Transition to pyproject.toml

.github/workflows/ci.yml

@@ -35,30 +35,28 @@ 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,ase,biopython]
 
     # Note the use of the -Wa flag to show DeprecationWarnings
     # We test the package as-installed. 
-    - name: Unit tests
+    - name: Unit tests and doctests
       env:
         MATERIALS_PROJECT_API_KEY: ${{ secrets.MATERIALS_PROJECT_API_KEY }}
       run: |
@@ -67,14 +65,8 @@ jobs:
         python -Wa -m pytest --pyargs crystals --full-trace
     
     - name: Build documentation
-      run: |
-        python setup.py build_sphinx
-    
-    - name: Doctests
-      run: |
-        python -m sphinx -b doctest docs build
-        python -m doctest README.md
-
+      run:
+        sphinx-build -M html docs build/docs
 
   release:
     if: startsWith(github.ref, 'refs/tags/v')
@@ -93,8 +85,8 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
-        pip install -r dev-requirements.txt
+        pip install build
+        pip install .[development,ase,biopython]
 
     - name: Create release description
       run: |
@@ -103,7 +95,7 @@ jobs:
 
     - name: Create source distribution
       run: |
-        python setup.py sdist
+        python -m build
 
     - name: Create release
       uses: softprops/action-gh-release@v2

.readthedocs.yml

@@ -20,5 +20,7 @@ build:
 
 python:
   install:
-    - requirements: requirements.txt
-    - requirements: dev-requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - development

crystals/base.py

@@ -170,6 +170,7 @@ def chemical_composition(self) -> Dict[str, float]:
 
         Example
         -------
+        >>> from crystals import Crystal
         >>> c = Crystal.from_cod(1508819)
         >>> c.chemical_composition # doctest: +SKIP
         OrderedDict([('H',  0.441),
@@ -196,6 +197,7 @@ def chemical_formula(self) -> str:
 
         Example
         -------
+        >>> from crystals import Crystal
         >>> c = Crystal.from_cod(1508819)
         >>> c.chemical_formula
         'C15 H19 Cl N4 O4'

crystals/lattice.py

@@ -322,6 +322,7 @@ def bounded_reflections(
 
         Examples
         --------
+        >>> from crystals import Crystal
         >>> cryst = Crystal.from_database('C')
         >>> refls = cryst.bounded_reflections(1.5) # 1.5 inverse Angstroms
         >>> list(refls)
@@ -491,7 +492,7 @@ def cyclic(iterable: Iterable[Any]) -> Iterable[Iterable[Any]]:
     Examples
     --------
     >>> list(cyclic((1,2,3)))
-    [(1,2,3), (2,3,1), (3,1,2)]
+    [(1, 2, 3), (3, 1, 2), (2, 3, 1)]
     """
     iterable = tuple(iterable)
     n = len(iterable)

pyproject.toml

@@ -0,0 +1,81 @@
+[build-system]
+requires = ["build", "setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "crystals.__version__"}
+
+[project]
+name = "crystals"
+dynamic = ["version"]
+authors = [
+  { name="Laurent P. René de Cotret", email="[email protected]" },
+]
+maintainers = [
+  { name="Laurent P. René de Cotret", email="[email protected]" },
+]
+description = "Data structures for crystallography"
+readme = "README.md"
+license = {file = "LICENSE"}
+requires-python = ">=3.7, <4"
+dependencies = [
+    "numpy        >= 1.20, < 3",
+    "spglib       >= 1.15, < 3",
+    "pycifrw      >= 4.4.1, < 5",
+    "requests     >= 2, < 3",
+]
+keywords=["crystallography", "material science", "structural biology"]
+classifiers = [
+    "Environment :: Console",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+development = [
+    "sphinx >= 3",
+    "sphinx_rtd_theme >= 0.4",
+    "pytest >= 6",
+    "wheel",
+]
+biopython = ["biopython >= 1, <2"]
+ase = ["ase >= 3, <4"]
+
+[project.urls]
+Documentation = "https://crystals.readthedocs.io/"
+Repository = "https://github.com/LaurentRDC/crystals"
+"Bug Tracker" = "https://github.com/LaurentRDC/crystals/issues"
+
+[project.scripts]
+spam-cli = "crystals.__main__:main"
+
+# See here for an explanation of how to include package data:
+# https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data
+[tool.setuptools.package-data]
+crystals = ["cifs/*.cif"]
+
+[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", 
+]