Merge master

.github/workflows/publish.yaml

@@ -5,68 +5,25 @@ on:
     types: [published]
   workflow_dispatch:
 
-
 jobs:
-  fix_release_deps:
-    permissions: write-all
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.12'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip pip-tools setuptools
-
-    - name: Set configuration
-      run: |
-        git config --global user.name "${GITHUB_ACTOR}"
-        git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
-
-    - name: Create requirements files
-      run: |
-        python tools/generate_requirements_txt.py
-        pip-compile -o requirements_full.txt pyproject.toml
-        git add requirements_full.txt requirements.txt
-        git commit -m "Updated requirements.txt files" || true
-
-    - name: Bump version to new tag
-      run: |
-        python -m pip install bump-my-version
-        bump-my-version bump --new-version $GITHUB_REF_NAME patch
-        git commit -am "Bump version to: $GITHUB_REF_NAME"
-
-    - name: Push back changes to master and tag
-      run: |
-        git tag --force $GITHUB_REF_NAME HEAD
-        git push --force --tags
-        git switch -C master
-        git push --set-upstream -f origin master
-
   deploy:
-    needs: fix_release_deps
     runs-on: ubuntu-latest
     environment: release
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
 
     steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ github.ref_name }}
-
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.12'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install build setuptools>=61.2 wheel
-        python -m build --no-isolation
-
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build setuptools>=61.2 wheel
+          python -m build --no-isolation
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yaml

@@ -0,0 +1,76 @@
+name: Tests for MORS
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup system
+        run: |
+          sudo apt-get update
+          sudo apt-get install libnetcdff-dev netcdf-bin
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v3
+        id: cache-virtualenv
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Build MORS
+        if: steps.cache-virtualenv.outputs.cache-hit != 'true'
+        run: |
+          python -m pip install -e .[develop]
+
+      - uses: actions/cache@v3
+        id: cache-fwl-data
+        with:
+          path: /home/runner/work/fwl_data
+          key: fwl-data-1
+
+      - name: Test with pytest
+        run: |
+          export FWL_DATA="/home/runner/work/fwl_data"
+          coverage run -m pytest
+
+      - name: Report coverage
+        run: |
+          coverage json
+          export TOTAL=$(python -c "import json;print(json.load(open('coverage.json'))['totals']['percent_covered_display'])")
+          echo "total=$TOTAL" >> $GITHUB_ENV
+          echo "### Total coverage: ${TOTAL}%" >> $GITHUB_STEP_SUMMARY
+          echo $'\n```' >> $GITHUB_STEP_SUMMARY
+          coverage report >> $GITHUB_STEP_SUMMARY
+          echo $'\n```' >> $GITHUB_STEP_SUMMARY
+
+      - name: Make coverage badge
+        if: ${{ github.ref == 'refs/heads/master' && matrix.python-version == '3.10' }}
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.GIST_TOKEN }}
+          gistID: a25c37a328839edd00bb32d8527aec30
+          filename: covbadge.svg
+          label: Coverage
+          message: ${{ env.total }}%
+          minColorRange: 50
+          maxColorRange: 90
+          valColorRange: ${{ env.total }}

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+      - docs

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -0,0 +1,41 @@
+# Contributing guidelines
+
+### Building the documentation
+
+The documentation is written in [markdown](https://www.markdownguide.org/basic-syntax/), and uses [mkdocs](https://www.mkdocs.org/) to generate the pages.
+
+To build the documentation for yourself:
+
+```console
+pip install -e .[docs]
+mkdocs serve
+```
+
+You can find the documentation source in the [docs](https://github.com/FormingWorlds/MORS/tree/main/docs) directory.
+If you are adding new pages, make sure to update the listing in the [`mkdocs.yml`](https://github.com/FormingWorlds/MORS/blob/main/mkdocs.yml) under the `nav` entry.
+
+The documentation is hosted on [readthedocs](https://fwl-mors.readthedocs.io).
+
+### Making a release
+
+The versioning scheme we use is [CalVer](https://calver.org/).
+
+0. Update requirements files:
+
+```console
+python tools/requirements_txt.py
+pip-compile -o requirements_full.txt pyproject.toml
+```
+
+1. Bump the version (`release`/`patch`) as needed
+
+```console
+bump-my-version release
+# 24.7.11
+```
+
+2. Commit and push your changes.
+
+3. Make a new [release](https://github.com/FormingWorlds/MORS/releases). Make sure to set the tag to the specified version, e.g. `24.7.11`.
+
+4. The [upload to pypi](https://pypi.org/project/fwl-mors) is triggered when a release is published and handled by [this workflow](https://github.com/FormingWorlds/MORS/actions/workflows/publish.yaml).