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tox.ini
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tox.ini
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[tox]
envlist = py38, py39, py310, py311, bioformats, czi, base-imageio, dv, lif, nd2, omezarr, sldy, bfio, upstreams, lint
skip_missing_interpreters = true
toxworkdir={env:TOX_WORK_DIR:.tox}
[testenv:lint]
skip_install = true
deps = pre-commit
commands = pre-commit run --all-files --show-diff-on-failure
[testenv:bioformats]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
deps =
bioformats_jar
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_bioformats_reader.py {posargs}
[testenv:czi]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
deps =
aicspylibczi>=3.1.1
fsspec>=2022.8.0
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_czi_reader.py {posargs}
[testenv:base-imageio]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
base-imageio
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_default_reader.py aicsimageio/tests/writers/extra_writers/test_timeseries_writer.py aicsimageio/tests/writers/extra_writers/test_two_d_writer.py {posargs}
[testenv:dv]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
dv
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_dv_reader.py {posargs}
[testenv:lif]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
deps = readlif>=0.6.4
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_lif_reader.py {posargs}
[testenv:nd2]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
nd2
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_nd2_reader.py {posargs}
[testenv:sldy]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/sldy_reader/ {posargs}
[testenv:bfio]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
bfio
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_ome_tiled_tiff_reader.py {posargs}
[testenv:omezarr]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_ome_zarr_reader.py {posargs}
[testenv:upstreams]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
deps =
dask @ git+https://github.com/dask/dask@main
distributed @ git+https://github.com/dask/distributed@main
fsspec @ git+https://github.com/fsspec/filesystem_spec@master
s3fs @ git+https://github.com/fsspec/s3fs@main
xarray @ git+https://github.com/pydata/xarray@main
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/ --ignore-glob="**/extra_readers/*" --ignore-glob="**/extra_writers/*" {posargs}
[testenv]
passenv =
AWS_*
JAVA_HOME
CI
setenv =
PYTHONPATH = {toxinidir}
extras =
test
commands =
pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/ --ignore-glob="**/extra_readers/*" --ignore-glob="**/extra_writers/*" {posargs}