pyproject.toml

[tool.poetry]
name = "geoapps"
version = "0.12.0"
license = "MIT"
description = "Open-sourced Applications in Geoscience"
authors = ["Mira Geoscience <support@mirageoscience.com>"]
maintainers = [
    "Benjamin Kary <benjamink@mirageoscience.com>",
    "Dominique Fournier <dominiquef@mirageoscience.com>",
]
repository = "https://github.com/MiraGeoscience/geoapps"
documentation = "https://mirageoscience-geoapps.readthedocs-hosted.com/"
homepage = "https://www.mirageoscience.com/mining-industry-software/python-integration/"
readme = "package.rst"

packages = [
    { include = "geoapps" },
    { include = "geoapps-assets" },
]
exclude = [
    "geoapps-assets/**/*.geoh5",
    "geoapps-assets/uijson/**",
]

include = [
    { path = "COPYING" },
    { path = "COPYING.LESSER" },
    { path = "LICENSE" },
    { path = "README.rst" },
    { path = "THIRD_PARTY_SOFTWARE.rst" },
    { path = "docs/**/THIRD_PARTY_SOFTWARE.rst" },
]

keywords = ["geology", "geophysics", "earth sciences"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Scientific/Engineering :: Physics",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
    "Natural Language :: English",
]

[tool.poetry.scripts]
start_notebook = { callable = "geoapps.scripts.start_notebook:main", extras = ["apps"] }

[tool.poetry.dependencies]
python = "^3.10, < 3.11"

dask = {version = "2024.6.*", extras = ["distributed"]}  # also in simpeg[dask]
discretize = "0.10.*"  # also in simpeg, octree-creation-app
distributed = "2024.6.*"  # because conda-lock doesn't take dask extras into account
fiona = "~1.9.2"
fsspec = "2022.*"  # also in simpeg
gdal = "~3.6.3"
pandas = "~2.2.1"  # also in simpeg
scikit-image = "~0.20.0"
scikit-learn = "~1.4.0"  # also in simpeg
tqdm = "^4.66.1"  # also in las-geoh5
numpy = "~1.26.0" # also in geoh5py, simpeg
notebook = "~7.3.2"
plotly = "~5.19.0"
pydiso = "0.1.*"  # not imported, but required at runtime for simpeg
scipy = "~1.14.0"

## dependencies for UI
#---------------------
dash = "~2.12"  # also in geoapps-utils[dash]
dash-daq = "~0.5.0"
flask = "~3.0.3"  # also in geoapps-utils[dash]
ipyfilechooser = "~0.6.0"
pyqtwebengine = "~5.15.2"  # also in geoapps-utils[dash]
pyside2 = "~5.15.2"  # also in geoapps-utils[dash]

## pip dependencies from Git repositories
#----------------------------------------
geoh5py = {version = ">=0.10.0rc1, <0.11.0a.dev", source = "pypi", allow-prereleases = true}
#geoh5py = {git = "https://github.com/MiraGeoscience/geoh5py.git", rev = "release/0.10.0"}

octree-creation-app = {version = ">=0.2.0rc1, <0.3.0a.dev", source = "pypi", allow-prereleases = true}
#octree-creation-app = {git = "https://github.com/MiraGeoscience/octree-creation-app.git", rev = "release/0.2.0"}

geoapps-utils = {version = ">=0.4.0rc1, <0.5.0a.dev", source = "pypi", allow-prereleases = true}
#geoapps-utils = {git = "https://github.com/MiraGeoscience/geoapps-utils.git", rev = "release/0.4.0"}

mira-simpeg = {version = ">=0.21.2.1rc1, <0.21.2.2a.dev", source="pypi", allow-prereleases = true, extras = ["dask"]}
#mira-simpeg = {git = "https://github.com/MiraGeoscience/simpeg.git", rev = "release/0.21.2.1", extras = ["dask"]}

param-sweeps = {version = ">=0.2.0rc1, <0.3.0a.dev", source = "pypi", allow-prereleases = true}
#param-sweeps = {git = "https://github.com/MiraGeoscience/param-sweeps.git", rev = "release/0.2.0"}

peak-finder-app = {version = ">=0.2.0rc1, <0.3.0a.dev", source = "pypi", allow-prereleases = true}

simpeg-drivers = {version = ">=0.2.0rc1, <0.3.0a.dev", source = "pypi", allow-prereleases = true}
#simpeg-drivers = {url = "https://github.com/MiraGeoscience/simpeg-drivers/archive/refs/heads/release/0.1.1.zip"}
#simpeg-drivers = {url = "http://localhost:8888/simpeg-drivers.tar.gz"}

simpeg-archive = {version = "~0.11.0", source = "pypi", allow-prereleases = true}
#simpeg-archive = {url = "https://github.com/MiraGeoscience/simpeg/archive/refs/heads/feature/simpeg_archive.tar.gz"}


## indirect dependencies, forcing them here for installation through Conda not pip
#---------------------------------------------------------------------------------
Pillow = "~10.3.0"  # from geoh5py
empymod = "~2.2.1"  # from simpeg and geoana
geoana = ">=0.5.0, <0.6.0"  # from simpeg
h5py = "^3.2.1"  # from geoh5py
mkl = "2023.2, <2024.1"  # from simpeg
properties = "~0.6.0"  # from simpeg-archive
pydantic = "^2.5.2"  # from geoapps-utils, octrree-creation-app
pymatsolver = {version = "0.2.*", source = "pypi"}
zarr = "~2.14.2"  # from simpeg[dask], simpeg-drivers

# force some versions to resolve incompatible resolution between PyPI and Conda
#-------------------------------------------------------------------------------
tzdata = "2023.4"  # through pandas from SimPEG (constraint copied from simpeg-drivers)
tbb = { version = "2021.12.*", source = "pypi" }  # through mkl from SimPEG

## about pip dependencies
# to be specified to work with conda-lock
# - from PyPI: my_package = { version = "1.2.3", source = "pypi" }
# - from URL: !!! no actual lock, as tag or branch can move and installation will fetch current !!!
#   - for a tag:   my_package = { url = "https://github.com/ORGANISATION/REPO/archive/refs/tags/TAG.tar.gz" }
#   - for a branch: my_package = { url = "https://github.com/ORGANISATION/REPO/archive/refs/heads/BRANCH.tar.gz" }
# - to actually lock on a revision: my_package = { git = "https://github.com/ORGANISATION/REPO.git", rev = "GIT_REV" }
#   (where rev value is a tag, a branch name or a commit hash). Can also use ``branch`` or ``tag`` instead of ``rev``

[tool.conda-lock.dependencies]
libblas = "*=*mkl"  # because simpeg already brings in the MKL
ipywidgets = ">=8.1.0"
widgetsnbextension = ">=4.0"
jupyterlab = ">=4.3.0"
jupyter_server = ">=2.15.0"
jupyter_client = ">=8.6.0"
matplotlib = ">=3.0.0"  # also in simpeg and geoana

[tool.poetry.group.dev.dependencies]
Pygments = "*"
jupyter-book = "^1.0"
jupytext = "^1.14"
pylint = "*"
pytest = "*"
pytest-cov = "*"
readthedocs-sphinx-ext = "*"
semver = "*"
sphinx = "^5.0"
tomli = "*"

[tool.conda-lock]
platforms = ['win-64', 'linux-64']
channels = ['conda-forge']

[tool.ruff]
target-version = "py310"

[tool.ruff.lint]
ignore = [
    "B028",  # no-explicit-stacklevel for warnings.warn()
    "E501",  # line-too-long - code is reformatted (do not care about comments and docstring)
    "F401",  # unsused-import - covered by pycln
    "A005", # TO DO (stdlib-module-shadowing: Module shadows a Python standard-library module)
    "RUF005", # TO DO
    "B007", # TO DO
    "B011", # TO DO
    "B904", # TO DO
    "C408", # TO DO
    "C414", # TO DO
    "C416", # TO DO
    "C419", # TO DO
    "C901", # TO DO
    "RUF005",  # collection-literal-concatenation - wrong suggestion with numpy arrays
    "RUF012", # TO DO
    "RUF013", # TO DO
    "RUF015", # TO DO
    "UP038", # TO DO
    "TID252", # TO DO
]
select = [
    "A",  # flake8-builtins
    "B",  # flake8-bugbear
    "B006",  # Do not use mutable data structures for argument defaults
    "B9",  # flake8-bugbear opiniated warnings
    "BLE",  # flake8-blind-except
    "C4",  # flake8-comprehensions
    "C9",  # mccabe
    "E",  # pycodestyle errors
    "F",  # pyflakes
    "I",  # isort
    "RUF",  # ruff rules
    "TID", # flake8-tidy-imports
    "UP",  # pyupgrade
    "W",  # pycodestyle warnings
]

[tool.ruff.lint.mccabe]
max-complexity = 18

[tool.ruff.lint.isort]
lines-after-imports = 2

[tool.ruff.format]
# default formatting is just fine

[tool.mypy]
warn_unused_configs = true
ignore_missing_imports = true
scripts_are_modules = true
show_error_context = true
show_column_numbers = true
check_untyped_defs = true

plugins = [
    'numpy.typing.mypy_plugin'
]

[tool.pytest.ini_options]
#addopts =

[tool.coverage.run]
branch = true
source = ["geoapps"]
omit = []

[tool.coverage.report]
exclude_lines = [
    "raise NotImplementedError",
    "pass",
    "if TYPE_CHECKING",
    "pragma: no cover"
]

fail_under = 35

[tool.coverage.html]
skip_empty = true
skip_covered = true

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