Pyscf systems [CI-debugging PR]

.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/sccache-action@v0.0.3
+        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/sccache-action@v0.0.3
+        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

@@ -40,7 +40,7 @@ jobs:
 
           # check the build on a stock Ubuntu 20.04, including cmake 3.16
           - os: ubuntu-20.04
-            rust-version: "1.64"
+            rust-version: "1.65"
             container: ubuntu:20.04
             rust-target: x86_64-unknown-linux-gnu
             build-type: debug
@@ -100,6 +100,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/sccache-action@v0.0.3
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |
@@ -140,6 +142,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/sccache-action@v0.0.3
+        with:
+          version: "v0.5.4"
 
       - name: Setup sccache environnement variables
         run: |

.github/workflows/torch-tests.yml

@@ -19,22 +19,22 @@ 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
-            torch-version: 2.0.*
+            torch-version: 2.1.*
             python-version: "3.11"
             cargo-test-flags: --release
             do-valgrind: true
 
           - os: macos-11
-            torch-version: 2.0.*
+            torch-version: 2.1.*
             python-version: "3.11"
             cargo-test-flags: --release
 
           - os: windows-2019
-            torch-version: 2.0.*
+            torch-version: 2.1.*
             python-version: "3.11"
             cargo-test-flags: --release
 
@@ -60,6 +60,8 @@ jobs:
 
       - name: Setup sccache
         uses: mozilla-actions/sccache-action@v0.0.3
+        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

.readthedocs.yml

@@ -12,7 +12,7 @@ build:
     - cmake
   tools:
     python: "3.11"
-    rust: "1.64"
+    rust: "1.70"
   jobs:
     post_install:
       # install rascaline-torch with the CPU version of PyTorch. We can not use

CONTRIBUTING.rst

@@ -57,7 +57,7 @@ on rascaline:
 - **the rust compiler**: you will need both ``rustc`` (the compiler) and
   ``cargo`` (associated build tool). You can install both using `rustup`_, or
   use a version provided by your operating system. We need at least Rust version
-  1.64 to build rascaline.
+  1.65 to build rascaline.
 - **Python**: you can install ``Python`` and ``pip`` from your operating system.
   We require a Python version of at least 3.6.
 - **tox**: a Python test runner, cf https://tox.readthedocs.io/en/latest/. You
@@ -123,9 +123,29 @@ Github CI workflows.
 You can also run only a subset of tests with one of these commands:
 
 - ``cargo test`` runs everything
-- ``cargo test --test=<test-name>`` to run only the tests in ``tests/<test-name>.rs``;
-    - ``cargo test --test=python-api`` (or ``tox`` directly) to run Python tests only;
-    - ``cargo test --test=c-api`` to run the C API tests only;
+- ``cargo test --package=rascaline`` to run the calculators tests;
+- ``cargo test --package=rascaline-c-api`` to run the C/C++ tests only;
+
+  - ``cargo test --test=run-cxx-tests`` will run the unit tests for the C/C++
+    API. If `valgrind`_ is installed, it will be used to check for memory
+    errors. You can disable this by setting the `RASCALINE_DISABLE_VALGRIND`
+    environment variable to 1 (`export RASCALINE_DISABLE_VALGRIND=1` for most
+    Linux/macOS shells);
+  - ``cargo test --test=check-cxx-install`` will build the C/C++ interfaces,
+    install them and the associated CMake files and then try to build a basic
+    project depending on this interface with CMake;
+
+- ``cargo test --package=rascaline-torch`` to run the C++ TorchScript extension
+  tests only;
+
+  - ``cargo test --test=run-torch-tests`` will run the unit tests for the
+    TorchScript C++ extension;
+  - ``cargo test --test=check-cxx-install`` will build the C++ TorchScript
+    extension, install it and then try to build a basic project depending on
+    this extension with CMake;
+
+- ``cargo test --package=rascaline-python`` (or ``tox`` directly, see below) to
+  run Python tests only;
 - ``cargo test --lib`` to run unit tests;
 - ``cargo test --doc`` to run documentation tests;
 - ``cargo bench --test`` compiles and run the benchmarks once, to quickly ensure
@@ -135,10 +155,8 @@ You can add some flags to any of above commands to further refine which tests
 should run:
 
 - ``--release`` to run tests in release mode (default is to run tests in debug mode)
-- ``-- <filter>`` to only run tests whose name contains filter, for example ``cargo test -- spherical_harmonics``
-- ``--package rascaline`` to run tests defined in the rascaline crate (the core implementation)
-- ``--package rascaline-c-api`` to run tests defined in the rascaline-c-api
-  crate (the C API implementation)
+- ``-- <filter>`` to only run tests whose name contains filter, for example
+  ``cargo test -- spherical_harmonics``
 
 Also, you can run individual python tests using `tox`_
 if you wish to test only specific functionalities, for example:
@@ -156,6 +174,25 @@ The latter command ``tox -e format`` will use tox to do actual formatting instea
 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/rascaline-json-schema/Cargo.toml

@@ -4,7 +4,7 @@ version = "0.1.0"
 authors = ["Luthaf <luthaf@luthaf.fr>"]
 edition = "2021"
 publish = false
-rust-version = "1.64"
+rust-version = "1.65"
 
 [[bin]]
 name = "rascaline-json-schema"

docs/requirements.txt

@@ -10,7 +10,7 @@ myst-parser     # markdown => rst translation, used in extensions/rascaline_json
 
 # dependencies for the tutorials
 --extra-index-url https://download.pytorch.org/whl/cpu
-metatensor[torch] @ https://github.com/lab-cosmo/metatensor/archive/2248a3c.zip
+metatensor[torch] >=0.1.0,<0.2.0
 torch
 chemfiles
 matplotlib

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