tox.ini

[base]
name = blue_cwl
path = src/blue_cwl
testdeps =
    pytest
    libsonata
    voxcell
    nexusforge
basetemp=tmptestdir/{envname}

minversion = 3.18

[tox]
envlist =
    lint
    docs
    coverage
    check-packaging
    py{310,311,312}

[testenv]
deps = {[base]testdeps}
extras = viz
commands_pre = /bin/mkdir -p {[base]basetemp}
commands = python -m pytest --basetemp=tmptestdir/{envname} tests/unit {posargs}
allowlist_externals =
    /bin/mkdir
    ./tests/functional/certificate.sh


[testenv:functional]
deps =
    {[base]testdeps}
    brainbuilder==0.18.4
passenv =
    NEXUS_TOKEN
    NEXUS_BASE
    NEXUS_ORG
    NEXUS_PROJ
    MODULESHOME
    MODULEPATH
    LOADEDMODULES
    _LMFILES_
setenv =
    NEXUS_BASE = {env:NEXUS_BASE:https://staging.nise.bbp.epfl.ch/nexus/v1}
    NEXUS_ORG = {env:NEXUS_ORG:bbp_test}
    NEXUS_PROJ =  {env:NEXUS_PROJ:studio_data_11}
    SALLOC_ACCOUNT = {env:SALLOC_ACCOUNT:proj30}
commands_pre =
    /bin/mkdir -p {[base]basetemp}
commands = python -m pytest --basetemp=tmptestdir/{envname} tests/functional


[testenv:functional-{nexus_ok,cell_composition,cell_position,placeholder_emodel_assignment,placeholder_morphology_assignment,connectome_placeholder,connectome_filtering}]
deps =
    {[base]testdeps}
    cell_position: brainbuilder==0.18.4
    connectome_distance: connectome-manipulator==0.0.1.dev0
passenv =
    NEXUS_TOKEN
    NEXUS_BASE
    NEXUS_ORG
    NEXUS_PROJ
    USER
    MODULESHOME
    MODULEPATH
    LOADEDMODULES
    _LMFILES_
setenv = 
    NEXUS_BASE = {env:NEXUS_BASE:https://staging.nise.bbp.epfl.ch/nexus/v1}
    NEXUS_ORG = {env:NEXUS_ORG:bbp_test}
    NEXUS_PROJ =  {env:NEXUS_PROJ:studio_data_11}
    MODULEPATH=/gpfs/bbp.cscs.ch/ssd/apps/bsd/modules/_meta
    SALLOC_ACCOUNT = {env:SALLOC_ACCOUNT:proj30}
commands_pre =
    /bin/mkdir -p {[base]basetemp}
commands =
    nexus_ok: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_nexus_ok.py
    cell_composition: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_cell_composition.py
    cell_position: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_cell_position.py
    placeholder_emodel_assignment: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_placeholder_emodel_assignment.py
    connectome_placeholder: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_connectome_generation_placeholder.py
    connectome_filtering: python -m pytest --basetemp=tmptestdir/{envname} tests/functional/test_connectome_filtering_synapses.py

[testenv:check-packaging]
skip_install = true
deps =
    build
    twine
commands =
    python -m build -o {envtmpdir}/dist
    twine check {envtmpdir}/dist/*

[testenv:lint]
deps =
    ruff
    pylint
    mypy
    types-requests
    types-PyYAML
commands =
    ruff format --check {[base]path}
    ruff check {[base]path}
    pylint {[base]path}
    mypy --show-error-codes --ignore-missing-imports {[base]path}

[testenv:format]
deps =
    ruff
commands =
    ruff check --fix --select I {[base]path}
    ruff format {[base]path} tests

[testenv:coverage]
deps =
    {[base]testdeps}
    coverage[toml]
    pytest-cov
extras = viz
commands =
    python -m pytest --cov={[base]name} --basetemp=tmptestdir/{envname} tests/unit {posargs}
    coverage xml
    coverage html

[coverage:run]
# app is tested in functional tests
omit = */blue_cwl/app/*

[testenv:docs]
changedir = doc
extras = docs
commands =
    sphinx-build -b html \
        {toxinidir}/doc/source \
        {toxinidir}/doc/build/html \
        -d {toxinidir}/doc/build/doctrees \
        -W -T
allowlist_externals =
    /bin/mkdir


[pycodestyle]
# E731: do not assign a lambda expression, use a def
# W503: line break after binary operator
# W504: line break before binary operator
# E501: line too long (checked with pylint)
ignore = E731,W503,W504,E501,E203

[pydocstyle]
# D413: no blank line after last section
# D415: First line should end with a period, question mark, or exclamation point
# D417: Missing argument description
add-ignore = D413, D415, D417
convention = google

[gh-actions]
python =
    3.10: py310, lint
    3.11: py311, docs
    3.12: py312, check-packaging