Fix outdated setup.py find_namespace_packages and add test_egg_sources_txt_is_complete

CHANGES.md

@@ -8,7 +8,12 @@ nav_order: 4
 
 ## v2023.10.4
 
-- Bug fixes for MPRester and packaged data.
+### 🐛 Bug Fixes
+
+- Fix missing `potcar_summary_stats.json.gz` in `setup.package_data` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3372>
+- Bug fixes for MPRester and packaged data by @shyuep
+
+**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.10.3...v2023.10.4>
 
 ## v2023.10.3
 
@@ -67,12 +72,66 @@ nav_order: 4
 
 **Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>
 
+### 🛠 Enhancements
+
+- Add an input arg check for `Kpoints.automatic_density_by_lengths` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3299>
+
+### 🏥 Package Health
+
+- Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3303>
+- Move `py.typed` to package root by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3307>
+- Consistent casing `setup->setUp` across test classes by @janosh in <https://github.com/materialsproject/pymatgen/pull/3305>
+
+**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>
+
 ## v2023.9.2
 
-- VaspInputSets now allow structure to be None for stateless initialization.
-- MatPESStaticSet designed for generating PES data. (@SophiaRuan, @JiQi535)
-- Breaking: Bump minimum Python version to 3.9, in line with numpy.
-- Add `properties` to Structure and Molecule, with ASE adaptor support (@gpetretto, @Andrew-S-Rosen)
+- Add `Lattice` property `params_dict` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3239>
+- Generate SupercellTransformation from minimum boundary distance by @JiQi535 in <https://github.com/materialsproject/pymatgen/pull/3238>
+- More concise `test_from_boundary_distance`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3242>
+- Breaking: remove deprecated keyword `properties` from `Species`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3243>
+- Typo in Docs for PeriodicsSite by @jmmshn in <https://github.com/materialsproject/pymatgen/pull/3249>
+- Fix `Vasprun.converged_electronic` check if `ALGO=CHI` in `INCAR` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3250>
+- Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module by @janosh in <https://github.com/materialsproject/pymatgen/pull/3237>
+- Fix `ruff` D212 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3251>
+- Fix some Kpoints generated using wrong mesh types by @matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3245>
+- read `mag` from OSZICAR by @chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3146>
+- Use `numpy.testing.assert_allclose` over `assert np.allclose` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3253>
+- Don't let tests pollute the `pymatgen` repo by @janosh in <https://github.com/materialsproject/pymatgen/pull/3255>
+- Update `compatibility.md` by @mbercx in <https://github.com/materialsproject/pymatgen/pull/3260>
+- Google-style doc string return types by @janosh in <https://github.com/materialsproject/pymatgen/pull/3258>
+- Quasi-RRHO Thermochemistry Analysis Module by @arepstein in <https://github.com/materialsproject/pymatgen/pull/2028>
+- Add keyword `check_occu: bool = True` to `CifParser.get_structures()` by @jonathanjdenney in <https://github.com/materialsproject/pymatgen/pull/2836>
+- Fix bug in feff inputs.py by @kaifengZheng in <https://github.com/materialsproject/pymatgen/pull/3256>
+- Cancel concurrent CI runs to save budget by @janosh in <https://github.com/materialsproject/pymatgen/pull/3263>
+- Fix `Procar.get_projection_on_elements` for structures with multiple same-element ionic sites by @Na-Kawa in <https://github.com/materialsproject/pymatgen/pull/3261>
+- Fix `TestMPScanStaticSet.test_as_from_dict()` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3266>
+- Bump activesupport from 7.0.6 to 7.0.7.2 in /docs by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3267>
+- Fix `TestMPStaticSet` using `MPRelaxSet` in `test_user_incar_kspacing` and `test_kspacing_override`  by @janosh in <https://github.com/materialsproject/pymatgen/pull/3268>
+- Fix `nelectrons` not updating when replacing species in `Molecule` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3269>
+- Add `properties` to Structure and Molecule by @gpetretto in <https://github.com/materialsproject/pymatgen/pull/3264>
+- Fix `CifParser.get_structures(check_occu=False)` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3272>
+- Add `PotcarSingle.__repr__` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3273>
+- `__str__` to `__repr__` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3274>
+- Ion: handle dissolved gas formulas by @rkingsbury in <https://github.com/materialsproject/pymatgen/pull/3275>
+- Add VASP input set `MatPESStaticSet` by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3254>
+- Fix `test_valid_magmom_struct()` error message regex by @janosh in <https://github.com/materialsproject/pymatgen/pull/3276>
+- fix tests of MatPESStaticSet  by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3281>
+- Breaking: bump minimum Python version to 3.9 by @janosh in <https://github.com/materialsproject/pymatgen/pull/3283>
+- Breaking: Update `AseAtomsAdaptor` to handle `Structure.properties`/`Molecule.properties` by @Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3270>
+- Slightly relax the constraint satisfy condition of get_primitive_structure() by @fyalcin in <https://github.com/materialsproject/pymatgen/pull/3285>
+- [WIP] add custodian modified incar settings to incar and modify tests by @SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3284>
+- Add keyword `bandgap_tol: float = 1e-4` to `MPScanRelaxSet` by @janosh in <https://github.com/materialsproject/pymatgen/pull/3287>
+- `np.(arange->linspace)` in `io/vasp/optics.py` `get_delta`, `get_setp` and `epsilon_imag` by @LucasGVerga in <https://github.com/materialsproject/pymatgen/pull/3286>
+- MatPESStaticSet restore GGA tag removal if xc_functional.upper() == "R2SCAN" by @janosh in <https://github.com/materialsproject/pymatgen/pull/3288>
+- Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3294>
+- Bump cython from 3.0.0 to 3.0.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3292>
+- Bump scipy from 1.11.1 to 1.11.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3291>
+- Bump plotly from 5.11.0 to 5.16.1 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3289>
+- Bump joblib from 1.3.1 to 1.3.2 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3290>
+- Bump mp-api from 0.33.3 to 0.35.1 by @dependabot in <https://github.com/materialsproject/pymatgen/pull/3293>
+- xyz.**iter**() -> iter(xyz) by @janosh in <https://github.com/materialsproject/pymatgen/pull/3228>
+- Deprecate overlooked `from/as_..._string` methods by @janosh in <https://github.com/materialsproject/pymatgen/pull/3295>
 
 ## v2023.8.10
 

setup.py

@@ -24,10 +24,7 @@
 
 setup(
     name="pymatgen",
-    packages=find_namespace_packages(
-        include=["pymatgen.*", "pymatgen.analysis.*", "pymatgen.io.*", "pymatgen.ext.*", "cmd_line"],
-        exclude=["pymatgen.*.tests", "pymatgen.*.*.tests", "pymatgen.*.*.*.tests"],
-    ),
+    packages=find_namespace_packages(include=["pymatgen.*", "pymatgen.**.*", "cmd_line"]),
     version="2023.10.4",
     python_requires=">=3.9",
     install_requires=[

tasks.py

@@ -228,7 +228,6 @@ def release(ctx, version=None, nodoc=False):
 
     ctx.run("rm -f dist/*.*", warn=True)
     ctx.run("python setup.py sdist bdist_wheel", warn=True)
-    check_egg_sources_txt_for_completeness()
     ctx.run("twine upload --skip-existing dist/*.whl", warn=True)
     ctx.run("twine upload --skip-existing dist/*.tar.gz", warn=True)
     # post_discourse(ctx, warn=True)
@@ -249,24 +248,3 @@ def open_doc(ctx):
 def lint(ctx):
     for cmd in ["ruff", "mypy", "black", "pylint"]:
         ctx.run(f"{cmd} pymatgen")
-
-
-def check_egg_sources_txt_for_completeness():
-    """Check that all source and data files in pymatgen/ are listed in pymatgen.egg-info/SOURCES.txt."""
-    src_txt = "pymatgen.egg-info/SOURCES.txt"
-    if not os.path.exists(src_txt):
-        raise FileNotFoundError(f"{src_txt} not found. Run `pip install .` to create")
-
-    with open(src_txt) as file:
-        sources = file.read()
-
-    for src_file in sources.splitlines():
-        if not os.path.exists(src_file):
-            raise ValueError(f"{src_file} does not exist!")
-
-    for ext in ("py", "json", "json.gz", "yaml", "csv"):
-        for filepath in glob(f"pymatgen/**/*.{ext}", recursive=True):
-            if "/tests/" in filepath or "dao" in filepath:
-                continue
-            if filepath not in sources:
-                raise ValueError(f"{filepath} not found in {src_txt}")

tests/test_pkg.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+import os
+from glob import glob
+
+import pytest
+
+src_txt_path = "pymatgen.egg-info/SOURCES.txt"
+src_txt_missing = not os.path.isfile(src_txt_path)
+
+
+@pytest.mark.skipif(src_txt_missing, reason=f"{src_txt_path} not found. Run `pip install .` to create")
+def test_egg_sources_txt_is_complete():
+    """Check that all source and data files in pymatgen/ are listed in pymatgen.egg-info/SOURCES.txt."""
+
+    with open(src_txt_path) as file:
+        sources = file.read()
+
+    # check that all files listed in SOURCES.txt exist
+    for src_file in sources.splitlines():
+        assert os.path.exists(src_file), f"{src_file!r} does not exist!"
+
+    # check that all files in pymatgen/ are listed in SOURCES.txt
+    for ext in ("py", "json", "json.gz", "yaml", "csv"):
+        for filepath in glob(f"pymatgen/**/*.{ext}", recursive=True):
+            if "/tests/" in filepath or filepath.endswith("dao.py"):
+                continue
+            if filepath not in sources:
+                raise ValueError(
+                    f"{filepath} not found in {src_txt_path}. check setup.py package_data for outdated inclusion rules."
+                )