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

Author: stefdoerr

.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

.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}

conda_deps_linux.txt

@@ -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  

conda_deps_linux_aarch64.txt

@@ -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
 

conda_deps_osx.txt

@@ -89,7 +89,7 @@ Command line interface
 ~~~~~~~~~~~~~~~~~~~~~~
 
 
-.. autoprogram:: scripts.train:get_argparse()
+.. autoprogram:: torchmdnet.scripts.train:get_argparse()
    :prog: torchmd-train
 
 

conda_deps_win.txt

@@ -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 = "[email protected]" }]
+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"