From f470e7382a4f4e9e8f7cdca778d18e687e3ed8a1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 22 Nov 2024 22:10:55 +0800
Subject: [PATCH] Build(deps): Bump torch from 1.11.0 to 2.2.0 (#13)

* Build(deps): Bump torch from 1.11.0 to 2.2.0

Bumps [torch](https://github.com/pytorch/pytorch) from 1.11.0 to 2.2.0.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/compare/v1.11.0...v2.2.0)

---
updated-dependencies:
- dependency-name: torch
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* update environment

* update installation and dependency

* update README

* fix pydantic

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Han Yang <hanyang@microsoft.com>
---
 README.md        |  1 +
 environment.yaml | 18 ++++++++----------
 pyproject.toml   | 10 +++++++---
 setup.py         | 15 +++++++++++++++
 4 files changed, 31 insertions(+), 13 deletions(-)
 create mode 100644 setup.py

diff --git a/README.md b/README.md
index 2f2caa4..9c7d56b 100644
--- a/README.md
+++ b/README.md
@@ -24,6 +24,7 @@ To install the package, run the following command under the root of the folder:
 conda env create -f environment.yaml
 conda activate mattersim
 pip install -e .
+python setup.py build_ext --inplace
 ```
 
 ## Usage
diff --git a/environment.yaml b/environment.yaml
index ebb26ab..b50beec 100644
--- a/environment.yaml
+++ b/environment.yaml
@@ -3,21 +3,19 @@ channels:
   - pyg
   - pytorch
   - conda-forge
+  - nvidia
 dependencies:
   - python=3.9
-  - pytorch==1.11.0
-  - pytorch-sparse=0.6.15
-  - pytorch-scatter=2.0.9
+  - 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
-  - pip:
-    - seekpath
-    - torch==1.11.0+cu113
-    - torchvision==0.12.0+cu113
-    - torchaudio==0.11.0+cu113
-    - --extra-index-url https://download.pytorch.org/whl/cu113
+  - loguru
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 01685bb..0ec74fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,16 +22,20 @@ classifiers = [
 dependencies = [
     "ase>=3.23.0",
     "e3nn==0.5.0",
+    "seekpath",
     "numpy<2",
     "pymatgen",
     "torch_geometric==2.5.3",
-    "torch==1.11.0",
+    "torch==2.2.0",
     "torch_runstats==0.2.0",
     "torchmetrics>=0.10.0",
     "torch-ema==0.3",
     "opt_einsum_fx",
     "azure-storage-blob",
     "azure-identity",
+    "mp-api",
+    "emmet-core<0.84",
+    "pydantic==2.9.2"
 ]
 
 [project.optional-dependencies]
@@ -43,8 +47,8 @@ dev = [
 
 
 [project.urls]
-"Homepage" = "https://github.com/msr-ai4science/mattersim"
-"Bug Tracker" = "https://github.com/msr-ai4science/mattersim/issues"
+"Homepage" = "https://github.com/microsoft/mattersim"
+"Bug Tracker" = "https://github.com/microsoft/mattersim/issues"
 
 [tool.setuptools]
 package-dir = {"" = "src"}
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..529707d
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,15 @@
+from setuptools import setup, Extension
+import numpy as np
+from Cython.Build import cythonize
+
+extensions = [
+    Extension(
+        "mattersim.datasets.utils.threebody_indices",
+        ["src/mattersim/datasets/utils/threebody_indices.pyx"],
+        include_dirs=[np.get_include()]
+    )
+]
+
+setup(
+    ext_modules=cythonize(extensions)
+)
\ No newline at end of file