pyproject.toml

# Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/
[build-system]
requires = ["setuptools>=42", "wheel", "versioneer[toml]==0.29", "tomli"]

build-backend = "setuptools.build_meta"

[project]
name = "sophios"
dynamic = ["version"]
authors = [{name = "Jake Fennick", email = "jake.fennick@axleinfo.com"}]
description = "DSL for inferring the edges of a CWL workflow DAG"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
requires-python = ">=3.8"
dependencies = [
    # NOTE: This 'graphviz' refers to the python bindings to the underlying
    # system binary graphviz package (i.e. the `dot` executable) which we need to
    # install separately using either `conda install graphviz` or `sudo apt install graphviz`.
    # This 'graphviz' is equivalent to `conda install python-graphviz` or
    # `sudo apt install python3-graphviz` ONLY.
    "graphviz",
    "jsonschema",
    "pyyaml",
    "requests",
    "mergedeep",
    "networkx",
    "cwl-utils>=0.32",
    # CommandInputParameter attr changed from `type_` to `type` and back to `type_`
    # between versions 0.30, 0.31, 0.32
    # See https://github.com/common-workflow-language/cwl-utils/releases/
    "typeguard",
    "pydantic>=2.6",
    "pydantic-settings",
    "pydantic[email]",
    "docker",
    # FYI also need uidmap to run podman rootless
    "podman",
    # We are using the official release for these packages for now
    "toil[cwl]",
    "fastapi",
    "python-jose",
    "uvicorn",
    "referencing"
]

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

[project.urls]
Homepage = "https://github.com/PolusAI/workflow-inference-compiler"
"Bug Tracker" = "https://github.com/PolusAI/workflow-inference-compiler/issues"

[project.optional-dependencies]

test = [
    "pre-commit",
    "py", # See https://github.com/kevlened/pytest-parallel/pull/119
    "pytest",
    "pytest-cov",
    "pytest-parallel",
    "coverage",
    "mypy",
    "numpy",
    "scipy",
    "pylint",
    "autopep8",
    "pre-commit",
    "hypothesis",
    "hypothesis-jsonschema",
]
# 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
mypy-types = [
    "lxml-stubs",
    "types-Pillow",
    "types-PyYAML",
    "types-Pygments",
    "types-colorama",
    "types-decorator",
    "types-docutils",
    "types-html5lib",
    "types-jsonschema",
    "types-psutil",
    "types-python-jose",
    "types-pytz",
    "types-redis",
    "types-requests",
    "types-setuptools",
    "types-six",
    "types-urllib3",
]
# NOTE: toil and cwltool have a somewhat continuous release model. However,
# there can be updates and bugfixes in main that have not yet been released.
# If you need to install from source, simply run `pip install .[runners-src]`
# This will overwrite the existing release versions, so if you want to revert
# to the release versions, `pip uninstall toil cwltool` and then `pip install .`
# toml language has problem with underscore in array name
runners = [
    "toil[cwl]",
    "cwl-utils",
]
runners-src = [
    "toil[cwl] @ git+https://github.com/sameeul/toil.git",
    "cwltool @ git+https://github.com/sameeul/cwltool.git",
    "cwl-utils @ git+https://github.com/sameeul/cwl-utils.git",
]
# See docs/requirements.txt
doc = [
    "sphinx",
    "myst-parser",
    "sphinx-autodoc-typehints",
]
plots = ["matplotlib"]
cyto = ["ipycytoscape"] # only for DAG visualization
all_except_runner_src = ["sophios[test,doc,plots,cyto,mypy-types]"]
all = ["sophios[test,doc,plots,cyto,runners-src,mypy-types]"]

[project.scripts]
sophios = "sophios.main:main"
cwl_subinterpreter = "sophios.cwl_subinterpreter:main"
cwltool_filterlog = "sophios.run_local:cwltool_main"
# Need an extra entrypoint to avoid mixing up WIC cli flags with cwltool cli flags
cwltool_filterlog_pf = "sophios.run_local:cwltool_main_pf"

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

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

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

[tool.setuptools.package-data]
"*" = ["*.txt"]
"sophios" = ["**/*.json"]

[tool.aliases]
test = "pytest --workers 8"

[tool.versioneer]
VCS = "git"
style = "pep440-pre"
versionfile_source = "src/sophios/_version.py"
versionfile_build = "sophios/_version.py"
tag_prefix = "v"

[tool.build_sphinx]
source_dir = "docs"
# Based on https://packaging.python.org/en/latest/tutorials/packaging-projects/

[tool.mypy]
# See https://docs.pydantic.dev/latest/integrations/mypy/#enabling-the-plugin
plugins = ["pydantic.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 = ["sophios._version", "versioneer"]
ignore_errors = true

[[tool.mypy.overrides]]
module = [
    "graphviz.*",
    "mergedeep.*",
    "networkx.*",
    "matplotlib.*",
    "ipywidgets.*",
    "scipy.*",
    "ruamel.*",
    "toil.*",
    "version.*",
    "podman.*",
]
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 = ""


[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"