Use binary distribution (wheels) to install pymatgen in test suite (#…

…4073)

* comment tweaks

* pin python 3.12 in CI

* try to install from sdist

* try to add test files dir

* uncomment resolution

* set lower pin for bs4 from year 2017

* remove duplicate in dep declare

* drop quotes

* remove duplicated comment

* sort optional dependencies

* TEST: test exclude a required file from sdist would lead to CI failure

* Revert "TEST: test exclude a required file from sdist would lead to CI failure"

This reverts commit 0dba028.

* perhaps install from wheels?

* skip failing test as dgl doesn't support torch 2.4.1

* revert pyproject in favor in separate PR

* fix missing @

.github/workflows/issue-metrics.yml

@@ -26,7 +26,7 @@ jobs:
           # Calculate the last day of the previous month
           last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
 
-          #Set an environment variable with the date range
+          # Set an environment variable with the date range
           echo "$first_day..$last_day"
           echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
 

.github/workflows/release.yml

@@ -1,4 +1,5 @@
-name: Release # makes PyPI releases
+# Make PyPI releases
+name: Release
 
 on:
   release:
@@ -26,12 +27,12 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        name: Install Python
+      - name: Install Python
+        uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
-      - name: Build sdist
+      - name: Build source distribution
         run: |
           pip install build
           python -m build --sdist
@@ -66,7 +67,7 @@ jobs:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     permissions:
-      # For pypi trusted publishing
+      # For PyPI trusted publishing
       id-token: write
     steps:
       - name: Set up Python
@@ -81,9 +82,12 @@ jobs:
           merge-multiple: true
           path: dist
 
-      - name: Publish to PyPi or TestPyPI
+      - name: Publish to PyPI or TestPyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true
           verbose: true
-          repository-url: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.task == 'test-release' && 'https://test.pypi.org/legacy/' || '' }}
+          repository-url: >
+            ${{ github.event_name == 'workflow_dispatch' &&
+            github.event.inputs.task == 'test-release' &&
+            'https://test.pypi.org/legacy/' || '' }}

.github/workflows/test.yml

@@ -71,7 +71,8 @@ jobs:
       - name: Install ubuntu-only conda dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |
-          micromamba install -n pmg -c conda-forge bader enumlib openff-toolkit packmol pygraphviz tblite --yes
+          micromamba install -n pmg -c conda-forge bader enumlib \
+            openff-toolkit packmol pygraphviz tblite --yes
 
       - name: Install pymatgen and dependencies via uv
         run: |
@@ -84,7 +85,12 @@ jobs:
           # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
           pip install torch==2.2.1
 
-          uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
+          # Install from wheels to test the content
+          uv pip install build
+          python -m build --wheel
+
+          uv pip install dist/*.whl
+          uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
@@ -101,6 +107,8 @@ jobs:
           echo "$(realpath vampire-5.0/)" >> $GITHUB_PATH
 
       - name: pytest split ${{ matrix.split }}
+        env:
+          PMG_TEST_FILES_DIR: "${{ github.workspace }}/tests/files"
         run: |
           micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

tests/transformations/test_advanced_transformations.py

@@ -185,6 +185,7 @@ def test_apply_transformation(self):
         for struct_trafo in alls:
             assert "energy" not in struct_trafo
 
+    @pytest.mark.skip(reason="dgl don't support torch 2.4.1+, #4073")
     def test_m3gnet(self):
         pytest.importorskip("matgl")
         enum_trans = EnumerateStructureTransformation(refine_structure=True, sort_criteria="m3gnet_relax")
@@ -200,6 +201,7 @@ def test_m3gnet(self):
         # Check ordering of energy/atom
         assert alls[0]["energy"] / alls[0]["num_sites"] <= alls[-1]["energy"] / alls[-1]["num_sites"]
 
+    @pytest.mark.skip(reason="dgl don't support torch 2.4.1+, #4073")
     def test_callable_sort_criteria(self):
         matgl = pytest.importorskip("matgl")
         from matgl.ext.ase import Relaxer