Transition to pyproject.toml

.github/workflows/ci.yml

@@ -32,42 +32,32 @@ jobs:
       if: startsWith(runner.os, 'Linux')
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/*requirements.txt') }}
+        key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
 
     - uses: actions/cache@v4
       if: startsWith(runner.os, 'macOS')
       with:
         path: ~/Library/Caches/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/*requirements.txt') }}
+        key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
 
     - uses: actions/cache@v4
       if: startsWith(runner.os, 'Windows')
       with:
         path: ~\AppData\Local\pip\Cache
-        key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('**/*requirements.txt') }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml') }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install numpy wheel
-        pip install -r requirements.txt
-        pip install -r dev-requirements.txt
+        pip install .[development]
 
-    # We run the tests on the installed package, with all optional dependencies
-    # Note the use of the -Wa flag to show DeprecationWarnings
-    - name: Unit tests
+    - name: Unit tests and doc tests
       run: |
-        python -m pip install .[diffshow]
-        cd ~
-        python -Wa -m pytest --pyargs skued --import-mode=importlib
+        python -Wa -m pytest
     
     - name: Build documentation
       run: |
-        python setup.py build_sphinx
-    
-    - name: Doctests
-      run: |
-        python -m sphinx -b doctest docs build
+        sphinx-build -M html docs build/docs
 
 
   release:
@@ -87,8 +77,8 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
-        pip install -r dev-requirements.txt
+        pip install build
+        pip install .[development]
 
     - name: Create release description
       run: |
@@ -97,7 +87,7 @@ jobs:
 
     - name: Create source distribution
       run: |
-        python setup.py sdist
+        python -m build
 
     - name: Create release
       uses: softprops/action-gh-release@v2

.readthedocs.yml

@@ -14,5 +14,7 @@ build:
 
 python:
   install:
-    - requirements: requirements.txt
-    - requirements: dev-requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - development

CONTRIBUTING.md

@@ -115,10 +115,9 @@ Once you've fixed all merge conflicts, do:
 
 ### Build environment setup
 
-To create an appropriate development environment, you need to install the base requirements (`requirements.txt`) as well as extra, development requirements (`dev-requirements.txt`)
+To create an appropriate development environment, you need to install the base requirements as well as extra, development requirements:
 
-    pip install -r requirements
-    pip install -r dev-requirements
+    pip install .[development]
 
 ## Guidelines
 

MANIFEST.in

@@ -1,8 +1,6 @@
 include README.md
 include CHANGELOG.rst
 include LICENSE.txt 
-include requirements.txt 
-include dev-requirements.txt
 
 recursive-include skued/baseline/data *
 recursive-include skued/simulation/data *

docs/installation.rst

@@ -9,7 +9,7 @@ Installation
 Requirements
 ============
 
-Scikit-ued works on Linux, Mac OS X and Windows. It requires Python 3.7+. Packages requirements are `listed here <https://github.com/LaurentRDC/scikit-ued/blob/master/requirements.txt>`_.
+Scikit-ued works on Linux, Mac OS X and Windows. It requires Python 3.7+. Packages requirements are `listed here <https://github.com/LaurentRDC/scikit-ued/blob/master/pyproject.toml>`_.
 
 Install scikit-ued
 ==================

pyproject.toml

@@ -0,0 +1,75 @@
+[build-system]
+requires = ["build", "setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "skued.__version__"}
+
+[project]
+name = "scikit-ued"
+dynamic = ["version"]
+authors = [
+  { name="Laurent P. René de Cotret", email="[email protected]" },
+]
+maintainers = [
+  { name="Laurent P. René de Cotret", email="[email protected]" },
+]
+description = "Collection of algorithms and functions for ultrafast electron scattering"
+readme = "README.md"
+license = {file = "LICENSE"}
+requires-python = ">=3.7, <4"
+dependencies = [
+    "crystals     >= 1.3.1, < 2",
+    "npstreams    >= 1.6.5, < 2",
+    "numpy        >= 1.17, < 3",
+    "pywavelets   >= 1.0.0, < 2",
+    "scikit-image >= 0.19, < 1",
+    # See https://github.com/scipy/scipy/issues/17740
+    "scipy        >= 1.5.0, < 2, != 1.10.0",
+    "pyyaml       >= 3.1",
+    "matplotlib   >= 3.5, <4",
+]
+keywords=["ultrafast electron scattering"]
+classifiers = [
+    "Environment :: Console",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+
+[project.optional-dependencies]
+development = [
+    "Sphinx >= 3",
+    "sphinx_rtd_theme >= 0.4",
+    "pytest >= 6",
+    "black",
+]
+diffshow = ["pyqtgraph>=0.12,<1", "PyQt5"]
+
+[project.urls]
+Documentation = "https://scikit-ued.readthedocs.io/"
+Repository = "https://github.com/LaurentRDC/scikit-ued"
+"Bug Tracker" = "https://github.com/LaurentRDC/scikit-ued/issues"
+
+[project.scripts]
+skued-cli = "skued.__main__:main"
+
+[tool.black]
+line-length = 120
+include = '\.pyi?$'
+
+[tool.isort]
+profile = "black"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+log_cli_level = "INFO"
+# Very cool ability for pytest to also run doctests on package contents with `-doctest-modules`
+addopts = [
+    "--doctest-modules", 
+]

skued/__main__.py

@@ -10,9 +10,7 @@
 from . import __version__
 from .io import WITH_PYQTGRAPH, diffshow
 
-parser = argparse.ArgumentParser(
-    prog="skued", description=f"scikit-ued {__version__} command-line utilities."
-)
+parser = argparse.ArgumentParser(prog="skued", description=f"scikit-ued {__version__} command-line utilities.")
 
 subparsers = parser.add_subparsers(title="command", dest="command")
 

skued/affine.py

@@ -39,9 +39,7 @@ def affine_map(array):
         extended_matrix[:3, :3] = array
         return extended_matrix
     else:
-        raise ValueError(
-            "Array shape not 3x3 or 4x4, and thus is not a transformation matrix."
-        )
+        raise ValueError("Array shape not 3x3 or 4x4, and thus is not a transformation matrix.")
 
 
 def transform(matrix, array):