acellera-gufe 1.13.1__tar.gz

acellera_gufe-1.13.1/.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# https://github.com/OpenFreeEnergy/gufe/pull/421 -- big auto format MMH
+d27100a5b7b303df155e2b6d7874883d105e24bf
+# https://github.com/OpenFreeEnergy/gufe/pull/431 -- fix some files that didn't get formatted MMH
+f8c49d59e756130a995d02dfe04d7a91acb1d791

acellera_gufe-1.13.1/.github/PULL_REQUEST_TEMPLATE/release-prep.md

@@ -0,0 +1,22 @@
+---
+name: Release preparation
+about: Prepare a new release for this package
+title: 'Release : '
+labels: 'release-prep'
+assignees: ''
+
+---
+
+To create a new release, please do the following:
+- [ ] make any changes to the repo needed to accommodate the release
+    - [ ] check `environment.yml` for any updates needed; create any issues needed to update versions in next release cycle
+- [ ] run [`rever`](https://regro.github.io/rever-docs/index.html#rever-releaser-of-versions) to generate the `CHANGELOG` entry from `news` items: `rever <version_number>`
+    - inspect `CHANGELOG`, adjust as necessary
+- [ ] merge this PR into `main`
+
+
+After you have merged this PR, please also:
+- [ ]  create a release here in GitHub, including generating detailed release notes
+    - [ ] in the summary release notes, also link to the `CHANGELOG` entry for this release in the `gufe` docs
+- [ ]  await automated PR on `conda-forge` [`gufe-feedstock` `meta.yaml`](https://github.com/conda-forge/gufe-feedstock/blob/main/recipe/meta.yaml)
+    - [ ] review and merge

acellera_gufe-1.13.1/.github/pull_request_template.md

@@ -0,0 +1,27 @@
+<!--
+Thank you for pull request.
+Below are a few things we ask you kindly to self-check before getting a review. Remove checks that are not relevant.
+-->
+
+<!--
+Please note any issues this fixes using [closing keywords]( https://help.github.com/articles/closing-issues-using-keywords/ ):
+-->
+
+<!--
+see https://regro.github.io/rever-docs/news.html for details on how to add news entry (you do not need to run the rever command)
+-->
+Tips
+* Comment "pre-commit.ci autofix" to have pre-commit.ci atomically format your PR.
+  Since this will create a commit, it is best to make this comment when you are finished with your work.
+
+## LLM / AI generated code disclosure
+<!-- Please update this disclosure to reflect if you did or did not use LLMs / AI to generate code -->
+LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
+If yes, please provide details here:
+
+## Checklist
+* [ ] Added a ``news`` entry
+* [ ] Filled in the AI-generated code disclosure.
+
+## Developers certificate of origin
+- [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer Certificate of Origin** at <https://developercertificate.org/>.

acellera_gufe-1.13.1/.github/workflows/ci.yaml

@@ -0,0 +1,153 @@
+name: "CI"
+on:
+  # Allow for workflows to be manuallly triggered
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+      - stable
+      - epic/*
+      - release
+  schedule:
+    # At 07:00 UTC on Monday and Thursday.
+    - cron: "0 7 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.OS }}
+    name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🎨-${{ matrix.py3Dmol }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest']
+        py3Dmol: ["no"]
+        python-version:
+          - "3.12"
+          - "3.13"
+          - "3.14"
+        include:
+          - os: "macos-latest"
+            python-version: "3.14"
+          - os: "ubuntu-latest"
+            python-version: "3.12"
+            py3Dmol: "yes"
+
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v3
+        with:
+          micromamba-binary-path: ~/.local/bin/micromamba
+          environment-file: environment.yml
+          environment-name: gufe
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install py3Dmol (optional)"
+        if: ${{ matrix.py3Dmol == 'yes' }}
+        run: micromamba install py3Dmol
+
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import gufe; print(gufe.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: Cache Pooch data
+        uses: actions/cache@v5
+        with:
+          path: |
+            # linux cache location
+            ~/.cache/gufe
+            # osx cache location
+            ~/Library/Caches/gufe
+          # When files are added or changed in a pooch registry
+          # bump this key to create a new cache, for example if
+          # the key is pooch-${{ matrix.os }}-1 change it to pooch-${{ matrix.os }}-2
+          key: pooch-${{ matrix.os }}-0
+
+      - name: "Run tests"
+        run: |
+          pytest -n 2 -v --cov=gufe --cov-report=xml
+
+      - name: codecov
+        if: ${{ github.repository == 'OpenFreeEnergy/gufe'
+                && github.event != 'schedule' }}
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          fail_ci_if_error: False
+          verbose: True
+
+
+  package_build_and_test:
+    runs-on: ubuntu-latest
+    name: "package build and install test"
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: environment.yml
+          environment-name: gufe
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.12
+          init-shell: bash
+
+      - name: "install extra deps"
+        run: pip install pipx wheel twine readme-renderer
+
+      - name: "build sdist"
+        run: pipx run build --sdist --outdir dist
+
+      - name: "check package build"
+        run: |
+          dist=$(ls -t1 dist/gufe-*tar.gz | head -n1)
+          test -n "${dist}" || { echo "no distribution found"; exit 1; }
+          twine check $dist
+
+      - name: "install from source dist"
+        working-directory: ./dist
+        run: python -m pip install gufe-*tar.gz
+
+      - name: "install checks"
+        working-directory: ./dist
+        run: |
+          python -Ic "import gufe; print(gufe.__version__)"
+
+      - name: "run tests"
+        working-directory: ./dist
+        run: pytest -n auto --pyargs gufe

acellera_gufe-1.13.1/.github/workflows/clean_cache.yaml

@@ -0,0 +1,31 @@
+# from https://docs.github.com/en/actions/how-tos/manage-workflow-runs/manage-caches#force-deleting-cache-entries
+name: Cleanup github runner caches on closed pull requests
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write
+    steps:
+      - name: Cleanup
+        run: |
+          echo "Fetching list of cache keys"
+          cacheKeysForPR=$(gh cache list --ref $BRANCH --limit 100 --json id --jq '.[].id')
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh cache delete $cacheKey
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ github.token }}
+          GH_REPO: ${{ github.repository }}
+          BRANCH: refs/pull/${{ github.event.pull_request.number }}/merge

acellera_gufe-1.13.1/.github/workflows/conda_cron.yaml

@@ -0,0 +1,91 @@
+name: "conda_cron"
+on:
+  # Allow for manual trigger of workflow
+  workflow_dispatch:
+  schedule:
+    # At 07:00 UTC every day
+    - cron: "0 7 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  condacheck:
+    runs-on: ${{ matrix.OS }}
+    name: "daily conda check"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest']
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          path: gufe_repo
+
+      - name: Get Latest Version
+        id: latest-version
+        working-directory: gufe_repo
+        run: |
+          REPO="${{ github.repository }}"
+          VERSION=$(curl -s -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            "https://api.github.com/repos/$REPO/releases/latest" | jq -r '.tag_name | ltrimstr("v")')
+          echo $VERSION
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: gufe
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+            gufe=${{ steps.latest-version.outputs.VERSION }}
+            pooch
+            pytest
+            pytest-xdist
+            pygithub
+          condarc: |
+            channels:
+              - conda-forge
+          init-shell: bash
+
+      - name: Cache Pooch data
+        uses: actions/cache@v5
+        with:
+          path: |
+            # linux cache location
+            ~/.cache/gufe
+            # osx cache location
+            ~/Library/Caches/gufe
+          # When files are added or changed in a pooch registry
+          # bump this key to create a new cache, for example if
+          # the key is pooch-${{ matrix.os }}-1 change it to pooch-${{ matrix.os }}-2
+          key: pooch-${{ matrix.os }}-0
+
+      - id: run-tests
+        name: run tests
+        run: |
+          python -c 'import gufe;print(gufe.__version__)'
+          pytest -n auto --pyargs gufe
+
+      - name: raise-or-close-issue
+        if: ${{ always() }}
+        working-directory: gufe_repo
+        env:
+          CI_OUTCOME: ${{ steps.run-tests.outcome }}
+          TITLE: "[CI] CONDA CRON FAILURE ${{ matrix.os }} python ${{ matrix.python-version }}"
+          GITHUB_TOKEN: ${{ github.token }}
+        run: python devtools/raise-or-close-issue.py

acellera_gufe-1.13.1/.github/workflows/griffe-api-break-check.yaml

@@ -0,0 +1,59 @@
+name: "API break check"
+
+on:
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  griffe:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Fetch base branch
+        run: |
+          git fetch --no-tags origin "${{ github.base_ref }}:refs/remotes/origin/${{ github.base_ref }}"
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+
+      - name: Run Griffe
+        id: griffe
+        run: |
+          python -m pip install -U griffe
+
+          mkdir -p api-break-result
+          set +e
+
+          {
+            echo '$ griffe check "gufe" -s src --no-inspection --no-color --verbose -a origin/${{ github.base_ref }}'
+            griffe check "gufe" -s src --no-inspection --no-color --verbose -a "origin/${{ github.base_ref }}"
+            status=$?
+          } > api-break-result/griffe.log 2>&1
+
+          echo "status=$status" >> "$GITHUB_OUTPUT"
+
+      - name: Upload Griffe result
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: api-break-result
+          path: api-break-result/
+          retention-days: 7
+
+      - name: Fail if API break detected
+        if: steps.griffe.outputs.status != '0'
+        run: exit 1

acellera_gufe-1.13.1/.github/workflows/griffe-api-break-comment.yaml

@@ -0,0 +1,103 @@
+name: "API break check comment"
+
+on:
+  workflow_run:
+    workflows:
+      - "API break check"
+    types:
+      - completed
+
+permissions:
+  actions: read
+  issues: write
+  pull-requests: write
+
+jobs:
+  comment:
+    if: github.event.workflow_run.event == 'pull_request'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download Griffe result
+        uses: actions/download-artifact@v4
+        with:
+          name: api-break-result
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path: api-break-result
+
+      - name: Update PR comment
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const fs = require("fs");
+
+            const prs = context.payload.workflow_run.pull_requests;
+            if (!prs || prs.length === 0) {
+              core.info("No PR found for this workflow_run.");
+              return;
+            }
+
+            const prNumber = prs[0].number;
+            const identifier = "<!-- api-break-check -->";
+            const runUrl = context.payload.workflow_run.html_url;
+            const conclusion = context.payload.workflow_run.conclusion;
+
+            let log = "";
+            try {
+              log = fs.readFileSync("api-break-result/griffe.log", "utf8");
+            } catch (err) {
+              log = "Could not read Griffe log artifact.";
+            }
+
+            // Treat artifact contents as untrusted display text.
+            log = log.replaceAll("```", "`\u200b``");
+
+            // Truncate if log is really long
+            const maxLogChars = 60000;
+            if (log.length > maxLogChars) {
+              log = log.slice(0, maxLogChars) + "\n\n[truncated]";
+            }
+
+            const statusLine =
+              conclusion === "success"
+                ? "No API break detected ✅"
+                : "🚨 API breaking changes detected! 🚨";
+
+            const body = `${identifier}
+            ${statusLine}
+
+            [View workflow run](${runUrl})
+
+            <details>
+            <summary>Griffe output</summary>
+
+            \`\`\`text
+            ${log}
+            \`\`\`
+
+            </details>
+            `;
+
+            const { data: comments } = await github.rest.issues.listComments({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: prNumber,
+            });
+
+            for (const comment of comments) {
+              if (comment.body && comment.body.includes(identifier)) {
+                await github.rest.issues.deleteComment({
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  comment_id: comment.id,
+                });
+              }
+            }
+
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: prNumber,
+              body,
+            });

acellera_gufe-1.13.1/.github/workflows/mypy.yaml

@@ -0,0 +1,45 @@
+name: "mypy"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -leo pipefail {0}
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: gufe
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.12
+            rdkit=2025.03.4
+            mypy
+          init-shell: bash
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: "Lint with mypy"
+        run: |
+          mypy --version
+          mypy

acellera_gufe-1.13.1/.gitignore

@@ -0,0 +1,165 @@
+docs/generated/*
+
+# custom ignores
+.xxrun
+.idea/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*~
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# vim
+*.swp
+
+# Rever
+rever/