Merge branch 'main' into stable

.github/CODE_OF_CONDUCT.rst

@@ -0,0 +1,49 @@
+Code of Conduct
+===============
+
+- Be friendly and patient
+- Be respectful
+- Be welcoming
+- Be considerate
+- Focus on what's best for the community
+- Gracefully accept constructive criticism
+- Show courtesy and respect towards other community members
+- Be respectful of different viewpoints and experiences
+- Use welcoming and inclusive language
+
+Reporting an issue
+------------------
+If you see a violation of the code of conduct, please report it to anyone belonging to the [BioRetroSynth organization](https://github.com/orgs/brsynth/people).  If the person who is harassing you belongs to the team, he will recuse himself from handling your incident. We will respond as promptly as we can.
+To protect volunteers from abuse and burnout, we reserve the right to reject any report we believe to have been made with the deliberate intention of deceiving or misleading the committee.
+
+Enforcement
+-----------
+Upon receiving a report, the Maintainer core team will meet privately to discuss
+the matter and determine the best course of action.
+
+Possible responses may include:
+
+- taking no further action (if we determine no violation occurred)
+- a private reprimand from the core members to the individual(s) involved. In
+  this case, a core member will deliver that reprimand via email, copying the
+  rest of the core.
+- a public reprimand. In this case a core member will deliver the reprimand via
+  the same channel as the violation occurred (e.g., via comment on PR or issue)
+- an imposed vacation (e.g., asking the individual to refrain from participating
+  for a week). A core member will deliver a request for the individual to take
+  such a "vacation" voluntarily, but if they don't disagree then a temporary
+  ban may be imposed.
+- a permanent or temporary ban from the repository
+
+Once a resolution is agreed upon, but before it is enacted, the core will
+contact the original reporter and discuss the resolution and will note any
+feedback for the record, but is not obligated to act on such feedback.
+
+The core will never publicly discuss the issue; any public statements will be
+made by core members.
+
+If the incident involves a core member, the core member must recuse themselves
+from the response process.
+
+This policy was modified from
+`django project <https://www.djangoproject.com/conduct/enforcement-manual>`_

.github/CONTRIBUTING.rst

@@ -0,0 +1,65 @@
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+Ways you can help
+-----------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/brsynth/neo4jsbml/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version, versions of Neo4j and SBML specification.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with
+"enhancement" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Same as Implement Features
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/brsynth/neo4jsbml/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* This will hopefully become a community-driven project and contributions
+  are welcome :)
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring.
+2. Passing ``pytest``
+
+   .. code-block:: console
+
+        $ python -m pytest
+
+3. Passing `super-linter <https://github.com/marketplace/actions/super-linter>`_
+
+This policy was modified from
+`planemo project <https://github.com/galaxyproject/planemo/blob/master/CONTRIBUTING.rst>`_

.github/linters/.flake8

@@ -1,3 +1,4 @@
 [flake8]
 max-line-length = 320
 extend-ignore = E203,E262,F401
+exclude = docs/conf.py

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
      tag: ${{ steps.tag_label.outputs.tag }}
      changelog: ${{ steps.tag_raw.outputs.changelog }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -36,7 +36,7 @@ jobs:
   Changelog:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -56,12 +56,21 @@ jobs:
           PROJECT=$(echo "$GITHUB_REPOSITORY" | sed -e 's/\// /g' | awk '{print $2}')
           echo "$USER $PROJECT"
           github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
-      - name: 'Upload Artifact Changelog'
+      - uses: docker://pandoc/core:2.9
+        with:
+          args: -o CHANGELOG.data.rst CHANGELOG.md
+      - name: 'Upload Artifact Changelog - md'
         uses: actions/upload-artifact@v3
         with:
-          name: changelog-artifact
+          name: changelog-md-artifact
           path: CHANGELOG.md
           retention-days: 1
+      - name: 'Upload Artifact Changelog - rst'
+        uses: actions/upload-artifact@v3
+        with:
+          name: changelog-rst-artifact
+          path: CHANGELOG.data.rst
+          retention-days: 1
 
   Version:
     needs: TagRaw
@@ -70,7 +79,7 @@ jobs:
       version_path: ${{ steps.update_version.outputs.version_path }}
       version_dir: ${{ steps.update_version.outputs.version_dir }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: 'Update _version.py'
         id: update_version
         env:
@@ -81,6 +90,9 @@ jobs:
           sed -i "2s/.*/__version__ = \"$TAG\"/" "$VERSION_PATH"
           echo "version_path=$VERSION_PATH" >> "$GITHUB_OUTPUT"
           echo "version_dir=$VERSION_DIR" >> "$GITHUB_OUTPUT"
+
+          RECIPE_PATH=$(find . -name meta.yaml | head -n 1)
+          sed -i "2s/.*/{% set version = \"$TAG\" %}/" "$RECIPE_PATH"
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
         with:
@@ -93,7 +105,7 @@ jobs:
     steps:
       # Get Data
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -102,10 +114,15 @@ jobs:
         with:
           name: version-artifact
           path: ${{ needs.Version.outputs.version_dir }}
-      - name: 'Download Artifact Changelog'
+      - name: 'Download Artifact Changelog - md'
+        uses: actions/download-artifact@v3
+        with:
+          name: changelog-md-artifact
+      - name: 'Download Artifact Changelog - rst'
         uses: actions/download-artifact@v3
         with:
-          name: changelog-artifact
+          name: changelog-rst-artifact
+          path: docs/
       # Commit
       - name: 'Commit files'
         run: |
@@ -133,13 +150,13 @@ jobs:
     needs: [Commit, TagRaw]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           persist-credentials: false
           fetch-depth: 0
       - name: 'Bump version and push tag'
         id: tag
-        uses: mathieudutour/github-tag-action@v6.0
+        uses: mathieudutour/github-tag-action@v6.1
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           release_branches: stable
@@ -158,7 +175,7 @@ jobs:
         shell: bash -l {0} # activate env conda
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Deploying miniconda'
         uses: conda-incubator/setup-miniconda@v2
         with:

.github/workflows/lint.yml

@@ -8,12 +8,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
           fetch-depth: 0
       - name: Lint Code Base
-        uses: github/super-linter@v4
+        uses: github/super-linter@v5
         env:
           DEFAULT_BRANCH: ${{ github.ref }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

@@ -7,20 +7,22 @@ on:
   pull_request:
     branches:
       - main
+  schedule:
+    - cron:  '0 0 * * 1'
 
 jobs:
 
   Build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
       - name: 'Setup Neo4j with APOC'
@@ -41,36 +43,3 @@ jobs:
         run: |
           pip install --no-deps .
           python -m pytest tests
-
-  Coverage:
-    needs: [Build]
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: 'Checkout'
-        uses: actions/checkout@v3
-        with:
-          ref: ${{ github.ref }}
-      - name: 'Setup Neo4j with APOC'
-        uses: mdanics/[email protected]
-      - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: "latest"
-          environment-file: recipes/workflow.yaml
-          python-version: '3.9'
-          mamba-version: "*"
-          channel-priority: true
-          use-mamba: true
-      - name: 'Run tests'
-        run: |
-          pip install --no-deps .
-          coverage run -m pytest
-          coverage lcov
-      - name: 'Coveralls'
-        uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: ./coverage.lcov

.gitignore

@@ -24,3 +24,6 @@ debug
 papier
 cmd.sh
 *.xml
+# Docs
+_build
+generated

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+   os: ubuntu-22.04
+   tools:
+     python: "mambaforge-4.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+conda:
+  environment: recipes/workflow.yaml
+
+formats:
+  - pdf
+  - epub

CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## [0.10.1](https://github.com/brsynth/neo4jsbml/tree/0.10.1) (2023-03-17)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.10.0...0.10.1)
+
+## [0.10.0](https://github.com/brsynth/neo4jsbml/tree/0.10.0) (2023-03-17)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.9.2...0.10.0)
+
+**Merged pull requests:**
+
+- chore\(deps\): bump mathieudutour/github-tag-action from 6.0 to 6.1 [\#6](https://github.com/brsynth/neo4jsbml/pull/6) ([dependabot[bot]](https://github.com/apps/dependabot))
+- Read the docs [\#5](https://github.com/brsynth/neo4jsbml/pull/5) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
+## [0.9.2](https://github.com/brsynth/neo4jsbml/tree/0.9.2) (2023-02-23)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.9.1...0.9.2)
+
+## [0.9.1](https://github.com/brsynth/neo4jsbml/tree/0.9.1) (2023-02-21)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.9.0...0.9.1)
+
 ## [0.9.0](https://github.com/brsynth/neo4jsbml/tree/0.9.0) (2023-01-27)
 
 [Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.8.3...0.9.0)