fragility_id_regex"]
-            if re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c]) == None:
-                ds_comp_filt.append(0)
-            elif (re.search(damage_state_attribute_mapping["fragility_id_regex"][frag_reg], comp_ds_list["comp_id"][c])).string == comp_ds_list["comp_id"][c]:
-                ds_comp_filt.append(1)
+            if match and match.string == cid:
+                ds_comp_filt.append(True)
             else:
-                ds_comp_filt.append(0)    
+                ds_comp_filt.append(False)    
         
+        ds_comp_filt = np.array(ds_comp_filt) # Convert to array for boolean indexing
+
         ds_seq_filt = damage_state_attribute_mapping['ds_index'] == comp_ds_list['ds_seq_id'][c]
         if comp_ds_list['ds_sub_id'][c] == 1:
             ds_sub_filt = np.logical_or(damage_state_attribute_mapping['sub_ds_index'] ==1, damage_state_attribute_mapping['sub_ds_index'].isnull())
@@ -329,74 +337,73 @@ def build_simulated_inputs(model_dir):
         if sum(ds_filt) != 1:
             sys.exit('error!, Could not find damage state attrubutes')
         else:
-            ds_attr = damage_state_attribute_mapping.to_numpy()[ds_filt,:] #FZ# Changed to numpy array to filter out
-            ds_attr = pd.DataFrame(ds_attr, columns = list(damage_state_attribute_mapping.columns)) #FZ# Changed back to DataFrame
+            ds_attr = damage_state_attribute_mapping[ds_filt].iloc[0] # Series access
         
         ## Populate data for each damage state
         # Basic Component and DS identifiers
         comp_ds_info['comp_id'].append(comp_ds_list['comp_id'][c])
         comp_ds_info['comp_type_id'].append(comp_ds_list['comp_id'][c][0:5]) # first 5 characters indicate the type
         comp_ds_info['comp_idx'].append(c)
-        comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'][0])
-        # comp_ds_info['ds_sub_id'][c] = str2double(strrep(ds_attr.sub_ds_index{1},'NA','1'))
-        comp_ds_info['ds_sub_id'].append(ds_attr['sub_ds_index'][0])
-        if np.isnan(comp_ds_info['ds_sub_id'][c]):
-            comp_ds_info['ds_sub_id'][c] = 1.0
+        comp_ds_info['ds_seq_id'].append(ds_attr['ds_index'])
+        
+        sub_id = ds_attr['sub_ds_index']
+        if pd.isna(sub_id): sub_id = 1.0
+        comp_ds_info['ds_sub_id'].append(sub_id)
             
         # Set Component Attributes
-        comp_ds_info['system'].append(comp_attr['system_id'][0])
-        comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'][0])
-        comp_ds_info['structural_system'].append(comp_attr['structural_system'][0])
-        comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt'][0]) # component_attributes.csv does not have structural_system_alt field 
-        comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'][0])
-        comp_ds_info['unit'].append(comp_attr['unit'][0]) #FZ# Check w.r.t. matlab output
-        comp_ds_info['unit_qty'].append(comp_attr['unit_qty'][0])
-        comp_ds_info['service_location'].append(comp_attr['service_location'][0]) #FZ# Check w.r.t. matlab output
+        comp_ds_info['system'].append(comp_attr['system_id'])
+        comp_ds_info['subsystem_id'].append(comp_attr['subsystem_id'])
+        comp_ds_info['structural_system'].append(comp_attr['structural_system'])
+        comp_ds_info['structural_system_alt'].append(comp_attr['structural_system_alt']) # component_attributes.csv does not have structural_system_alt field
+        comp_ds_info['structural_series_id'].append(comp_attr['structural_series_id'])
+        comp_ds_info['unit'].append(comp_attr['unit']) #FZ# Check w.r.t. matlab output
+        comp_ds_info['unit_qty'].append(comp_attr['unit_qty'])
+        comp_ds_info['service_location'].append(comp_attr['service_location']) #FZ# Check w.r.t. matlab output
                    
         # Set Damage State Attributes
-        comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'][0])
-        comp_ds_info['safety_class'].append(ds_attr['safety_class'][0])
-        comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'][0])
-        comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'][0])
-        comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'][0])
-        comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'][0])
-        comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'][0])
-        comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'][0])
-        comp_ds_info['affects_access'].append(ds_attr['affects_access'][0])
-        comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'][0])
-        comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'][0])
-        comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'][0])
-        comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'][0])
-        comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'][0])
-        comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'][0])
-        comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'][0])    
-        comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'][0])
-        comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'][0])                
-        comp_ds_info['crew_size'].append(ds_attr['crew_size'][0])
-        comp_ds_info['permit_type'].append(ds_attr['permit_type'][0])
-        comp_ds_info['redesign'].append(ds_attr['redesign'][0])
-        comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'][0])
-        comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'][0])
-        comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'][0])
-        comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'][0])
-        comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'][0])
-        comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'][0])
-        
-        if comp_ds_info['tmp_repair_class'][c] > 0: # only grab values for components with temp repair times
-            time_lower_quantity = ds_attr['time_lower_quantity'][0]
-            time_upper_quantity = ds_attr['time_upper_quantity'][0]
+        # Map fields (legacy mapping logic preserved where simple)
+        comp_ds_info['is_sim_ds'].append(ds_attr['is_sim_ds'])
+        comp_ds_info['safety_class'].append(ds_attr['safety_class'])
+        comp_ds_info['affects_envelope_safety'].append(ds_attr['affects_envelope_safety'])
+        comp_ds_info['ext_falling_hazard'].append(ds_attr['exterior_falling_hazard'])
+        comp_ds_info['int_falling_hazard'].append(ds_attr['interior_falling_hazard'])
+        comp_ds_info['global_hazardous_material'].append(ds_attr['global_hazardous_material'])
+        comp_ds_info['local_hazardous_material'].append(ds_attr['local_hazardous_material'])
+        comp_ds_info['weakens_fire_break'].append(ds_attr['weakens_fire_break'])
+        comp_ds_info['affects_access'].append(ds_attr['affects_access'])
+        comp_ds_info['damages_envelope_seal'].append(ds_attr['damages_envelope_seal'])
+        comp_ds_info['affects_roof_function'].append(ds_attr['affects_roof_function'])
+        comp_ds_info['obstructs_interior_space'].append(ds_attr['obstructs_interior_space'])
+        comp_ds_info['impairs_system_operation'].append(ds_attr['impairs_system_operation'])
+        comp_ds_info['causes_flooding'].append(ds_attr['causes_flooding'])
+        comp_ds_info['interior_area_factor'].append(ds_attr['interior_area_factor'])
+        comp_ds_info['interior_area_conversion_type'].append(ds_attr['interior_area_conversion_type'])    
+        comp_ds_info['exterior_surface_area_factor'].append(ds_attr['exterior_surface_area_factor'])
+        comp_ds_info['exterior_falling_length_factor'].append(ds_attr['exterior_falling_length_factor'])                
+        comp_ds_info['crew_size'].append(ds_attr['crew_size'])
+        comp_ds_info['permit_type'].append(ds_attr['permit_type'])
+        comp_ds_info['redesign'].append(ds_attr['redesign'])
+        comp_ds_info['long_lead_time'].append(impedance_options['default_lead_time'] * ds_attr['long_lead'])
+        comp_ds_info['requires_shoring'].append(ds_attr['requires_shoring'])
+        comp_ds_info['resolved_by_scaffolding'].append(ds_attr['resolved_by_scaffolding'])
+        comp_ds_info['tmp_repair_class'].append(ds_attr['tmp_repair_class'])
+        comp_ds_info['tmp_repair_time_lower'].append(ds_attr['tmp_repair_time_lower'])
+        comp_ds_info['tmp_repair_time_upper'].append(ds_attr['tmp_repair_time_upper'])
         
-            comp_ds_info['tmp_repair_time_lower_qnty'].append(time_lower_quantity)
-            comp_ds_info['tmp_repair_time_upper_qnty'].append(time_upper_quantity)
+        tmp_class = ds_attr['tmp_repair_class']
+        if tmp_class > 0:
+            comp_ds_info['tmp_repair_time_lower_qnty'].append(ds_attr['time_lower_quantity'])
+            comp_ds_info['tmp_repair_time_upper_qnty'].append(ds_attr['time_upper_quantity'])
         else:
             comp_ds_info['tmp_repair_time_lower_qnty'].append(np.nan)
             comp_ds_info['tmp_repair_time_upper_qnty'].append(np.nan)
     
-        comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'][0])
+        comp_ds_info['tmp_crew_size'].append(ds_attr['tmp_crew_size'])
     
         # Subsystem attributes
-        subsystem_filt = subsystems['id'] == comp_attr['subsystem_id'][0]
-        if comp_ds_info['subsystem_id'][c] == 0:
+        sub_id = comp_attr['subsystem_id']
+        subsystem_filt = subsystems['id'] == sub_id
+        if sub_id == 0:
             # No subsytem
             comp_ds_info['n1_redundancy'].append(0)
             comp_ds_info['parallel_operation'].append(0)
@@ -404,10 +411,10 @@ def build_simulated_inputs(model_dir):
         elif sum(subsystem_filt) != 1:
             sys.exit('error! Could not find damage state attrubutes')
         else:
-            # Set Damage State Attributes
-            comp_ds_info['n1_redundancy'].append(np.array(subsystems['n1_redundancy'])[subsystem_filt][0])
-            comp_ds_info['parallel_operation'].append(np.array(subsystems['parallel_operation'])[subsystem_filt][0])
-            comp_ds_info['redundancy_threshold'].append(np.array(subsystems['redundancy_threshold'])[subsystem_filt][0])
+            sub_row = subsystems[subsystem_filt].iloc[0]
+            comp_ds_info['n1_redundancy'].append(sub_row['n1_redundancy'])
+            comp_ds_info['parallel_operation'].append(sub_row['parallel_operation'])
+            comp_ds_info['redundancy_threshold'].append(sub_row['redundancy_threshold'])
     
     damage['comp_ds_table'] = comp_ds_info
     

From f02fb9c070e9eaa3489999a30c86f79494ebca59 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 15:31:44 -0800
Subject: [PATCH 10/15] fix(input_builder): apply code cleanup and best
 practices

- **Resource Management:** Switched from `json.loads(open(...).read())` to `with open(...)` context managers for all file reads. This ensures file handles are properly closed, preventing resource leaks.
- **Exceptions:** Replaced `sys.exit('error...')` with `raise ValueError('error...')`. Raising exceptions is preferred for library/module code as it allows the calling application to handle the error rather than abruptly terminating the interpreter.
- **Repair Cost Logic:** Fixed checking for 'repair_cost_ratio_engineering' using `if key not in dict` instead of `if key in dict.keys() == False`. Refactored the calculation to use efficient Numpy array accumulation instead of loop-based list updates.
- **CSV Loading:** Removed redundant arguments (`header=0`, `encoding='unicode_escape'`) where standard `pd.read_csv` defaults suffice, aligning with clean codebase standards.
---
 src/atc138/input_builder.py | 37 +++++++++++++++++++++++++------------
 1 file changed, 25 insertions(+), 12 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 69fbc02..67370ea 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -68,7 +68,8 @@ def build_simulated_inputs(model_dir):
     for each assessment. Data is formated as json structures or csv tables'''
     
     # 1. Building Model: Basic data about the building being assessed
-    building_model = json.loads(open(os.path.join(model_dir, 'building_model.json')).read())
+    with open(os.path.join(model_dir, 'building_model.json'), 'r') as f:
+        building_model = json.load(f)
     
     # If number of stories is 1, change individual values to lists in order to work with later code
     if building_model['num_stories'] == 1:
@@ -150,12 +151,15 @@ def build_simulated_inputs(model_dir):
     Data is formated as json structures.'''
     
     # 1. Simulated damage consequences - various building and story level consequences of simulated data, for each realization of the monte carlo simulation.
-    damage_consequences = json.loads(open(os.path.join(model_dir, 'damage_consequences.json')).read())
+    with open(os.path.join(model_dir, 'damage_consequences.json'), 'r') as f:
+        damage_consequences = json.load(f)
     
     # 2. Simulated utility downtimes for electrical, water, and gas networks for each realization of the monte carlo simulation.
     # If file exists load it 
-    if os.path.exists(os.path.join(model_dir, 'utility_downtime.json')) == True:
-        functionality = json.loads(open(os.path.join(model_dir, 'utility_downtime.json')).read())
+    utility_path = os.path.join(model_dir, 'utility_downtime.json')
+    if os.path.exists(utility_path):
+        with open(utility_path, 'r') as f:
+            functionality = json.load(f)
     # else If no data exist, assume there is no consequence of network downtime
     else:
         num_reals = len(damage_consequences["repair_cost_ratio_total"])
@@ -168,7 +172,9 @@ def build_simulated_inputs(model_dir):
     
     
     # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
-    sim_damage = json.loads(open(os.path.join(model_dir, 'simulated_damage.json')).read())
+    # 3. Simulated component damage per tenant unit for each realization of the monte carlo simulation
+    with open(os.path.join(model_dir, 'simulated_damage.json'), 'r') as f:
+        sim_damage = json.load(f)
     
     # Write in individual dictionaries part of larger 'damage' dictionary 
     damage = {'story' : {}, 'tenant_units' : {}}
@@ -225,7 +231,7 @@ def build_simulated_inputs(model_dir):
         occ_id = tenant_units.loc[tu, 'occupancy_id'] # Use .loc for pandas safety
         fnc_requirements_filt = tenant_function_requirements['occupancy_id'] == occ_id
         if sum(fnc_requirements_filt) != 1:
-            sys.exit(f'error! Tenant Unit Requirements for Occupancy ID {occ_id} Not Found')
+            raise ValueError(f'error! Tenant Unit Requirements for Occupancy ID {occ_id} Not Found')
         
         # Accessing filtered rows. Original input builder used filtered Series assignment.
         req_row = tenant_function_requirements[fnc_requirements_filt].iloc[0]
@@ -305,7 +311,7 @@ def build_simulated_inputs(model_dir):
         # Find the component attributes of this component
         comp_attr_filt = component_attributes['fragility_id'] == comp_ds_list['comp_id'][c]
         if sum(comp_attr_filt) != 1:
-            sys.exit('error! Could not find component attrubutes')
+            raise ValueError('error! Could not find component attrubutes')
         else:
             comp_attr = component_attributes[comp_attr_filt].iloc[0] # Changed to Series access for robust scalar extraction
                   
@@ -335,7 +341,7 @@ def build_simulated_inputs(model_dir):
         ds_filt = ds_comp_filt & ds_seq_filt & ds_sub_filt
         
         if sum(ds_filt) != 1:
-            sys.exit('error!, Could not find damage state attrubutes')
+             raise ValueError('error!, Could not find damage state attrubutes')
         else:
             ds_attr = damage_state_attribute_mapping[ds_filt].iloc[0] # Series access
         
@@ -421,11 +427,18 @@ def build_simulated_inputs(model_dir):
     ## Check missing data
     # Engineering Repair Cost Ratio - Assume is the sum of all component repair
     # costs that require redesign
-    if 'repair_cost_ratio_engineering' in damage_consequences.keys() == False:
+    ## Check missing data
+    # Engineering Repair Cost Ratio - Assume is the sum of all component repair
+    # costs that require redesign
+    if 'repair_cost_ratio_engineering' not in damage_consequences:
         eng_filt = np.array(damage['comp_ds_table']['redesign']).astype(bool)
-        damage_consequences['repair_cost_ratio_engineering'] = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
-        for s in range(len(sim_damage['story'])):
-            damage_consequences['repair_cost_ratio_engineering'] = damage_consequences['repair_cost_ratio_engineering'] + np.sum(sim_damage['story'][s]['repair_cost'][:,eng_filt], axis = 1)
+        # Re-calc using numpy arrays
+        costs = np.zeros(len(damage_consequences['repair_cost_ratio_total']))
+        if 'story' in sim_damage:
+             for s in range(len(sim_damage['story'])):
+                 story_costs = np.array(sim_damage['story'][s]['repair_cost'])
+                 costs += np.sum(story_costs[:, eng_filt], axis=1)
+        damage_consequences['repair_cost_ratio_engineering'] = costs.tolist()
     
 
     # Convert tenant_units dataframe to dictionary

From f8b1bf3acbd8ff7dc8037e72ff968ed8b723b768 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 15:34:16 -0800
Subject: [PATCH 11/15] fix(input_builder): usage of idempotent list wrapping
 for single-story models

- Updated the normalization logic for single-story building models to check if attributes are already lists/sequences before wrapping them.
- This idempotency ensures that if the input `building_model.json` is already correctly formatted (as a list) logic doesn't corrupt the data by creating nested lists (e.g. `[[val]]` instead of `[val]`).
---
 src/atc138/input_builder.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 67370ea..24d0b7b 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -74,10 +74,12 @@ def build_simulated_inputs(model_dir):
     # If number of stories is 1, change individual values to lists in order to work with later code
     if building_model['num_stories'] == 1:
         for key in ['area_per_story_sf', 'ht_per_story_ft', 'occupants_per_story', 'stairs_per_story', 'struct_bay_area_per_story']:
-            building_model[key] = [building_model[key]]
+            if not isinstance(building_model[key], list):
+                building_model[key] = [building_model[key]]
     if building_model['num_stories'] == 1:
         for key in ['edge_lengths']:
-            building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
+            if not isinstance(building_model[key][0], list):
+                building_model[key] = [[building_model[key][0]], [building_model[key][1]]]
     
     # 2. List of tenant units within the building and their basic attributes
     tenant_unit_list = pd.read_csv(os.path.join(model_dir, 'tenant_unit_list.csv'))

From bfdab302793f86ac95e03dd0a9c129fa86444a67 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 15:36:55 -0800
Subject: [PATCH 12/15] fix(input_builder): finalize docstrings and output
 cleanup

- Activated the function docstring for `build_simulated_inputs` to improve code discoverability and documentation in IDEs.
---
 src/atc138/input_builder.py | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/atc138/input_builder.py b/src/atc138/input_builder.py
index 24d0b7b..181b3d5 100644
--- a/src/atc138/input_builder.py
+++ b/src/atc138/input_builder.py
@@ -40,17 +40,20 @@ def recursive_update(d, u):
 
 
 def build_simulated_inputs(model_dir):
-    # """
-    # Code for generating simulated_inputs.json file
-    # Adapted from original build_inputs.py for atc138 package.
-    
-    # Parameters
-    # ----------
-    # model_dir: string
-    #     directory containing input files.
-    # """
-
-    print(f"Building inputs from: {model_dir}")
+    """
+    Generates simulated_inputs dictionary from raw input files in the model directory.
+    Based on the original build_inputs.py script.
+    
+    Parameters
+    ----------
+    model_dir: string
+        Path to the directory containing raw input files.
+        
+    Returns
+    -------
+    simulated_inputs: dict
+        The complete dictionary of inputs.
+    """
         
     ''' PULL STATIC DATA
     If the location of this directory differs, updat the static_data_dir variable below. '''

From fbece1d06f4273d1609659f88c356170fcfd62c0 Mon Sep 17 00:00:00 2001
From: Adam Zsarnoczay <33822153+zsarnoczay@users.noreply.github.com>
Date: Tue, 3 Feb 2026 15:42:22 -0800
Subject: [PATCH 13/15] fix(repair_schedule): enforce scalar extraction for
 system indices

- Updated index retrieval in `fn_set_repair_constraints` to explicitly extract the scalar integer from `np.where` results.
- Added `[0]` (resulting in `[0][0]`) to `np.where(...)` calls when looking up 'interior', and 'structural' system indices.
- This ensures the indices are passed as native integers (or scalar numpy ints) rather than single-element arrays, preventing dimension mismatch errors when finding constraints or indexing into matrices.
---
 src/atc138/repair_schedule/other_repair_schedule_functions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/atc138/repair_schedule/other_repair_schedule_functions.py b/src/atc138/repair_schedule/other_repair_schedule_functions.py
index d5f27ca..4a1aa41 100644
--- a/src/atc138/repair_schedule/other_repair_schedule_functions.py
+++ b/src/atc138/repair_schedule/other_repair_schedule_functions.py
@@ -435,8 +435,8 @@ def fn_set_repair_constraints(systems, repair_type, conditionTag):
     # Interior Constraints
     if repair_type == 'full':
         # Interiors are delayed by structural repairs
-        interiors_idx = np.where(np.array(systems['name']) == 'interior')[0] #FZ# [0] is done to convert tuple to np array
-        structure_idx = np.where(np.array(systems['name']) == 'structural')[0]
+        interiors_idx = np.where(np.array(systems['name']) == 'interior')[0][0] #FZ [0] is done to convert tuple to np array # [0][0] to get scalar
+        structure_idx = np.where(np.array(systems['name']) == 'structural')[0][0]
  
         sys_constraint_matrix[:,interiors_idx] = structure_idx+1 #FZ# +1 is done to replace with the system id which starts with 1, but python indexing starts at 0. 
         

From dfa2ef98fdd5c8d1ed6edc0e1cb6ff204becfac4 Mon Sep 17 00:00:00 2001
From: dustin-cook <dustintcook@gmail.com>
Date: Thu, 5 Feb 2026 15:41:21 -0500
Subject: [PATCH 14/15] Update readme

Updates readme to reflect CLI installation process
---
 README.md | 46 +++++++++++++++++++++-------------------------
 1 file changed, 21 insertions(+), 25 deletions(-)

diff --git a/README.md b/README.md
index f5a26c0..05d392e 100644
--- a/README.md
+++ b/README.md
@@ -2,43 +2,39 @@
 This is translation of Matlab codebase into Python for quantifying building-specific functional recovery and reoccupancy based on a probabilistic performance-based earthquake engineering framework.
 
 ## Requirements
-- The `requirements.txt` file defines the Python package dependencies required to run this codebase. Follow the instructions below to install all required depenedancies listed in the 'requirements.txt' file.
-- Recommended Python version: `3.9` (the codebase was developed and tested with Python 3.9).
 
-Installation (using a virtual environment is recommended):
+- **Python Version**: 3.9 or later (recommend 3.9)
+- **Package Manager**: pip (comes with Python)
 
-```powershell
-# create a virtual environment
-python -m venv .venv
+### Installation
 
-# activate the virtual environment (PowerShell)
-.\.venv\Scripts\Activate.ps1
+The ATC-138 Functional Recovery Assessment tool is distributed as a Python package. Install it using pip:
 
-# upgrade pip (optional but recommended)
-python -m pip install --upgrade pip
 
-# install dependencies from requirements.txt
-pip install -r requirements.txt
-```
+```bash
+# Create and activate a virtual environment (recommended)
+python -m venv .venv
 
-If you prefer conda:
+# Activate virtual environment
+# On Windows (PowerShell):
+.\.venv\Scripts\Activate.ps1
+# On macOS/Linux:
+source .venv/bin/activate
 
-```bash
-conda create -n frec python=3.9
-conda activate frec
-pip install -r requirements.txt
+# Install the package in editable mode
+pip install -e .
 ```
 
-If you run into platform-specific dependency issues, please refer to the package error messages and install any missing system libraries before re-running `pip install -r requirements.txt`.
-Original Matlab code is from Dr. Dustin Cook's Github directory https://github.com/OpenPBEE/PBEE-Recovery.
 
-### Method Description
-The method for quantifying building-specific functional recovery is based on the performance-based earthquake engineering framework. To quantify building function, the method maps component-level damage to system-level performance, and system-level performance to building function using a series of fault trees that describe the interdependencies between the functions of various building components. The method defines the recovery of function and occupancy at the tenant unit level, where a building can be made up of one-to-many tenant units, each with a possible unique set of requirements to regain building function; the recovery state of the building is defined as an aggregation of all the tenant units within the building. The method propagates uncertainty through the assessment using a Monte Carlo simulation. Details of the method are fully described in Cook, Liel, Haselton, and Koliou, 2022. "A Framework for Operationalizing the Assessment of Post Earthquake Functional Recovery of Buildings", Earthquake Spectra.
+### Verify Installation
+
+After installation, verify that the CLI is available:
 
-### Implementation Details
-The method is developed as part of the consequence module of the Performance-Based Earthquake Engineering framework and uses simulations of component damage from the FEMA P-58 method as an fundamental input. Therefore, this implementation will not perform a FEMA P-58 assessment, and instead, expects the simulations of component damage, from a FEMA P-58 assessment to be provided as inputs. Along with other information about the building, the buildings tenant units, and some analysis options, this implementation will perform the functional recovery assessment method, and provide simulated recovery times for each realization provided. The implementation runs an assessment for a single building at a single intensity level. The implementation of the method does not handle demo and replace conditions and predicts building function based on component damage simulation and recovery times assuming damage will be repaired in-kind. Building failure, demo, and replacement conditions can be handled as a post-process by either overwriting realizations where global failure occurs or only inputting realizations that are scheduled for repair.
+```bash
+atc138 --help
+```
 
-The method is employs Python v 3.9; running this implementation using other versions of Python may not perform as expected.
+You should see the command help output with available options.
 
 ## Running an Assessment
  - **Step 1**: Build the inputs json file of simulated inputs. Title the file "simulated_inputs.json" and place it in a directory of the model name within the "inputs" drirectory. This json data file can either be constructed manually following the inputs schema or using the build script as discussed in the _Building the Inputs File section_ below.

From 9519b9ebb51251a79f1b700b6182e1476977b295 Mon Sep 17 00:00:00 2001
From: hgp297 <hgp@berkeley.edu>
Date: Fri, 6 Feb 2026 12:31:12 -0800
Subject: [PATCH 15/15] doc: revised running instructions in README

- Rewrote "Running an Assessment" with CLI and import instructions.
- Changed file nomenclature
- Removed instructions on manually building inputs. This now instructs
  the user to place any default overrides into the input directory.
---
 README.md | 61 +++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 39 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index 05d392e..0e7f15d 100644
--- a/README.md
+++ b/README.md
@@ -37,13 +37,38 @@ atc138 --help
 You should see the command help output with available options.
 
 ## Running an Assessment
- - **Step 1**: Build the inputs json file of simulated inputs. Title the file "simulated_inputs.json" and place it in a directory of the model name within the "inputs" drirectory. This json data file can either be constructed manually following the inputs schema or using the build script as discussed in the _Building the Inputs File section_ below.
- - **Step 2**: Open the Python file "driver_PBEErecovery.py" and set the "model_name", "model_dir", and "outputs_dir" variables.
- - **Step 3**: Run the script
- - **Step 4**: Simulated assessment outputs will be saved as a json file in a directory of your choice
+
+An assessment can be run directly from the command line, or as imported within a Python workflow. If `simulated_inputs.json` does not exist, it will be created using default inputs within `src/atc138/data`. Various assessment options can be overridden by placing them in file `optional_inputs.json` file within the input directory. This file can be customized for each assessment if desired and will be set as default values if not specified.
+
+### Running from the command line
+
+With the input directory containing the necessary inputs, perform an assessment by running:
+
+```bash
+python -m atc138.cli dir/to/inputs dir/to/outputs
+```
+
+ For example, the ICSB example case is run with:
+
+```bash
+python -m atc138.cli ./examples/ICSB ./examples/ICSB/output
+```
+
+### Imported via Python script
+
+Ensure that the `src/` directory is on the path of the main script. Then:
+
+```python
+from src.atc138 import driver
+
+example_dir = './examples/ICSB'
+output_dir = './examples/ICSB/output'
+
+driver.run_analysis(example_dir, output_dir, seed=985)
+```
 
 ## Example Inputs
-Four example inputs are provided to help illustrate both the construction of the inputs file and the implementation. These files are located in the inputs/example_inputs directory and can be run through the assessment by setting the variable names accordingly in **step 2** above.
+Four example inputs are provided to help illustrate both the construction of the inputs file and the implementation. These files are located in the `examples/` directory and can be run through the assessment by setting the variable names accordingly above.
 
 ## Definition of I/O
 A brief description of the various input and output variables are provided below. A detailed schema of all expected input and output subfields is provided in the schema directory.
@@ -76,18 +101,8 @@ A brief description of the various input and output variables are provided below
  - **functionality['impeding_factors']**: Python dictionary
    Python dictionary containing the simulated impeding factors delaying the start of system repair
 
-## Building the Inputs File
-Instead of manually defining the inputs matlab data file based on the inputs schema, the inputs file can be built from a simpler set of building inputs, taking advantage of default assessment assumptions and component, system, and tenant attributes contained within the _static_tables_ directory.
-
-### Instructions
- - **Step 1**: Copy the scripts build_inputs.py and optional_inputs.py from the _Inputs2Copy_ directory to the directory where you want to build the simulated_inputs.json inputs file
- - **Step 2**: Add the requried building specific input files listed below to the same directory
- - **Step 3**: Modify the optional_inputs.py file as needed and run it before running the build_inputs.py file
- - **Step 4**: Make sure the diectory for the static data tables in build_inputs.py is correctly pointing to the location of the _static_tables_ directory under the heading # Load required data tables
- - **Step 5**: Run the build script
-
-#### Option for Customizing Static Data 
-If you would like to modify the static data tables listed below for a specifc model, simply copy the static data tables listed below to the build script directory, modify the files, and specifiy the path to the location of the modified files (same directory as the build script).
+## Manually building the Inputs File
+By default, the inputs file are built from a simpler set of building inputs, taking advantage of default assessment assumptions and component, system, and tenant attributes contained within the _data_ directory. If you would like to manually modify the data tables listed below for a specific model, simply copy the files to the input directory and modify them.
 
 ### Required Building Specific Data
 Each file listed below contains data specific to the building performance model and simulated damage given for a specific level of shaking. Each file listed will need to be created for each unique assessment and saved in the root directory of the build script. Data are contained in either json  or csv format.
@@ -97,7 +112,7 @@ Each file listed below contains data specific to the building performance model
      - story: [int] building story where this tenant unit is located (ground floor is listed at 1)
      - area: [number] total gross plan area of the tenant unit, in square feet
      - perim_area: [number] total exterior perimeter area (elevation) of the tenant unit, is square feet
-     - occupancy_id: [int] foreign key to the _occupancy_id_ attribute of the tenant_function_requirements.csv table in the _static_tables_ directory
+     - occupancy_id: [int] foreign key to the _occupancy_id_ attribute of the tenant_function_requirements.csv table in the _data_ directory
  - **comp_ds_list.csv**: Table that lists each component and damage state populated in the building performance model; one row per each component's damage state. This table requires the following attributes:
      - comp_id: [string] unique FEMA P-58 component identifier
      - ds_seq_id: [int] interger index of the sequential parent damage state (i.e., damage state 1, 2, 3, 4);
@@ -113,15 +128,17 @@ Each file listed below contains data specific to the building performance model
      - tenant_unit{tu}.num_comps: [array: 1 × damage states] The total number of components associated with each damage state (should be uniform for damage state of the same component stack).
 
 ### Optional Building Specific Data
-The file(s) listed below contain data that is optional for the assessment. If the files do not exist, the method will make simplifying assumptions to account for the missing data (as noted below). Save in the root directory of the build script.
+The file(s) listed below contain data that is optional for the assessment. If the files do not exist, the method will make simplifying assumptions to account for the missing data (as noted below). Save in the input directory of your analysis.
  - **utility_downtime.json**: Regional utility simulated downtimes for gas, water, and electrical power networks. Contains all variables within the _functionality['utilities']_ dictionary defined in the inputs schema.
 
 ### Default Optional Inputs
-The Python file listed below defines additional assessment inputs based on set of default values. Copy the file from the _Inputs2Copy_ directory, place it in the root directory of the build script, and modify it as you see if (or build the script programmatically)
- - **optional_inputs.py**: Defines default variables for the impedance_options, repair_time_options, functionality_options, and regional_impact variables listed in the inputs schema.
+The Python file listed below defines additional assessment inputs based on set of default values. Place this file in the input directory of your analysis.
+ - **optional_inputs.json**: Defines default variables for the impedance_options, repair_time_options, functionality_options, and regional_impact variables listed in the inputs schema.
+
+<!-- How does a user modify the static tables (now data) without touching the original data files? -->
 
 ### Static Data
-The csv tables listed below contain default component, damage state, system, and tenant function attributes that can be used to populate the required assessment inputs according to the methodology. Either in build_inputs.py point to the location of these tables in the _static_tables_ directory, or copy and modify them as you see fit and place them in the root directory of the build script.
+The csv tables listed below contain default component, damage state, system, and tenant function attributes that can be used to populate the required assessment inputs according to the methodology. Either in `input_builder.py` point to the location of these tables in the _data_ directory, or copy and modify them as you see fit and place them in the root directory of the build script.
  - **component_attributes.csv**: Attributes of components in the FEMA P-58 fragility database that are required for the functional recovery assessment.
  - **damage_state_attribute_mapping.csv**: Attributes of damage state in the FEMA P-58 fragility database and their affect on function and reoccupancy.
  - **subsystems.csv**: Attributes of each default subsystem considered in the method.