Update Nuclei Segmentation - Developing Tribolium Castaneum Embryo - 2D StarDist

bioimageiobot commented 4 months ago

This is an automatic PR created by the @bioimageiobot regarding changes to the resource item 10.5281/zenodo.10406343. The following version(s) will be added:

10491807 (version from 2024-01-11)

Please review the changes and make sure the new item or version(s) pass the following check list:

[ ] Passed the bioimage.io CI tests: static (and dynamic) validations
[ ] The meta information for the RDF item is complete
- [ ] The tags are complete and describe the model
- [ ] Naming is intuitive and descriptive, example: Multi-Organ Nucleus Segmentation (StarDist 2D)
- [ ] Authors are provided
- [ ] Documentation is complete
- For models, include an overview, describe how the model is trained, what is the training data, how to use the model, how to validate the results and list the references. TODO: Model documentation template.
[ ] Approved by at least one of the bioimage.io admin team member.

Maintainers: @cfusterbarcelo

Note: If you updated or re-uploaded another version for the current item on Zenodo, this PR won't be changed automatically. To proceed, you can do the following:

Block this version, but keep looking for future versions: Edit the current resource.yaml and keep the top-level status field as accepted, but change the status under the current version to blocked.
Accept this version and keep looking for future versions: Merge this PR for now.
Keep proposed version(s) (and this resource in general if it is new) as pending: Close this PR without merging.

Then wait for the CI on the main branch to complete. It should detect the new version(s) and create another PR for the new version(s).

Previous PRs of this resource: https://github.com/bioimage-io/collection-bioimage-io/pull/697

bioimageiobot commented 4 months ago

preview

FynnBe commented 4 months ago

the specified conda env failed to install:

channels: [defaults, conda-forge]
dependencies:
- python>=3.7
- bioimageio.core>=0.5.0
- pip
- pip: [stardist>=0.8.5, 'tensorflow>=2.14,<3']
name: '10491807'

from the log it looks like pip install stardist failed with ModuleNotFoundError: No module named 'numpy.distutils'

pip log

Installing pip packages: stardist>=0.8.5, tensorflow>=2.14,<3 Collecting stardist>=0.8.5 (from -r /home/runner/work/collection-bioimage-io/collection-bioimage-io/artifacts/static_validation_artifact/10.5281/zenodo.10406343/10491807/mambaf4GUyYuwTWO (line 1)) Downloading stardist-0.8.5.tar.gz (885 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 885.6/885.6 kB 13.5 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [18 lines of output] Traceback (most recent call last): File "/home/runner/micromamba/envs/10491807/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/home/runner/micromamba/envs/10491807/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/micromamba/envs/10491807/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) ^^^^^^^^^^^^^^^^^^^^^ File "/tmp/pip-build-env-p6n3rrua/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/pip-build-env-p6n3rrua/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-p6n3rrua/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line [311](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/7987134736/job/21809134837?pr=722#step:4:315), in run_setup exec(code, locals()) File "", line 4, in ModuleNotFoundError: No module named 'numpy.distutils' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error × Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output. note: This error originates from a subprocess, and is likely not a problem with pip. critical libmamba pip failed to install packages

FynnBe commented 4 months ago

in https://stackoverflow.com/a/70592872 I found that the fix might be to pin numpy to 1.21.5 (numpy-1.26.3 was installed)

FynnBe commented 4 months ago

so I propose you try to update environment.yaml to

channels: [defaults, conda-forge]
dependencies:
- python>=3.7
- bioimageio.core>=0.5.0
- pip
- numpy==1.21.5  # see https://github.com/bioimage-io/collection-bioimage-io/pull/722#issuecomment-1956302487
- pip: [stardist>=0.8.5, 'tensorflow>=2.14,<3']
name: stardist

bioimage-io / collection-bioimage-io

Update Nuclei Segmentation - Developing Tribolium Castaneum Embryo - 2D StarDist #722