New setup (#358)

* updated installation for cuda 12.6 * new setup.py pyproject.toml installation * cleanup * fix tests and deprecations * most deps are added now by the pip package * cleanup deps more * better handling of CUDA builds * correct building and installation * reorganize CI * install nnpops later * fix nnpops installation on correct OSs * nnpops is installing pytorch-cpu from conda which is messing with the torch used to compile from pip * pytorch doesn't generate pip packages anymore for old osx machines * be a bit more flexible with specific builds * fix docs building * fix python version * delayed import of NNPops to fix issues in docs generation * fixed paths to scripts module * undo commenting out
torchmd · Feb 12, 2025 · 1502491 · 1502491
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -17,12 +17,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os:
-          [
+        os: [
             "ubuntu-latest",
             "ubuntu-22.04-arm",
             "macos-latest",
-            "macos-13",
+            # "macos-13",
             "windows-2022",
           ]
         python-version: ["3.10"]
@@ -50,41 +49,47 @@ jobs:
           conda-remove-defaults: "true"
         if: matrix.os == 'macos-13'
 
-      - name: Install OS-specific conda dependencies
+      - name: Install OS-specific compilers
         run: |
           if [[ "${{ matrix.os }}" == "ubuntu-22.04-arm" ]]; then
-            conda install --file conda_deps_linux_aarch64.txt --channel conda-forge --override-channels
+            conda install gxx --channel conda-forge --override-channels
           elif [[ "${{ runner.os }}" == "Linux" ]]; then
-            conda install --file conda_deps_linux.txt --channel conda-forge --override-channels
+            conda install gxx --channel conda-forge --override-channels
           elif [[ "${{ runner.os }}" == "macOS" ]]; then
-            conda install --file conda_deps_osx.txt --channel conda-forge --override-channels
+            conda install clangxx llvm-openmp pybind11 --channel conda-forge --override-channels
           elif [[ "${{ runner.os }}" == "Windows" ]]; then
-            conda install --file conda_deps_win.txt --channel conda-forge --override-channels
+            conda install vc vc14_runtime vs2015_runtime --channel conda-forge --override-channels
           fi
 
-      - name: Install testing packages
-        run: conda install -y -c conda-forge flake8 pytest psutil
-
       - name: List the conda environment
         run: conda list
 
+      - name: Install testing packages
+        run: conda install -y -c conda-forge flake8 pytest psutil python-build
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
       - name: Build and install the package
         run: |
           if [[ "${{ runner.os }}" == "Windows" ]]; then
             export LIB="C:/Miniconda/envs/test/Library/lib"
-            pip -vv install .
-          else
-            pip -vv install .
           fi
+          python -m build            
+          pip install dist/*.whl
         env:
           WITH_CUDA: "0"
 
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      # - name: Install nnpops
+      #   if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
+      #   run: conda install nnpops --channel conda-forge --override-channels
+
+      - name: List the conda environment
+        run: conda list
 
       - name: Run tests
         run: pytest -v -s --durations=10

diff --git a/.github/workflows/docs_build.yaml b/.github/workflows/docs_build.yaml
@@ -8,29 +8,30 @@ on:
     branches:
       - "main"
 
-
 jobs:
   build-docs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: "3.10"
+          channels: conda-forge
+          conda-remove-defaults: "true"
+
+      - name: Install compiler
+        run: conda install gxx --channel conda-forge --override-channels
 
-    - name: Set up Env
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        environment-file: environment.yml
-        init-shell: bash
-        generate-run-shell: true
+      - name: Install docs dependencies
+        run: |
+          pip install -vv .
+          pip install -r docs/requirements.txt
+        shell: bash -el {0}
 
-    - name: Install docs dependencies
-      run: |
-        pip install -vv .
-        pip install -r docs/requirements.txt
-      shell: bash -el {0}
-
-    - name: Build Sphinx Documentation
-      run: |
-        cd docs
-        make html
-      shell: bash -el {0}
+      - name: Build Sphinx Documentation
+        run: |
+          cd docs
+          make html
+        shell: bash -el {0}
diff --git a/conda_deps_linux.txt b/conda_deps_linux.txt
diff --git a/conda_deps_linux_aarch64.txt b/conda_deps_linux_aarch64.txt
diff --git a/conda_deps_osx.txt b/conda_deps_osx.txt
diff --git a/conda_deps_win.txt b/conda_deps_win.txt
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -54,8 +54,7 @@ It is recommended to install the same version as the one used by torch.
 
 .. code-block:: shell
 
-   conda install -c conda-forge cuda-nvcc cuda-libraries-dev cuda-version gxx pytorch=*=*cuda*
-
+   conda install -c conda-forge python=3.10 cuda-version=12.6 cuda-nvvm cuda-nvcc cuda-libraries-dev
 
 
 * CUDA<12  

diff --git a/docs/source/models.rst b/docs/source/models.rst
@@ -342,7 +342,7 @@ To implement a new architecture, you need to follow these steps:
                 **shared_args,
             )
 
-4. Add any new parameters required to initialize your module to scripts.train.get_args:
+4. Add any new parameters required to initialize your module to torchmdnet.scripts.train.get_args:
 
     .. code-block:: python
 

diff --git a/docs/source/torchmd-train.rst b/docs/source/torchmd-train.rst
@@ -89,7 +89,7 @@ Command line interface
 ~~~~~~~~~~~~~~~~~~~~~~
 
 
-.. autoprogram:: scripts.train:get_argparse()
+.. autoprogram:: torchmdnet.scripts.train:get_argparse()
    :prog: torchmd-train
 
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,38 @@
+[project]
+name = "torchmd-net"
+description = "TorchMD-NET provides state-of-the-art neural networks potentials for biomolecular systems"
+authors = [{ name = "Acellera", email = "info@acellera.com" }]
+readme = "README.md"
+requires-python = ">=3.8"
+dynamic = ["version"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Operating System :: POSIX :: Linux",
+]
+dependencies = [
+  "h5py",
+  # "nnpops",
+  "torch==2.5.1.*",
+  "torch_geometric",
+  "lightning",
+  "tqdm",
+  "pandas",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/torchmd/torchmd-net"
+"Bug Tracker" = "https://github.com/torchmd/torchmd-net/issues"
+
+[project.scripts]
+torchmd-train = "torchmdnet.scripts.train:main"
+
+[tool.setuptools_scm]
+
+[tool.setuptools.packages.find]
+where = [""]
+include = ["torchmdnet*"]
+namespaces = false
+
+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8", "torch==2.5.1.*"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
@@ -2,33 +2,17 @@
 # Distributed under the MIT License.
 # (See accompanying file README.md file or copy at http://opensource.org/licenses/MIT)
 
-import subprocess
-from setuptools import setup, find_packages
+from setuptools import setup
 import torch
-from torch.utils.cpp_extension import (
-    BuildExtension,
-    CUDAExtension,
-    include_paths,
-    CppExtension,
-)
+from torch.utils.cpp_extension import BuildExtension, CUDAExtension, CppExtension
 import os
-import sys
-
-is_windows = sys.platform == "win32"
 
-try:
-    version = (
-        subprocess.check_output(["git", "describe", "--abbrev=0", "--tags"])
-        .strip()
-        .decode("utf-8")
-    )
-except Exception:
-    print("Failed to retrieve the current version, defaulting to 0")
-    version = "0"
 
 # If WITH_CUDA is defined
 if os.environ.get("WITH_CUDA", "0") == "1":
     use_cuda = True
+elif os.environ.get("WITH_CUDA", "0") == "0":
+    use_cuda = False
 else:
     use_cuda = torch.cuda._is_compiled()
 
@@ -37,13 +21,12 @@ def set_torch_cuda_arch_list():
     """Set the CUDA arch list according to the architectures the current torch installation was compiled for.
     This function is a no-op if the environment variable TORCH_CUDA_ARCH_LIST is already set or if torch was not compiled with CUDA support.
     """
-    if not os.environ.get("TORCH_CUDA_ARCH_LIST"):
-        if use_cuda:
-            arch_flags = torch._C._cuda_getArchFlags()
-            sm_versions = [x[3:] for x in arch_flags.split() if x.startswith("sm_")]
-            formatted_versions = ";".join([f"{y[0]}.{y[1]}" for y in sm_versions])
-            formatted_versions += "+PTX"
-            os.environ["TORCH_CUDA_ARCH_LIST"] = formatted_versions
+    if use_cuda and not os.environ.get("TORCH_CUDA_ARCH_LIST"):
+        arch_flags = torch._C._cuda_getArchFlags()
+        sm_versions = [x[3:] for x in arch_flags.split() if x.startswith("sm_")]
+        formatted_versions = ";".join([f"{y[0]}.{y[1]}" for y in sm_versions])
+        formatted_versions += "+PTX"
+        os.environ["TORCH_CUDA_ARCH_LIST"] = formatted_versions
 
 
 set_torch_cuda_arch_list()
@@ -61,30 +44,15 @@ def set_torch_cuda_arch_list():
     name="torchmdnet.extensions.torchmdnet_extensions",
     sources=[os.path.join(extension_root, "torchmdnet_extensions.cpp")]
     + neighbor_sources,
-    include_dirs=include_paths(),
     define_macros=[("WITH_CUDA", 1)] if use_cuda else [],
 )
 
 if __name__ == "__main__":
     setup(
-        name="torchmd-net",
-        version=version,
-        packages=find_packages(),
         ext_modules=[extensions],
         cmdclass={
             "build_ext": BuildExtension.with_options(
                 no_python_abi_suffix=True, use_ninja=False
             )
         },
-        include_package_data=True,
-        entry_points={
-            "console_scripts": ["torchmd-train = torchmdnet.scripts.train:main"]
-        },
-        package_data={
-            "torchmdnet": (
-                ["extensions/torchmdnet_extensions.so"]
-                if not is_windows
-                else ["extensions/torchmdnet_extensions.dll"]
-            )
-        },
     )
diff --git a/tests/test_calculator.py b/tests/test_calculator.py
@@ -3,7 +3,7 @@
 # (See accompanying file README.md file or copy at http://opensource.org/licenses/MIT)
 
 import torch
-from torch.testing import assert_allclose
+from torch.testing import assert_close
 import pytest
 from os.path import dirname, join
 from torchmdnet.calculators import External
@@ -15,6 +15,8 @@
 @pytest.mark.parametrize("box", [None, torch.eye(3)])
 @pytest.mark.parametrize("use_cuda_graphs", [True, False])
 def test_compare_forward(box, use_cuda_graphs):
+    from copy import deepcopy
+
     if use_cuda_graphs and not torch.cuda.is_available():
         pytest.skip("CUDA not available")
     checkpoint = join(dirname(dirname(__file__)), "tests", "example.ckpt")
@@ -48,14 +50,19 @@ def test_compare_forward(box, use_cuda_graphs):
         checkpoint, z.unsqueeze(0), use_cuda_graph=use_cuda_graphs, device=device
     )
     calc.model = model
+    # Path the model
+    model = deepcopy(model)
+    model.representation_model.distance.check_errors = not use_cuda_graphs
+    model.representation_model.static_shapes = use_cuda_graphs
+    model.representation_model.distance.resize_to_fit = not use_cuda_graphs
     calc_graph.model = model
     if box is not None:
         box = (box * 2 * args["cutoff_upper"]).unsqueeze(0)
     for _ in range(10):
         e_calc, f_calc = calc.calculate(pos, box)
         e_pred, f_pred = calc_graph.calculate(pos, box)
-        assert_allclose(e_calc, e_pred)
-        assert_allclose(f_calc, f_pred)
+        assert_close(e_calc, e_pred)
+        assert_close(f_calc, f_pred)
 
 
 def test_compare_forward_multiple():
@@ -72,5 +79,5 @@ def test_compare_forward_multiple():
         torch.cat([torch.zeros(len(z1)), torch.ones(len(z2))]).long(),
     )
 
-    assert_allclose(e_calc, e_pred)
-    assert_allclose(f_calc, f_pred.view(-1, len(z1), 3))
+    assert_close(e_calc, e_pred)
+    assert_close(f_calc, f_pred.view(-1, len(z1), 3), rtol=1e-4, atol=1e-5)
diff --git a/tests/test_equivariance.py b/tests/test_equivariance.py
@@ -24,7 +24,7 @@ def test_scalar_invariance():
 
     y = model(z, pos, batch)[0]
     y_rot = model(z, pos @ rotate, batch)[0]
-    torch.testing.assert_allclose(y, y_rot)
+    torch.testing.assert_close(y, y_rot)
 
 
 def test_vector_equivariance():
@@ -50,4 +50,4 @@ def test_vector_equivariance():
 
     y = model(z, pos, batch)[0]
     y_rot = model(z, pos @ rotate, batch)[0]
-    torch.testing.assert_allclose(y @ rotate, y_rot)
+    torch.testing.assert_close(y @ rotate, y_rot)