From 474e7d5be76d8a38fe89ccdb578fa410d0163c1b Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 13:46:45 +0000 Subject: [PATCH 01/24] Generate repo contents with `python-template` --- .codespell_ignore.txt | 0 .editorconfig | 21 +++++++ .github/PULL_REQUEST_TEMPLATE.md | 26 +++++++++ .github/dependabot.yml | 15 +++++ .github/workflows/auto-merge.yml | 23 ++++++++ .github/workflows/check-links.yml | 20 +++++++ .github/workflows/ci.yml | 38 +++++++++++++ .gitignore | 4 +- .markdownlint.yaml | 4 ++ .pre-commit-config.yaml | 45 +++++++++++++++ .taplo.toml | 4 ++ .vscode/extensions.json | 9 +++ .vscode/settings.json | 11 ++++ README.md | 95 +++++++++++++++++++++++++++++++ mkdocs.yml | 45 +++++++++++++++ muse2_data_analysis/__init__.py | 7 +++ muse2_data_analysis/__main__.py | 1 + pyproject.toml | 67 ++++++++++++++++++++++ tests/__init__.py | 1 + tests/test_muse2_data_analysis.py | 8 +++ 20 files changed, 442 insertions(+), 2 deletions(-) create mode 100644 .codespell_ignore.txt create mode 100644 .editorconfig create mode 100644 .github/PULL_REQUEST_TEMPLATE.md create mode 100644 .github/dependabot.yml create mode 100644 .github/workflows/auto-merge.yml create mode 100644 .github/workflows/check-links.yml create mode 100644 .github/workflows/ci.yml create mode 100644 .markdownlint.yaml create mode 100644 .pre-commit-config.yaml create mode 100644 .taplo.toml create mode 100644 .vscode/extensions.json create mode 100644 .vscode/settings.json create mode 100644 mkdocs.yml create mode 100644 muse2_data_analysis/__init__.py create mode 100644 muse2_data_analysis/__main__.py create mode 100644 pyproject.toml create mode 100644 tests/__init__.py create mode 100644 tests/test_muse2_data_analysis.py diff --git a/.codespell_ignore.txt b/.codespell_ignore.txt new file mode 100644 index 0000000..e69de29 diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..7ec55f1 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,21 @@ +root = true + +[*] +charset = utf-8 +insert_final_newline = true +trim_trailing_whitespace = true +indent_style = space +indent_size = 4 +max_line_length = 88 + +[*.md] +indent_size = 2 + +[*.yaml] +indent_size = 2 + +[*.yml] +indent_size = 2 + +[Makefile] +indent_style = tab diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..ba00034 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,26 @@ +# Description + +_Please include a summary of the change and which issue is fixed (if any). Please also +include relevant motivation and context. List any dependencies that are required for +this change._ + +Close # (issue) + +## Type of change + +- [ ] Documentation (non-breaking change that adds or improves the documentation) +- [ ] New feature (non-breaking change which adds functionality) +- [ ] Optimization (non-breaking, back-end change that speeds up the code) +- [ ] Bug fix (non-breaking change which fixes an issue) +- [ ] Breaking change (whatever its nature) + +## Key checklist + +- [ ] All tests pass (eg. `python -m pytest`) +- [ ] Pre-commit hooks run successfully (eg. `pre-commit run --all-files`) + +## Further checks + +- [ ] Code is commented, particularly in hard-to-understand areas +- [ ] Tests added or an issue has been opened to tackle that in the future. + (Indicate issue here: # (issue)) diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..b406f0f --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,15 @@ +# To get started with Dependabot version updates, you'll need to specify which +# package ecosystems to update and where the package manifests are located. +# Please see the documentation for all configuration options: +# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates + +version: 2 +updates: + - package-ecosystem: uv + directory: / + schedule: + interval: weekly + - package-ecosystem: github-actions + directory: / + schedule: + interval: weekly diff --git a/.github/workflows/auto-merge.yml b/.github/workflows/auto-merge.yml new file mode 100644 index 0000000..0089531 --- /dev/null +++ b/.github/workflows/auto-merge.yml @@ -0,0 +1,23 @@ +name: Dependabot and Pre-commit auto-merge + +on: + pull_request: + +permissions: + contents: write + pull-requests: write # Needed if in a private repository + +jobs: + auto-merge: + runs-on: ubuntu-latest + if: ${{ github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]' }} + steps: + - name: Enable auto-merge for Dependabot PRs + run: | + gh pr review --approve "$PR_URL" + gh pr merge --auto --merge "$PR_URL" + env: + PR_URL: ${{ github.event.pull_request.html_url }} + # GitHub provides this variable in the CI env. You don't + # need to add anything to the secrets vault. + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml new file mode 100644 index 0000000..c0626fb --- /dev/null +++ b/.github/workflows/check-links.yml @@ -0,0 +1,20 @@ +name: Check links in Markdown files +on: + schedule: + - cron: 0 0 * * 1 # midnight every Monday + push: + branches: [main] + pull_request: + workflow_dispatch: + +jobs: + check-links: + name: Linkspector + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - name: Run linkspector + uses: umbrelladocs/action-linkspector@v1 + with: + github_token: ${{ secrets.github_token }} + reporter: github-pr-review diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..1c3d4aa --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,38 @@ +name: Test and build + +on: + push: + branches: [main] + pull_request: + workflow_dispatch: + workflow_call: + +jobs: + test: + runs-on: ${{matrix.os}} + strategy: + fail-fast: false + matrix: + os: + - ubuntu-latest + - windows-latest + - macos-latest + python-version: ['3.13'] + + steps: + - uses: actions/checkout@v6 + - uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + prune-cache: false + activate-environment: true + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: uv sync + + - name: Run mypy + run: mypy . + + - name: Run tests + run: pytest diff --git a/.gitignore b/.gitignore index b7faf40..09be0ef 100644 --- a/.gitignore +++ b/.gitignore @@ -182,9 +182,9 @@ cython_debug/ .abstra/ # Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore # that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, +# and can be added to the global gitignore or merged into this file. However, if you prefer, # you could uncomment the following to ignore the entire vscode folder # .vscode/ diff --git a/.markdownlint.yaml b/.markdownlint.yaml new file mode 100644 index 0000000..3453c97 --- /dev/null +++ b/.markdownlint.yaml @@ -0,0 +1,4 @@ +# Disable checks here +MD013: false +MD007: + indent: 4 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..b804884 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,45 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: check-merge-conflict + - id: debug-statements + - id: trailing-whitespace + - id: end-of-file-fixer + - id: pretty-format-json + args: [--autofix, --indent, '4', --no-sort] + - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks + rev: v2.14.0 + hooks: + - id: pretty-format-yaml + args: [--autofix, --indent, '2', --offset, '2'] + - repo: https://github.com/python-jsonschema/check-jsonschema + rev: 0.33.1 + hooks: + - id: check-dependabot + - id: check-github-actions + - id: check-github-workflows + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.12.0 + hooks: + - id: ruff-check + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.16.1 + hooks: + - id: mypy + - repo: https://github.com/igorshubovych/markdownlint-cli + rev: v0.45.0 + hooks: + - id: markdownlint-fix + - repo: https://github.com/codespell-project/codespell + rev: v2.4.1 + hooks: + - id: codespell + args: [-I, .codespell_ignore.txt] + - repo: https://github.com/ComPWA/taplo-pre-commit + rev: v0.9.3 + hooks: + - id: taplo-format # Format TOML files + - id: taplo-lint diff --git a/.taplo.toml b/.taplo.toml new file mode 100644 index 0000000..33c6825 --- /dev/null +++ b/.taplo.toml @@ -0,0 +1,4 @@ +[formatting] +compact_inline_tables = true +column_width = 88 +indent_string = " " diff --git a/.vscode/extensions.json b/.vscode/extensions.json new file mode 100644 index 0000000..2d06122 --- /dev/null +++ b/.vscode/extensions.json @@ -0,0 +1,9 @@ +{ + "recommendations": [ + "ms-python.mypy-type-checker", + "ms-python.python", + "editorconfig.editorconfig", + "davidanson.vscode-markdownlint", + "charliermarsh.ruff" + ] +} diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..d4817cc --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,11 @@ +{ + "[python]": { + "editor.formatOnSave": true, + "editor.defaultFormatter": "charliermarsh.ruff" + }, + "editor.rulers": [ + 88 + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} diff --git a/README.md b/README.md index 2f8d054..c98d5e0 100644 --- a/README.md +++ b/README.md @@ -1 +1,96 @@ # MUSE2 data analysis + +Python scripts and Jupyter notebooks for analysing and visualising MUSE2 data files. + +This is a Python application that uses [uv] for packaging and dependency management. +It provides [`pre-commit`][pre-commit] hooks for various linters +and formatters and automated tests using [`pytest`][pytest] and [GitHub Actions]. +Pre-commit hooks are automatically kept updated with a dedicated GitHub Action, this can +be removed and replaced with [pre-commit.ci] if using a public repo. The package version +is dynamically generated from the most recent git tag using +[`setuptools-scm`][setuptools-scm]. + +It was developed by the [Imperial College Research Software Engineering Team]. + +## Usage + +To get started: + +1. [Download and install uv] following the instructions for your OS. +1. Activate a git repository (required for `pre-commit` and the package versioning with +`setuptools-scm`): + + ```bash + git init + ``` + +1. Install the package and dependencies and set up the virtual environment: + + ```bash + uv sync + ``` + +1. Activate the virtual environment, or just preface your commands with `uv run` to use +the virtual environment (see [uv activate] for more info): + + ```bash + source .venv/bin/activate + + ``` + + or + + ```bash + uv run + ``` + +1. Install the pre-commit git hooks: + + ```bash + uv run pre-commit install + ``` + +1. Update the pre-commit hooks + + ```bash + uv run pre-commit autoupdate + ``` + +1. Run the main app: + + ```bash + uv run python -m muse2_data_analysis + ``` + +1. Run the tests: + + ```bash + uv run pytest + ``` + +1. Create an initial commit (it's possible there might be some failures in pre-commit): + + ```bash + git add . + git commit -m "Initial commit" + ``` + +## Updating Dependencies + +Use the commands `uv add ` and `uv remove ` to add or remove dependencies. + +- Use the optional flag `--dev` to add/remove development dependencies. +- Include the optional flag `--group ` to add/remove dependencies from specific groups. +- These will automatically update the `pyproject.toml` file. + +For further information, see the [uv] docs for managing dependencies. + +[uv]: https://docs.astral.sh/uv +[pre-commit]: https://pre-commit.com/ +[pytest]: https://pytest.org/ +[GitHub Actions]: https://github.com/features/actions +[pre-commit.ci]: https://pre-commit.ci +[setuptools-scm]: https://setuptools-scm.readthedocs.io/en/latest/ +[Imperial College Research Software Engineering Team]: https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/service-offering/research-software-engineering/ +[Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ +[uv activate]: https://docs.astral.sh/uv/pip/environments/ diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..4dba205 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,45 @@ +site_name: MUSE2 data analysis +watch: [muse2_data_analysis] + +theme: + name: material + +extra_css: + - stylesheets/extra.css + +markdown_extensions: + - admonition + - pymdownx.details + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.snippets: + check_paths: true + - pymdownx.superfences + - toc: + permalink: ¤ + +plugins: + - search + - gen-files: + scripts: + - docs/gen_ref_nav.py + - literate-nav: + nav_file: SUMMARY.md + - section-index + - mkdocstrings: + default_handler: python + handlers: + python: + options: + show_source: true + show_root_heading: true + show_category_heading: true + merge_init_into_class: true + +nav: + - MUSE2 data analysis documentation: index.md + # defer to gen-files + literate-nav + - Code Reference: reference/ diff --git a/muse2_data_analysis/__init__.py b/muse2_data_analysis/__init__.py new file mode 100644 index 0000000..4a10ba2 --- /dev/null +++ b/muse2_data_analysis/__init__.py @@ -0,0 +1,7 @@ +"""The main module for MUSE2 data analysis.""" + +from contextlib import suppress +from importlib.metadata import PackageNotFoundError, version + +with suppress(PackageNotFoundError): + __version__ = version(__name__) diff --git a/muse2_data_analysis/__main__.py b/muse2_data_analysis/__main__.py new file mode 100644 index 0000000..0bd4893 --- /dev/null +++ b/muse2_data_analysis/__main__.py @@ -0,0 +1 @@ +"""The entry point for the MUSE2 data analysis program.""" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..fb6acf1 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,67 @@ +[project] +name = "muse2_data_analysis" +dynamic = ["version"] +description = "Python scripts and Jupyter notebooks for analysing and visualising MUSE2 data files." +authors = [ + {name = "Alex Dewar", email = "a.dewar@imperial.ac.uk"}, + {name = "Imperial College London RSE Team", email = "ict-rse-team@imperial.ac.uk"}, +] +requires-python = ">=3.13" + +dependencies = [] + +[dependency-groups] +dev = [ + "ruff>=0.14.13", + "mypy>=1.19.1", + "pip-tools>=7.5.2", + "pre-commit>=4.5.1", + "pytest>=9.0.2", + "pytest-cov>=7.0.0", + "pytest-mock>=3.15.1", +] + + +[tool.mypy] +disallow_any_explicit = true +disallow_any_generics = true +warn_unreachable = true +warn_unused_ignores = true +disallow_untyped_defs = true +exclude = [".venv/", "docs/"] + +[[tool.mypy.overrides]] +module = "tests.*" +disallow_untyped_defs = false + +[tool.pytest.ini_options] +addopts = "-v -p no:warnings --cov=muse2_data_analysis --cov-branch --cov-report=html --cov-report=xml --doctest-modules --ignore=muse2_data_analysis/__main__.py --ignore=docs/" + +[tool.ruff] +target-version = "py313" + +[tool.ruff.lint] +select = [ + "D", # pydocstyle + "E", # pycodestyle + "F", # Pyflakes + "I", # isort + "UP", # pyupgrade + "RUF", # ruff +] +pydocstyle.convention = "google" + +[tool.ruff.lint.per-file-ignores] +"tests/*" = [ + "D100", # Missing docstring in public module + "D104", # Missing docstring in public package +] + +[build-system] +requires = ["setuptools>=78", "setuptools-scm"] +build-backend = "setuptools.build_meta" + +[tool.setuptools] +packages = ["muse2_data_analysis"] + +[tool.setuptools_scm] diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..f513847 --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""Unit tests for MyProject.""" diff --git a/tests/test_muse2_data_analysis.py b/tests/test_muse2_data_analysis.py new file mode 100644 index 0000000..de7943b --- /dev/null +++ b/tests/test_muse2_data_analysis.py @@ -0,0 +1,8 @@ +"""Tests for the main module.""" + +from muse2_data_analysis import __version__ + + +def test_version(): + """Check that the version is acceptable.""" + assert isinstance(__version__, str) From d2aabec89599ef4741adff64a80b3c5e4c7f92d0 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 13:51:46 +0000 Subject: [PATCH 02/24] Remove unneeded `pip-tools` dep and generate `uv.lock` --- pyproject.toml | 1 - uv.lock | 418 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 418 insertions(+), 1 deletion(-) create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index fb6acf1..46acedd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,6 @@ dependencies = [] dev = [ "ruff>=0.14.13", "mypy>=1.19.1", - "pip-tools>=7.5.2", "pre-commit>=4.5.1", "pytest>=9.0.2", "pytest-cov>=7.0.0", diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..b731c79 --- /dev/null +++ b/uv.lock @@ -0,0 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minimum Python version to 3.14 I don't think we need to worry about backwards compatibility. Apart from anything, we're using `uv`, which should make it dead simple to install Python 3.14. --- .github/workflows/ci.yml | 2 +- pyproject.toml | 4 +-- uv.lock | 55 +--------------------------------------- 3 files changed, 4 insertions(+), 57 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1c3d4aa..cec2968 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: - ubuntu-latest - windows-latest - macos-latest - python-version: ['3.13'] + python-version: ['3.14'] steps: - uses: actions/checkout@v6 diff --git a/pyproject.toml b/pyproject.toml index 46acedd..9a695ea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = [ {name = "Alex Dewar", email = "a.dewar@imperial.ac.uk"}, {name = "Imperial College London RSE Team", email = "ict-rse-team@imperial.ac.uk"}, ] -requires-python = ">=3.13" +requires-python = ">=3.14" dependencies = [] @@ -37,7 +37,7 @@ disallow_untyped_defs = false addopts = "-v -p no:warnings --cov=muse2_data_analysis --cov-branch --cov-report=html --cov-report=xml --doctest-modules --ignore=muse2_data_analysis/__main__.py --ignore=docs/" [tool.ruff] -target-version = "py313" +target-version = "py314" [tool.ruff.lint] select = [ diff --git a/uv.lock b/uv.lock index b731c79..5de8647 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,6 @@ version = 1 revision = 3 -requires-python = ">=3.13" +requires-python = ">=3.14" [[package]] name = "cfgv" @@ -26,32 +26,6 @@ version = "7.13.1" source = { registry = "https://pypi.org/simple" } sdist = { url = "https://files.pythonhosted.org/packages/23/f9/e92df5e07f3fc8d4c7f9a0f146ef75446bf870351cd37b788cf5897f8079/coverage-7.13.1.tar.gz", hash = "sha256:b7593fe7eb5feaa3fbb461ac79aac9f9fc0387a5ca8080b0c6fe2ca27b091afd", size = 825862, upload-time = "2025-12-28T15:42:56.969Z" } wheels = [ - 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pyproject.toml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) delete mode 100644 muse2_data_analysis/__main__.py diff --git a/muse2_data_analysis/__main__.py b/muse2_data_analysis/__main__.py deleted file mode 100644 index 0bd4893..0000000 --- a/muse2_data_analysis/__main__.py +++ /dev/null @@ -1 +0,0 @@ -"""The entry point for the MUSE2 data analysis program.""" diff --git a/pyproject.toml b/pyproject.toml index 9a695ea..fd67e8d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ module = "tests.*" disallow_untyped_defs = false [tool.pytest.ini_options] -addopts = "-v -p no:warnings --cov=muse2_data_analysis --cov-branch --cov-report=html --cov-report=xml --doctest-modules --ignore=muse2_data_analysis/__main__.py --ignore=docs/" +addopts = "-v -p no:warnings --cov=muse2_data_analysis --cov-branch --cov-report=html --cov-report=xml --doctest-modules --ignore=docs/" [tool.ruff] target-version = "py314" From e0ce6159bdcb3828ac6067fa3989169732a4a69f Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 15:17:58 +0000 Subject: [PATCH 05/24] Add functions for finding and running `muse2` --- muse2_data_analysis/__init__.py | 2 ++ muse2_data_analysis/muse2.py | 47 +++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 muse2_data_analysis/muse2.py diff --git a/muse2_data_analysis/__init__.py b/muse2_data_analysis/__init__.py index 4a10ba2..94ce630 100644 --- a/muse2_data_analysis/__init__.py +++ b/muse2_data_analysis/__init__.py @@ -3,5 +3,7 @@ from contextlib import suppress from importlib.metadata import PackageNotFoundError, version +from .muse2 import find_muse2, run_muse2 # noqa: F401 + with suppress(PackageNotFoundError): __version__ = version(__name__) diff --git a/muse2_data_analysis/muse2.py b/muse2_data_analysis/muse2.py new file mode 100644 index 0000000..eb6b526 --- /dev/null +++ b/muse2_data_analysis/muse2.py @@ -0,0 +1,47 @@ +"""Tools for running the muse2 command-line program. + +If the MUSE2_PATH environment variable is set, this will be used, otherwise muse2 will +be searched for on the PATH. +""" + +import os +import shutil +import subprocess as sp +from pathlib import Path + +_muse2_path: Path | None = None + + +def find_muse2() -> Path: + """Get the path to muse2, if any. + + Raises an exception if muse2 is not found. + """ + # Cache path + global _muse2_path + if _muse2_path: + return _muse2_path + + path = os.getenv("MUSE2_PATH") or shutil.which("muse2") + if not path: + raise RuntimeError( + "Could not find path to muse2. Either set the MUSE2_PATH environment " + "variable or installing muse2 to your PATH (e.g. by running 'cargo " + "install muse2')" + ) + + _muse2_path = Path(path) + return _muse2_path + + +def run_muse2(*args: str) -> str: + """Run muse2 with the specified arguments, returning combined stdout and stderr. + + Raises an exception if muse2 is not found. + """ + muse2 = find_muse2() + output = sp.run((muse2, *args), text=True, stdout=sp.PIPE, stderr=sp.STDOUT) + if output.returncode != 0: + raise RuntimeError(f"Error running muse2: {output.stdout}") + + return output.stdout From 7298513350ecec8311ecdc04d5fcdca306daeac2 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 15:38:01 +0000 Subject: [PATCH 06/24] run_muse2: Set MUSE2_USE_DEFAULT_SETTINGS env var --- muse2_data_analysis/muse2.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/muse2_data_analysis/muse2.py b/muse2_data_analysis/muse2.py index eb6b526..658ce6f 100644 --- a/muse2_data_analysis/muse2.py +++ b/muse2_data_analysis/muse2.py @@ -40,7 +40,13 @@ def run_muse2(*args: str) -> str: Raises an exception if muse2 is not found. """ muse2 = find_muse2() - output = sp.run((muse2, *args), text=True, stdout=sp.PIPE, stderr=sp.STDOUT) + output = sp.run( + (muse2, *args), + text=True, + stdout=sp.PIPE, + stderr=sp.STDOUT, + env={"MUSE2_USE_DEFAULT_SETTINGS": "1"}, # ignore user's settings file + ) if output.returncode != 0: raise RuntimeError(f"Error running muse2: {output.stdout}") From 4c56ed5ba117ee859986528f9bf9b08962e56dfb Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 17:55:46 +0000 Subject: [PATCH 07/24] pre-commit: Add `nbstripout` hook --- .pre-commit-config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b804884..232ac90 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,6 +25,10 @@ repos: - id: ruff-check args: [--fix, --exit-non-zero-on-fix] - id: ruff-format + - repo: https://github.com/kynan/nbstripout + rev: 0.8.1 + hooks: + - id: nbstripout - repo: https://github.com/pre-commit/mirrors-mypy rev: v1.16.1 hooks: From c6fce4f9a6cbd1c197eda585d1f6098ebd5b0cb8 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 18:09:47 +0000 Subject: [PATCH 08/24] Add some helper functions for notebooks --- data/.gitignore | 3 +++ data/README.txt | 1 + muse2_data_analysis/helpers.py | 38 ++++++++++++++++++++++++++++++++++ 3 files changed, 42 insertions(+) create mode 100644 data/.gitignore create mode 100644 data/README.txt create mode 100644 muse2_data_analysis/helpers.py diff --git a/data/.gitignore b/data/.gitignore new file mode 100644 index 0000000..ff7b252 --- /dev/null +++ b/data/.gitignore @@ -0,0 +1,3 @@ +* +!README.txt +!.gitignore diff --git a/data/README.txt b/data/README.txt new file mode 100644 index 0000000..b9fdf48 --- /dev/null +++ b/data/README.txt @@ -0,0 +1 @@ +This is a placeholder directory for input/output data for example analyses. diff --git a/muse2_data_analysis/helpers.py b/muse2_data_analysis/helpers.py new file mode 100644 index 0000000..0f578f7 --- /dev/null +++ b/muse2_data_analysis/helpers.py @@ -0,0 +1,38 @@ +"""Helper functions for notebooks.""" + +from pathlib import Path + +from . import run_muse2 + +DATA_DIR = Path(__file__).parent.parent.absolute() / "data" +EXAMPLE_NAME = "muse1_default" +_INPUT_DIR = DATA_DIR / f"{EXAMPLE_NAME}_input" +_OUTPUT_DIR = DATA_DIR / f"{EXAMPLE_NAME}_output" + + +def get_example_input_dir() -> Path: + """Get the directory for example input data. + + If the folder does not exist, we create it by extracting an example from muse2. + """ + if _INPUT_DIR.exists(): + return _INPUT_DIR + + run_muse2("example", "extract", EXAMPLE_NAME, str(_INPUT_DIR)) + return _INPUT_DIR + + +def get_example_output_dir() -> Path: + """Get the directory for example output data. + + If the folder does not exist, we create it by running an example model with muse2. + """ + if _OUTPUT_DIR.exists(): + return _OUTPUT_DIR + + # Ensure INPUT_DIR exists + get_example_input_dir() + + # Run the example model + run_muse2("run", str(_INPUT_DIR), "--output-dir", str(_OUTPUT_DIR)) + return _OUTPUT_DIR From 7d09eb80d78f5569fed1481f937bb72175c9cc1e Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 18:17:58 +0000 Subject: [PATCH 09/24] pre-commit: Drop `taplo-lint` hook It makes network requests which are currently failing for me. --- .pre-commit-config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 232ac90..6032b14 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -46,4 +46,3 @@ repos: rev: v0.9.3 hooks: - id: taplo-format # Format TOML files - - id: taplo-lint From b457cc18b60e62d1aace7a82ef7aff82abb88b58 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Fri, 23 Jan 2026 18:18:07 +0000 Subject: [PATCH 10/24] Add notebooks from MUSE2 repo, using helpers --- .pre-commit-config.yaml | 1 + notebooks/capacity.ipynb | 152 ++++ notebooks/prices.ipynb | 84 +++ pyproject.toml | 2 +- uv.lock | 1491 +++++++++++++++++++++++++++++++++++++- 5 files changed, 1711 insertions(+), 19 deletions(-) create mode 100644 notebooks/capacity.ipynb create mode 100644 notebooks/prices.ipynb diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6032b14..7cd5eee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,6 +8,7 @@ repos: - id: end-of-file-fixer - id: pretty-format-json args: [--autofix, --indent, '4', --no-sort] + exclude: \.ipynb$ - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks rev: v2.14.0 hooks: diff --git a/notebooks/capacity.ipynb b/notebooks/capacity.ipynb new file mode 100644 index 0000000..1af6afd --- /dev/null +++ b/notebooks/capacity.ipynb @@ -0,0 +1,152 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Calculating agent capacity\n", + "\n", + "This notebook contains example data processing using the output of the [`muse1_default`] example\n", + "model.\n", + "\n", + "Output files are mostly in CSV format. The format of output files is documented [here][output-format].\n", + "\n", + "We begin by loading the `model.toml` input file to get the list of milestone years.\n", + "\n", + "[`muse1_default`]: ../../examples/muse1_default/\n", + "[output-format]: https://energysystemsmodellinglab.github.io/MUSE2/file_formats/output_files.html" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "import tomllib\n", + "\n", + "import pandas as pd\n", + "\n", + "sys.path.append(\"..\")\n", + "\n", + "from muse2_data_analysis.helpers import get_example_input_dir, get_example_output_dir\n", + "\n", + "input_dir = get_example_input_dir()\n", + "output_dir = get_example_output_dir()\n", + "\n", + "with (input_dir / \"model.toml\").open(\"rb\") as f:\n", + " model = tomllib.load(f)\n", + "\n", + "# We need to know the milestone years for processing the assets file\n", + "years = model[\"milestone_years\"]" + ] + }, + { + "cell_type": "markdown", + "id": "2", + "metadata": {}, + "source": [ + "## Load and process output data\n", + "\n", + "We next load the output data. In this case, we want to calculate how much capacity was invested in\n", + "different processes for different agents. This information can be found in the `assets.csv` output\n", + "file.\n", + "\n", + "The `assets.csv` file contains information about different assets, including when they were\n", + "commissioned and decommissioned as well as their capacity. To calculate the overall capacity for a\n", + "given agent and process type, we have to process this data. Note that different assets owned by the\n", + "same agent may have the same process ID if the agent has reinvested in the same process type in a\n", + "different year." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3", + "metadata": {}, + "outputs": [], + "source": [ + "# The assets.csv file contains info about which assets were invested in and when\n", + "assets = pd.read_csv(output_dir / \"assets.csv\")\n", + "\n", + "# Assets with no decommission_year are effectively decommissioned after time horizon\n", + "assets[\"decommission_year\"] = assets[\"decommission_year\"].fillna(years[-1] + 1)\n", + "\n", + "# Calculate capacity for each type of process for each agent\n", + "capacity = pd.DataFrame()\n", + "for year in years:\n", + " active = assets[\n", + " (year >= assets[\"commission_year\"]) & (year < assets[\"decommission_year\"])\n", + " ]\n", + "\n", + " # This only works because each agent is responsible for one and only one commodity\n", + " cap_sum = active.groupby([\"agent_id\", \"process_id\"])[\"capacity\"].sum().reset_index()\n", + "\n", + " df = pd.DataFrame(cap_sum)\n", + " df[\"year\"] = year\n", + "\n", + " capacity = pd.concat([capacity, df])\n", + "\n", + "capacity" + ] + }, + { + "cell_type": "markdown", + "id": "4", + "metadata": {}, + "source": [ + "## Plot results\n", + "\n", + "Finally, we plot the results.\n", + "\n", + "Note that each of the agents has invested in only one process type; otherwise there would be\n", + "multiple bars per plot here." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5", + "metadata": {}, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "\n", + "agents = capacity[\"agent_id\"].unique()\n", + "_, axes = plt.subplots(1, len(agents))\n", + "for ax, agent in zip(axes, agents):\n", + " capacity[capacity[\"agent_id\"] == agent].pivot(\n", + " index=\"year\", columns=\"process_id\", values=\"capacity\"\n", + " ).plot(kind=\"bar\", ax=ax)\n", + " ax.set_title(agent)\n", + " ax.set_xlabel(\"Year\")\n", + " ax.set_ylabel(\"Capacity\")\n", + " ax.legend(title=\"Process\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "muse2-data-analysis", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.14.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/prices.ipynb b/notebooks/prices.ipynb new file mode 100644 index 0000000..97aaa0c --- /dev/null +++ b/notebooks/prices.ipynb @@ -0,0 +1,84 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "# Plotting commodity prices\n", + "\n", + "This notebook shows how to plot commodity prices, using the [`muse1_default`] example model.\n", + "\n", + "We first load the prices from the `commodity_prices.csv` output file.\n", + "\n", + "[`muse1_default`]: ../../examples/muse1_default/" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "\n", + "import pandas as pd\n", + "\n", + "sys.path.append(\"..\")\n", + "\n", + "from muse2_data_analysis.helpers import get_example_output_dir\n", + "\n", + "output_dir = get_example_output_dir()\n", + "prices = pd.read_csv(output_dir / \"commodity_prices.csv\")\n", + "prices.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "from matplotlib import pyplot as plt\n", + "\n", + "COMMODITY_ID = \"heat\"\n", + "\n", + "# This won't work if there are multiple regions\n", + "assert prices[\"region_id\"].nunique() == 1\n", + "\n", + "_, ax = plt.subplots()\n", + "\n", + "prices[prices[\"commodity_id\"] == COMMODITY_ID].pivot(\n", + " index=\"milestone_year\", columns=\"time_slice\", values=\"price\"\n", + ").plot(kind=\"bar\", ax=ax)\n", + "\n", + "ax.set_xlabel(\"Milestone year\")\n", + "ax.set_ylabel(\"Price\")\n", + "ax.legend(title=\"Time slice\");" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "muse2-data-analysis", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.14.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pyproject.toml b/pyproject.toml index fd67e8d..2a3cad8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ authors = [ ] requires-python = ">=3.14" -dependencies = [] +dependencies = ["matplotlib>=3.10.8", "notebook>=7.5.2", "pandas>=3.0.0"] [dependency-groups] dev = [ diff --git a/uv.lock b/uv.lock index 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"2025-10-07T21:16:34.951Z" }, +] From 1e8e3c0794f6cc4f3da913e302f0add0f7873534 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 10:10:40 +0000 Subject: [PATCH 11/24] CI: Use lychee cf. Linkspector for checking links --- .github/workflows/check-links.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml index c0626fb..f3cea05 100644 --- a/.github/workflows/check-links.yml +++ b/.github/workflows/check-links.yml @@ -9,12 +9,9 @@ on: jobs: check-links: - name: Linkspector + name: Lychee link checker runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - - name: Run linkspector - uses: umbrelladocs/action-linkspector@v1 - with: - github_token: ${{ secrets.github_token }} - reporter: github-pr-review + - id: lychee + uses: lycheeverse/lychee-action@v2 From 4d7732e3261c925f6fcf502cf1d618abea2c9b71 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 10:41:20 +0000 Subject: [PATCH 12/24] Update README.md --- README.md | 73 +++++++++---------------------------------------------- 1 file changed, 12 insertions(+), 61 deletions(-) diff --git a/README.md b/README.md index c98d5e0..d13da3b 100644 --- a/README.md +++ b/README.md @@ -1,28 +1,18 @@ # MUSE2 data analysis -Python scripts and Jupyter notebooks for analysing and visualising MUSE2 data files. +> :warning: **Note that this repository is currently a work in progress.** :warning: -This is a Python application that uses [uv] for packaging and dependency management. -It provides [`pre-commit`][pre-commit] hooks for various linters -and formatters and automated tests using [`pytest`][pytest] and [GitHub Actions]. -Pre-commit hooks are automatically kept updated with a dedicated GitHub Action, this can -be removed and replaced with [pre-commit.ci] if using a public repo. The package version -is dynamically generated from the most recent git tag using -[`setuptools-scm`][setuptools-scm]. +This repository contains Python scripts and Jupyter notebooks for analysing and +visualising [MUSE2] data files. -It was developed by the [Imperial College Research Software Engineering Team]. +We recommend using [uv] for installing dependencies and managing your virtual +environment. ## Usage To get started: 1. [Download and install uv] following the instructions for your OS. -1. Activate a git repository (required for `pre-commit` and the package versioning with -`setuptools-scm`): - - ```bash - git init - ``` 1. Install the package and dependencies and set up the virtual environment: @@ -44,53 +34,14 @@ the virtual environment (see [uv activate] for more info): uv run ``` -1. Install the pre-commit git hooks: - - ```bash - uv run pre-commit install - ``` - -1. Update the pre-commit hooks - - ```bash - uv run pre-commit autoupdate - ``` - -1. Run the main app: - - ```bash - uv run python -m muse2_data_analysis - ``` - -1. Run the tests: - - ```bash - uv run pytest - ``` - -1. Create an initial commit (it's possible there might be some failures in pre-commit): - - ```bash - git add . - git commit -m "Initial commit" - ``` - -## Updating Dependencies - -Use the commands `uv add ` and `uv remove ` to add or remove dependencies. - -- Use the optional flag `--dev` to add/remove development dependencies. -- Include the optional flag `--group ` to add/remove dependencies from specific groups. -- These will automatically update the `pyproject.toml` file. - -For further information, see the [uv] docs for managing dependencies. +There are some example notebooks in the [`notebooks`] folder to get you started. +[MUSE2]: https://github.com/EnergySystemsModellingLab/MUSE2 [uv]: https://docs.astral.sh/uv -[pre-commit]: https://pre-commit.com/ -[pytest]: https://pytest.org/ -[GitHub Actions]: https://github.com/features/actions -[pre-commit.ci]: https://pre-commit.ci -[setuptools-scm]: https://setuptools-scm.readthedocs.io/en/latest/ -[Imperial College Research Software Engineering Team]: https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/service-offering/research-software-engineering/ [Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ [uv activate]: https://docs.astral.sh/uv/pip/environments/ +[`notebooks`] ./notebooks + +## Copyright + +Copyright © 2026 Imperial College London From d612d22cecf4c7afda626d837dd04ff27f910245 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 11:22:35 +0000 Subject: [PATCH 13/24] MyProject => muse2_data_analysis Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- tests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/__init__.py b/tests/__init__.py index f513847..a3c5152 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -1 +1 @@ -"""Unit tests for MyProject.""" +"""Unit tests for muse2_data_analysis.""" From 273c436f474b85d57bc195885b7b0147f5bc6fcd Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 11:23:22 +0000 Subject: [PATCH 14/24] README.md: Missing colon for link Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d13da3b..6eb8792 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,7 @@ There are some example notebooks in the [`notebooks`] folder to get you started. [uv]: https://docs.astral.sh/uv [Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ [uv activate]: https://docs.astral.sh/uv/pip/environments/ -[`notebooks`] ./notebooks +[`notebooks`]: ./notebooks ## Copyright From d976d070947ef2d5d9ffd3088342e1b2910c3066 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 11:30:10 +0000 Subject: [PATCH 15/24] Fix: Include existing env vars when invoking `muse2` --- muse2_data_analysis/muse2.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/muse2_data_analysis/muse2.py b/muse2_data_analysis/muse2.py index 658ce6f..5a8696a 100644 --- a/muse2_data_analysis/muse2.py +++ b/muse2_data_analysis/muse2.py @@ -45,7 +45,10 @@ def run_muse2(*args: str) -> str: text=True, stdout=sp.PIPE, stderr=sp.STDOUT, - env={"MUSE2_USE_DEFAULT_SETTINGS": "1"}, # ignore user's settings file + env={ + **os.environ, + "MUSE2_USE_DEFAULT_SETTINGS": "1", # ignore user's settings file + }, ) if output.returncode != 0: raise RuntimeError(f"Error running muse2: {output.stdout}") From 304c8028f13f6840a959f05f990f18a079e4d661 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 11:32:03 +0000 Subject: [PATCH 16/24] Use `check=True` for `sp.run` This is better than hand-rolling the error-checking code. --- muse2_data_analysis/muse2.py | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/muse2_data_analysis/muse2.py b/muse2_data_analysis/muse2.py index 5a8696a..6925d36 100644 --- a/muse2_data_analysis/muse2.py +++ b/muse2_data_analysis/muse2.py @@ -40,17 +40,20 @@ def run_muse2(*args: str) -> str: Raises an exception if muse2 is not found. """ muse2 = find_muse2() - output = sp.run( - (muse2, *args), - text=True, - stdout=sp.PIPE, - stderr=sp.STDOUT, - env={ - **os.environ, - "MUSE2_USE_DEFAULT_SETTINGS": "1", # ignore user's settings file - }, - ) - if output.returncode != 0: - raise RuntimeError(f"Error running muse2: {output.stdout}") + + try: + output = sp.run( + (muse2, *args), + text=True, + stdout=sp.PIPE, + stderr=sp.STDOUT, + env={ + **os.environ, + "MUSE2_USE_DEFAULT_SETTINGS": "1", # ignore user's settings file + }, + check=True, + ) + except sp.CalledProcessError as e: + raise RuntimeError(f"Error running muse2: {e.stdout}") return output.stdout From 94002105f49f575c789bcb468cf047efee181d67 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Mon, 26 Jan 2026 11:34:26 +0000 Subject: [PATCH 17/24] Remove unnecessary `sys.path.append` from notebooks The user should just install the `muse2_data_analysis` into their virtualenv instead. --- notebooks/capacity.ipynb | 5 +---- notebooks/prices.ipynb | 6 +----- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/notebooks/capacity.ipynb b/notebooks/capacity.ipynb index 1af6afd..aa22048 100644 --- a/notebooks/capacity.ipynb +++ b/notebooks/capacity.ipynb @@ -25,13 +25,10 @@ "metadata": {}, "outputs": [], "source": [ - "import sys\n", "import tomllib\n", "\n", "import pandas as pd\n", "\n", - "sys.path.append(\"..\")\n", - "\n", "from muse2_data_analysis.helpers import get_example_input_dir, get_example_output_dir\n", "\n", "input_dir = get_example_input_dir()\n", @@ -130,7 +127,7 @@ ], "metadata": { "kernelspec": { - "display_name": "muse2-data-analysis", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, diff --git a/notebooks/prices.ipynb b/notebooks/prices.ipynb index 97aaa0c..9b2d3d8 100644 --- a/notebooks/prices.ipynb +++ b/notebooks/prices.ipynb @@ -21,12 +21,8 @@ "metadata": {}, "outputs": [], "source": [ - "import sys\n", - "\n", "import pandas as pd\n", "\n", - "sys.path.append(\"..\")\n", - "\n", "from muse2_data_analysis.helpers import get_example_output_dir\n", "\n", "output_dir = get_example_output_dir()\n", @@ -62,7 +58,7 @@ ], "metadata": { "kernelspec": { - "display_name": "muse2-data-analysis", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, From a717b9d539f259f76bf58cac125ecfbfd6323e88 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Tue, 27 Jan 2026 14:16:24 +0000 Subject: [PATCH 18/24] Add instructions for activating venv on Windows --- README.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6eb8792..9dda12f 100644 --- a/README.md +++ b/README.md @@ -21,14 +21,22 @@ To get started: ``` 1. Activate the virtual environment, or just preface your commands with `uv run` to use -the virtual environment (see [uv activate] for more info): +the virtual environment (see [uv docs] for more info). + + To activate on Linux/macOS: ```bash source .venv/bin/activate ``` - or + To activate on Windows: + + ```powershell + .venv\Scripts\activate + ``` + + Or run the command directly: ```bash uv run @@ -39,7 +47,7 @@ There are some example notebooks in the [`notebooks`] folder to get you started. [MUSE2]: https://github.com/EnergySystemsModellingLab/MUSE2 [uv]: https://docs.astral.sh/uv [Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ -[uv activate]: https://docs.astral.sh/uv/pip/environments/ +[uv docs]: https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment [`notebooks`]: ./notebooks ## Copyright From 3014850f30c0a87a03c13e8c032cf1eec373159a Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Tue, 27 Jan 2026 15:42:05 +0000 Subject: [PATCH 19/24] Rename vars in notebooks --- notebooks/capacity.ipynb | 8 ++++---- notebooks/prices.ipynb | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/notebooks/capacity.ipynb b/notebooks/capacity.ipynb index aa22048..b5673a8 100644 --- a/notebooks/capacity.ipynb +++ b/notebooks/capacity.ipynb @@ -31,10 +31,10 @@ "\n", "from muse2_data_analysis.helpers import get_example_input_dir, get_example_output_dir\n", "\n", - "input_dir = get_example_input_dir()\n", - "output_dir = get_example_output_dir()\n", + "INPUT_DIR = get_example_input_dir()\n", + "OUTPUT_DIR = get_example_output_dir()\n", "\n", - "with (input_dir / \"model.toml\").open(\"rb\") as f:\n", + "with (INPUT_DIR / \"model.toml\").open(\"rb\") as f:\n", " model = tomllib.load(f)\n", "\n", "# We need to know the milestone years for processing the assets file\n", @@ -67,7 +67,7 @@ "outputs": [], "source": [ "# The assets.csv file contains info about which assets were invested in and when\n", - "assets = pd.read_csv(output_dir / \"assets.csv\")\n", + "assets = pd.read_csv(OUTPUT_DIR / \"assets.csv\")\n", "\n", "# Assets with no decommission_year are effectively decommissioned after time horizon\n", "assets[\"decommission_year\"] = assets[\"decommission_year\"].fillna(years[-1] + 1)\n", diff --git a/notebooks/prices.ipynb b/notebooks/prices.ipynb index 9b2d3d8..b57854f 100644 --- a/notebooks/prices.ipynb +++ b/notebooks/prices.ipynb @@ -25,8 +25,8 @@ "\n", "from muse2_data_analysis.helpers import get_example_output_dir\n", "\n", - "output_dir = get_example_output_dir()\n", - "prices = pd.read_csv(output_dir / \"commodity_prices.csv\")\n", + "INPUT_DIR = get_example_output_dir()\n", + "prices = pd.read_csv(INPUT_DIR / \"commodity_prices.csv\")\n", "prices.head()" ] }, From 3fc289a164f45ef246f8e15d2090ebe0040bfcb9 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Tue, 27 Jan 2026 15:46:00 +0000 Subject: [PATCH 20/24] VS Code: Recommend Jupyter extension --- .vscode/extensions.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 2d06122..14113cf 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,7 +1,8 @@ { "recommendations": [ - "ms-python.mypy-type-checker", "ms-python.python", + "ms-python.mypy-type-checker", + "ms-toolsai.jupyter", "editorconfig.editorconfig", "davidanson.vscode-markdownlint", "charliermarsh.ruff" From 793fc2aff38c654f49f995b0aea9db86926f9f1e Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Tue, 27 Jan 2026 15:47:30 +0000 Subject: [PATCH 21/24] Provide instructions on viewing notebooks --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9dda12f..4b88369 100644 --- a/README.md +++ b/README.md @@ -42,13 +42,22 @@ the virtual environment (see [uv docs] for more info). uv run ``` -There are some example notebooks in the [`notebooks`] folder to get you started. +There are some example notebooks in the [`notebooks`] folder to get you started. You can +view these with Jupyter notebook, like so: + +```bash +uv run jupyter notebook +``` + +If you are using Visual Studio Code, you can also view them directly in your IDE with +[the Jupyter extension]. [MUSE2]: https://github.com/EnergySystemsModellingLab/MUSE2 [uv]: https://docs.astral.sh/uv [Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ [uv docs]: https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment [`notebooks`]: ./notebooks +[the Jupyter extension]: https://code.visualstudio.com/docs/datascience/jupyter-notebooks ## Copyright From cb644a854b69a33bb7324d0d3005d14b89c4f27b Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Tue, 27 Jan 2026 16:07:07 +0000 Subject: [PATCH 22/24] Add instructions on adding to `PATH` or setting env vars --- README.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/README.md b/README.md index 4b88369..d8faa76 100644 --- a/README.md +++ b/README.md @@ -42,6 +42,25 @@ the virtual environment (see [uv docs] for more info). uv run ``` +1. Make sure the Python code can find your MUSE2 installation. (If you have not yet +installed MUSE2, [follow the instructions here][install-muse2].) + + There are two ways you can do this: + + 1. Make sure the `muse2` executable is on your [`PATH`]: + + - [Instructions for Windows][windows-path] + - [Instructions for Linux][linux-path] + - [Instructions for macOS][macos-path] + + (If you installed MUSE2 with `cargo`, it should already be on your `PATH`.) + + 1. Set the `MUSE2_PATH` environment variable to the full path of the `muse2` + executable file. + + You can either do this by [setting the environment variable from within + Jupyter][jupyter-envvar] or from your shell before you launch Jupyter notebook. + There are some example notebooks in the [`notebooks`] folder to get you started. You can view these with Jupyter notebook, like so: @@ -56,6 +75,12 @@ If you are using Visual Studio Code, you can also view them directly in your IDE [uv]: https://docs.astral.sh/uv [Download and install uv]: https://docs.astral.sh/uv/getting-started/installation/ [uv docs]: https://docs.astral.sh/uv/pip/environments/#creating-a-virtual-environment +[install-muse2]: https://energysystemsmodellinglab.github.io/MUSE2/#getting-started +[`PATH`]: https://en.wikipedia.org/wiki/PATH_(variable) +[windows-path]: https://stackoverflow.com/a/41895179 +[linux-path]: https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere +[macos-path]: https://apple.stackexchange.com/a/41586 +[jupyter-envvar]: https://stackoverflow.com/a/44251637 [`notebooks`]: ./notebooks [the Jupyter extension]: https://code.visualstudio.com/docs/datascience/jupyter-notebooks From b05da63d2b7aea034768fbe11ff43aa5705f9f23 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Wed, 28 Jan 2026 08:39:47 +0000 Subject: [PATCH 23/24] Apply Copilot fixes for wording Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- .github/workflows/auto-merge.yml | 2 +- muse2_data_analysis/muse2.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/auto-merge.yml b/.github/workflows/auto-merge.yml index 0089531..28a395b 100644 --- a/.github/workflows/auto-merge.yml +++ b/.github/workflows/auto-merge.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest if: ${{ github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]' }} steps: - - name: Enable auto-merge for Dependabot PRs + - name: Enable auto-merge for bot PRs run: | gh pr review --approve "$PR_URL" gh pr merge --auto --merge "$PR_URL" diff --git a/muse2_data_analysis/muse2.py b/muse2_data_analysis/muse2.py index 6925d36..19e8f0b 100644 --- a/muse2_data_analysis/muse2.py +++ b/muse2_data_analysis/muse2.py @@ -26,7 +26,7 @@ def find_muse2() -> Path: if not path: raise RuntimeError( "Could not find path to muse2. Either set the MUSE2_PATH environment " - "variable or installing muse2 to your PATH (e.g. by running 'cargo " + "variable or install muse2 to your PATH (e.g. by running 'cargo " "install muse2')" ) From 9618677a9751edc7e4555db39aa1b45b17a91191 Mon Sep 17 00:00:00 2001 From: Alex Dewar Date: Wed, 28 Jan 2026 08:40:27 +0000 Subject: [PATCH 24/24] Remove unused `mkdocs.yml` file --- mkdocs.yml | 45 --------------------------------------------- 1 file changed, 45 deletions(-) delete mode 100644 mkdocs.yml diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index 4dba205..0000000 --- a/mkdocs.yml +++ /dev/null @@ -1,45 +0,0 @@ -site_name: MUSE2 data analysis -watch: [muse2_data_analysis] - -theme: - name: material - -extra_css: - - stylesheets/extra.css - -markdown_extensions: - - admonition - - pymdownx.details - - pymdownx.highlight: - anchor_linenums: true - line_spans: __span - pygments_lang_class: true - - pymdownx.inlinehilite - - pymdownx.snippets: - check_paths: true - - pymdownx.superfences - - toc: - permalink: ¤ - -plugins: - - search - - gen-files: - scripts: - - docs/gen_ref_nav.py - - literate-nav: - nav_file: SUMMARY.md - - section-index - - mkdocstrings: - default_handler: python - handlers: - python: - options: - show_source: true - show_root_heading: true - show_category_heading: true - merge_init_into_class: true - -nav: - - MUSE2 data analysis documentation: index.md - # defer to gen-files + literate-nav - - Code Reference: reference/