Merge pull request #517 from hakonanes/from-setup-to-pyproject

Change build backend from setuptools to Hatch

.github/workflows/build.yml

@@ -14,11 +14,11 @@ jobs:
     name: code style
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: psf/black@stable
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
@@ -34,23 +34,6 @@ jobs:
         run: |
           black --diff --line-length 77 doc/tutorials/*.ipynb
 
-  # Make sure all necessary files will be included in a release
-  manifest:
-    name: check manifest
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-
-      - name: Install dependencies
-        run: |
-          pip install manifix
-
-      - name: Check MANIFEST.in file
-        run: |
-          python setup.py manifix
-
   build-with-pip:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
@@ -68,17 +51,17 @@ jobs:
             DEPENDENCIES: diffpy.structure==3.0.2  matplotlib==3.5
             LABEL: -oldest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install depedencies and package
         shell: bash
         run: |
-          pip install -U -e .'[doc, tests]'
+          pip install -U -e .'[doc,tests,coverage]'
 
       - name: Install oldest supported version
         if: ${{ contains(matrix.LABEL, 'oldest') }}

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
       - id: black-jupyter

README.rst

@@ -1,15 +1,8 @@
-.. raw:: html
-
-    <p>
-      <h1>
-        <a href="https://orix.readthedocs.io"><img valign="middle" src="https://github.com/raw/pyxem/orix/develop/doc/_static/img/orix_logo.png" width="50" alt="orix logo"/></a>
-        orix
-      </h1>
-    </p>
-
-.. Content above here until EXCLUDE plus one line is excluded from the long description
-.. in the source distributions uploaded to PyPI
-.. EXCLUDE
+|logo| orix
+===========
+
+.. |logo| image:: https://github.com/raw/pyxem/orix/develop/doc/_static/img/orix_logo.png
+  :width: 50
 
 orix is an open-source Python library for analysing orientations and crystal symmetry.
 

doc/conf.py

@@ -6,8 +6,10 @@
 import inspect
 import os
 from os.path import dirname, relpath
+from pathlib import Path
 import re
 import sys
+import tomllib
 
 from numpydoc.docscrape_sphinx import SphinxDocString
 
@@ -20,9 +22,14 @@
 # sys.path.insert(0, os.path.abspath("."))
 sys.path.append("../")
 
-project = "orix"
-copyright = f"2018-{str(datetime.now().year)}, {orix.__author__}"
-author = orix.__author__
+top_dir = Path(__file__).parent.parent
+
+with open(top_dir / "pyproject.toml", "rb") as f:
+    metadata = tomllib.load(f)
+
+project = metadata["project"]["name"]
+author = metadata["project"]["authors"][0]["name"]
+copyright = f"2018-{str(datetime.now().year)}, {author}"
 release = orix.__version__
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -120,10 +127,10 @@
 # modifications to point nbviewer and Binder to the GitHub develop
 # branch links when the documentation is launched from a kikuchipy
 # version with "dev" in the version
-if "dev" in orix.__version__:
+if "dev" in release:
     release_version = "develop"
 else:
-    release_version = "v" + orix.__version__
+    release_version = "v" + release
 # This is processed by Jinja2 and inserted before each notebook
 nbsphinx_prolog = (
     r"""
@@ -234,14 +241,14 @@ def linkcode_resolve(domain, info):
     fn = relpath(fn, start=startdir).replace(os.path.sep, "/")
 
     if fn.startswith("orix/"):
-        m = re.match(r"^.*dev0\+([a-f\d]+)$", orix.__version__)
+        m = re.match(r"^.*dev0\+([a-f\d]+)$", release)
         pre_link = "https://github.com/pyxem/orix/blob/"
         if m:
             return pre_link + "%s/%s%s" % (m.group(1), fn, linespec)
-        elif "dev" in orix.__version__:
+        elif "dev" in release:
             return pre_link + "develop/%s%s" % (fn, linespec)
         else:
-            return pre_link + "v%s/%s%s" % (orix.__version__, fn, linespec)
+            return pre_link + "v%s/%s%s" % (release, fn, linespec)
     else:
         return None
 

doc/dev/building_writing_documentation.rst

@@ -112,7 +112,7 @@ We use :doc:`nbval <nbval:index>` for this.
 The tutorial notebooks can be run interactively in the browser with the help of Binder.
 When creating a server from the orix source code, Binder installs the packages listed in
 the ``environment.yml`` configuration file, which must include all ``doc`` dependencies
-in ``setup.py`` necessary to run the notebooks.
+in ``pyproject.toml`` necessary to run the notebooks.
 
 Writing API reference
 ---------------------

orix/__init__.py

@@ -1,8 +1,4 @@
-__name__ = "orix"
 __version__ = "0.14.dev0"
-__author__ = "orix developers"
-__author_email__ = "pyxem.team@gmail.com"
-__description__ = "orix is an open-source Python library for handling crystal orientation mapping data."
 # Sorted by line contributions (ideally excluding lines in notebook files)
 __credits__ = [
     "Håkon Wiik Ånes",

pyproject.toml

@@ -0,0 +1,109 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "orix"
+# conf.py assumes orix developers to be first author
+authors = [{name = "orix developers"}]
+description = "orix is an open-source Python library for handling crystal orientation mapping data"
+license = {file = "LICENSE"}
+readme = {file = "README.rst", content-type = "text/x-rst"}
+dynamic = ["version"]
+classifiers=[
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "dask[array]",
+    "diffpy.structure       >= 3.0.2",
+    "h5py",
+    "matplotlib             >= 3.5",
+    "matplotlib-scalebar",
+    "numba",
+    "numpy",
+    "numpy-quaternion",
+    "pooch                  >= 0.13",
+    # TODO: Remove once https://github.com/diffpy/diffpy.structure/issues/97 is fixed
+    "pycifrw",
+    "scipy",
+    "tqdm",
+]
+
+[project.optional-dependencies]
+doc = [
+    "ipykernel",  # Used by nbsphinx to execute notebooks
+    "memory_profiler",
+    "nbconvert                      >= 7.16.4",
+    "nbsphinx                       >= 0.7",
+    "numpydoc",
+    "pydata-sphinx-theme",
+    "scikit-image",
+    "scikit-learn",
+    "sphinx                         >= 3.0.2",
+    "sphinx-codeautolink[ipython]",
+    "sphinx-copybutton              >= 0.2.5",
+    "sphinx-design",
+    "sphinx-gallery",
+    "sphinxcontrib-bibtex           >= 1.0",
+]
+tests = [
+    "numpydoc",
+    "pytest                         >= 5.4",
+    "pytest-rerunfailures",
+    "pytest-xdist",
+]
+coverage = [
+    "coverage                       >= 5.0",
+    "pytest-cov                     >= 2.8.1",
+]
+dev = [
+    "black[jupyter]",
+    "hatch",
+    "isort                          >= 5.10",
+    "outdated",
+    "pre-commit                     >= 1.16",
+    "orix[doc,tests,coverage]",
+]
+
+[tool.hatch.version]
+path = "orix/__init__.py"
+
+[tool.coverage.report]
+precision = 2
+
+[tool.coverage.run]
+branch = true
+source = ["orix"]
+relative_files = true
+omit = [
+    "orix/__init__.py",
+    "orix/tests/**/*.py",
+]
+
+[tool.pytest.ini_options]
+addopts = [
+    "-ra",
+    "--ignore=doc/_static/img/colormap_banners/create_colormap_banners.py",
+    "--ignore=examples/*/*.py",
+]
+doctest_optionflags = "NORMALIZE_WHITESPACE"
+filterwarnings = [
+    "ignore:Deprecated call to `pkg_resources:DeprecationWarning",
+    "ignore:pkg_resources is deprecated as an API:DeprecationWarning",
+]
+
+[tool.isort]
+profile = "black"
+filter_files = true
+force_sort_within_sections = true