Update v1

.github/dependabot.yml

@@ -10,5 +10,5 @@ updates:
     schedule:
       interval: "daily"
     open-pull-requests-limit: 99
-    target-branch: "update-v1"
+    target-branch: "master"
     versioning-strategy: lockfile-only

.github/workflows/elasticapp.yml

@@ -0,0 +1,61 @@
+name: elasticapp (Elastica++ based backend) tests
+
+# trigger run only on changes to the backend folder.
+on:
+  push:
+    paths:
+      - backend/**
+  pull_request:
+    paths:
+      - backend/**
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.11"] #, "3.12"]
+        os: [ubuntu-latest] # , macos-latest]
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          uv-version: latest
+      - name: Compile OpenMP
+        env:
+          OMP_NUM_THREADS: 2
+        run: |
+          sudo apt-get update; sudo apt-get install -y libomp5 libomp-dev
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up cache
+        uses: actions/cache@v5
+        with:
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
+            ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install PyElastica and dependencies
+        run: |
+          make install-dev-deps PYTHON_VERSION=${{ matrix.python-version }}
+          uv cache prune --ci
+
+      - name: Run elasticapp tests
+        run: |
+          source .venv/bin/activate
+          cd backend
+          make clean-build
+          make test
+          # pytest backend/tests/py

.github/workflows/main.yml

@@ -3,14 +3,6 @@ name: CI
 
 # Controls when the action will run.
 on: [push, pull_request]
-# Older settings:
-# Triggers the workflow on push request events for the master branch,
-# and pull request events for all branches.
-#on:
-#  push:
-#    branches: [ master ]
-#  pull_request:
-#    branches: [ '**' ]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -52,7 +44,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       # Set up cache
       - name: Set up cache
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ${{ matrix.path }}
           key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
@@ -62,7 +54,7 @@ jobs:
       # Install dependencies
       - name: Install dependencies
         run: |
-          make install-dev-deps
+          make install-dev-deps PYTHON_VERSION=${{ matrix.python-version }}
           uv cache prune --ci
           source .venv/bin/activate
       # Runs a single command using the runners shell
@@ -102,7 +94,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Set up cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ matrix.path }}
           key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
@@ -111,14 +103,14 @@ jobs:
             ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
       - name: Install dependencies
         run: |
-          make install-dev-deps
+          make install-dev-deps PYTHON_VERSION=${{ matrix.python-version }}
           uv cache prune --ci
           source .venv/bin/activate
       - name: Test PyElastica using pytest
         if: startsWith(runner.os, 'macOS')
         run: |
           make test_coverage_xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -7,6 +7,10 @@ __pycache__/
 *.so
 
 *.swp
+.vscode
+docs/_gallery
+docs/gen_modules
+docs/sg_execution_times.rst
 
 # Distribution / packaging
 .Python
@@ -215,6 +219,7 @@ sample_prog.py
 
 # txt files
 *.txt
+!CMakelists.txt
 
 # movie or video file formats
 *.mp4
@@ -237,3 +242,6 @@ outcmaes/*
 
 # csv files
 *.csv
+
+# ./backend dependencies
+deps

.pre-commit-config.yaml

@@ -1,17 +1,20 @@
 default_language_version:
   python: python3
 
-default_stages: [commit, push]
+default_stages: [pre-commit, pre-push]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.5.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: check-json
       - id: check-yaml
+      - id: check-toml
       - id: end-of-file-fixer
         exclude: LICENSE
+      - id: check-added-large-files
+      - id: mixed-line-ending
 
   - repo: local
     hooks:

.readthedocs.yaml

@@ -4,6 +4,8 @@ version: 2
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-24.04
+  apt_packages:
+    - ffmpeg
   tools: { python: "3.10" }
   jobs:
     create_environment:
@@ -14,6 +16,7 @@ build:
     install:
       - "true"
 
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html

CONTRIBUTING.md

@@ -121,7 +121,7 @@ Please don't hesitate improving [documentation](https://github.com/GazzolaLab/Py
 
 We also have many related projects in separate repositories that utilize the PyElastica as a core library.
 Since the package is often used for research purpose, many on-going projects are typically not published.
-If you are interested in hearing more, please contact one of our the maintainer.
+If you are interested in hearing more, please contact the maintainer.
 
 ### Pull requests
 

Makefile

@@ -2,15 +2,24 @@
 PYTHON := python3
 PYTHONPATH := `pwd`
 AUTOFLAKE_ARGS := -r
+PYTHON_VERSION :=
 
 #* Installation
 .PHONY: install
 install:
+ifdef PYTHON_VERSION
+	uv sync --python $(PYTHON_VERSION)
+else
 	uv sync
+endif
 
 .PHONY: install-dev-deps
 install-dev-deps:
+ifdef PYTHON_VERSION
+	uv sync --all-groups --all-extras --python $(PYTHON_VERSION)
+else
 	uv sync --all-groups --all-extras
+endif
 
 
 .PHONY: build
@@ -25,7 +34,7 @@ pre-commit-install:
 .PHONY: black
 black:
 	uv run black --version
-	uv run black --config pyproject.toml elastica tests examples
+	uv run black --config pyproject.toml elastica tests examples backend
 
 .PHONY: black-check
 black-check:
@@ -35,7 +44,7 @@ black-check:
 .PHONY: flake8
 flake8:
 	uv run flake8 --version
-	uv run flake8 elastica tests
+	uv run flake8 elastica
 
 .PHONY: autoflake-check
 autoflake-check:
@@ -45,7 +54,7 @@ autoflake-check:
 .PHONY: autoflake-format
 autoflake-format:
 	uv run autoflake --version
-	uv run autoflake --in-place $(AUTOFLAKE_ARGS) elastica tests examples
+	uv run autoflake --in-place $(AUTOFLAKE_ARGS) elastica tests examples backend
 
 .PHONY: format-codestyle
 format-codestyle: black autoflake-format
@@ -62,15 +71,15 @@ mypy:
 
 .PHONY: test
 test:
-	uv run pytest -c pyproject.toml
+	uv run pytest -c pyproject.toml tests
 
 .PHONY: test_coverage
 test_coverage:
-	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica -c pyproject.toml
+	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica -c pyproject.toml tests
 
 .PHONY: test_coverage_xml
 test_coverage_xml:
-	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica --cov-report=xml -c pyproject.toml
+	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica --cov-report=xml -c pyproject.toml tests
 
 .PHONY: check-codestyle
 check-codestyle: black-check flake8 autoflake-check
@@ -103,8 +112,12 @@ pytestcache-remove:
 build-remove:
 	rm -rf build/ dist/
 
+.PHONY: doc-remove
+doc-remove:
+	rm -rf docs/_build docs/gen_modules/ docs/sg_execution_times.rst docs/_gallery/
+
 .PHONY: cleanup
-cleanup: pycache-remove dsstore-remove ipynbcheckpoints-remove pytestcache-remove mypycache-remove build-remove
+cleanup: pycache-remove dsstore-remove ipynbcheckpoints-remove pytestcache-remove mypycache-remove build-remove doc-remove
 
 all: format-codestyle cleanup test
 

README.md

@@ -1,12 +1,12 @@
 <div align='center'>
 <h1> PyElastica </h1>
 
-[![CI][badge-CI]][link-CI] [![Documentation Status][badge-docs-status]][link-docs-status] [![codecov][badge-codecov]][link-codecov] [![Downloads][badge-pepy-download-count]][link-pepy-download-count] [![DOI][badge-doi]][link-doi] [![Binder][badge-binder]][link-binder] [![Gitter][badge-gitter]][link-gitter]
+[![CI][badge-CI]][link-CI] [![Documentation Status][badge-docs-status]][link-docs-status] [![codecov][badge-codecov]][link-codecov] [![Downloads][badge-pepy-download-count]][link-pepy-download-count] [![DOI][badge-doi]][link-doi] [![Gitter][badge-gitter]][link-gitter]
  </div>
 
 PyElastica is the python implementation of **Elastica**: an *open-source* project for simulating assemblies of slender, one-dimensional structures using Cosserat Rod theory.
 
-[![gallery][link-readme-gallary]][link-project-website]
+[![gallery][link-readme-gallery]][link-project-website]
 
 Visit [www.cosseratrods.org][link-project-website] for more information and learn about Elastica and Cosserat rod theory.
 
@@ -84,13 +84,6 @@ We ask that any publications which use Elastica cite as following:
 - [Controlling a CyberOctopus soft arm with muscle-like actuation](https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=9683318) (UIUC, 2020) (IEEE CDC 2021)
 - [Energy shaping control of a CyberOctopus soft arm](https://ieeexplore.ieee.org/document/9304408) (UIUC, 2020) (IEEE CDC 2020)
 
-## Tutorials
-[![Binder][badge-binder-tutorial]][link-binder]
-
-We have created several Jupyter notebooks and Python scripts to help users get started with PyElastica. The Jupyter notebooks are available on Binder, allowing you to try out some of the tutorials without having to install PyElastica.
-
-We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder ([`examples/Visualization`](examples/Visualization)).
-
 ## Contribution
 
 If you would like to participate, please read our [contribution guideline](CONTRIBUTING.md). Private development branches are moved to [elastica-python](https://github.com/GazzolaLab/elastica-python) repository; access is limited to the core developers, collaborators, and maintainers.
@@ -113,7 +106,7 @@ _Names arranged alphabetically_
 
 [//]: # (Collection of URLs.)
 
-[link-readme-gallary]: https://github.com/skim0119/PyElastica/blob/assets_logo/assets/alpha_gallery.gif
+[link-readme-gallery]: https://github.com/skim0119/PyElastica/blob/assets_logo/assets/alpha_gallery.gif
 
 [link-project-website]: https://cosseratrods.org
 [link-lab-website]: http://mattia-lab.com/
@@ -122,7 +115,6 @@ _Names arranged alphabetically_
 [badge-pypi]: https://badge.fury.io/py/pyelastica.svg
 [badge-CI]: https://github.com/GazzolaLab/PyElastica/workflows/CI/badge.svg
 [badge-docs-status]: https://readthedocs.org/projects/pyelastica/badge/?version=latest
-[badge-binder]: https://mybinder.org/badge_logo.svg
 [badge-pepy-download-count]: https://pepy.tech/badge/pyelastica
 [badge-codecov]: https://codecov.io/gh/GazzolaLab/PyElastica/branch/master/graph/badge.svg
 [badge-gitter]: https://badges.gitter.im/PyElastica/community.svg
@@ -133,7 +125,5 @@ _Names arranged alphabetically_
 [link-pepy-download-count]: https://pepy.tech/project/pyelastica
 [link-codecov]: https://codecov.io/gh/GazzolaLab/PyElastica
 
-[badge-binder-tutorial]: https://img.shields.io/badge/Launch-PyElastica%20Tutorials-579ACA.svg?logo=data:image/png;base64,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
-[link-binder]: https://mybinder.org/v2/gh/GazzolaLab/PyElastica/master?filepath=examples%2FBinder%2F0_PyElastica_Tutorials_Overview.ipynb
 [link-gitter]: https://gitter.im/PyElastica/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
 [link-doi]: https://zenodo.org/badge/latestdoi/254172891

backend/.clang-format

@@ -0,0 +1,17 @@
+---
+# We'll use defaults from the Google style.
+# See http://clang.llvm.org/docs/ClangFormat.html for help.
+Language: Cpp
+BasedOnStyle: Google
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+PointerAlignment: Left
+DerivePointerAlignment: false
+FixNamespaceComments: true
+IncludeCategories:
+  - Regex: "^<.*"
+    Priority: 1
+  - Regex: ".*"
+    Priority: 2
+NamespaceIndentation: All
+SortIncludes: false