update packaging for release on pypi

.github/workflows/dca_tests.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10"]
     steps:
       - name: Test DCA
         uses: actions/checkout@v4

README.md

@@ -32,6 +32,15 @@ If you are installing with `pip` you can run
 $ pip install -e . -r requirements.txt
 ```
 
+Note: DCA only requires a CPU-only `pytorch`. If you wish to, **before** installing DCA as in the above instructions,
+you can install a CPU-only `pytorch` by following the `pytorch` [installation guide](https://pytorch.org/get-started/locally/).
+
+
+```bash
+$ pip install torch --index-url https://download.pytorch.org/whl/cpu
+```
+
+
 ## Datasets
 The 4 datasets used in the DCA paper can be found in the following locations
 * [M1](https://zenodo.org/record/583331) - We used indy_20160627_01.mat

docs/source/conf.py

@@ -12,7 +12,6 @@
 #
 import os
 import sys
-import sphinx_rtd_theme
 
 # Get the project root dir, which is the parent parent dir of this
 project_root = os.path.dirname(os.path.dirname(os.getcwd()))
@@ -68,7 +67,6 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

pyproject.toml

@@ -1,3 +1,33 @@
 [build-system]
-requires = ["setuptools>=42"]
+requires = ["setuptools>=61", "wheel"]  # [CHANGE] upgraded setuptools to 61+ for full pyproject.toml metadata support
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "DynamicalComponentsAnalysis"
+version = "1.1.0"
+description = "Dynamical Components Analysis"
+readme = "README.md"
+requires-python = ">=3.6"
+authors = [
+    { name="Jesse Livezey", email="jesse.livezey@gmail.com" },
+    { name="David Clark" }
+]
+license = { file = "LICENSE.txt" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent"
+]
+dynamic = ["dependencies"]
+
+[project.urls]
+Homepage = "https://github.com/BouchardLab/DynamicalComponentsAnalysis"
+"Bug Tracker" = "https://github.com/BouchardLab/DynamicalComponentsAnalysis/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}

requirements.txt

@@ -4,5 +4,4 @@ h5py
 pandas
 scikit-learn
 matplotlib
---extra-index-url https://download.pytorch.org/whl/cpu
 torch

src/dca/cov_util.py

@@ -812,8 +812,8 @@ def __get__(self, obj, objtype):
 
 @memoized
 def pv_permutation(T, N):
-    A = np.arange((T * N)**2, dtype=np.int).reshape((T * N, T * N))
-    A_perm = np.zeros((T**2, N**2), dtype=np.int)
+    A = np.arange((T * N)**2, dtype=int).reshape((T * N, T * N))
+    A_perm = np.zeros((T**2, N**2), dtype=int)
     for i in range(T):
         for j in range(T):
             row_idx = i * T + j