From 78fe3e511e598e4bc9547c249cb7bc071a655d4e Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 06:58:45 +1000 Subject: [PATCH 01/15] Build docs with uv from a locked environment Manage the docs build environment with astral-sh/setup-uv and uv sync instead of pip-installing uv into a setup-python interpreter. Track uv.lock and install with --frozen so the documentation is built from pinned, reproducible dependency versions, with the uv cache reused across runs. --- .github/workflows/docs.yml | 20 +- uv.lock | 4665 ++++++++++++++++++++++++++++++++++++ 2 files changed, 4673 insertions(+), 12 deletions(-) create mode 100644 uv.lock diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 8ef3b7cd..7f08cd27 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -22,17 +22,15 @@ jobs: - uses: actions/checkout@v4 with: persist-credentials: false - - uses: actions/setup-python@v5 + - uses: astral-sh/setup-uv@v6 with: - python-version: '3.14' + enable-cache: true - name: Install pandoc run: sudo apt-get install -y pandoc - name: Install Python dependencies - run: | - python -m pip install uv - uv pip install --system -e ".[docs]" + run: uv sync --python 3.14 --extra docs --no-default-groups --frozen - name: Build documentation - run: python -m sphinx.cmd.build docs doc_build -j2 + run: uv run python -m sphinx.cmd.build docs doc_build -j2 - name: Deploy to atomicateam/docs uses: JamesIves/github-pages-deploy-action@v4 with: @@ -58,21 +56,19 @@ jobs: - uses: actions/checkout@v4 with: persist-credentials: false - - uses: actions/setup-python@v5 + - uses: astral-sh/setup-uv@v6 if: github.event.action != 'closed' with: - python-version: '3.14' + enable-cache: true - name: Install pandoc if: github.event.action != 'closed' run: sudo apt-get install -y pandoc - name: Install Python dependencies if: github.event.action != 'closed' - run: | - python -m pip install uv - uv pip install --system -e ".[docs]" + run: uv sync --python 3.14 --extra docs --no-default-groups --frozen - name: Build documentation if: github.event.action != 'closed' - run: python -m sphinx.cmd.build docs doc_build -j2 + run: uv run python -m sphinx.cmd.build docs doc_build -j2 - name: Deploy / update / remove preview uses: rossjrw/pr-preview-action@v1 with: diff --git a/uv.lock 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upload-time = "2025-09-14T22:18:19.088Z" }, +] From 88357b6728ae1e5fa4134ef8bcda054eaf066cd7 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 07:12:48 +1000 Subject: [PATCH 02/15] Add GitHub Actions test workflow using uv Run the test suite on GitHub Actions across Ubuntu, macOS, and Windows, driving pytest directly with uv (uv sync + uv run pytest) rather than tox. The pytest configuration in tox.ini [pytest] is reused as-is, so junit and coverage reports are still produced; test results are published with mikepenz/action-junit-report. The Azure Pipelines test job is left in place for now, until deployment is also migrated. Pin the Python version via a tracked .python-version file instead of hardcoding it, and update the docs workflow to rely on it as well. --- .github/workflows/docs.yml | 4 ++-- .github/workflows/tests.yml | 42 +++++++++++++++++++++++++++++++++++++ .gitignore | 2 +- .python-version | 1 + 4 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/tests.yml create mode 100644 .python-version diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 7f08cd27..d49119f6 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -28,7 +28,7 @@ jobs: - name: Install pandoc run: sudo apt-get install -y pandoc - name: Install Python dependencies - run: uv sync --python 3.14 --extra docs --no-default-groups --frozen + run: uv sync --extra docs --no-default-groups --frozen - name: Build documentation run: uv run python -m sphinx.cmd.build docs doc_build -j2 - name: Deploy to atomicateam/docs @@ -65,7 +65,7 @@ jobs: run: sudo apt-get install -y pandoc - name: Install Python dependencies if: github.event.action != 'closed' - run: uv sync --python 3.14 --extra docs --no-default-groups --frozen + run: uv sync --extra docs --no-default-groups --frozen - name: Build documentation if: github.event.action != 'closed' run: uv run python -m sphinx.cmd.build docs doc_build -j2 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 00000000..0f7bc6dd --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,42 @@ +name: Tests + +on: + workflow_dispatch: + pull_request: + +permissions: + contents: read + checks: write + pull-requests: write + +jobs: + test: + name: Tests (${{ matrix.os }}) + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + runs-on: ${{ matrix.os }} + steps: + - name: Checkout sources + uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + # Python version comes from .python-version (read automatically by uv) + - name: Install dependencies + run: uv sync --extra test --no-default-groups --frozen + + # pytest config (junit, coverage, -n 2) lives in tox.ini [pytest]; these + # flags add the notebook (nbval) validation that tox layered on top + - name: Run tests + run: uv run pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope --durations=25 + + - name: Publish test results + uses: mikepenz/action-junit-report@v6 + if: always() + with: + report_paths: junit/test-results.xml diff --git a/.gitignore b/.gitignore index f6b572b9..f8747c3f 100644 --- a/.gitignore +++ b/.gitignore @@ -73,7 +73,7 @@ target/ .ipynb_checkpoints # pyenv -.python-version +# .python-version is intentionally tracked to pin the Python version for uv # celery beat schedule file celerybeat-schedule diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..6324d401 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.14 From 227d80cf27f625080c0e772e4b6987c43d8b6142 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:33:52 +1000 Subject: [PATCH 03/15] Add PyPI publish workflow gated on tests Publish to PyPI whenever main is updated (any push, not only PR merges), after the full cross-platform test suite passes. The test workflow is made reusable (workflow_call) and invoked as a dependency, so publishing only proceeds when every matrix leg succeeds. Follow current packaging best practices: build sdist and wheel with uv on a job with no publishing rights, then publish from a separate job using PyPI Trusted Publishing (OIDC) via a dedicated pypi environment, so no API token is stored. skip-existing avoids failures when main is pushed without a version bump. The Azure Pipelines deploy job is left in place for now. --- .github/workflows/publish.yml | 58 +++++++++++++++++++++++++++++++++++ .github/workflows/tests.yml | 1 + 2 files changed, 59 insertions(+) create mode 100644 .github/workflows/publish.yml diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 00000000..e10e7b89 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,58 @@ +name: Publish + +# Publish to PyPI whenever main is updated (any push, not only PR merges), +# but only after the full test suite passes. +on: + push: + branches: [main] + +# Ceiling for the reusable test job (its junit reporter needs checks: write); +# the build/publish jobs narrow this further at the job level. +permissions: + contents: read + checks: write + pull-requests: write + +jobs: + # Run the full cross-platform test suite (reusable workflow) + test: + uses: ./.github/workflows/tests.yml + + # Build sdist + wheel once, on a job with no publishing privileges + build: + needs: test + runs-on: ubuntu-latest + permissions: + contents: read + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + - name: Build sdist and wheel + run: uv build + - uses: actions/upload-artifact@v4 + with: + name: dist + path: dist/ + + # Publish via PyPI Trusted Publishing (OIDC) - no API token/secret needed + publish: + needs: build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/atomica + permissions: + id-token: write + steps: + - uses: actions/download-artifact@v4 + with: + name: dist + path: dist/ + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + # main can be pushed without a version bump; skip instead of failing + # when the version already exists on PyPI + skip-existing: true diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 0f7bc6dd..c5ee3807 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -3,6 +3,7 @@ name: Tests on: workflow_dispatch: pull_request: + workflow_call: permissions: contents: read From fe493c97ca340f513c92dad0319d6e8e4da8502b Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:35:09 +1000 Subject: [PATCH 04/15] Remove Azure Pipelines PyPI deploy job PyPI publishing is now handled by the GitHub Actions publish workflow, so drop the Azure deploy job to avoid two systems publishing to PyPI on main. The Azure tox test job is kept for now. --- azure-pipelines.yml | 24 +----------------------- 1 file changed, 1 insertion(+), 23 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index e4bd6a54..2c07d1e7 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -46,27 +46,5 @@ jobs: # reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov' # Documentation is built and published via GitHub Actions (.github/workflows/docs.yml) - -- job: 'deploy' - dependsOn: 'tox' - condition: and(ne(variables['Build.Reason'], 'Schedule'),and(succeeded(), eq(variables['Build.SourceBranch'], 'refs/heads/main'))) - pool: - vmImage: 'ubuntu-latest' - steps: - - task: UsePythonVersion@0 - displayName: 'Select python version' - inputs: - versionSpec: '3.14' - - script: | - python -m pip install build - python -m pip install twine - python -m build - displayName: 'Build Atomica' - - task: TwineAuthenticate@1 - displayName: 'Twine Authenticate' - inputs: - pythonUploadServiceConnection: pypi_atomica - - script: | - python -m twine upload -r "pypi_atomica" --config-file $(PYPIRC_PATH) dist/* - displayName: 'Upload to PyPI' +# PyPI publishing is handled via GitHub Actions (.github/workflows/publish.yml) From e306fc712ed71d3b3486e95a05731f5d4c80187d Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:45:03 +1000 Subject: [PATCH 05/15] Tidy comments in publish workflow --- .github/workflows/publish.yml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index e10e7b89..d04249b6 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -1,24 +1,23 @@ name: Publish - # Publish to PyPI whenever main is updated (any push, not only PR merges), -# but only after the full test suite passes. +# but only after the full test suite passes + on: push: branches: [main] -# Ceiling for the reusable test job (its junit reporter needs checks: write); -# the build/publish jobs narrow this further at the job level. permissions: contents: read checks: write pull-requests: write jobs: - # Run the full cross-platform test suite (reusable workflow) + + # Run pre-deployment tests test: uses: ./.github/workflows/tests.yml - # Build sdist + wheel once, on a job with no publishing privileges + # Build build: needs: test runs-on: ubuntu-latest @@ -36,7 +35,7 @@ jobs: name: dist path: dist/ - # Publish via PyPI Trusted Publishing (OIDC) - no API token/secret needed + # Publish publish: needs: build runs-on: ubuntu-latest @@ -53,6 +52,5 @@ jobs: - name: Publish to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: - # main can be pushed without a version bump; skip instead of failing - # when the version already exists on PyPI + # main can be pushed without a version bump; skip instead of failing when the version already exists on PyPI skip-existing: true From 86ac15a6a243f8817b19f2b366525e9e89208254 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:49:19 +1000 Subject: [PATCH 06/15] Surface coverage in the Actions run summary Add a CodeCoverageSummary step that renders the Cobertura coverage.xml into the GitHub Actions job summary, so coverage is visible in the run without posting a PR comment. Run it only on the Linux matrix leg (Docker action; coverage is identical across platforms) and never fail the build on it. --- .github/workflows/tests.yml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c5ee3807..fe150697 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -41,3 +41,20 @@ jobs: if: always() with: report_paths: junit/test-results.xml + + # Surface coverage in the Actions run summary (no PR comment). Only on + # Linux: this is a Docker action, and coverage is the same across the OS + # matrix, so one report avoids duplication. + - name: Coverage summary + uses: irongut/CodeCoverageSummary@v1.3.0 + if: always() && matrix.os == 'ubuntu-latest' + continue-on-error: true + with: + filename: coverage.xml + format: markdown + output: both + - name: Add coverage to job summary + if: always() && matrix.os == 'ubuntu-latest' + continue-on-error: true + shell: bash + run: cat code-coverage-results.md >> "$GITHUB_STEP_SUMMARY" From a5dd10bc208e4b9cc2de4b54cf707c3719f1d9f9 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:51:36 +1000 Subject: [PATCH 07/15] Use coverage.py markdown output for the coverage summary Replace the irongut/CodeCoverageSummary Docker action with coverage.py's built-in markdown report piped to the Actions job summary. This drops a third-party dependency, stays in sync with the installed coverage version, and needs no Docker. --- .github/workflows/tests.yml | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index fe150697..2b980d2d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -42,19 +42,13 @@ jobs: with: report_paths: junit/test-results.xml - # Surface coverage in the Actions run summary (no PR comment). Only on - # Linux: this is a Docker action, and coverage is the same across the OS - # matrix, so one report avoids duplication. + # Surface coverage in the Actions run summary (no PR comment) using + # coverage.py's own markdown output - no third-party action needed. Only + # once (Linux); coverage is the same across the OS matrix. - name: Coverage summary - uses: irongut/CodeCoverageSummary@v1.3.0 - if: always() && matrix.os == 'ubuntu-latest' - continue-on-error: true - with: - filename: coverage.xml - format: markdown - output: both - - name: Add coverage to job summary if: always() && matrix.os == 'ubuntu-latest' continue-on-error: true shell: bash - run: cat code-coverage-results.md >> "$GITHUB_STEP_SUMMARY" + run: | + echo "## Coverage" >> "$GITHUB_STEP_SUMMARY" + uv run coverage report --format=markdown >> "$GITHUB_STEP_SUMMARY" From d2208a8590751c7ccbd74fa908689a9227f9db91 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:57:35 +1000 Subject: [PATCH 08/15] Remove Azure Pipelines CI has fully migrated to GitHub Actions (tests, docs, and PyPI publishing), so drop azure-pipelines.yml and its dead build-status badge from the README. --- README.md | 2 -- azure-pipelines.yml | 50 --------------------------------------------- 2 files changed, 52 deletions(-) delete mode 100644 azure-pipelines.yml diff --git a/README.md b/README.md index 6b70d192..fcf321da 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ # Atomica -[![Build Status](https://dev.azure.com/AtomicaTeam/Atomica/_apis/build/status/atomicateam.atomica?branchName=master)](https://dev.azure.com/AtomicaTeam/Atomica/_build/latest?definitionId=1&branchName=master) - [![PyPi version](https://badgen.net/pypi/v/atomica/)](https://pypi.org/project/atomica) Atomica is a simulation engine for compartmental models. It can be used to simulate disease epidemics, health care cascades, and many other things. diff --git a/azure-pipelines.yml b/azure-pipelines.yml deleted file mode 100644 index 2c07d1e7..00000000 --- a/azure-pipelines.yml +++ /dev/null @@ -1,50 +0,0 @@ -schedules: -- cron: "0 13 * * *" - displayName: Nightly build - branches: - include: - - main - - develop - -jobs: -- job: 'tox' - variables: - python.version: '3.14' - TOXENV: 'py314' - strategy: - matrix: - linux: - imageName: 'ubuntu-latest' - mac: - imageName: 'macos-latest' - windows: - imageName: 'windows-latest' - pool: - vmImage: $(imageName) - steps: - - task: UsePythonVersion@0 - displayName: 'Use Python $(python.version)' - inputs: - versionSpec: '$(python.version)' - - - script: python -m pip install --upgrade pip && python -m pip install tox tox-uv - displayName: 'Install Tox' - - - script: tox -e $(TOXENV) - displayName: 'Run Tox tests' - - - task: PublishTestResults@2 - inputs: - testResultsFiles: '**/test-*.xml' - testRunTitle: 'Publish test results for Python $(python.version)' - condition: succeededOrFailed() - - - task: PublishCodeCoverageResults@2 - inputs: - codeCoverageTool: Cobertura - summaryFileLocation: '$(System.DefaultWorkingDirectory)/**/coverage.xml' -# reportDirectory: '$(System.DefaultWorkingDirectory)/**/htmlcov' - -# Documentation is built and published via GitHub Actions (.github/workflows/docs.yml) -# PyPI publishing is handled via GitHub Actions (.github/workflows/publish.yml) - From 8add7985ca88b895931b6e58c066979d7138da15 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 09:57:35 +1000 Subject: [PATCH 09/15] Move pytest configuration to pytest.ini Extract the [pytest] section from tox.ini into a dedicated pytest.ini at the repo root. It stays at the root (not tests/) so testpaths spanning tests/ and docs/ still resolve. tox continues to read this config for local runs. --- pytest.ini | 16 ++++++++++++++++ tox.ini | 18 ++---------------- 2 files changed, 18 insertions(+), 16 deletions(-) create mode 100644 pytest.ini diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 00000000..690b475b --- /dev/null +++ b/pytest.ini @@ -0,0 +1,16 @@ +[pytest] +addopts = -ra -v -n 2 --junitxml=junit/test-results.xml --color=no --cov=atomica --cov-report=xml --cov-report=html --log-level=DEBUG +junit_family=xunit1 +console_output_style = count +testpaths = tests docs/examples docs/tutorial +python_files = test_tox_*.py +norecursedirs = atomica_apps .ipynb_checkpoints +# Enable headless matplotlib testing and suppress deprecation warnings +env = + MPLBACKEND = agg + +# Ignore deprecation warnings as not relevant for testing purposes +filterwarnings = + ignore::DeprecationWarning + ignore::PendingDeprecationWarning + ignore::UserWarning:.*openpyxl diff --git a/tox.ini b/tox.ini index 72b15fb1..11efb24d 100644 --- a/tox.ini +++ b/tox.ini @@ -22,20 +22,6 @@ extras = docs commands = python -m sphinx.cmd.build docs {posargs:doc_build} -j2 -[pytest] -addopts = -ra -v -n 2 --junitxml=junit/test-results.xml --color=no --cov=atomica --cov-report=xml --cov-report=html --log-level=DEBUG -junit_family=xunit1 -console_output_style = count -testpaths = tests docs/examples docs/tutorial -python_files = test_tox_*.py -norecursedirs = atomica_apps .ipynb_checkpoints -# Enable headless matplotlib testing and suppress deprecation warnings -env = - MPLBACKEND = agg - -# Ignore deprecation warnings as not relevant for testing purposes -filterwarnings = - ignore::DeprecationWarning - ignore::PendingDeprecationWarning - ignore::UserWarning:.*openpyxl +# pytest configuration lives in pytest.ini (at the repo root, so testpaths that +# span tests/ and docs/ resolve correctly) From 2c34e4ab27aeaaef57ac2dbaabc4f6d60ea0c7c9 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 10:03:02 +1000 Subject: [PATCH 10/15] Drop tox Remove tox.ini now that CI runs pytest and Sphinx directly via uv. Update the README to run the suite with pip/pytest or uv (matching CI) instead of tox, and refresh the workflow comment that referenced tox.ini. --- .github/workflows/tests.yml | 4 ++-- README.md | 10 +++++----- tox.ini | 27 --------------------------- 3 files changed, 7 insertions(+), 34 deletions(-) delete mode 100644 tox.ini diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 2b980d2d..bebd0e1f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -31,8 +31,8 @@ jobs: - name: Install dependencies run: uv sync --extra test --no-default-groups --frozen - # pytest config (junit, coverage, -n 2) lives in tox.ini [pytest]; these - # flags add the notebook (nbval) validation that tox layered on top + # pytest config (junit, coverage, -n 2) lives in pytest.ini; these flags + # add the notebook (nbval) validation on top - name: Run tests run: uv run pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope --durations=25 diff --git a/README.md b/README.md index fcf321da..c9647b04 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ pip install -e . ## Running tests -Atomica includes a suite of tests, some of which get automatically run and others that are used manually. The automated test suite can be executed with `pytest`, and can be run from within an isolated environment using `tox`. To use the tests, you will need to follow the steps above to perform a 'Git installation' because the tests are not included in the PyPI distribution. After installation, you can run individual test scripts from the `tests` directory with commands like: +Atomica includes a suite of tests, some of which get automatically run and others that are used manually. The automated test suite can be executed with `pytest`. To use the tests, you will need to follow the steps above to perform a 'Git installation' because the tests are not included in the PyPI distribution. After installation, you can run individual test scripts from the `tests` directory with commands like: ``` python tests/testworkflow.py @@ -57,16 +57,16 @@ which will install the additional development dependencies. Then, to run the aut pytest ``` -To run the tests in an isolated virtual environment, from the root directory, run +Alternatively, if you use [uv](https://docs.astral.sh/uv/), you can run the suite in a managed environment that matches CI, without installing the dependencies manually: ``` -tox +uv run --extra test pytest ``` -If you don't have `tox`, install it using `pip install tox`. To test against a specific Python version, pass it as an argument, e.g. +To also validate the example and tutorial notebooks (as CI does), add the nbval options: ``` -tox -e py312 +uv run --extra test pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope ``` ## Claude Code integration diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 11efb24d..00000000 --- a/tox.ini +++ /dev/null @@ -1,27 +0,0 @@ -[tox] -envlist = py314 -requires = - tox-uv>=1 - -[testenv] -description = Run basic usage tests -runner = uv-venv-runner - -# Change directory so that we make sure we are using the package-installed version -changedir = {envtmpdir} -extras = test - -commands = - pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope {toxinidir} {posargs} - -[testenv:docs] -description = Build the documentation -runner = uv-venv-runner -changedir = {toxinidir} -extras = docs -commands = - python -m sphinx.cmd.build docs {posargs:doc_build} -j2 - -# pytest configuration lives in pytest.ini (at the repo root, so testpaths that -# span tests/ and docs/ resolve correctly) - From 1a24b036ade0be21f621bda46fa45a865b6e7c56 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 10:31:39 +1000 Subject: [PATCH 11/15] Rework README around uv-based workflow Restructure installation and usage around uv (uv add, editable installs, branch dependencies), and move the test instructions to run via uv run --extra test pytest, matching the GitHub Actions CI. Group advanced usage and troubleshooting notes together. --- README.md | 74 +++++++++++++++++++++++++++++++------------------------ 1 file changed, 42 insertions(+), 32 deletions(-) diff --git a/README.md b/README.md index c9647b04..993eb1fc 100644 --- a/README.md +++ b/README.md @@ -8,88 +8,98 @@ For detailed documentation, visit [https://atomica.tools/docs](https://atomica.t ## Installation -Atomica requires Python 3.10 or later and is distributed via PyPI. To install, run +Atomica requires Python 3.11 or later and is distributed via PyPI. To install, run ``` pip install atomica ``` -## Git installation - -If you want to install a different branch of Atomica, or plan to make changes to the Atomica source code, you will need to install Atomica via Git rather than via PyPI. This can be performed using +Atomica is mainly used as the modelling platform for downstream analyses. Therefore, the most common usage is to set up an analysis-specific repository, and simply include `atomica` as a dependency that will be installed automatically via PyPI. We recommend using [uv](https://docs.astral.sh/uv/) to manage Python environments, in which case `atomica` can be added as a dependency using ``` -git clone https://github.com/atomicateam/atomica.git -cd atomica -pip install -e . +uv add atomica ``` -## Running tests +## Claude Code integration + +Atomica ships an MCP server (`atomica.mcp`) that exposes tools for querying framework and databook files and a set of built-in workflow skills (MCP prompts). The tools let Claude read compartments, parameters, transitions, and variable metadata directly from `.xlsx` framework files, as well as read and write data in `.xlsx` databook files. The skills guide Claude through multi-step workflows such as producing a structured summary of a framework. -Atomica includes a suite of tests, some of which get automatically run and others that are used manually. The automated test suite can be executed with `pytest`. To use the tests, you will need to follow the steps above to perform a 'Git installation' because the tests are not included in the PyPI distribution. After installation, you can run individual test scripts from the `tests` directory with commands like: +To register the server with Claude Code, run the following from within your project directory: ``` -python tests/testworkflow.py +claude mcp add atomica -- uv run python -m atomica.mcp ``` -Note that many of the tests open `matplotlib` figures as part of the test. If the test script is run on a machine without a display available, the error +Once added, the tools and skills are available automatically in any Claude Code session for that project. If you use Atomica across multiple projects and want the MCP server available in all of them without repeating the `claude mcp add` step, register it at the user level instead: ``` -_tkinter.TclError: couldn't connect to display "localhost:0.0" +claude mcp add -s user atomica -- uv run python -m atomica.mcp ``` -will be raised. In that case, simply set the `matplotlib` backend to `agg` which allows the calls to succeed with a display present. For example, run +The Atomica MCP will then be used whenever you are working within a project that has `atomica` as a dependency. + +## Advanced usage + +### Using a branch in a downstream project + +To use an Atomica branch in a downstream project with `uv`, you can add the Git repository directly as a dependency ``` -export MPLBACKEND=agg -python tests/testworkflow.py +uv add git+https://github.com/atomicateam/atomica --branch ``` -To run the automated suite, install the test dependencies using +For more information on this usage, see https://docs.astral.sh/uv/concepts/projects/dependencies/. + +### Developer installation + +If you want to install a different branch of Atomica, or plan to make changes to the Atomica source code, you will need to install Atomica via Git rather than via PyPI. ``` -pip install -e ".[test]" +git clone https://github.com/atomicateam/atomica.git +cd atomica +pip install -e . ``` -which will install the additional development dependencies. Then, to run the automated suite, from the root directory (the one containing `README.md`) run: +If using `uv`, simply cloning the repository is sufficient, and scripts can be run with `uv run`. If you are developing Atomica in parallel with your own analysis repository, it would be recommended to clone `atomica` and then install it in your analysis repository as an editable package with `uv` ``` -pytest +uv add --editable ../ ``` -Alternatively, if you use [uv](https://docs.astral.sh/uv/), you can run the suite in a managed environment that matches CI, without installing the dependencies manually: +In which case you can edit your local copy of Atomica and have it reflected in your analysis code. + +### Running tests + +Atomica includes a suite of tests. The automated test suite can be executed with `pytest`. ``` uv run --extra test pytest ``` -To also validate the example and tutorial notebooks (as CI does), add the nbval options: +Note the inclusion of the extra `test` dependencies that are not installed by default. Many of the tests open `matplotlib` figures as part of the test. If the test script is run on a machine without a display available, the error ``` -uv run --extra test pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope +_tkinter.TclError: couldn't connect to display "localhost:0.0" ``` -## Claude Code integration - -Atomica ships an MCP server (`atomica.mcp`) that exposes tools for querying framework and databook files and a set of built-in workflow skills (MCP prompts). The tools let Claude read compartments, parameters, transitions, and variable metadata directly from `.xlsx` framework files, as well as read and write data in `.xlsx` databook files. The skills guide Claude through multi-step workflows such as producing a structured summary of a framework. - -To register the server with Claude Code, run the following from within your project directory: +will be raised. In that case, simply set the `matplotlib` backend to `agg` which allows the calls to succeed with a display present. For example, run ``` -claude mcp add atomica -- uv run python -m atomica.mcp +export MPLBACKEND=agg +uv run --extra test pytest ``` -Once added, the tools and skills are available automatically in any Claude Code session for that project. If you use Atomica across multiple projects and want the MCP server available in all of them without repeating the `claude mcp add` step, register it at the user level instead: +To also validate the example and tutorial notebooks, include the `nbval` options: ``` -claude mcp add -s user atomica -- uv run python -m atomica.mcp +uv run --extra test pytest --nbval-lax --current-env --nbval-cell-timeout=600 --dist loadscope ``` -The Atomica MCP will then be used whenever you are working within a project that has `atomica` as a dependency. +This will reproduce the automated testing that is executed on GitHub as part of the CI workflow. ### Adding custom skills -Skills are plain Markdown files in `atomica/mcp/skills/`. To add a new workflow, drop a `.md` file into that directory — it is registered as an MCP prompt automatically when the server starts, with no code changes required. The first `# Heading` line becomes the prompt description shown in the MCP client. +The MCP server publishes a set of skills, which are plain Markdown files in `atomica/mcp/skills/`. To add a new workflow, add a `.md` file into that directory — it is registered as an MCP prompt automatically when the server starts, with no code changes required. The first `# Heading` line becomes the prompt description shown in the MCP client. ## Troubleshooting From 68e96eaedf4e0975ee44331d9095b15718a6f089 Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 10:33:12 +1000 Subject: [PATCH 12/15] Require Python 3.11 networkx (pulled in via hyperopt) requires Python >=3.11, so 3.10 could not actually resolve the dependency set. Bump requires-python to >=3.11, drop the 3.10 classifier to match the README, and relock. --- pyproject.toml | 3 +- uv.lock | 1167 +++++------------------------------------------- 2 files changed, 109 insertions(+), 1061 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d7a11d0c..52340007 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,13 +20,12 @@ classifiers = [ "Programming Language :: Python", "Topic :: Software Development :: Libraries :: Python Modules", "Development Status :: 5 - Production/Stable", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Programming Language :: Python :: 3.14" ] -requires-python = ">=3.10" +requires-python = ">=3.11" dependencies = [ "matplotlib", diff --git a/uv.lock b/uv.lock index 9b3fbc37..5451bd94 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,6 @@ version = 1 revision = 3 -requires-python = ">=3.10" +requires-python = ">=3.11" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", "python_full_version >= '3.14' and sys_platform == 'emscripten'", @@ -8,10 +8,9 @@ resolution-markers = [ "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'", "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'", "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", - 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The lazy imports in framework.py/model.py are kept so networkx is only loaded when validation runs. --- pyproject.toml | 1 + uv.lock | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 52340007..bd673f97 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,6 +36,7 @@ dependencies = [ "openpyxl", "pyswarm", "hyperopt", + "networkx", "sciris", "tqdm", "mcp>=2.0", diff --git a/uv.lock b/uv.lock index 5451bd94..9dbb4e7c 100644 --- a/uv.lock +++ b/uv.lock @@ -69,6 +69,7 @@ dependencies = [ { name = "hyperopt" }, { name = "matplotlib" }, { name = "mcp" }, + { name = "networkx" }, { name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" }, { name = "numpy", version = "2.5.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" }, { name = "openpyxl" }, @@ -131,6 +132,7 @@ requires-dist = [ { name = "nbconvert", marker = "extra == 'test'" }, { name = "nbsphinx", marker = "extra == 'docs'" }, { name = "nbval", marker = "extra == 'test'" }, + { name = "networkx" }, { name = "numpy", specifier = ">=1.10.1" }, { name = "openpyxl" }, { name = "pandas" }, @@ -3604,8 +3606,8 @@ name = "uvicorn" version = "0.52.4" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "click" }, - { name = "h11" }, + { name = "click", marker = "sys_platform != 'emscripten'" }, + { name = "h11", marker = "sys_platform != 'emscripten'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/f2/0f/3f86e61397dd33bf2ccf28188c40db6a740658aeebbbf6e7dbc101a1f487/uvicorn-0.52.4.tar.gz", hash = "sha256:73acfee47a0b133c5de13d219492d62d8a31e935f4fe6e41a232451a15379f86", size = 100627, upload-time = "2026-08-19T06:27:41.821Z" } wheels = [ From 2660b550e2fdd333d4d1f5da439496f56f5fb2ec Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 10:47:24 +1000 Subject: [PATCH 14/15] Add status badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 993eb1fc..713e5b65 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # Atomica [![PyPi version](https://badgen.net/pypi/v/atomica/)](https://pypi.org/project/atomica) +[![Tests](https://github.com/atomicateam/atomica/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/atomicateam/atomica/actions/workflows/tests.yml) Atomica is a simulation engine for compartmental models. It can be used to simulate disease epidemics, health care cascades, and many other things. From b71080a5c7ca9f72d4cdb04bcee4319ffa6318fd Mon Sep 17 00:00:00 2001 From: Romesh Abeysuriya Date: Tue, 1 Sep 2026 10:47:30 +1000 Subject: [PATCH 15/15] Increment version --- atomica/version.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/atomica/version.py b/atomica/version.py index 2c99f4e0..89e207db 100644 --- a/atomica/version.py +++ b/atomica/version.py @@ -3,5 +3,5 @@ Standard location for module version number and date. """ -version = "1.32.3" -versiondate = "2026-08-27" +version = "1.32.4" +versiondate = "2026-09-01"