Testing CI

.coveragerc

@@ -0,0 +1,12 @@
+[run]
+omit =
+    */_version.py
+    */data/*
+
+[report]
+exclude_lines =
+    if __name__ == "__main__"
+    pragma: no cover
+    pragma: no-cover
+    -no-cov
+    raise NotImplementedError

.github/workflows/ci.yml

@@ -3,105 +3,72 @@ name: CI
 on:
   push:
     branches:
-      - "master"
-      - "dev"
       - "main"
   pull_request:
     branches:
-      - "master"
-      - "dev"
       - "main"
   schedule:
     # Run a cron job once daily
     - cron: "0 0 * * *"
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
-    name: ${{ matrix.name }}
-    runs-on: ${{ matrix.os }}
+    name: "tests"
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: Linux, Python 3.9
-            os: ubuntu-latest
-            python-version: "3.9"
-            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-
-          - name: MacOS, Python 3.9
-            os: macOS-latest
-            python-version: "3.9"
-            conda-installer: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-MacOSX-x86_64.sh
+        os: ['ubuntu', 'macos']
+        python-version:
+          - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          installer-url: ${{ matrix.conda-installer }}
+          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           activate-environment: test
           channel-priority: true
           environment-file: devtools/conda-envs/env.yaml
-          auto-activate-base: false
           use-mamba: true
+          miniforge-variant: Mambaforge
 
       - name: Additional info about the build
-        shell: bash
         run: |
           uname -a
           df -h
           ulimit -a
+
       - name: Environment Information
-        shell: bash -l {0}
         run: |
           conda info --all
           conda list
           mamba --version
+
       - name: Install package
-        shell: bash -l {0}
         run: |
           python -m pip install -e .
+
       - name: Run tests
         shell: bash -l {0}
         run: |
           pytest -v --cov=cinnabar --cov-report=xml --cov-report=term --color=yes cinnabar/tests/
-      - uses: codecov/codecov-action@v2
+
+      - uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
           fail_ci_if_error: true # optional (default = false)
           verbose: true # optional (default = false)
-
-  lint-format:
-    name: Lint & format checks
-    runs-on: ubuntu-18.04
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-          python-version: "3.9"
-          activate-environment: test
-          channel-priority: true
-          environment-file: devtools/conda-envs/env.yaml
-          auto-activate-base: false
-          use-mamba: true
-
-      - name: Additional info about the build
-        shell: bash
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-      - name: Environment Information
-        shell: bash -l {0}
-        run: |
-          conda info --all
-          conda list
-      - name: Install package
-        shell: bash -l {0}
-        run: |
-          python -m pip install --no-deps .

devtools/conda-envs/env.yaml

@@ -24,5 +24,4 @@ dependencies:
   # testing
   - pytest
   - pytest-cov
-  - codecov
   - nbval