Update ci.yaml

.github/workflows/ci.yaml

@@ -1,16 +1,14 @@
-#!/bin/bash
 name: CI
+run-name: "${{ github.event_name }}: ${{ github.ref }}"
 
 on:
   push:
-    branches:
-      - "master"
   pull_request:
     branches:
       - "master"
   schedule:
-    # Run a cron job once weekly on Monday
-    - cron: "0 3 * * 1"
+    - cron: "0 3 * * 1"  # weekly on Monday
+  workflow_dispatch:
 
 jobs:
   test:
@@ -20,14 +18,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     env:
       CI_OS: ${{ matrix.os }}
       PYVER: ${{ matrix.python-version }}
       PACKAGE: "opencadd"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Additional info about the build
         shell: bash
@@ -36,36 +34,41 @@ jobs:
           df -h
           ulimit -a
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: 'Setup conda environment'
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: test
+          create-args: python=${{ matrix.python-version }}
           environment-file: devtools/conda-envs/test_env.yaml
-          channels: conda-forge,defaults,bioconda
+          micromamba-version: latest
+          generate-run-shell: true
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+              - defaults
+              - bioconda
 
       # TODO: Remove this step when patched theseus makes it to CF
       - name: Build patched mmligner
-        shell: bash -l {0}
+        shell: micromamba-shell {0}
         run: |
-          conda activate base
-          conda install conda-build
+          micromamba install conda-build
           conda build devtools/conda-recipes/mmligner/
 
       - name: Install package
-        shell: bash -l {0}
+        shell: micromamba-shell {0}
         run: |
-          conda install -c local mmligner pip
+          micromamba install -c local mmligner pip
           python -m pip install . --no-deps
-          conda list
+          micromamba list
 
       - name: Run tests
-        shell: bash -l {0}
+        shell: micromamba-shell {0}
         run: |
           pytest -v --cov=${PACKAGE} --cov-report=xml --color=yes ${PACKAGE}/tests/
 
       - name: CodeCov
+        if: github.event_name == 'push' && github.ref_name == 'master'
         uses: codecov/codecov-action@v1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -77,35 +80,24 @@ jobs:
   lint-format:
     runs-on: ubuntu-latest
     env:
-      CI_OS: ubuntu-latest
       PACKAGE: "opencadd"
-      PYVER: "3.8"
 
     steps:
       - name: Checkout the code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: 'Setup Python'
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          activate-environment: test
-          environment-file: devtools/conda-envs/test_env.yaml
-          channels: conda-forge,defaults,bioconda
+          python-version: '3.x'
 
       - name: Install linter and formatter
-        shell: bash -l {0}
         run: |
-          conda install -y pylint black
+          python -m pip install pylint black
 
       - name: Run pylint
-        shell: bash -l {0}
-        run: |
-          pylint $PACKAGE/
+        run: pylint $PACKAGE/
 
       - name: Run black check
-        shell: bash -l {0}
         if: always()
-        run: |
-          black --check -l 99 $PACKAGE/
+        run: black --check -l 99 $PACKAGE/