merge proper pyscf systems into bond-atom expansion branch

.codecov.yml

@@ -1,15 +1,11 @@
 coverage:
-  ignore:
-    - tests/.*
   status:
     project:
       default:
         target: 80%
     patch: off
+  ignore:
+    - "tests/.*"
+    - "examples/.*"
 
-comment: off
-
-fixes:
-  # map coverage collected inside tox virtual environments
-  # to the source dir in git
-  - ".tox/all-deps/lib/*/site-packages/::python/"
+comment: false

.github/workflows/coverage.yml

@@ -38,7 +38,7 @@ jobs:
       - name: install python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install tox
+          python -m pip install tox coverage
 
       - name: install lcov
         run: sudo apt install -y lcov
@@ -47,10 +47,12 @@ jobs:
         uses: actions/cache@v3
         with:
           path: .tox
-          key: tox-${{ matrix.os }}-${{ hashFiles('pyproject.toml', 'setup.cfg', 'tox.ini') }}
+          key: tox-${{ hashFiles('pyproject.toml', 'setup.cfg', 'tox.ini') }}
 
       - name: Setup sccache
         uses: mozilla-actions/[email protected]
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |
@@ -69,10 +71,22 @@ jobs:
           lcov --remove coverage.info '/usr/*' "$(pwd)/rascaline-c-api/tests/*" "$(pwd)/rascaline-c-api/examples/*" --output-file coverage.info
 
       - name: collect Python coverage
-        run: tox -e all-deps
+        run: |
+          tox -e all-deps
+          tox -e torch-tests
+        env:
+          # Use the CPU only version of torch when building/running the code
+          PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+
+      - name: combine Python coverage files
+        run: |
+            coverage combine --append \
+              ./.coverage \
+              ./python/rascaline-torch/.coverage
+            coverage xml
 
       - name: upload to codecov.io
         uses: codecov/codecov-action@v3
         with:
           fail_ci_if_error: true
-          files: target/tarpaulin/cobertura.xml,.tox/coverage.xml,coverage.info
+          files: target/tarpaulin/cobertura.xml,coverage.xml,coverage.info

.github/workflows/python-tests.yml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         include:
           - os: ubuntu-20.04
-            python-version: "3.7"
+            python-version: "3.8"
           - os: ubuntu-20.04
             python-version: "3.11"
           - os: macos-11
@@ -47,6 +47,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/[email protected]
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |
@@ -73,7 +75,7 @@ jobs:
     name: Python ${{ matrix.python-version }} / check build
     strategy:
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
         os: [ubuntu-20.04]
     steps:
       - uses: actions/checkout@v3

.github/workflows/rust-tests.yml

@@ -100,6 +100,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/[email protected]
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |
@@ -140,6 +142,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/[email protected]
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |

.github/workflows/torch-tests.yml

@@ -19,7 +19,7 @@ jobs:
         include:
           - os: ubuntu-20.04
             torch-version: 1.11.*
-            python-version: "3.7"
+            python-version: "3.8"
             cargo-test-flags: --release
 
           - os: ubuntu-20.04
@@ -60,6 +60,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/[email protected]
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |

.gitignore

@@ -3,10 +3,12 @@ target/
 Cargo.lock
 
 .tox/
-.coverage
 build/
 dist/
 *.egg-info
 __pycache__/
 .vscode
 *.DS_Store
+htmlcov/
+.coverage
+coverage.xml

CONTRIBUTING.rst

@@ -176,6 +176,24 @@ of just testing it.
 .. _`cargo` : https://doc.rust-lang.org/cargo/
 .. _valgrind: https://valgrind.org/
 
+Inspecting Python code coverage
+-------------------------------
+
+The code coverage is reported at `codecov`_. You can also inspect the coverage locally.
+To get the full coverage first combine all reports and open produced html file in a
+browser
+
+.. code-block:: bash
+
+    tox
+    coverage combine --append \
+        ./.coverage \
+        ./python/rascaline-torch/.coverage
+    coverage html
+    firefox htmlcov/index.html
+
+.. _codecov: https://codecov.io/gh/lab-cosmo/metatensor
+
 Writing your own calculator
 ---------------------------
 

docs/src/conf.py

@@ -140,6 +140,7 @@ def setup(app):
     "metatensor": ("https://lab-cosmo.github.io/metatensor/latest/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "skmatter": ("https://scikit-matter.readthedocs.io/en/latest/", None),
     "torch": ("https://pytorch.org/docs/stable/", None),
     "python": ("https://docs.python.org/3", None),

docs/src/devdoc/explanations/index.rst

@@ -12,3 +12,4 @@ to give you more clarity and understanding of what rascaline is all about.
 
     architecture
     interfaces
+    radial-integral