From 151850e5ed52c21ce645a350e367eb593623013f Mon Sep 17 00:00:00 2001
From: Thomas Duigou <thomas.duigou@inrae.fr>
Date: Thu, 6 Feb 2025 19:03:49 +0100
Subject: [PATCH] ci(test): now make use of coveralls

---
 .github/workflows/test.yml            | 59 +++++----------------
 .github/workflows/test_deprecated.yml | 74 +++++++++++++++++++++++++++
 2 files changed, 87 insertions(+), 46 deletions(-)
 create mode 100644 .github/workflows/test_deprecated.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5498024..00178dc 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,25 +1,17 @@
 name: Test code
 
-on:
-
-    push:
-        branches: [ '*' ]
-        # paths: [ '**.py' ]
+on: [push, pull_request]
 
 jobs:
 
     Test:
 
-        runs-on: ${{ matrix.os }}-latest
-        strategy:
-            matrix:
-                os: ["ubuntu", "macos", "windows"]
+        runs-on: ubuntu-latest
         defaults:
             run:
                 shell: bash -l {0}
         
         steps:
-
             - name: Checkout code
               uses: actions/checkout@v4
 
@@ -31,46 +23,21 @@ jobs:
                 activate-environment: test-env
                 conda-remove-defaults: "true"
 
-            - name: Install dev dependencies with conda
-              run: |
-                  conda env update -n test-env --file environment-dev.yml
-              
             - name: Install as package
               run: |
-                  pip -v install --no-deps --editable .
+                    pip -v install --no-deps --editable .
 
-            - name: Run tests with coverage
-              run: |
-                  coverage run -m pytest -xs
-            
-            - name: Generate coverage report
-              if: matrix.os == 'ubuntu'
+            - name: Install dependencies for testing
               run: |
-                  coverage report --format markdown > coverage.md
+                    conda install --channel conda-forge pytest
+                    pip install coveralls
 
-            - name: Extract coverage percentage
-              if: matrix.os == 'ubuntu'
+            - name: Run tests
               run: |
-                  export COV_PERCENT=$(coverage report --format total)
-                  echo "COV_PERCENT=$COV_PERCENT" >> $GITHUB_ENV
+                    coverage run -m pytest tests
 
-            - name: Create Coverage Badge
-              if: matrix.os == 'ubuntu'
-              uses: schneegans/dynamic-badges-action@v1.7.0
-              with:
-                auth: ${{ secrets.GIST_SECRET }}
-                gistID: 056fdf29a6c0ab5b61a62f21468be178
-                filename: molecule-signature-coverage.json
-                label: coverage
-                message: ${{ env.COV_PERCENT }}%
-                valColorRange: ${{ env.COV_PERCENT }}
-                minColorRange: 50
-                maxColorRange: 90
-
-            - name: Upload coverage report
-              if: matrix.os == 'ubuntu'
-              uses: actions/upload-artifact@v4
-              with:
-                name: coverage
-                path: coverage.md
-                compression-level: 0
+            - name: Report using coveralls
+              run: |
+                    coveralls
+              env:
+                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test_deprecated.yml b/.github/workflows/test_deprecated.yml
new file mode 100644
index 0000000..2dd33a5
--- /dev/null
+++ b/.github/workflows/test_deprecated.yml
@@ -0,0 +1,74 @@
+name: Test code (deprecated)
+
+on:
+    push:
+        branches-ignore: [ '*' ]  # Prevents this workflow from running
+
+jobs:
+
+    Test:
+
+        runs-on: ${{ matrix.os }}-latest
+        strategy:
+            matrix:
+                os: ["ubuntu", "macos", "windows"]
+        defaults:
+            run:
+                shell: bash -l {0}
+        
+        steps:
+
+            - name: Checkout code
+              uses: actions/checkout@v4
+
+            - name: Install regular dependencies with conda
+              uses: conda-incubator/setup-miniconda@v3
+              with:
+                miniforge-version: "latest"
+                environment-file: environment.yml
+                activate-environment: test-env
+                conda-remove-defaults: "true"
+
+            - name: Install dev dependencies with conda
+              run: |
+                  conda env update -n test-env --file environment-dev.yml
+              
+            - name: Install as package
+              run: |
+                  pip -v install --no-deps --editable .
+
+            - name: Run tests with coverage
+              run: |
+                  coverage run -m pytest -xs
+            
+            - name: Generate coverage report
+              if: matrix.os == 'ubuntu'
+              run: |
+                  coverage report --format markdown > coverage.md
+
+            - name: Extract coverage percentage
+              if: matrix.os == 'ubuntu'
+              run: |
+                  export COV_PERCENT=$(coverage report --format total)
+                  echo "COV_PERCENT=$COV_PERCENT" >> $GITHUB_ENV
+
+            - name: Create Coverage Badge
+              if: matrix.os == 'ubuntu'
+              uses: schneegans/dynamic-badges-action@v1.7.0
+              with:
+                auth: ${{ secrets.GIST_SECRET }}
+                gistID: 056fdf29a6c0ab5b61a62f21468be178
+                filename: molecule-signature-coverage.json
+                label: coverage
+                message: ${{ env.COV_PERCENT }}%
+                valColorRange: ${{ env.COV_PERCENT }}
+                minColorRange: 50
+                maxColorRange: 90
+
+            - name: Upload coverage report
+              if: matrix.os == 'ubuntu'
+              uses: actions/upload-artifact@v4
+              with:
+                name: coverage
+                path: coverage.md
+                compression-level: 0