Migrate to pyproject (#575)

* migrate to pyproject setup

* fix typo in prototypes + add latex-->unicode decoding for special chars

Author: esoteric-ephemera

.github/workflows/release.yml

@@ -20,15 +20,15 @@ jobs:
       - name: Install dependencies
         run: |
           conda install --quiet --yes -c conda-forge openbabel pip ruamel.yaml
-          pip install -r requirements.txt
-          pip install -e .[tests]
+          pip install -e .[strict,tests]
 
       - name: Test
-        run: pytest
+        run: pytest -n auto tests
 
       - name: Build packages
         run: |
-          python setup.py sdist bdist_wheel
+          pip install --upgrade build
+          python -m build
 
       - name: Publish
         uses: pypa/gh-action-pypi-publish@master

.github/workflows/tests.yml

@@ -24,12 +24,11 @@ jobs:
         shell: bash -l {0}
         run: |
           conda install --quiet --yes -c conda-forge openbabel pip ruamel.yaml
-          python${{ matrix.python-version }} -m pip install -r requirements.txt
-          python${{ matrix.python-version }} -m pip install -e .[tests,cli]
+          python${{ matrix.python-version }} -m pip install -e .[strict,tests,cli]
 
       - name: Test
         shell: bash -l {0}
-        run: python${{ matrix.python-version }} -m pytest --cov=robocrys --cov-report=xml --cov-config=.coveragerc tests/
+        run: python${{ matrix.python-version }} -m pytest -n auto --cov=robocrys --cov-report=xml --cov-config=.coveragerc tests/
 
   docs:
     runs-on: ubuntu-latest
@@ -44,8 +43,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -e .[docs,cli]
+          pip install -e .[strict,docs,cli]
 
       - name: Build
         run: sphinx-build docs/src docs_build

.mypy.ini

@@ -0,0 +1,101 @@
+
+[build-system]
+requires = ["setuptools>=80.0.0","setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+root = "."
+relative_to = "__file__"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["tests", "docs", "dev_scripts"]
+include = ["robocrys"]
+
+[tool.setuptools.package-data]
+"robocrys.condense" = ["*.json.gz"]
+
+[project]
+name = "robocrys"
+dynamic = ["version"]
+requires-python = ">=3.10"
+description="Automatic generation of crystal structure descriptions"
+license = {text = "Modified BSD"}
+authors = [
+    {name = "Alex Ganose", email="aganose@lbl.gov"},
+]
+dependencies = [
+    "spglib>=2.5.0",
+    "numpy",
+    "scipy",
+    "pymatgen>=2024.1.26",
+    "inflect",
+    "networkx",
+    "matminer>=0.9.2",
+    "monty",
+    "pubchempy",
+    "pybtex",
+]
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Information Technology",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Other/Nonlisted Topic",
+    "Operating System :: OS Independent",
+]
+keywords=["crystal-structure", "crystallography", "materials-science"]
+
+[project.urls]
+Homepage = "https://github.com/hackingmaterials/robocrystallographer"
+Documentation = "https://hackingmaterials.lbl.gov/robocrystallographer/"
+
+[project.optional-dependencies]
+docs = [
+    "sphinx>=5.3.0",
+    "sphinx-argparse==0.5.2",
+    "sphinx_rtd_theme==3.0.2",
+    "sphinx-autodoc-typehints==3.0.1",
+]
+dev = ["tqdm", "pybel", "pebble", "maggma"]
+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+cli = ["mp_api"]
+lint = [
+    "coverage==7.11.0",
+    "codacy-coverage==1.3.11",
+    "pycodestyle==2.14.0",
+    "mypy==1.18.2",
+    "pydocstyle==6.1.1",
+    "flake8==7.3.0",
+    "pylint==4.0.2",
+    "black==25.9.0",
+]
+strict = [
+    "spglib==2.6.0",
+    "numpy==2.2.6,",
+    "scipy==1.15.3",
+    "pymatgen==2025.10.7",
+    "inflect==7.5.0",
+    "networkx==3.4.2",
+    "matminer==0.9.3",
+    "monty==2025.3.3",
+    "pubchempy==1.0.5",
+    "pybtex==0.25.1",
+]
+
+[project.scripts]
+robocrys = "robocrys.cli:main"
+
+[tool.mypy]
+ignore_missing_imports = true

pyproject.toml

@@ -5,9 +5,16 @@
 
 from __future__ import annotations
 
-from robocrys._version import __version__
+from importlib.metadata import PackageNotFoundError, version
+
 from robocrys.condense.condenser import StructureCondenser
 from robocrys.describe.describer import StructureDescriber
 from robocrys.util import common_formulas
 
 __all__ = ["__version__", "StructureDescriber", "StructureCondenser", "common_formulas"]
+
+try:
+    __version__ = version("robocrys")
+except PackageNotFoundError:
+    # package is not installed
+    pass

requirements.txt

@@ -171,9 +171,18 @@ def get_mineral_description(self) -> str:
             spg_symbol = htmlify_spacegroup(self._da.spg_symbol)
             formula = htmlify(formula)
 
-        mineral_name = get_mineral_name(self._da.mineral)
+        if mineral_name := get_mineral_name(self._da.mineral):
+            # replace latex-like characters with unicode
+            latex_reps = {
+                "$\\mu$": "\u03BC",
+                "\\'{c}": "\u0107",
+            }
+            if self.fmt in {"html", "unicode"} and any(
+                k in mineral_name for k in latex_reps
+            ):
+                for k, v in latex_reps.items():
+                    mineral_name = mineral_name.replace(k, v)
 
-        if mineral_name:
             desc = f"{formula} is {mineral_name} structured and"
         else:
             desc = f"{formula}"