pyproject.toml

[tool.poetry]
name = "nexusLIMS"
version = "1.4.3"
description = "The NIST Electron Microscopy Nexus LIMS project"
authors = ["Joshua Taillon <joshua.taillon@nist.gov>"]
maintainers = ["Joshua Taillon <joshua.taillon@nist.gov>"]
readme = "README.md"
repository = "https://github.com/usnistgov/NexusLIMS.git"
documentation = "http://pages.nist.gov/NexusLIMS"
license = "NIST Public License"
# necessary if we want to have a package name with capitals... see
#  https://github.com/python-poetry/poetry/issues/1538#issuecomment-555753130
packages = [
    {include = "nexusLIMS"}
]

[tool.poetry.dependencies]
python = ">=3.8.1,<3.11"
lxml = "^4.9.2"
requests = "^2.28.1"
requests_ntlm = "^1.1.0"
pytz = "^2022.7"
hyperspy = "1.7.3"
scikit-learn = "^1.2.0"
python-dotenv = "^0.21.0"
defusedxml = "^0.7.1"

[tool.poetry.dev-dependencies]
pytest = "^7.2"
coverage = "^7.0.0"
pytest-mpl = "^0.16.1"
pytest-cov = "^4.0.0"
Sphinx = "^4.3.1"
sphinx-bootstrap-theme = "^0.8.0"
tox = "^4.0"

[tool.poetry.scripts]


[tool.poetry.group.dev.dependencies]
black = "^23.1.0"
isort = "^5.12.0"
pylint = "^2.16.4"
ruff = "^0.0.259"
sphinxcontrib-towncrier = "^0.3.2a0"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.isort]
profile = "black"
src_paths = ["nexusLIMS", "tests"]

[tool.pylint.format]
max-line-length = "88"
good-names = ["f", "i", "j", "k", "v", "s"]
ignore-long-lines = "^\\s*(# |\\.\\. _.*: |``/feed)(<?https?://\\S+>|\\S+)?$"

[tool.pylint.Main]
extension-pkg-allow-list = ["lxml"]

[tool.pylint.MASTER]
init-hook="from pylint.config import find_default_config_files; import os, sys; sys.path.append(os.path.dirname(next(find_default_config_files())))"
ignore="dev_scripts"

[tool.pylint."MESSAGES CONTROL"]
disable = "locally-disabled"

[tool.ruff]
select = [
    "F", "E", "W", "I", "N", "D", "YTT", "UP", "S", "FBT", "B", "A", "COM", "C4",
    "DTZ", "T10", "EM", "EXE", "ISC", "ICN", "G", "INP", "PIE", "T20", "PYI",
    "PT", "Q", "RSE", "RET", "SLF", "SIM", "TID", "TCH", "ARG", "PTH", "ERA", "PL",
    "TRY", "RUF"
]
ignore = ["N999", "UP006", "UP007", "UP035", "B905", "RUF007"]

[tool.ruff.per-file-ignores]
"tests/*" = ["S"]

[tool.ruff.pydocstyle]
convention = "numpy"

[tool.towncrier]
directory = "docs/changes"
package = "nexusLIMS"
package_dir = "nexusLIMS"
title_format = "v{version} ({project_date})"
filename = "docs/development_log.rst"
issue_format = "`#{issue} <https://gitlab.nist.gov/gitlab/nexuslims/NexusMicroscopyLIMS/-/issues/{issue}>`_"

[[tool.towncrier.type]]
directory = "feature"
name = "New features"
showcontent = true

[[tool.towncrier.type]]
directory = "bugfix"
name = "Bug fixes"
showcontent = true

[[tool.towncrier.type]]
directory = "enhancement"
name = "Enhancements"
showcontent = true

[[tool.towncrier.type]]
directory = "doc"
name = "Documentation improvements"
showcontent = true

[[tool.towncrier.type]]
directory = "misc"
name = "Miscellaneous/Development changes"
showcontent = true

[[tool.towncrier.type]]
directory = "removal"
name = "Deprecations and/or Removals"
showcontent = true

[tool.tox]
legacy_tox_ini = """
[tox]
isolated_build = true
envlist = 
    lint
    py{38, 39, 310}

[testenv]
passenv = *
allowlist_externals = poetry
commands = 
    poetry install
    poetry run pytest tests/ --cov=nexusLIMS --cov=tests \
        --cov-config=tests/.coveragerc \
        --cov-report html:tests/coverage \
        --cov-report term-missing \
        --junitxml=tests/test_report.xml \
        --mpl --mpl-baseline-path=tests/files/figs

[testenv:gen_mpl_baseline]
passenv = *
description = use pytest-mpl to generate baseline figures for comparison
commands = 
    poetry install
    poetry run pytest tests/test_extractors.py \
        -k TestThumbnailGenerator \
        --mpl-generate-path=tests/files/figs

[testenv:docs]
passenv = *
description = invoke sphinx-build to build the HTML docs
commands = 
    poetry install
    poetry run python -m sphinx.cmd.build ./docs ./_build -n -E -a -j auto -b html

[testenv:lint]
passenv = *
description = run liniting scripts
commands = 
    poetry install
    poetry run isort . --check-only
    poetry run black --check .
    poetry run ruff check nexusLIMS tests
    poetry run pylint nexusLIMS tests
"""