Update the code for the latest versions of metatensor and metatomic

.github/workflows/build-wheels.yml

@@ -52,7 +52,7 @@ jobs:
             rust-target: x86_64-pc-windows-msvc
             cibw-arch: AMD64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -63,7 +63,7 @@ jobs:
           target: ${{ matrix.rust-target }}
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -89,7 +89,7 @@ jobs:
             MACOSX_DEPLOYMENT_TARGET=11
             FEATOMIC_NO_LOCAL_DEPS=1
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: wheel-${{ matrix.os }}-${{ matrix.cibw-arch }}
           path: ./wheelhouse/*.whl
@@ -140,7 +140,7 @@ jobs:
           - {torch-version: '2.9', cibw-python: 'cp312-*'}
           - {torch-version: '2.10', cibw-python: 'cp313-*'}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -151,7 +151,7 @@ jobs:
           target: ${{ matrix.rust-target }}
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -202,7 +202,7 @@ jobs:
                               --exclude libc10.so \
                               -w {dest_dir} {wheel}
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: torch-single-version-wheel-${{ matrix.torch-version }}-${{ matrix.os }}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
@@ -227,17 +227,17 @@ jobs:
             os: windows-2022
             arch: x86_64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Download wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           pattern: torch-single-version-wheel-*-${{ matrix.os }}-${{ matrix.arch }}
           merge-multiple: false
           path: dist
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -272,7 +272,7 @@ jobs:
       - name: check wheels with twine
         run: twine check wheelhouse/*
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: torch-wheel-${{ matrix.os }}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
@@ -281,12 +281,12 @@ jobs:
     runs-on: ubuntu-24.04
     name: sdist
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -304,7 +304,7 @@ jobs:
           ./scripts/package-featomic.sh dist/cxx/
           ./scripts/package-featomic-torch.sh dist/cxx/
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         with:
           name: sdist
           path: |
@@ -320,27 +320,27 @@ jobs:
       pull-requests: write
     steps:
       - name: Download featomic wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           path: wheels
           pattern: wheel-*
           merge-multiple: true
 
       - name: Download featomic-torch wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           path: wheels
           pattern: torch-wheel-*
           merge-multiple: true
 
       - name: Download sdists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           path: wheels
           name: sdist
 
       - name: Re-upload a single wheels artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: wheels
           path: |
@@ -356,7 +356,7 @@ jobs:
 
       - name: upload to GitHub release (featomic)
         if: startsWith(github.ref, 'refs/tags/featomic-v')
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           files: |
             wheels/cxx/featomic-cxx-*.tar.gz
@@ -367,7 +367,7 @@ jobs:
 
       - name: upload to GitHub release (featomic-torch)
         if: startsWith(github.ref, 'refs/tags/featomic-torch-v')
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           files: |
             wheels/cxx/featomic-torch-cxx-*.tar.gz

.github/workflows/coverage.yml

@@ -18,10 +18,10 @@ jobs:
       - name: free disk space
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -76,7 +76,7 @@ jobs:
             coverage xml
 
       - name: upload to codecov.io
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           fail_ci_if_error: true
           files: target/tarpaulin/cobertura.xml,coverage.xml,coverage.info

.github/workflows/docs.yml

@@ -21,15 +21,15 @@ jobs:
       - name: free disk space
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
         with:
           toolchain: stable
 
       - name: setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
 
@@ -45,7 +45,7 @@ jobs:
           PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
 
       - name: store documentation as github artifact to be downloaded by users
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: docs
           path: docs/build/html/*

.github/workflows/python-tests.yml

@@ -27,10 +27,10 @@ jobs:
           - os: windows-2022
             python-version: "3.13"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -71,10 +71,12 @@ jobs:
         python-version: ['3.10', '3.13']
         os: [ubuntu-24.04]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0 # we need the full history to get the git version info
 
       - name: set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/rust-tests.yml

@@ -73,7 +73,7 @@ jobs:
         if: matrix.os == 'ubuntu-24.04'
         run: sudo rm -rf /usr/share/dotnet /usr/local/lib/android || true
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
         working-directory: /
 
       - name: setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         if: "!matrix.container"
         with:
           python-version: "3.13"
@@ -135,7 +135,7 @@ jobs:
     runs-on: ubuntu-24.04
     name: check examples / benchmarks
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master
@@ -172,7 +172,7 @@ jobs:
           - rust-version: stable
             rust-target: x86_64-unknown-linux-gnu
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: setup rust
         uses: dtolnay/rust-toolchain@master

.github/workflows/torch-tests.yml

@@ -58,7 +58,7 @@ jobs:
           apt install -y cmake make gcc g++ git curl python3.10 python3.10-venv
           update-alternatives --install /usr/local/bin/python python /usr/bin/python3.10 1
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -74,7 +74,7 @@ jobs:
       # we get torch from pip to run the C++ test
       - name: setup Python
         if: matrix.container != 'ubuntu:22.04'
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

docs/requirements.txt

@@ -10,9 +10,9 @@ myst-parser     # markdown => rst translation, used in extensions/featomic_json_
 
 # dependencies for the tutorials
 --extra-index-url https://download.pytorch.org/whl/cpu
-metatensor-operations >=0.4.0,<0.5
-metatensor-torch >=0.8.4,<0.9
-metatomic-torch >= 0.1.11,<0.2
+metatensor-operations >=0.5.0-rc2,<0.6
+metatensor-torch >=0.9.0-rc6,<0.10
+metatomic-torch >= 0.1.12-rc2,<0.2
 torch
 chemfiles
 matplotlib

featomic-torch/CMakeLists.txt

@@ -122,8 +122,8 @@ find_package(Torch 2.3 REQUIRED)
 #
 # When updating METATENSOR_TORCH_FETCH_VERSION, you will also have to update the
 # SHA256 sum of the file in `FetchContent_Declare`.
-set(METATENSOR_TORCH_FETCH_VERSION "0.8.2")
-set(REQUIRED_METATENSOR_TORCH_VERSION "0.8")
+set(METATENSOR_TORCH_FETCH_VERSION "0.9.0-rc6")
+set(REQUIRED_METATENSOR_TORCH_VERSION "0.9")
 if (FEATOMIC_FETCH_METATENSOR_TORCH)
     message(STATUS "Fetching metatensor-torch from github")
 
@@ -132,7 +132,7 @@ if (FEATOMIC_FETCH_METATENSOR_TORCH)
     FetchContent_Declare(
         metatensor_torch
         URL      ${URL_ROOT}/metatensor-torch-v${METATENSOR_TORCH_FETCH_VERSION}/metatensor-torch-cxx-${METATENSOR_TORCH_FETCH_VERSION}.tar.gz
-        URL_HASH SHA256=0be618d0cdcfca86cd0c25f47d360b6a2410ebb09ece8d21f153e933ce64bb55
+        URL_HASH SHA256=73afb6795a04e6e31a993d11e35183d3aa3e97b2d30e14b1a4a04c45263a13bc
     )
 
     FetchContent_MakeAvailable(metatensor_torch)
@@ -150,7 +150,7 @@ endif()
 #
 # When updating METATOMIC_TORCH_FETCH_VERSION, you will also have to update the
 # SHA256 sum of the file in `FetchContent_Declare`.
-set(METATOMIC_TORCH_FETCH_VERSION "0.1.11")
+set(METATOMIC_TORCH_FETCH_VERSION "0.1.12-rc2")
 set(REQUIRED_METATOMIC_TORCH_VERSION "0.1")
 if (FEATOMIC_FETCH_METATENSOR_TORCH)
     message(STATUS "Fetching metatomic-torch from github")
@@ -160,7 +160,7 @@ if (FEATOMIC_FETCH_METATENSOR_TORCH)
     FetchContent_Declare(
         metatomic_torch
         URL      ${URL_ROOT}/metatomic-torch-v${METATOMIC_TORCH_FETCH_VERSION}/metatomic-torch-cxx-${METATOMIC_TORCH_FETCH_VERSION}.tar.gz
-        URL_HASH SHA256=cd500ab1371fb1d284b9ae514e7feaa205eca231437dd2d527fbf3852e673eef
+        URL_HASH SHA256=38a0de4d9320487405b13ed208013895b829ab74cf9bb774e88c5b628368fc49
     )
 
     FetchContent_MakeAvailable(metatomic_torch)

featomic-torch/src/autograd.cpp

@@ -245,7 +245,8 @@ std::vector<torch::Tensor> PositionsGrad<scalar_t>::forward(
     auto systems_start = systems_start_ivalue.toIntList();
 
     auto samples = dX_dr->samples();
-    const auto* sample_ptr = samples->as_metatensor().values().data();
+    const auto sample_values = samples->as_metatensor().values_cpu();
+    const auto* sample_ptr = sample_values.data();
 
     always_assert(samples->names().size() == 3);
     always_assert(samples->names()[0] == "sample");
@@ -331,7 +332,8 @@ std::vector<torch::Tensor> PositionsGrad<scalar_t>::backward(
     auto dB_d_dA_dr = grad_outputs[0]; // gradient of B w.r.t. dA/dr (output of forward)
 
     auto samples = dX_dr->samples();
-    const auto* sample_ptr = samples->as_metatensor().values().data();
+    const auto sample_values = samples->as_metatensor().values_cpu();
+    const auto* sample_ptr = sample_values.data();
 
     always_assert(samples->names().size() == 3);
     always_assert(samples->names()[0] == "sample");
@@ -436,7 +438,8 @@ std::vector<torch::Tensor> CellGrad<scalar_t>::forward(
     always_assert(all_cells.requires_grad());
 
     auto samples = dX_dH->samples();
-    const auto* sample_ptr = samples->as_metatensor().values().data();
+    const auto sample_values = samples->as_metatensor().values_cpu();
+    const auto* sample_ptr = sample_values.data();
 
     always_assert(samples->names().size() == 1);
     always_assert(samples->names()[0] == "sample");
@@ -517,9 +520,10 @@ std::vector<torch::Tensor> CellGrad<scalar_t>::backward(
     auto dB_d_dA_dH = grad_outputs[0]; // gradient of B w.r.t. dA/dH (output of forward)
 
     auto samples = dX_dH->samples();
-    const auto* sample_ptr = samples->as_metatensor().values().data();
     always_assert(samples->names().size() == 1);
     always_assert(samples->names()[0] == "sample");
+    const auto samples_values = samples->as_metatensor().values_cpu();
+    const auto* samples_ptr = samples_values.data();
 
     // ========================= extract pointers =========================== //
     // TODO: remove all CPU <=> device data movement by rewriting the VJP
@@ -571,7 +575,7 @@ std::vector<torch::Tensor> CellGrad<scalar_t>::backward(
             // dB_d_dA_dX.shape == [samples, features...]
             #pragma omp for
             for (int64_t grad_sample_i=0; grad_sample_i<samples->count(); grad_sample_i++) {
-                auto sample_i = sample_ptr[grad_sample_i];
+                auto sample_i = samples_ptr[grad_sample_i];
                 auto system_i = static_cast<int64_t>(systems[sample_i].item<int32_t>());
 
                 for (int64_t i=0; i<n_features; i++) {

featomic-torch/src/calculator.cpp

@@ -50,7 +50,7 @@ static metatensor_torch::TensorBlock block_to_torch(
     }
 
     auto torch_values = torch::from_blob(
-        values.data(),
+        const_cast<double*>(values.data()),
         sizes,
         [tensor](void*) mutable {
             // this function holds a copy of `tensor`, which will make sure that