v0.16.0

[jwindhager]

• Version upgrades
  • CellProfiler
  • GitHub actions workflows
  • Python dependencies, including readimc, xtiff, deepcell, tensorflow
• New features
  • napari #27
  • Mask expansion #106
  • Xpra-enabled Docker images
  • Cellpose-enabled Docker images #118
  • Jupyter Notebook, Jupyter Lab
• Multi-stage Dockerfile
  • Single requirements.txt
  • Separate venvs for steinbock and CellProfiler
  • Prepared for tensorflow-enabled arm64-based image #98
  • Only run fixuid when $RUN_FIXUID is set #156
• Minor bugfixes and improvements, including:
  • Capture stderr of subprocesses
  • Improved packaging (pyproject.toml, setup.cfg)
  • Fix missing error message #151
• Development environment
  • Pre-commit hooks
  • Black-compatible configuration
• Updated test skeletons #95
• Documentation updates, including
  • Improved mkdocs configuration
  • Rename "framework" to "toolkit"
  • Updated installation instructions #160

[codecov-commenter]

Codecov Report

Base: 32.61% // Head: 30.65% // Decreases project coverage by -1.97% :warning:

Coverage data is based on head (c050e87) compared to base (f05cfe5). Patch coverage: 10.57% of modified lines in pull request are covered.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #164 +/- ## ========================================== - Coverage 32.61% 30.65% -1.97% ========================================== Files 60 66 +6 Lines 2287 2512 +225 ========================================== + Hits 746 770 +24 - Misses 1541 1742 +201 ``` | [Impacted Files](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup) | Coverage Δ | | |---|---|---| | [steinbock/\_cli/\_cli.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL19jbGkvX2NsaS5weQ==) | `0.00% <0.00%> (ø)` | | | [steinbock/\_cli/apps.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL19jbGkvYXBwcy5weQ==) | `0.00% <0.00%> (ø)` | | | [steinbock/\_cli/utils.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL19jbGkvdXRpbHMucHk=) | `0.00% <ø> (ø)` | | | [steinbock/\_cli/visualization.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL19jbGkvdmlzdWFsaXphdGlvbi5weQ==) | `0.00% <0.00%> (ø)` | | | [steinbock/classification/\_cli/ilastik.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL2NsYXNzaWZpY2F0aW9uL19jbGkvaWxhc3Rpay5weQ==) | `0.00% <0.00%> (ø)` | | | [steinbock/export/\_cli/\_cli.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL2V4cG9ydC9fY2xpL19jbGkucHk=) | `0.00% <0.00%> (ø)` | | | [steinbock/export/\_cli/data.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL2V4cG9ydC9fY2xpL2RhdGEucHk=) | `0.00% <0.00%> (ø)` | | | [steinbock/export/data.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL2V4cG9ydC9kYXRhLnB5) | `74.35% <0.00%> (ø)` | | | [steinbock/export/graphs.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL2V4cG9ydC9ncmFwaHMucHk=) | `90.62% <0.00%> (ø)` | | | [steinbock/measurement/\_cli/cellprofiler.py](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup#diff-c3RlaW5ib2NrL21lYXN1cmVtZW50L19jbGkvY2VsbHByb2ZpbGVyLnB5) | `0.00% <0.00%> (ø)` | | | ... and [24 more](https://codecov.io/gh/BodenmillerGroup/steinbock/pull/164?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BodenmillerGroup)

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