pymetadata 0.6.1__tar.gz → 0.6.2__tar.gz

{pymetadata-0.6.1 → pymetadata-0.6.2}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.6.1"
+current_version = "0.6.2"
 commit = true
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
@@ -7,7 +7,9 @@ search = "{current_version}"
 replace = "{new_version}"
 regex = false
 ignore_missing_version = false
-tag = true
+# 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} → {new_version}"

pymetadata-0.6.2/.github/CODEOWNERS

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

pymetadata-0.6.2/.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/`

pymetadata-0.6.2/.github/rulesets/apply.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+#
+# Apply the repository policies of pymetadata: the merge settings of the
+# repository and the rulesets in this directory. 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="${1:-matthiaskoenig/pymetadata}"
+DIR="$(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

pymetadata-0.6.2/.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"
+          }
+        ]
+      }
+    }
+  ]
+}

pymetadata-0.6.2/.github/rulesets/main.json

@@ -0,0 +1,17 @@
+{
+  "name": "main",
+  "target": "branch",
+  "enforcement": "active",
+  "bypass_actors": [],
+  "conditions": {
+    "ref_name": {
+      "include": ["refs/heads/main"],
+      "exclude": []
+    }
+  },
+  "rules": [
+    {"type": "deletion"},
+    {"type": "non_fast_forward"},
+    {"type": "required_linear_history"}
+  ]
+}

pymetadata-0.6.2/.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"}
+  ]
+}

{pymetadata-0.6.1 → pymetadata-0.6.2}/.github/workflows/ci-cd.yml

@@ -2,14 +2,19 @@ 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
+# least privilege by default, the release and sync jobs raise what they need
 permissions:
   contents: read
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  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/') }}
 
@@ -51,8 +56,24 @@ jobs:
       run:
         uvx --with tox-uv tox -e py${{ matrix.python-version }}
 
-  release:
+  tests:
+    # the one check the branch protection requires; the names of the matrix
+    # jobs change with the matrix, this name does not
+    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
@@ -85,3 +106,20 @@ jobs:
         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

{pymetadata-0.6.1 → pymetadata-0.6.2}/.github/workflows/docs.yml

@@ -2,18 +2,24 @@ 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:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   # never cancel a running deployment, it would leave the site half published
-  group: pages
   cancel-in-progress: false
 
 jobs:
-  build:
+  docs:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: docs
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
@@ -42,7 +48,7 @@ jobs:
           path: site
 
   deploy:
-    needs: build
+    needs: docs
     # only the default branch publishes to https://matthiaskoenig.github.io/pymetadata
     if: github.ref == 'refs/heads/develop'
     runs-on: ubuntu-latest

{pymetadata-0.6.1 → pymetadata-0.6.2}/.github/workflows/ruff.yml

@@ -2,17 +2,23 @@ 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.ref }}
-  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
   ruff:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: ruff
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:

{pymetadata-0.6.1 → pymetadata-0.6.2}/.github/workflows/ty.yml

@@ -2,17 +2,23 @@ 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.ref }}
-  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
 
 jobs:
   ty:
+    # required by the branch protection, see .github/rulesets/develop.json
+    name: ty
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:

{pymetadata-0.6.1 → pymetadata-0.6.2}/CITATION.cff

@@ -8,7 +8,7 @@ authors:
     given-names: "Matthias"
     orcid: "https://orcid.org/0000-0003-1725-179X"
     affiliation: "Humboldt-University Berlin, Faculty of Life Science, Institute for Biology, Biology, Berlin; University Lübeck; University Hospital Schleswig-Holstein, Campus Lübeck, First Department of Medicine, Germany"
-version: "0.6.1"
+version: "0.6.2"
 date-released: "2026-09-07"
 doi: "10.5281/zenodo.5308801"
 license: MIT

{pymetadata-0.6.1 → pymetadata-0.6.2}/CLAUDE.md

@@ -32,10 +32,18 @@ tox -e ty                       # ty type check (config in [tool.ty] in pyprojec
 uvx ty check                    # same check, straight from the working tree
 ```
 
-Release steps are in `docs/development.md` (there is no separate `RELEASE.md`);
-version bumps go through `uvx bump-my-version bump [major|minor|patch]` (updates
-`src/pymetadata/__init__.py` and `CITATION.cff`), and pushing the tag triggers
-the PyPI release workflow.
+`develop` is the default branch and takes every change through a pull request;
+direct pushes are rejected by the rulesets in `.github/rulesets/` (applied with
+`.github/rulesets/apply.sh`), which require the `tests`, `ruff`, `ty` and `docs`
+checks. `main` only tracks the latest release and is fast-forwarded by the
+`sync-main` job of the release workflow, never by hand.
+
+Release steps are in `docs/development.md` (there is no separate `RELEASE.md`):
+the release is prepared on a branch, `uvx bump-my-version bump [major|minor|patch]`
+updates `src/pymetadata/__init__.py` and `CITATION.cff` and commits without
+tagging (`tag = false`, a squash merge would rewrite the commit), and the tag is
+created on `develop` after the pull request was merged, which triggers the PyPI
+release workflow.
 
 Documentation is [Zensical](https://zensical.org/): markdown sources in `docs/`,
 configured in `zensical.toml`, built into the gitignored `site/`

{pymetadata-0.6.1 → pymetadata-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: pymetadata
-Version: 0.6.1
+Version: 0.6.2
 Summary: pymetadata are python utilities for working with metadata.
 Project-URL: Homepage, https://matthiaskoenig.github.io/pymetadata
 Project-URL: Documentation, https://matthiaskoenig.github.io/pymetadata

{pymetadata-0.6.1 → pymetadata-0.6.2}/docs/development.md

@@ -2,6 +2,83 @@
 
 Contributions are welcome. The repository is [matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata); development happens against the `develop` branch via pull requests.
 
+## Branch model
+
+Two branches are permanent:
+
+- **`develop`** is the default branch and the branch everything is integrated
+  into. The documentation on
+  [matthiaskoenig.github.io/pymetadata](https://matthiaskoenig.github.io/pymetadata)
+  is published from it.
+- **`main`** tracks the latest published release. It is fast-forwarded to the
+  released commit by the `sync-main` job of the `CI-CD` workflow after the
+  package went to pypi, so `main` and the newest version on pypi always agree.
+  Nothing is developed on `main` and nothing is merged into it by hand.
+
+Work happens on short lived branches off `develop`, which GitHub deletes after
+the merge. Releases are tagged on `develop`, see [Release](#release).
+
+## Pull requests
+
+Neither branch accepts a direct push, every change goes through a pull request
+against `develop`. This includes the maintainer, there is no bypass.
+
+A pull request can only be merged once the four required checks are green:
+
+| check   | workflow      | content                                                              |
+| ------- | ------------- | -------------------------------------------------------------------- |
+| `tests` | `ci-cd.yml`   | the test matrix, linux, macos and windows with python 3.11 to 3.14    |
+| `ruff`  | `ruff.yml`    | `ruff check` and `ruff format --check`                                |
+| `ty`    | `ty.yml`      | `tox r -e ty`                                                         |
+| `docs`  | `docs.yml`    | the zensical build including the api reference and the agent files    |
+
+`tests` aggregates the test matrix into a single job, so the name of the
+required check stays the same when the matrix changes.
+
+Further rules of a pull request:
+
+- conversations have to be resolved before the merge
+- an approval is dismissed when new commits are pushed
+- the history stays linear, i.e., a pull request is merged with squash or
+  rebase; merge commits are disabled
+- the maintainer is the code owner of the repository (`.github/CODEOWNERS`) and
+  is requested for review on every pull request. A pull request of a contributor
+  is therefore reviewed and merged by the maintainer, who has the only write
+  access. The rulesets themselves do not require an approval: on a personal
+  repository a ruleset cannot ask for an approval only from somebody else, and
+  requiring one would block the pull requests of the maintainer, who cannot
+  approve their own. Once a second person has write access, a ruleset requiring
+  an approving review of a code owner can be added
+
+[Auto-merge](https://docs.github.com/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/automatically-merging-a-pull-request)
+is enabled for the repository, so a pull request can be queued and is merged as
+soon as the checks pass and the required approval is there.
+
+### Repository policies { #repository-policies }
+
+The protection is implemented with
+[repository rulesets](https://docs.github.com/repositories/configuring-branches-and-merges-in-your-repository/managing-rulesets/about-rulesets).
+They are part of the repository in `.github/rulesets/` instead of only living in
+the web interface, so a change to a policy is reviewed like any other change:
+
+| ruleset                 | applies to | rules                                                                                                                                       |
+| ----------------------- | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------- |
+| `develop.json`          | `develop`  | pull request required, the four checks above, resolved conversations, linear history, no force push, no deletion. **No bypass, for anybody.** |
+| `main.json`             | `main`     | linear history, no force push, no deletion, no bypass. The fast-forward of the release workflow needs none, only a force push or a merge commit would be rejected |
+| `tags.json`             | all tags   | a tag cannot be deleted or moved, so a release tag keeps pointing at what was released                                                       |
+
+Changing a policy means changing the json and applying it:
+
+```bash
+.github/rulesets/apply.sh
+```
+
+The script is idempotent: it updates the rulesets which exist and creates the
+missing ones. It also sets the merge settings of the repository, i.e.,
+auto-merge, delete branch on merge, and squash and rebase as the only merge
+methods. It needs the [github cli](https://cli.github.com) authenticated as a
+user with admin permission on the repository.
+
 ## Setup development environment
 
 Development needs [uv](https://docs.astral.sh/uv/) and a checkout of the repository:
@@ -138,19 +215,36 @@ Run `ruff format` afterwards, since the rendered modules are not formatted.
 
 ## Release
 
-A release is made from `develop`:
+A release is made from `develop`. Since `develop` only accepts pull requests,
+the release is prepared on a branch and tagged once that pull request is merged:
+
+1. branch off `develop`: `git switch -c release/x.y.z develop`
+2. update the ontology modules, see [Regenerating the ontologies](#regenerating-the-ontologies), and commit the changes
+3. write the release notes for the version in `release-notes/x.y.z.md`
+4. make sure everything passes: `tox run-parallel`, `ruff check`, `tox r -e ty`
+5. check the version bump: `uvx bump-my-version bump [major|minor|patch] --dry-run -vv`
+6. bump the version: `uvx bump-my-version bump [major|minor|patch]`, which updates `src/pymetadata/__init__.py` and `CITATION.cff` and commits. It does not create the tag; a squash or rebase merge would rewrite the commit and leave the tag behind on a commit which is not part of `develop`
+7. push the branch, open the pull request against `develop` and merge it once the checks are green
+8. tag the merged commit on `develop` and push the tag:
+
+    ```bash
+    git switch develop
+    git pull
+    git tag x.y.z
+    git push origin x.y.z
+    ```
+
+    This starts the `CI-CD` workflow, which runs the test matrix, publishes to
+    [pypi](https://pypi.org/project/pymetadata/), creates the GitHub release
+    from `release-notes/x.y.z.md` and fast-forwards `main` to the tagged commit.
+    Check the version before pushing, a tag cannot be moved or deleted
+    afterwards.
 
-1. update the ontology modules, see [Regenerating the ontologies](#regenerating-the-ontologies), and commit the changes
-2. write the release notes for the version in `release-notes/`
-3. make sure everything passes: `tox run-parallel`, `ruff check`, `tox r -e ty`
-4. check the version bump: `uvx bump-my-version bump [major|minor|patch] --dry-run -vv`
-5. bump the version: `uvx bump-my-version bump [major|minor|patch]`, which updates `src/pymetadata/__init__.py` and `CITATION.cff`, commits and tags
-6. `git push --tags`, which triggers the release workflow publishing to [pypi](https://pypi.org/project/pymetadata/), followed by `git push`
-7. test the installation from pypi in a fresh environment:
+9. test the installation from pypi in a fresh environment:
 
     ```bash
     uv venv --python 3.14
     uv pip install pymetadata
     ```
 
-8. once Zenodo has archived the release, update the citation information, i.e., `date-released` in `CITATION.cff` and the version, date and version DOI of the release in the citation of `README.md` and `docs/index.md`. `bump-my-version` only updates the version, not the date and the DOI, which are only known after the release
+10. once Zenodo has archived the release, update the citation information, i.e., `date-released` in `CITATION.cff` and the version, date and version DOI of the release in the citation of `README.md` and `docs/index.md`. `bump-my-version` only updates the version, not the date and the DOI, which are only known after the release. These changes go in through a pull request like everything else

pymetadata-0.6.2/release-notes/0.6.2.md

@@ -0,0 +1,21 @@
+# Release notes for pymetadata 0.6.2
+![pymetadata](./docs/images/favicon/pymetadata-100x100-300dpi.png)
+
+We are pleased to release the next version of pymetadata including the
+following changes:
+
+## Features
+- `EntryFormat.ANTIMONY` for Antimony model files in COMBINE archives (`text/plain`)
+
+## Development
+- every change goes into `develop` through a pull request; the tests, `ruff`, `ty` and the documentation build have to pass before a merge is possible
+- `main` tracks the latest published release and is fast-forwarded to the released commit by the release workflow
+- the workflows also run on pull requests, so contributions from forks are tested
+- the branch protection is part of the repository as rulesets in `.github/rulesets/`, together with `CODEOWNERS` and a pull request template
+- the branch model, the pull request rules and the adjusted release process are documented in `docs/development.md`
+- the mkdocstrings options in `zensical.toml` use the plugin table directly, as required by zensical 0.0.60
+
+## Fixes
+- `RDFAnnotation` raises a `ValueError` for a qualifier which is not a `BQB` or `BQM`, instead of only for a missing one, so an invalid qualifier fails where it is passed
+
+Your pymetadata team

{pymetadata-0.6.1 → pymetadata-0.6.2}/src/pymetadata/__init__.py

@@ -7,7 +7,7 @@ from pathlib import Path
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 __author__ = "Matthias Koenig"
-__version__ = "0.6.1"
+__version__ = "0.6.2"
 
 
 program_name: str = "pymetadata"

{pymetadata-0.6.1 → pymetadata-0.6.2}/src/pymetadata/core/annotation.py

@@ -118,10 +118,10 @@ class RDFAnnotation:
         self.resource: str = resource
         self.provider: ProviderType = ProviderType.NONE
 
-        if not qualifier:
+        if not isinstance(qualifier, BQB | BQM):
             raise ValueError(
-                f"MIRIAM qualifiers are required for rdf annotation, but no "
-                f"qualifier for resource '{resource}' was provided."
+                f"MIRIAM qualifiers are required for rdf annotation, but "
+                f"'{qualifier}' was provided for resource '{resource}'."
             )
         if not resource:
             raise ValueError(
@@ -341,9 +341,7 @@ class RDFAnnotation:
             True if the qualifier is a MIRIAM qualifier and the term matches the
             pattern of its collection.
         """
-        valid_qualifier: bool = False
-        if self.qualifier:
-            valid_qualifier = self.check_qualifier(self.qualifier)
+        valid_qualifier: bool = self.check_qualifier(self.qualifier)
         valid_term: bool = True
         if self.collection and self.term:
             valid_term = self.check_miriam_term()

{pymetadata-0.6.1 → pymetadata-0.6.2}/src/pymetadata/omex.py

@@ -131,6 +131,7 @@ class EntryFormat(str, Enum):
     SCI = PURL_PREFIX + "application/x-scilab"
     XPP = PURL_PREFIX + "text/plain"
     SEDX = PURL_PREFIX + "application/x-sed-ml-archive"
+    ANTIMONY = PURL_PREFIX + "text/plain"
 
     H323 = PURL_PREFIX + "text/h323"
     ACX = PURL_PREFIX + "application/internet-property-stream"

{pymetadata-0.6.1 → pymetadata-0.6.2}/zensical.toml

@@ -96,13 +96,13 @@ icon = "fontawesome/brands/python"
 link = "https://pypi.org/project/pymetadata/"
 
 # API reference is rendered from the docstrings, see the `docs/api` pages
-[project.plugins.mkdocstrings.config]
+[project.plugins.mkdocstrings]
 default_handler = "python"
 
-[project.plugins.mkdocstrings.config.handlers.python]
+[project.plugins.mkdocstrings.handlers.python]
 paths = ["src"]
 
-[project.plugins.mkdocstrings.config.handlers.python.options]
+[project.plugins.mkdocstrings.handlers.python.options]
 docstring_style = "google"
 docstring_section_style = "table"
 show_source = false