sbml2cellml 0.1.0__tar.gz

sbml2cellml-0.1.0/.bumpversion.toml

@@ -0,0 +1,24 @@
+[tool.bumpversion]
+current_version = "0.1.0"
+commit = true
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+# no tag: the bump is merged into develop through a pull request, which
+# rewrites the commit, so the tag is created on develop afterwards
+tag = false
+sign_tags = false
+tag_name = "{new_version}"
+tag_message = "Bump version: {current_version} to {new_version}"
+allow_dirty = false
+message = "Bump version: {current_version} to {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "./src/sbml2cellml/__init__.py"
+
+[[tool.bumpversion.files]]
+filename = "./CITATION.cff"

sbml2cellml-0.1.0/.github/CODEOWNERS

@@ -0,0 +1 @@
+* @matthiaskoenig

sbml2cellml-0.1.0/.github/dependabot.yml

@@ -0,0 +1,16 @@
+# Keep the GitHub Actions used in the workflows up to date.
+# See https://docs.github.com/code-security/dependabot/dependabot-version-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # a single pull request for all action updates instead of one per action
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "ci"

sbml2cellml-0.1.0/.github/pull_request_template.md

@@ -0,0 +1,12 @@
+## Summary
+
+<!-- what does this change and why -->
+
+## Checklist
+
+- [ ] the pull request targets `develop`
+- [ ] tests were added or updated for the change
+- [ ] `tox run-parallel` passes locally (tests and `ty`)
+- [ ] `ruff check` and `ruff format` are clean, e.g., via `pre-commit run --all-files`
+- [ ] public functions and classes have type annotations and a docstring
+- [ ] user visible changes are in `release-notes/` and, if needed, in `docs/`

sbml2cellml-0.1.0/.github/rulesets/apply.sh

@@ -0,0 +1,61 @@
+#!/usr/bin/env bash
+#
+# Apply the repository policies of sbml2cellml: the merge settings of the
+# repository, the rulesets in this directory and the branch which may deploy
+# the documentation. The script is idempotent, i.e., a ruleset which already
+# exists is updated instead of added a second time, so it can be run again
+# after every change of the json files.
+#
+# The file name of a ruleset has to match the "name" in the json. A ruleset which
+# is removed from this directory stays on the repository, delete it with
+# `gh api -X DELETE repos/<owner>/<repo>/rulesets/<id>`.
+#
+# Requires the github cli (https://cli.github.com) authenticated as a user with
+# admin permission on the repository:
+#
+#   gh auth login
+#   .github/rulesets/apply.sh [owner/repo]
+#
+set -euo pipefail
+
+REPO="${1:-matthiaskoenig/sbml2cellml}"
+DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+echo "repository settings of ${REPO}"
+gh api -X PATCH "repos/${REPO}" \
+  -F allow_auto_merge=true \
+  -F delete_branch_on_merge=true \
+  -F allow_update_branch=true \
+  -F allow_squash_merge=true \
+  -F allow_rebase_merge=true \
+  -F allow_merge_commit=false \
+  --silent
+
+for path in "${DIR}"/*.json; do
+  name="$(basename "${path}" .json)"
+  id="$(gh api "repos/${REPO}/rulesets" --jq "map(select(.name == \"${name}\")) | .[0].id // empty")"
+  if [[ -n "${id}" ]]; then
+    gh api -X PUT "repos/${REPO}/rulesets/${id}" --input "${path}" --silent
+    echo "ruleset ${name} updated (${id})"
+  else
+    id="$(gh api -X POST "repos/${REPO}/rulesets" --input "${path}" --jq .id)"
+    echo "ruleset ${name} created (${id})"
+  fi
+done
+
+# The documentation workflow deploys from develop. Enabling GitHub Pages creates
+# the github-pages environment with a deployment policy for the default branch
+# of that moment (main here), which rejects every deployment from develop.
+echo "deployment branches of the github-pages environment"
+gh api -X PUT "repos/${REPO}/environments/github-pages" --silent --input - <<'JSON'
+{"deployment_branch_policy": {"protected_branches": false, "custom_branch_policies": true}}
+JSON
+policies="$(gh api "repos/${REPO}/environments/github-pages/deployment-branch-policies" \
+  --jq '.branch_policies[].name')"
+if grep -qx develop <<<"${policies}"; then
+  echo "develop may deploy"
+else
+  gh api -X POST "repos/${REPO}/environments/github-pages/deployment-branch-policies" \
+    -f name=develop -f type=branch --silent
+  echo "develop may deploy (added)"
+fi

sbml2cellml-0.1.0/.github/rulesets/develop.json

@@ -0,0 +1,61 @@
+{
+  "name": "develop",
+  "target": "branch",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": [
+        "refs/heads/develop"
+      ],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "non_fast_forward"
+    },
+    {
+      "type": "required_linear_history"
+    },
+    {
+      "type": "pull_request",
+      "parameters": {
+        "required_approving_review_count": 0,
+        "dismiss_stale_reviews_on_push": true,
+        "require_code_owner_review": false,
+        "require_last_push_approval": false,
+        "required_review_thread_resolution": true,
+        "allowed_merge_methods": [
+          "squash",
+          "rebase"
+        ],
+        "require_extra_approval_for_unattributed_changes": false
+      }
+    },
+    {
+      "type": "required_status_checks",
+      "parameters": {
+        "strict_required_status_checks_policy": false,
+        "do_not_enforce_on_create": false,
+        "required_status_checks": [
+          {
+            "context": "tests"
+          },
+          {
+            "context": "ruff"
+          },
+          {
+            "context": "ty"
+          },
+          {
+            "context": "docs"
+          }
+        ]
+      }
+    }
+  ]
+}

sbml2cellml-0.1.0/.github/rulesets/main.json

@@ -0,0 +1,22 @@
+{
+  "name": "main",
+  "target": "branch",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": [
+        "refs/heads/main"
+      ],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {
+      "type": "deletion"
+    },
+    {
+      "type": "non_fast_forward"
+    }
+  ]
+}

sbml2cellml-0.1.0/.github/rulesets/tags.json

@@ -0,0 +1,16 @@
+{
+  "name": "tags",
+  "target": "tag",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": ["~ALL"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "deletion"},
+    {"type": "non_fast_forward"}
+  ]
+}

sbml2cellml-0.1.0/.github/workflows/biomodels.yml

@@ -0,0 +1,68 @@
+name: biomodels
+
+on:
+  workflow_dispatch:
+
+concurrency:
+  group: biomodels
+  cancel-in-progress: false
+
+permissions:
+  contents: read
+
+jobs:
+  biomodels:
+    name: biomodels
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    permissions:
+      contents: write       # push the results branch
+      pull-requests: write  # open the pull request
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Install the python dev files
+        # the extension of libroadrunner links against libpython, which the
+        # standalone interpreters do not put on the library search path
+        run: |
+          sudo add-apt-repository -y ppa:deadsnakes/ppa
+          sudo apt-get update
+          sudo apt-get install -y python3.13-dev
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v10.1.0
+        with:
+          python-version: "3.13"
+          enable-cache: true
+      - name: Cache the BioModels downloads
+        uses: actions/cache@v6
+        with:
+          path: ~/.cache/sbml2cellml/biomodels
+          key: biomodels-${{ hashFiles('biomodels/models.json') }}
+          restore-keys: |
+            biomodels-
+      - name: Install dependencies
+        run: uv sync --extra dev
+      - name: Run the BioModels check
+        shell: bash
+        run: uv run sbml2cellml-biomodels run | tee biomodels-run.log
+      - name: Build the pull request body from the run summary
+        run: |
+          {
+            echo "Regenerated by the biomodels workflow with sbml2cellml-biomodels run."
+            tail -12 biomodels-run.log
+            echo "Review the changes of docs/biomodels.md before merging."
+          } > biomodels-summary.md
+      - name: Open a pull request with the results
+        uses: peter-evans/create-pull-request@v8
+        with:
+          token: ${{ secrets.BIOMODELS_TOKEN || github.token }}
+          branch: biomodels-results
+          base: develop
+          title: "Update the BioModels results"
+          commit-message: "Update the BioModels results"
+          body-path: biomodels-summary.md
+          delete-branch: true
+          add-paths: |
+            biomodels/results.json
+            docs/biomodels.md

sbml2cellml-0.1.0/.github/workflows/ci-cd.yml

@@ -0,0 +1,131 @@
+name: CI-CD
+
+on:
+  push:
+    # feature branches are tested through their pull request, tags release
+    branches: [develop, main]
+    tags: ['*']
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+# least privilege by default, the release job raises what it needs
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  # superseded branch runs are cancelled, release runs are never cancelled
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.13"]
+
+    steps:
+    - uses: actions/checkout@v7
+      with:
+        persist-credentials: false
+    - name: Install the python dev files (linux only)
+      # the extension of libroadrunner links against libpython, which the
+      # standalone interpreters do not put on the library search path
+      run: |
+        if [ "$RUNNER_OS" == "Linux" ]; then
+          sudo add-apt-repository -y ppa:deadsnakes/ppa
+          sudo apt-get update
+          sudo apt-get install -y python${{ matrix.python-version }}-dev
+        fi
+      shell: bash
+    - name: Install uv and set the python version
+      # astral-sh/setup-uv publishes no floating major tag beyond v7
+      uses: astral-sh/setup-uv@v10.1.0
+      with:
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+    - name: Cache the SBML test suite
+      # the complete SBML test suite runs on linux only
+      if: runner.os == 'Linux'
+      uses: actions/cache@v6
+      with:
+        path: ~/.cache/sbml2cellml
+        key: sbml-test-suite-3.5.0
+    - name: Test with tox
+      env:
+        # the complete SBML test suite runs on linux only
+        SBML2CELLML_TESTSUITE: ${{ runner.os == 'Linux' && '1' || '' }}
+      run:
+        uvx --with tox-uv tox -e py${{ matrix.python-version }}
+
+  tests:
+    # the one check the branch protection requires; the names of the matrix
+    # jobs change with the matrix, this name does not, see .github/rulesets/
+    name: tests
+    needs: test
+    if: always()
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    steps:
+    - name: Check the result of the test matrix
+      env:
+        RESULT: ${{ needs.test.result }}
+      run: |
+        echo "test matrix: $RESULT"
+        test "$RESULT" = "success"
+
+  release:
+    needs: tests
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    environment:
+      name: pypi
+      url: https://pypi.org/p/sbml2cellml
+    permissions:
+      id-token: write  # trusted publishing to PyPI
+      contents: write  # create the GitHub release
+    steps:
+    - uses: actions/checkout@v7
+      with:
+        persist-credentials: false
+    - name: Install uv
+      uses: astral-sh/setup-uv@v10.1.0
+      with:
+        python-version: "3.13"
+        enable-cache: true
+    - name: Build package
+      run: uvx hatch build
+    - name: Check the package
+      run: uvx twine check dist/*
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist
+    - name: Create GitHub release
+      uses: softprops/action-gh-release@v3
+      with:
+        body_path: "release-notes/${{ github.ref_name }}.md"
+        draft: false
+        prerelease: false
+
+  sync-main:
+    # main tracks the latest published release, see docs/development.md
+    needs: release
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    permissions:
+      contents: write  # fast-forward main to the released commit
+    steps:
+    - uses: actions/checkout@v7
+      with:
+        # a shallow clone cannot be pushed to another branch
+        fetch-depth: 0
+    - name: Fast-forward main to the release
+      # no --force: the push fails loudly if it would not be a fast-forward
+      run: git push origin HEAD:main

sbml2cellml-0.1.0/.github/workflows/docs.yml

@@ -0,0 +1,73 @@
+name: documentation
+
+on:
+  push:
+    # feature branches are built through their pull request
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  # one run per branch or pull request, so that a deployment of `develop` is
+  # never overtaken by the next one, which would leave the site half published
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  docs:
+    # the name the branch protection requires, see .github/rulesets/
+    name: docs
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v6
+      - name: Install the python dev files
+        # the extension of libroadrunner links against libpython, which the
+        # standalone interpreters do not put on the library search path
+        run: |
+          sudo add-apt-repository -y ppa:deadsnakes/ppa
+          sudo apt-get update
+          sudo apt-get install -y python3.13-dev
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v10.1.0
+        with:
+          python-version: "3.13"
+          enable-cache: true
+      - name: Install dependencies
+        run: uv sync --extra dev
+      - name: Build the documentation
+        # the API reference is rendered from the docstrings by mkdocstrings,
+        # so the package has to be importable
+        run: uv run zensical build --clean --strict
+      - name: Generate the agent facing files
+        # llms.txt, llms-full.txt and the markdown of every page
+        run: uv run python scripts/llms_txt.py
+      - name: Upload the site
+        uses: actions/upload-pages-artifact@v5
+        with:
+          path: site
+
+  deploy:
+    needs: docs
+    # only the default branch publishes to https://matthiaskoenig.github.io/sbml2cellml
+    if: github.ref == 'refs/heads/develop'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      pages: write     # deploy to GitHub Pages
+      id-token: write  # verify the deployment originates from this workflow
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

sbml2cellml-0.1.0/.github/workflows/ruff.yml

@@ -0,0 +1,37 @@
+name: ruff
+
+on:
+  push:
+    # feature branches are checked through their pull request
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+jobs:
+  ruff:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: ruff
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      # the ruff version is read from the dev dependencies in pyproject.toml
+      - name: Lint
+        # astral-sh/ruff-action publishes no floating major tag beyond v3
+        uses: astral-sh/ruff-action@v4.1.0
+        with:
+          args: check --output-format=github
+      - name: Format
+        uses: astral-sh/ruff-action@v4.1.0
+        with:
+          args: format --check --diff

sbml2cellml-0.1.0/.github/workflows/ty.yml

@@ -0,0 +1,45 @@
+name: ty
+
+on:
+  push:
+    # feature branches are checked through their pull request
+    branches: [develop, main]
+  pull_request:
+    branches: [develop, main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+jobs:
+  ty:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: ty
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Install the python dev files
+        # the extension of libroadrunner links against libpython, which the
+        # standalone interpreters do not put on the library search path
+        run: |
+          sudo add-apt-repository -y ppa:deadsnakes/ppa
+          sudo apt-get update
+          sudo apt-get install -y python3.13-dev
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v10.1.0
+        with:
+          python-version: "3.13"
+          enable-cache: true
+      - name: Type check with tox
+        env:
+          # render diagnostics as GitHub Actions workflow annotations
+          TY_OUTPUT_FORMAT: github
+        run:
+          uvx --with tox-uv tox -e ty

sbml2cellml-0.1.0/.gitignore

@@ -0,0 +1,35 @@
+# python
+__pycache__/
+*.pyc
+*.egg-info/
+
+# packaging artifacts (hatchling builds into dist/)
+dist/
+
+# environments, tool caches
+.venv/
+.tox/
+.pytest_cache/
+.ruff_cache/
+.coverage
+coverage.xml
+# build cache of zensical
+.cache/
+# scratch of the subagent-driven development workflow
+.superpowers/
+
+# rendered documentation, built by the `documentation` workflow
+site/
+
+# generated by the examples
+examples/results/
+# generated by sbml2cellml-testsuite (converted files of the run)
+testsuite/work/
+# generated by sbml2cellml-biomodels (converted files of the run)
+biomodels/work/
+
+# editors, operating system
+.idea/
+.vscode/
+*~
+.DS_Store

sbml2cellml-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+# Checks run before every commit, see `docs/development.md`.
+# Install once per checkout with `pre-commit install`.
+#
+# A commit only checks the changed files; `pre-commit run --all-files` checks
+# the whole repository, which is what a newly added hook should be tried with.
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: check-yaml
+    description: Check yaml files for parseable syntax
+  - id: check-toml
+    description: Check toml files for parseable syntax
+  - id: check-json
+    description: Check json files for parseable syntax
+  - id: check-added-large-files
+    description: Prevent large files from being committed
+    # testsuite/results.json and docs/testsuite.md, generated by
+    # `sbml2cellml-testsuite run`, are larger than the 500 kB default
+    args: [ --maxkb=2000 ]
+  - id: check-merge-conflict
+    description: Check for files that contain merge conflict strings
+  - id: check-symlinks
+    description: Check for symlinks which do not point to anything
+  - id: trailing-whitespace
+    description: Trim trailing whitespaces
+  - id: end-of-file-fixer
+    description: Fix empty lines at ends of files
+  - id: detect-private-key
+    description: Detects the presence of private keys
+  - id: check-case-conflict
+    description: Check for names which conflict on case insensitive filesystems
+  - id: mixed-line-ending
+    description: Normalize mixed line endings
+    args: [ --fix=lf ]
+  - id: debug-statements
+    description: Check for forgotten breakpoints and debugger imports
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.16.6
+  hooks:
+    # Run the linter.
+    - id: ruff-check
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]
+
+- repo: https://github.com/astral-sh/ty-pre-commit
+  # ty version.
+  rev: v0.0.81
+  hooks:
+    # Run the type checker on the whole project (see `[tool.ty]` in pyproject.toml).
+    # `--extra dev` syncs the environment with the dev dependencies, so that the
+    # test imports (pytest) resolve.
+    - id: ty
+      args: [ --extra, dev ]

sbml2cellml-0.1.0/.python-version

@@ -0,0 +1 @@
+3.13