Dev

.github/workflows/tests.yaml

@@ -1,42 +1,47 @@
-# This file runs the tests in `tests/`
-# They will run in parallel, and run on three operating systems:
-# Ubuntu, Windows and Mac.
-
 name: tests
 
 on:
   push:
     branches: [main]
   workflow_dispatch:
+    inputs:
+      operating_systems:
+        description: 'Operating systems to test on'
+        type: choice
+        default: 'all'
+        options:
+          - all
+          - ubuntu-latest
+          - windows-latest
+          - macos-latest
 
 jobs:
-
-  # Run tests on Ubuntu
-  tests-on-ubuntu:
+  # Generate matrix based on input
+  setup-matrix:
     runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
-
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install python and dependencies
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.13'
-          cache: 'pip'
-      - run: pip install -r requirements.txt
-
-      - name: Run tests
-        run: pytest
-
-      - name: List the environment variables
-        run: env
-
-  # Run tests on Windows
-  tests-on-windows:
-    runs-on: windows-latest
+      - name: Set matrix
+        id: set-matrix
+        run: |
+          if [[ "${{ inputs.operating_systems }}" == "all" || "${{ github.event_name }}" == "push" ]]; then
+            echo 'matrix=["ubuntu-latest", "windows-latest", "macos-latest"]' >> $GITHUB_OUTPUT
+          else
+            echo 'matrix=["${{ inputs.operating_systems }}"]' >> $GITHUB_OUTPUT
+          fi
+
+  # Run tests using matrix strategy
+  tests:
+    permissions:
+      contents: write
+    needs: setup-matrix
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ${{ fromJSON(needs.setup-matrix.outputs.matrix) }}
+
     steps:
-
       - name: Check out repository
         uses: actions/checkout@v4
 
@@ -45,31 +50,42 @@ jobs:
         with:
           python-version: '3.13'
           cache: 'pip'
-      - run: python -m pip install -r requirements.txt
-
-      - name: Run tests
-        run: pytest
-
-      - name: List the environment variables
-        run: env
-
-  # Run tests on Mac
-  tests-on-macos:
-    runs-on: macos-latest
-    steps:
-
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install python and dependencies
-        uses: actions/setup-python@v4
+
+      - name: Install requirements (Windows)
+        if: runner.os == 'Windows'
+        run: python -m pip install -r requirements.txt
+
+      - name: Install requirements (Unix)
+        if: runner.os != 'Windows'
+        run: pip install -r requirements.txt
+
+      - name: Run tests (with coverage for linux)
+        run: |
+          if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
+            pytest --cov --cov-report=xml
+          else
+            pytest
+          fi
+        shell: bash
+
+      - name: Generate coverage badge (for-the-badge style)
+        if: matrix.os == 'ubuntu-latest'
+        run: genbadge coverage -i coverage.xml -o images/coverage-badge.svg
+
+      - name: Upload coverage badge
+        if: matrix.os == 'ubuntu-latest'
+        uses: actions/upload-artifact@v4
         with:
-          python-version: '3.13'
-          cache: 'pip'
-      - run: pip install -r requirements.txt
-
-      - name: Run tests
-        run: pytest
-
-      - name: List the environment variables
-        run: env
+          name: coverage-badge
+          path: images/coverage-badge.svg
+
+      - name: Commit coverage badge
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add images/coverage-badge.svg
+          git commit -m "ci(tests): update coverage badge" || echo "No changes to commit"
+          git push
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CITATION.cff

@@ -14,6 +14,11 @@ authors:
     email: a.heather2@exeter.ac.uk
     affiliation: University of Exeter
     orcid: 'https://orcid.org/0000-0002-6596-3479'
+  - given-names: Thomas
+    family-names: Monks
+    email: t.m.w.monks@exeter.ac.uk
+    affiliation: University of Exeter
+    orcid: 'https://orcid.org/0000-0003-2631-4481'
 repository-code: >-
   https://github.com/pythonhealthdatascience/pydesrap_stroke
 abstract: >-

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, caste, color, 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 email 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
+[INSERT CONTACT METHOD].
+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](https://www.contributor-covenant.org/), version 2.1,
+available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct/>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/inclusion).
+
+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/>.