build: clean up environment.yaml and reorganize pyproject.toml (#28)

* clean up environment.yaml and reorganize pyproject.toml

* clean up environment.yaml

* add MANIFEST.in and configure the files to copy for building distribution

* update installation instruction in README.md

* update building workflow

* add 5M checkpoint

---------

Co-authored-by: Han Yang <[email protected]>

.github/workflows/build.yaml

@@ -28,12 +28,16 @@ jobs:
 
     - name: Install dependencies
       run: |
-        micromamba run -n mattersim pip install -e .
+        micromamba run -n mattersim uv pip install -e .
 
     - name: Install test dependencies
       run: |
-        micromamba run -n mattersim pip install -e ".[dev]"
+        micromamba run -n mattersim uv pip install -e ".[dev]"
+
+    - name: Build extension
+      run: |
+        micromamba run -n mattersim python setup.py build_ext --inplace
 
     - name: Run tests
       run: |
-        micromamba run -n mattersim pytest -s tests
+        micromamba run -n mattersim pytest -s tests

MANIFEST.in

@@ -0,0 +1,2 @@
+include src/mattersim/pretrained_models/*.pth
+include src/mattersim/datasets/utils/*.pyx

README.md

@@ -59,7 +59,7 @@ To install the package, run the following command under the root of the folder:
 ```bash
 mamba env create -f environment.yaml
 mamba activate mattersim
-pip install -e .
+uv pip install -e .
 python setup.py build_ext --inplace
 ```
 

environment.yaml

@@ -1,21 +1,15 @@
 name: mattersim
 channels:
-  - pyg
-  - pytorch
   - conda-forge
-  - nvidia
 dependencies:
   - python=3.9
-  - pytorch-sparse
-  - pytorch-scatter
-  - pytorch==2.2.0
-  - torchvision==0.17.0
-  - torchaudio==2.2.0
-  - pytorch-cuda=11.8
   - ca-certificates
   - openssl
   - numpy<2
   - phonopy==2.14.0
   - phono3py==2.3.0
-  - cython
-  - loguru
+  - cython>=0.29.32
+  - setuptools>=45
+  - wheel
+  - pip:
+    - uv

pyproject.toml

@@ -25,9 +25,12 @@ dependencies = [
     "seekpath",
     "numpy<2",
     "pymatgen",
-    "torch_geometric==2.5.3",
+    "loguru",
     "torch==2.2.0",
+    "torchvision==0.17.0",
+    "torchaudio==2.2.0",
     "torch_runstats==0.2.0",
+    "torch_geometric==2.5.3",
     "torchmetrics>=0.10.0",
     "torch-ema==0.3",
     "opt_einsum_fx",
@@ -41,8 +44,11 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     "pytest",
+    "pytest-cov",
     "pytest-testmon",
-    "pre-commit"
+    "pre-commit",
+    "ipython",
+    "ipykernel"
 ]
 
 
@@ -55,4 +61,4 @@ package-dir = {"" = "src"}
 
 [tool.setuptools.packages.find]
 where = ["src"]
-include = ["mattersim", "mattersim.*"]
+include = ["mattersim", "mattersim.*"]