Update the bond-atom PR branch with upstream progress

metatensor · Apr 8, 2024 · bd8fe3f · bd8fe3f
2 parents 892a3a9 + 5c2a798
commit bd8fe3f
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Showing 192 changed files with 5,791 additions and 4,459 deletions.
diff --git a/.github/workflows/build-wheels.yml b/.github/workflows/build-wheels.yml
@@ -3,7 +3,7 @@ name: Build Python wheels
 on:
   push:
     branches: [master]
-    tags: "*"
+    tags: ["*"]
   pull_request:
     # Check all PR
 
@@ -36,7 +36,7 @@ jobs:
             rust-target: x86_64-pc-windows-msvc
             cibw_arch: AMD64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -47,9 +47,9 @@ jobs:
           target: ${{ matrix.rust-target }}
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: install dependencies
         run: python -m pip install cibuildwheel
@@ -85,17 +85,17 @@ jobs:
     runs-on: ubuntu-20.04
     name: sdist
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - name: build sdist
         run: |
-          pip install wheel
-          python setup.py sdist
+          pip install build
+          python -m build --sdist .
       - uses: actions/upload-artifact@v3
         with:
           name: wheels

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -18,12 +18,12 @@ jobs:
       - name: free disk space
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
@@ -38,7 +38,9 @@ jobs:
       - name: install python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install tox coverage
+          # https://github.com/tox-dev/tox/issues/3238
+          python -m pip install tox==4.14.0
+          python -m pip install coverage
 
       - name: install lcov
         run: sudo apt install -y lcov
@@ -86,7 +88,8 @@ jobs:
             coverage xml
 
       - name: upload to codecov.io
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
           files: target/tarpaulin/cobertura.xml,coverage.xml,coverage.info
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -18,21 +18,22 @@ jobs:
       - name: free disk space
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
         with:
           toolchain: stable
 
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: install dependencies
         run: |
-          pip install tox
+          # https://github.com/tox-dev/tox/issues/3238
+          python -m pip install tox==4.14.0
           sudo apt install doxygen
 
       - name: build documentation

diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml
@@ -21,16 +21,16 @@ jobs:
           - os: ubuntu-20.04
             python-version: "3.8"
           - os: ubuntu-20.04
-            python-version: "3.11"
+            python-version: "3.12"
           - os: macos-11
-            python-version: "3.11"
+            python-version: "3.12"
           - os: windows-2019
-            python-version: "3.11"
+            python-version: "3.12"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -42,7 +42,9 @@ jobs:
       - name: install python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install tox
+          # https://github.com/tox-dev/tox/issues/3238
+          python -m pip install tox==4.14.0
+
           echo "tox_version=$(python -c 'import tox; print(tox.__version__)')" >> $GITHUB_ENV
 
       - name: Setup sccache
@@ -75,13 +77,13 @@ jobs:
     name: Python ${{ matrix.python-version }} / check build
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
         os: [ubuntu-20.04]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -94,7 +96,9 @@ jobs:
       - name: install python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install tox
+          # https://github.com/tox-dev/tox/issues/3238
+          python -m pip install tox==4.14.0
+
           echo "tox_version=$(python -c 'import tox; print(tox.__version__)')" >> $GITHUB_ENV
 
       - name: cache tox environments

diff --git a/.github/workflows/rust-tests.yml b/.github/workflows/rust-tests.yml
@@ -73,18 +73,18 @@ jobs:
         if: matrix.os == 'ubuntu-20.04'
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: "copy the code to C: drive"
         if: matrix.os == 'windows-2019'
         run: cp -r ${{ github.workspace }} ${{ matrix.working-directory }}
         working-directory: /
 
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         if: "!matrix.container"
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
@@ -127,13 +127,8 @@ jobs:
   prevent-bitrot:
     runs-on: ubuntu-20.04
     name: check examples / benchmarks
-    strategy:
-      matrix:
-        include:
-          - rust-version:
-            rust-target:
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
@@ -168,7 +163,7 @@ jobs:
           - rust-version: stable
             rust-target: x86_64-unknown-linux-gnu
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master

diff --git a/.github/workflows/torch-tests.yml b/.github/workflows/torch-tests.yml
@@ -23,6 +23,8 @@ jobs:
             cargo-test-flags: --release
 
           - os: ubuntu-20.04
+            # These should be updated to torch 2.2 and Python 3.12 once
+            # https://github.com/pytorch/pytorch/issues/118862 is solved
             torch-version: 2.1.*
             python-version: "3.11"
             cargo-test-flags: --release
@@ -39,7 +41,7 @@ jobs:
             cargo-test-flags: --release
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
@@ -48,7 +50,7 @@ jobs:
 
       # we get torch from pip to run the C++ test
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -11,8 +11,8 @@ build:
   apt_packages:
     - cmake
   tools:
-    python: "3.11"
-    rust: "1.70"
+    python: "3.12"
+    rust: "1.75"
   jobs:
     post_install:
       # install rascaline-torch with the CPU version of PyTorch. We can not use

diff --git a/README.rst b/README.rst
@@ -44,15 +44,15 @@ List of implemented representations
      - Core of representations in LODE (Long distance equivariant)
      - positions
    * - Sorted distances
-     - Each atomic center is represented by a vector of distance to its
-       neighbors within the spherical cutoff
+     - Each atom is represented by a vector of distance to its neighbors within
+       the spherical cutoff
      - no
    * - Neighbor List
      - Each pair is represented by the vector between the atoms. This is
        intended to be used as a starting point for more complex representations
      - positions
    * - AtomicComposition
-     - Obtaining the stoichiometric information of a structure
+     - Obtaining the stoichiometric information of a system
      - positions and cell
 
 .. inclusion-marker-representations-end

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,5 @@
-# sphinx dependencies
-sphinx < 7.2    # breathe is not compatible with sphinx 7.2 yet
+# sphinx and dependencies
+sphinx == 7.2.6
 furo            # sphinx theme
 breathe >=4.33  # C and C++ => sphinx through doxygen
 sphinx-gallery  # convert python files into nice documentation
@@ -10,7 +10,8 @@ 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] >=0.1.0,<0.2.0
+metatensor
+metatensor-torch >= 0.3.0,<0.4.0
 torch
 chemfiles
 matplotlib

diff --git a/docs/src/.gitignore b/docs/src/.gitignore
@@ -1 +1,2 @@
 examples
+sg_execution_times.rst
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -109,7 +109,11 @@ def setup(app):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["Thumbs.db", ".DS_Store"]
+exclude_patterns = [
+    "Thumbs.db",
+    ".DS_Store",
+    "sg_execution_times.rst",
+]
 
 
 autoclass_content = "both"
@@ -120,7 +124,7 @@ def setup(app):
     "filename_pattern": "/*",
     "examples_dirs": ["../../python/rascaline/examples"],
     "gallery_dirs": ["examples"],
-    "min_reported_time": 60,
+    "min_reported_time": 5,
     # Make the code snippet for rascaline functions clickable
     "reference_url": {"rascaline": None},
     "prefer_full_module": ["rascaline"],

diff --git a/docs/src/devdoc/explanations/radial-integral.rst b/docs/src/devdoc/explanations/radial-integral.rst
@@ -20,8 +20,8 @@ determined by specifying two ingredients:
 
 -  the atomic density function :math:`g(r)` as implemented in
    :ref:`python-atomic-density`, often chosen to be a Gaussian or Delta function, that
-   defined the type of density under consideration. For a given center atom :math:`i` in
-   the structure, the total density function :math:`\rho_i(\boldsymbol{r})` around is
+   defined the type of density under consideration. For a given central atom :math:`i` in
+   the system, the total density function :math:`\rho_i(\boldsymbol{r})` around is
    then defined as :math:`\rho_i(\boldsymbol{r}) = \sum_{j} g(\boldsymbol{r} -
    \boldsymbol{r}_{ij})`.
 
@@ -37,8 +37,8 @@ determined by specifying two ingredients:
    :math:`\hat{r}`, i.e. at the spherical angles :math:`(\theta, \phi)` that determine
    the orientation of the unit vector :math:`\hat{r} = \boldsymbol{r}/r`.
 
-The spherical expansion coefficient :math:`\langle nlm | \rho_i \rangle` (we ommit the
-chemical species index :math:`a` for simplicity) is then defined as
+The spherical expansion coefficient :math:`\langle nlm | \rho_i \rangle` (we omit the
+atom type index :math:`a` for simplicity) is then defined as
 
 .. math::
 
@@ -110,7 +110,7 @@ The key point is that the dependence on the vectorial position
 :math:`\boldsymbol{r}_{ij}` is split into a factor that contains information about the
 orientation of this vector, namely :math:`Y_{lm}(\hat{r}_{ij})`, which is just the
 spherical harmonic evaluated at :math:`\hat{r}_{ij}`, and a remaining part that captures
-the dependence on the distance of atom :math:`j` from the center atom :math:`i`, namely
+the dependence on the distance of atom :math:`j` from the central atom :math:`i`, namely
 :math:`I_{nl}(r_{ij})`, which we shall call the radial integral. The radial integral
 class computes and outputs this radial part :math:`I_{nl}(r_{ij})`. Since the angular
 part is just the usual spherical harmonic, this is the part that also depends on the