update .yml files

.github/workflows/docs.yml

@@ -36,8 +36,21 @@ jobs:
       - name: build documents
         run: make -C doc html
 
+      - name: Run tests and upload coverage
+        shell: bash -l {0}
+        run: |
+          conda activate test
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./doc/build/html

.github/workflows/main.yml

@@ -44,17 +44,12 @@ jobs:
           conda activate test
           conda install --file requirements/run.txt
           conda install --file requirements/test.txt
-          pip install -e .
-          
+          pip install .
+
       - name: Validate diffpy.structure
         shell: bash -l {0}
         run: |
           conda activate test
-          coverage run -m diffpy.structure.tests.run
+          coverage run -m pytest -vv -s
           coverage report -m
           codecov
-          
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/action@v3.0.0
+        with:
+          extra_args: --all-files