Refactor the CI and add pyproject.toml

theochem · Sep 13, 2024 · b55e554 · b55e554
1 parent 39d90f9
commit b55e554
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Showing 6 changed files with 344 additions and 114 deletions.
diff --git a/.github/workflows/ci_codecov.yml b/.github/workflows/ci_codecov.yml
@@ -21,19 +21,16 @@ on:
     - cron: "0 0 * * *"
 
 jobs:
-  run:
+  test:
     name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest]
-
-    env:
-      OS: ${{ matrix.os }}
-      python-version: "3.7"
+        python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Additional info about the build
       shell: bash
       run: |
@@ -42,7 +39,7 @@ jobs:
         ulimit -a
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
@@ -51,22 +48,27 @@ jobs:
       shell: bash
       run: |
         python -m pip install --upgrade pip
+        python -m pip install -r requirements_dev.txt
+        python -m pip install -U pytest pytest-cov codecov
+
+    - name: Install package
+      shell: bash
+      run: |
         python -m pip install .
         # pip install tox tox-gh-actions
-        python -m pip install -r requirements.txt
-        python -m pip install -U pytest pytest-cov
 
     - name: Run tests
       shell: bash
       run: |
-        pytest --cov=./ --cov-config=.coveragerc --cov-report=xml --color=yes procrustes/test/
+        python -m pytest -c pyproject.toml --cov-config=.coveragerc --cov-report=xml --color=yes selector
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3.1.0
+      uses: codecov/codecov-action@v4.5.0
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        # Temp fix for https://github.com/codecov/codecov-action/issues/1487
+        version: v0.6.0
         fail_ci_if_error: true
-        directory: ./coverage/reports/
         file: ./coverage.xml
-        verbose: true
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
diff --git a/.github/workflows/ci_tox.yml b/.github/workflows/ci_tox.yml
@@ -1,30 +1,63 @@
 name: CI Tox
+
 on:
-    push:
-        # branches: [master, tox]
-    pull_request:
-        branches: [master]
+  # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+  # Existing codes likely still have "master" as the primary branch
+  # Both are tracked here to keep legacy and new codes working
+  push:
+    branches:
+      - "master"
+      - "main"
+  pull_request:
+    branches:
+      - "master"
+      - "main"
+  schedule:
+    # Nightly tests run on master by default:
+    # Scheduled workflows run on the latest commit on the default or base branch.
+    # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
 
 jobs:
-    test:
-        strategy:
-            fail-fast: false
-            matrix:
-                os: [ubuntu-latest, macos-latest, windows-latest]
-                python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+  test:
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # os: [macOS-latest, windows-latest, ubuntu-latest]
+        os: [macos-13, windows-latest, ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Additional info about the build
+      shell: bash
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: x64
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -r requirements_dev.txt
+        # python -m pip install -U pytest pytest-cov codecov
+        python -m pytest -c pyproject.toml --cov-config=.coveragerc --cov-report=xml --color=yes procrustes
 
-        runs-on: ${{ matrix.os }}
-        steps:
-        - uses: actions/checkout@v3
-        - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v4
-          with:
-              python-version: ${{ matrix.python-version }}
-              architecture: x64
-        - name: Install dependencies
-          run: |
-              python -m pip install --upgrade pip
-              pip install tox tox-gh-actions
-        - name: Testing with tox
-          run: tox
+    - name: Install package
+      shell: bash
+      run: |
+        python -m pip install .
+        pip install tox tox-gh-actions
 
+    - name: Run tests
+      shell: bash
+      run: |
+        tox
diff --git a/README.md b/README.md
@@ -1,13 +1,12 @@
 Procrustes
 ==========
 
-[![This project supports Python 3.6+](https://img.shields.io/badge/Python-3.6+-blue.svg)](https://python.org/downloads)
+[![This project supports Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg)](https://python.org/downloads)
 [![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://opensource.org/licenses/)
 [![GitHub Actions CI Tox Status](https://github.com/theochem/procrustes/actions/workflows/ci_tox.yml/badge.svg?branch=master)](https://github.com/theochem/procrustes/actions/workflows/ci_tox.yml)
 [![Documentation Status](https://readthedocs.org/projects/procrustes/badge/?version=latest)](https://procrustes.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/theochem/procrustes/branch/master/graph/badge.svg?token=3L96J5QQOT)](https://codecov.io/gh/theochem/procrustes)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/theochem/procrustes/master?filepath=doc%2Fnotebooks%2F)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/theochem/procrustes.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/theochem/procrustes/context:python)
 
 The Procrustes library provides a set of functions for transforming a matrix to make it
 as similar as possible to a target matrix. For more information, visit
@@ -55,7 +54,7 @@ first, and then:
 
 ```bash
 # Create and activate myenv conda environment (optional, but recommended)
-conda create -n myenv python=3.6
+conda create -n myenv python=3.11
 conda activate myenv
 
 # Install the stable release.