continue (attempting to) fix setup and github workflows

.github/workflows/testing.yml

@@ -26,12 +26,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install --quiet -r requirements.txt -r requirements-ci.txt
+        pip install --quiet -r requirements.txt -r requirements-dev.txt
         pip install -e .
     - name: pytest
       run: |
         pytest --cov=pymatgen --cov-report=xml
-        
+
     - uses: codecov/codecov-action@v1
       if: matrix.python-version == 3.10
       with:

.gitignore

@@ -1,22 +1,139 @@
-.DS_Store
-*.egg-info
-*.o
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
 *.so
-*.pyc
-*.swp
-*.swo
-dist
-_build
-build
-.project
-.pydevproject
-.settings
-.externalToolBuilders
-.idea
-setuptools*
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
 .ipynb_checkpoints
-.tox
 
-pymatgen/\.vscode/
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm settings
+.idea*
+.DS_store
+.log
+
+docs_build
+examples/wip*
 
 .vscode/

pyproject.toml

@@ -1,21 +1,110 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools >= 65.0.0", "versioningit ~= 1.0", "wheel"]
+
+[project]
+authors = [
+  { name = "Matthew Kuner", email = "[email protected]" },
+  { name = "Janosh Riebesell"},
+  { name = "Jason Munro"},
+  { name = "Aaron Kaplan"},
+]
+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",
+  "Operating System :: OS Independent",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Information Analysis",
+  "Topic :: Scientific/Engineering :: Physics",
+  "Topic :: Scientific/Engineering :: Chemistry",
+  "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dependencies = [
+  "pymatgen",
+  "numpy"
+]
+description = "A comprehensive I/O validator for electronic structure calculations"
+dynamic = ["version"]
+keywords = ["io", "validation", "dft", "vasp"]
+license = { text = "modified BSD" }
+name = "pymatgen-io-validation"
+readme = "README.rst"
+requires-python = '>=3.8'
+
+[project.optional-dependencies]
+dev = ["pre-commit>=2.12.1"]
+#docs = ["jupyter-book>=0.13.1",]
+
+
+tests = ["pytest==7.4.2", "pytest-cov==4.1.0"]
+
+
+[tool.setuptools.dynamic]
+readme = { file = ["README.rst"] }
+
+#[project.urls]
+#repository = "https://github.com/materialsproject/pymatgen-io-validation"
+
+[tool.setuptools.packages.find]
+exclude = ["tests"]
+where = ["./"]
+
+[tool.versioningit.vcs]
+default-tag = "0.0.1"
+method = "git"
+
+[tool.isort]
+profile = "black"
+
 [tool.black]
 line-length = 120
-target-version = ['py38']
-include = '\.pyi?$'
-exclude = '''
-
-(
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-)
-'''
+
+[tool.blacken-docs]
+line-length = 120
+
+[tool.flake8]
+extend-ignore = "E203, W503, E501, F401, RST21"
+max-line-length = 120
+max-doc-length = 120
+min-python-version = "3.8.0"
+rst-roles = "class, func, ref, obj"
+select = "C, E, F, W, B, B950"
+
+[tool.mypy]
+ignore_missing_imports = true
+no_strict_optional = true
+
+[tool.coverage.run]
+branch = true
+include = ["pymatgen/*"]
+parallel = true
+
+[tool.coverage.paths]
+source = ["pymatgen/"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+
+[tool.pydocstyle]
+convention = 'google'
+match = '^pymatgen/(?!_).*\.py'
+inherit = false
+add-ignore = "D107, "
+
+[tool.autoflake]
+in-place = true
+remove-unused-variables = true
+remove-all-unused-imports = true
+expand-star-imports = true
+ignore-init-module-imports = true
+
+
+[tool.setuptools.packages.find]
+exclude = ["tests"]
+where = ["./"]

requirements.txt

@@ -1 +1,9 @@
-pymatgen==2022.4.19
+pymatgen==2023.10.11
+emmet-core==0.72.7
+pydantic==2.4.2
+pydantic-core==2.10.1
+pydantic-settings==2.0.3
+typing-extensions==4.8.0
+monty==2023.9.25
+numpy==1.26.1
+requests==2.31.0