pyproject.toml

# Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/
[build-system]
requires = ["jupyter_packaging~=0.7.9", "setuptools>=42,<68", "wheel", "versioneer[toml]==0.29"]
# NOTE: The above list mostly comes from https://github.com/nglviewer/nglview/pull/969/files
# NOTE: Use upper bound of <68 for setuptools due to 2to3 error.
# See https://stackoverflow.com/questions/72414481/error-in-anyjson-setup-command-use-2to3-is-invalid

build-backend = "setuptools.build_meta"

[project]
name = "mm-workflows"
dynamic = ["version"]
authors = [{name = "Jake Fennick", email = "jake.fennick@axleinfo.com"}]
description = "Molecular modeling workflows"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
requires-python = ">=3.8"
dependencies = [
    "requests",
    "beautifulsoup4", # Solely for parsing gromacs mdp options html
]

[project.readme]
file = "README.md"
content-type = "text/markdown"

[project.urls]
Homepage = "https://github.com/PolusAI/mm-workflows"
"Bug Tracker" = "https://github.com/PolusAI/mm-workflows/issues"

[project.optional-dependencies]

test = [
    "pre-commit",
    "mypy",
    "pylint",
    "autopep8",
]
# NOTE: The following list was generated using the command
# mypy --install-types
# When updating this list, also update .pre-commit-config.yaml
# Alternatively, the --non-interactive flag can be used install these automatically.
# See https://mypy.readthedocs.io/en/stable/command_line.html#miscellaneous
# toml language has problem with underscore in array name
mypy-types = [
    "pandas-stubs",
    "types-beautifulsoup4",
    "types-requests",
    "types-openpyxl",
    "types-pyyaml",
]

workflow-deps = [
    "matplotlib",
    "pandas",
    "numpy>=1.21.0",
    "mdanalysis",
    "nmrformd",
    "mdanalysis",
    "mdtraj",
    "rdkit",
    "pymol",
    "pdbfixer @ git+https://github.com/openmm/pdbfixer.git",
    "openmm",
]
# See docs/requirements.txt
doc = [
    "sphinx",
    "myst-parser",
    "sphinx-autodoc-typehints",
    "ipytree",
]

all = ["mm-workflows[test,workflow-deps,doc,mypy-types]"]

[project.scripts]
mm-workflows = "mm_workflows.main:main"

# Need the following defined in order to make versioneer work with git tags
[tool.setuptools.dynamic]
version = {attr = "mm_workflows.__version__"}

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = false

[tool.setuptools.packages.find]
where = ["src"]
namespaces = false

[tool.versioneer]
VCS = "git"
style = "pep440-pre"
versionfile_source = "src/mm_workflows/_version.py"
versionfile_build = "mm_workflows/_version.py"
tag_prefix = "''"
# Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/

[tool.mypy]
# See https://mypy.readthedocs.io/en/stable/running_mypy.html#follow-imports
follow_imports = "normal"

# Specifies the paths to use, after trying the paths from MYPYPATH environment variable.
# mypy_path = ''

# NOTE: mypy requires __init__.py files and/or namespace_packages = True. Otherwise, you will get
# "error: Cannot find implementation or library stub for module named 'module'"
namespace_packages = true

# Disallows defining functions without type annotations or with incomplete type annotations.
disallow_untyped_defs = true
# Disallows defining functions with incomplete type annotations.
disallow_incomplete_defs = true
# Type-checks the interior of functions without type annotations.
check_untyped_defs = true

# Warns about casting an expression to its inferred type.
warn_redundant_casts = true
# Warns about unneeded `# type: ignore` comments.
warn_unused_ignores = true
# Shows a warning when returning a value with type Any from a function declared with a non-Any return type.
warn_return_any = true

# A regular expression that matches file names, directory names and paths which
# mypy should ignore while recursively discovering files to check.
# Note that if you want to exclude multiple regexes, you have to concatenate
# them with |, and sometimes it doesn't even work. It is much easier to
# just use the [mypy-*] notation below with ignore_errors = True
# exclude =

# Allows disabling one or multiple error codes globally.
# disable_error_code = ["ignore-missing-imports"] # comma-separated list of strings

# Disallows usage of generic types that do not specify explicit type parameters.
# disallow_any_generics = False # NOTE: This one tends to generate a medium number of warnings, so enable with caution.

# Disallows all expressions in the module that have type Any.
# disallow_any_expr = False # NOTE: This one tends to generate a MASSIVE number of warnings, so enable with caution.

# Ignores all non-fatal errors.
ignore_errors = false

# Probably because it is in the root directory, I was unable to add
# versioneer to the exclude=regex above, but this works.

[[tool.mypy.overrides]]
module = ["BioSimSpace.*", "MDAnalysis.*", "pymol.*", "rdkit.*", "nmrformd.*", "setuptools.*", "parmed.*", "pdbfixer.*", "openmm.*", "mdtraj.*", "nglview.*", "ipytree.*", "ipywidgets.*"]
ignore_missing_imports = true


[tool.pytest.ini_options]
markers = [
    "fast: (i.e. for maximum speed, use 'pytest -m fast')",
    "slow: (i.e. for medium speed, use 'pytest -m \"not slow\"')",
    "serial: (These tests CANNOT be run in parallel with --workers n > 1)",
]
addopts = "--maxfail=2"
# Exit after first num failures or errors


[tool.codespell]
skip = "*.svg,*.html"
ignore-words = "codespellwords.txt"

# See https://pylint.pycqa.org/en/latest/user_guide/configuration/all-options.html

[tool.pylint.main]

# TODO: Add class and module docstrings.
disable=[
        "missing-class-docstring",
        "missing-module-docstring",
        "dangerous-default-value",
        "pointless-string-statement",
        "unused-variable",
        "fixme",
        "invalid-name",
    ]

# Specify a score threshold to be exceeded before program exits with error.
# Try to keep the threshold near the default of a perfect 10/10.
# However, for some reason, on github actions CI/CD the scores are slightly
# lower and fails, so let's use 9.25 instead of 9.50 for now.
fail-under=9.25

[tool.pylint.format]

# Regexp for a line that is allowed to be longer than the limit.
ignore-long-lines='^\s*(# )?(See )?(and )?<?https?://\S+>?$'

# Maximum number of characters on a single line.
max-line-length=120

# Maximum number of lines in a module.
max-module-lines=750

[tool.pylint.miscellaneous]

# List of note tags to take in consideration, separated by a comma.
notes="FIXME,XXX,TODO"