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wolearyc · Sep 17, 2024 · 9784f8b · 9784f8b
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diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -27,6 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install uv
+        uv pip install ${{ matrix.uv-arg }} --system -r deps/dev_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/torch_geometric_requirements.txt
         uv pip install ${{ matrix.uv-arg }} --system -r deps/torch_requirements.txt

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 **Ramannoodle** is a Python API for efficiently calculating Raman spectra from first principles calculations. Ramannoodle supports molecular-dynamics- and phonon-based Raman calculations and includes interfaces with VASP.
 
-Ramannoodle is designed from the ground up to be:
+Ramannoodle aims to be:
 
 1. **EFFICIENT**
 
@@ -33,9 +33,19 @@ Ramannoodle includes interfaces with:
 
 Ramannoodle can be installed via pip:
 
-`
+```
 $ pip install ramannoodle
-`
+```
+
+Due to idiosyncrasies with PyTorch's build system, installing ramannoodle's machine learning modules is slightly more involved. First, PyTorch must be installed ([pip commands](https://pytorch.org/get-started/locally/)). Then, corresponding torch-scatter and torch-sparse packages must be installed. Finally, Ramannoodle can then be installed with the appropriate options.
+
+For example, installation on a Linux system using PyTorch 2.4.1 (cpu implementation) is done as follows:
+
+```
+$ pip install torch==2.4.1+cpu --index-url https://download.pytorch.org/whl/cpu
+$ pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.4.0+cpu.html
+$ pip install ramannoodle[torch]
+```
 
 ## Documentation
 

diff --git a/deps/dev_requirements.txt b/deps/dev_requirements.txt
@@ -0,0 +1,5 @@
+flake8 == 7.1.0
+pre-commit == 3.7.1
+pylint == 3.2.6
+pytest == 8.3.1
+setuptools == 74.1.2
diff --git a/deps/requirements.txt b/deps/requirements.txt
@@ -1,23 +1,12 @@
 # numpy, scipy recommendations: https://scientific-python.org/specs/spec-0000/
 
-defusedxml >= 0.6.0;python_version=='3.10' # minimum working
-defusedxml >= 0.6.0;python_version=='3.11' # minimum working
-defusedxml >= 0.6.0;python_version=='3.12' # minimum working
-flake8 == 7.1.0
-numpy >= 1.24.0;python_version=='3.10' # minimum recommended
-numpy >= 1.24.0;python_version=='3.11' # minimum recommended
-numpy >= 1.26.0;python_version=='3.12' # minimum working
-pre-commit == 3.7.1
-pylint == 3.2.6
-pytest == 8.3.1
-scipy >= 1.10.0;python_version=='3.10' # minimum recommended
-scipy >= 1.10.0;python_version=='3.11' # minimum recommended
-scipy >= 1.11.2;python_version=='3.12' # minimum working
-setuptools == 74.1.2
-spglib >= 1.16.4;python_version=='3.10' # minimum working
-spglib >= 1.16.4;python_version=='3.11' # minimum working
-spglib >= 1.16.4;python_version=='3.12' # minimum working
-tabulate >= 0.8.8;python_version=='3.10' # minimum working
-tabulate >= 0.8.8;python_version=='3.11' # minimum working
-tabulate >= 0.8.8;python_version=='3.12' # minimum working
-tqdm >= 2.0
+defusedxml >= 0.6.0 # min working
+numpy >= 1.24.0;python_version=='3.10' # min recommended
+numpy >= 1.24.0;python_version=='3.11' # min recommended
+numpy >= 1.26.0;python_version=='3.12' # min working
+scipy >= 1.10.0;python_version=='3.10' # min recommended
+scipy >= 1.10.0;python_version=='3.11' # min recommended
+scipy >= 1.11.2;python_version=='3.12' # min working
+spglib >= 1.16.4 # min working
+tabulate >= 0.8.8 # min working
+tqdm >= 2.0 # min working
diff --git a/deps/torch_geometric_requirements.txt b/deps/torch_geometric_requirements.txt
@@ -1,20 +1,16 @@
-aiohttp >= 3.8.0;python_version=='3.10'
-aiohttp >= 3.8.3;python_version=='3.11'
-aiohttp >= 3.9.0;python_version=='3.12'
-dill >= 0.3.4
-frozenlist >= 1.2.0;python_version=='3.10'
-frozenlist >= 1.3.3;python_version=='3.11'
-frozenlist >= 1.4.1;python_version=='3.12'
-fsspec>= 2021.4.0;python_version=='3.10'
-fsspec>= 2021.4.0;python_version=='3.11'
-fsspec>=2021.4.0;python_version=='3.12'
-jinja2 >= 3.0.2
-pyparsing >= 3.0.0
-scikit-learn >= 1.2.0;python_version=='3.10'
-scikit-learn >= 1.2.0;python_version=='3.11'
-scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=="darwin"
-scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=="linux"
-scikit-learn >= 1.4.0;python_version=='3.12' and sys_platform=="win32"
-torch_geometric >= 2.3.0;python_version=='3.10'
-torch_geometric >= 2.3.0;python_version=='3.11'
-torch_geometric >= 2.3.0;python_version=='3.12'
+aiohttp >= 3.8.0;python_version=='3.10' # min working
+aiohttp >= 3.8.3;python_version=='3.11' # min working
+aiohttp >= 3.9.0;python_version=='3.12' # min working
+dill >= 0.3.4 # min working
+frozenlist >= 1.2.0;python_version=='3.10' # min working
+frozenlist >= 1.3.3;python_version=='3.11' # min working
+frozenlist >= 1.4.1;python_version=='3.12' # min working
+fsspec>= 2021.4.0;python_version=='3.10' # min working
+jinja2 >= 3.0.2 # min working
+pyparsing >= 3.0.0 # min working
+scikit-learn >= 1.2.0;python_version=='3.10' # min working
+scikit-learn >= 1.2.0;python_version=='3.11' # min working
+scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='darwin' # min working
+scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='linux' # min working
+scikit-learn >= 1.4.0;python_version=='3.12' and sys_platform=='win32' # min working
+torch_geometric >= 2.3.0 # min working
diff --git a/deps/torch_requirements.txt b/deps/torch_requirements.txt
@@ -1,4 +1,4 @@
 --index-url https://download.pytorch.org/whl/cpu
-torch==2.4.1;sys_platform=="darwin"
-torch==2.4.1+cpu;sys_platform=="linux"
-torch==2.4.1+cpu;sys_platform=="win32"
+torch==2.4.1;sys_platform=='darwin'
+torch==2.4.1+cpu;sys_platform=='linux'
+torch==2.4.1+cpu;sys_platform=='win32'
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,27 +14,37 @@ requires-python = ">=3.10"
 keywords = ["raman", "spectrum", "vasp", "dft", "phonons", "molecular", "dynamics", "polarizability" ]
 license = {text = "MIT"}
 dependencies = [
-    "numpy >= 1.24.0;python_version=='3.10'", # minimum recommended
-    "numpy >= 1.24.0;python_version=='3.11'", # minimum recommended
-    "numpy >= 1.26.0;python_version=='3.12'", # minimum working
-    "scipy >= 1.10.0;python_version=='3.10'", # minimum recommended
-    "scipy >= 1.10.0;python_version=='3.11'", # minimum recommended
-    "scipy >= 1.11.2;python_version=='3.12'", # minimum working
-    "spglib >= 1.16.4;python_version=='3.10'", # minimum working
-    "spglib >= 1.16.4;python_version=='3.11'", # minimum working
-    "spglib >= 1.16.4;python_version=='3.12'", # minimum working
-    "defusedxml >= 0.6.0;python_version=='3.10'", # minimum working
-    "defusedxml >= 0.6.0;python_version=='3.11'", # minimum working
-    "defusedxml >= 0.6.0;python_version=='3.12'", # minimum working
-    "tabulate >= 0.8.8;python_version=='3.10'", # minimum working
-    "tabulate >= 0.8.8;python_version=='3.11'", # minimum working
-    "tabulate >= 0.8.8;python_version=='3.12'", # minimum working
-    "torch >= 2.4.0",
-    "torch-geometric >= 2.5.3",
-    "torch-sparse >= 0.6.18",
+    "defusedxml >= 0.6.0", # min working
+    "numpy >= 1.24.0;python_version=='3.10'", # min recommended
+    "numpy >= 1.24.0;python_version=='3.11'", # min recommended
+    "numpy >= 1.26.0;python_version=='3.12'", # min working
+    "scipy >= 1.10.0;python_version=='3.10'", # min recommended
+    "scipy >= 1.10.0;python_version=='3.11'", # min recommended
+    "scipy >= 1.11.2;python_version=='3.12'", # min working
+    "spglib >= 1.16.4", # min working
+    "tabulate >= 0.8.8", # min working
+    "tqdm >= 2.0", # min working
 ]
 
 [project.optional-dependencies]
+torch = [
+    "aiohttp >= 3.8.0;python_version=='3.10'", # min working
+    "aiohttp >= 3.8.3;python_version=='3.11'", # min working
+    "aiohttp >= 3.9.0;python_version=='3.12'", # min working
+    "dill >= 0.3.4", # min working
+    "frozenlist >= 1.2.0;python_version=='3.10'", # min working
+    "frozenlist >= 1.3.3;python_version=='3.11'", # min working
+    "frozenlist >= 1.4.1;python_version=='3.12'", # min working
+    "fsspec>= 2021.4.0", # min working
+    "jinja2 >= 3.0.2", # min working
+    "pyparsing >= 3.0.0", # min working
+    "scikit-learn >= 1.2.0;python_version=='3.10'", # min working
+    "scikit-learn >= 1.2.0;python_version=='3.11'", # min working
+    "scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='darwin'", # min working
+    "scikit-learn >= 1.3.0;python_version=='3.12' and sys_platform=='linux'", # min working
+    "scikit-learn >= 1.4.0;python_version=='3.12' and sys_platform=='win32'", # min working
+    "torch_geometric >= 2.3.0", # min working
+]
 
 [project.urls]
 Documentation = "https://ramannoodle.readthedocs.io/en/latest/"