refactor: CI installation process to use 'uv' for faster dependency management

.github/workflows/main.yml

@@ -22,14 +22,15 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
+      - name: Install uv
         run: |
-          pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -e . --no-deps
+          pip install uv
+      - name: Install dependencies with uv
+        run: |
+          uv pip install ."[tests]"
 
       - name: Run tests
-        run: pytest
+        run: python -m pytest
 
   build-docs:
     if: github.event_name == 'push' && github.ref == 'refs/heads/master'
@@ -52,12 +53,12 @@ jobs:
         with:
           python-version: '3.9'
 
-      - name: Install dependencies
+      - name: Install uv
         run: |
-          pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install sphinx sphinx_rtd_theme sphinx-argparse
-          pip install -e . --no-deps
+          pip install uv
+      - name: Install dependencies with uv
+        run: |
+          uv pip install ."[docs]""
 
       - name: Build docs
         working-directory: docs

.github/workflows/publish.yml

@@ -19,12 +19,14 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: "3.x"
-    - name: Install dependencies
+    - name: Install uv
       run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel
-    - name: Build package (setup.py)
+        pip install uv
+    - name: Install project with uv
       run: |
-        python setup.py sdist bdist_wheel
+        uv pip install -e .
+    - name: Build package with uv
+      run: |
+        uv build
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

pyproject.toml

@@ -1,3 +1,51 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cdtools-py"
+description = "Tools for coherent diffractive imaging and ptychography"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { file = "LICENSE.txt" }
+authors = [
+	{ name = "Abe Levitan", email = "abraham.levitan@psi.ch" },
+	{ name = "Madelyn Cain" },
+	{ name = "Anastasiia Kutakh" }
+]
+maintainers = [
+	{ name = "Abe Levitan", email = "abraham.levitan@psi.ch" }
+]
+keywords = ["ptychography", "CDI", "imaging", "torch", "differentiable"]
+classifiers = [
+	"Programming Language :: Python :: 3",
+	"Operating System :: OS Independent",
+	"License :: OSI Approved :: MIT License"
+]
+urls = { "Homepage" = "https://github.com/cdtools-developers/cdtools", "Documentation" = "https://cdtools-developers.github.io/cdtools/" }
+dependencies = [
+	"numpy>=1.0",
+	"scipy>=1.0",
+	"matplotlib>=2.0",
+	"torch>=2.3.0",
+	"h5py>=2.1",
+	"python-dateutil",
+]
+dynamic = ["version"]
+
+[tool.setuptools.dynamic]
+version = {attr = "cdtools._version.__version__"}
+
+[project.optional-dependencies]
+tests = [
+	"pytest",
+	"pooch"
+]
+docs = [
+	"sphinx>=4.3.0",
+	"sphinx-argparse",
+	"sphinx_rtd_theme>=0.5.1"
+]
+
 [tool.ruff]
-# Decrease the maximum line length to 79 characters.
 line-length = 79

requirements.txt

@@ -1,11 +0,0 @@
-numpy>=1.0
-scipy>=1.0
-matplotlib>=2.0  # 2.0 introduces better colormaps which are used by default
-torch>=1.9.0 #1.9.0 implements support for autograd on indexed complex tensors
-h5py>=2.1
-python-dateutil
-pytest
-pooch
-sphinx>=4.3.0 # Fixes a bug with bulleted lists
-sphinx-argparse
-sphinx_rtd_theme>=0.5.1 # Fixes a bug with bulleted lists

setup.py

@@ -1,51 +0,0 @@
-import setuptools
-import os
-import re
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-# read version from src/cdtools/_version.py
-version_file = os.path.join("src/cdtools", "_version.py")
-with open(version_file) as f:
-    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", f.read(), re.M)
-if not version_match:
-    raise RuntimeError("Unable to find version string.")
-version = version_match.group(1)
-    
-setuptools.setup(
-    name="cdtools-py",
-    version=version,
-    python_requires='>3.8', # recommended minimum version for pytorch 2.3.0
-    author="Abe Levitan",
-    author_email="abraham.levitan@psi.ch",
-    description="Tools for coherent diffractive imaging and ptychography",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/cdtools-developers/cdtools",
-    install_requires=[
-        "numpy>=1.0",
-        "scipy>=1.0",
-        "matplotlib>=2.0", # 2.0 has better colormaps which are used by default
-        "python-dateutil",
-        "torch>=2.3.0", #2.3.0 is the earliest release for which L-BFGS works directly on complex-valued leaf tensors
-        "h5py>=2.1"],
-    extras_require={
-        'tests': [
-            "pytest",
-            "pooch",
-        ],
-        'docs': [
-            "sphinx>=4.3.0",
-            "sphinx-argparse",
-            "sphinx_rtd_theme>=0.5.1"
-        ]
-    },
-    package_dir={"": "src"},
-    packages=setuptools.find_packages("src"),
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "Operating System :: OS Independent",
-    ],
-)
-