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Models still included in manifest #48

Open FynnBe opened 1 year ago

FynnBe commented 1 year ago

Hi there, there are still models in the manifest file, that should be transfered to Zenodo: https://github.com/deepimagej/models/blob/6259f76df55ae002d50cd19d1bd23333a2230aed/manifest.bioimage.io.yaml#L183-L262

FynnBe commented 1 year ago

related issues: https://github.com/deepimagej/models/issues/47, https://github.com/bioimage-io/bioimage.io/issues/308

FynnBe commented 1 year ago

some of these models do not pass static validation:

log output ``` [[{'bioimageio_spec_version': '0.4.9', 'error': {'_schema': ['Minimal shape [ 1. 32. 32. 1.] of output output is too small for halo [0, 97, 97, 0].']}, 'id': 'validation_summary_latest_static', 'name': 'bioimageio.spec static validation of RDF with update to latest format version', 'nested_errors': {}, 'source_name': '/home/runner/work/collection-bioimage-io/collection-bioimage-io/scripts/../gh-pages/rdfs/deepimagej/MU-Lux_CTC_PhC-C2DL-PSC/latest/rdf.yaml', 'status': 'failed', 'traceback': None, 'warnings': {'name': "Unrecognized run mode 'deepimagej'", 'tags': "Missing tags corresponding to bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'framework': " "['tensorflow', 'pytorch', 'tensorflow.js']}, {'network': ['unet', 'densenet', 'resnet', " "'inception', 'shufflenet']}, {'task': ['semantic-segmentation', 'instance-segmentation', " "'object-detection', 'image-classification', 'denoising', 'image-restoration', " "'image-reconstruction', 'in-silico-labeling']}]", 'weights': {'keras_hdf5': "missing 'tensorflow_version' entry for weights format keras_hdf5"}}}], [{'bioimageio_spec_version': '0.4.9', 'error': {'_schema': ['Minimal shape [ 1. 20. 20. 1.] of output output is too small for halo [0, 10, 10, 0].']}, 'id': 'validation_summary_latest_static', 'name': 'bioimageio.spec static validation of RDF with update to latest format version', 'nested_errors': {}, 'source_name': '/home/runner/work/collection-bioimage-io/collection-bioimage-io/scripts/../gh-pages/rdfs/deepimagej/SMLMDensityMapEstimationDEFCoN/latest/rdf.yaml', 'status': 'failed', 'traceback': None, 'warnings': {'tags': "Missing tags corresponding to bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'task': " "['semantic-segmentation', 'instance-segmentation', 'object-detection', " "'image-classification', 'denoising', 'image-restoration', 'image-reconstruction', " "'in-silico-labeling']}]", 'weights': {'tensorflow_js': "missing 'tensorflow_version' entry for weights format tensorflow_js"}}}], [{'bioimageio_spec_version': '0.4.9', 'error': {'license': ['Must be one of: bzip2-1.0.6, Glulxe, Parity-7.0.0, OML, UCL-1.0, UPL-1.0, BSD-Protection, ' 'OCLC-2.0, eCos-2.0, Multics, IPL-1.0, IPA, eGenix, Glide, Entessa, FSFUL, Nunit, ' 'MPL-2.0-no-copyleft-exception, libpng-2.0, OLDAP-2.2.1, curl, ANTLR-PD, CC-BY-SA-2.0, ' 'LiLiQ-P-1.1, TCP-wrappers, Unicode-DFS-2016, ODbL-1.0, LPPL-1.3a, CERN-OHL-1.2, ADSL, ' 'CDDL-1.0, Motosoto, BUSL-1.1, OGL-UK-1.0, xinetd, Imlib2, SNIA, OGTSL, TMate, OCCT-PL, ' 'GPL-1.0-or-later, YPL-1.1, CECILL-2.0, PHP-3.0, BlueOak-1.0.0, Zimbra-1.3, OGC-1.0, ' 'NASA-1.3, SPL-1.0, Intel-ACPI, SISSL-1.2, OGL-Canada-2.0, CC-BY-3.0-US, copyleft-next-0.3.1, ' 'GFDL-1.1-invariants-or-later, GL2PS, MS-PL, SCEA, CC-BY-ND-2.5, SSPL-1.0, Spencer-86, ' 'LPPL-1.0, GPL-3.0-only, GPL-2.0-with-autoconf-exception, Giftware, CC-BY-NC-ND-3.0, ' 'CNRI-Python, GFDL-1.2-no-invariants-or-later, Afmparse, BSD-3-Clause-LBNL, NCGL-UK-2.0, ' 'GPL-1.0+, 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OLDAP-2.4, PostgreSQL, Net-SNMP, Ruby, OSET-PL-2.1, Dotseqn, CUA-OPL-1.0, ' 'Bahyph, LiLiQ-Rplus-1.1, LGPL-2.0+, wxWindows, AGPL-3.0, Abstyles, OLDAP-1.3, NTP-0, ' 'OLDAP-2.2, CC-BY-SA-3.0, SWL, BSD-3-Clause-Open-MPI, LGPL-2.1+, GFDL-1.2-invariants-only, ' 'Zend-2.0, GFDL-1.1-no-invariants-or-later, mpich2, NLOD-1.0, gnuplot, CERN-OHL-S-2.0, ' 'OGL-UK-2.0, NPL-1.1, Zed, VOSTROM, ZPL-2.0, CERN-OHL-W-2.0, CC-BY-NC-SA-2.0, APSL-2.0, ' 'LPL-1.0, ANTLR-PD-fallback, libtiff, HPND, GPL-3.0-or-later, Artistic-2.0, Unicode-DFS-20[15](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:16), ' 'CC-BY-NC-4.0, RPL-1.1, CC-BY-SA-1.0, Cube, ODC-By-1.0, copyleft-next-0.3.0, CC-BY-ND-4.0, ' 'ZPL-1.1, GFDL-1.3-or-later, CATOSL-1.1, GPL-2.0-with-classpath-exception, LGPL-2.0, ' 'BSD-2-Clause-Views, BSL-1.0, CNRI-Jython, Eurosym, CC-BY-SA-3.0-AT, CECILL-C, EPICS, ' 'CC-BY-NC-ND-2.0, GD, X11, MPL-1.1, GFDL-1.1-invariants-only, psfrag, RSCPL, YPL-1.0, ' 'SGI-B-1.1, CC-BY-ND-1.0, SGI-B-2.0, APAFML, Spencer-94, ISC, MIT-advertising, ' 'GFDL-1.2-invariants-or-later, CC-BY-NC-SA-2.5, CC-BY-1.0, OSL-2.1, CrystalStacker, FSFULLR, ' 'libselinux-1.0, MulanPSL-2.0, LGPL-3.0, OLDAP-2.5, Artistic-1.0-Perl, AFL-1.2, CAL-1.0, ' 'BSD-4-Clause, Interbase-1.0, NPOSL-3.0.']}, 'id': 'validation_summary_latest_static', 'name': 'bioimageio.spec static validation of RDF with update to latest format version', 'nested_errors': {}, 'source_name': '/home/runner/work/collection-bioimage-io/collection-bioimage-io/scripts/../gh-pages/rdfs/deepimagej/SkinLesionClassification/latest/rdf.yaml', 'status': 'failed', 'traceback': None, 'warnings': {'license': 'BSD2 is not a recognized SPDX license identifier. See https://spdx.org/licenses/', 'name': "Unrecognized run mode 'deepimagej'", 'tags': "Missing tags corresponding to bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'network': " "['unet', 'densenet', 'resnet', 'inception', 'shufflenet']}, {'task': " "['semantic-segmentation', 'instance-segmentation', 'object-detection', " "'image-classification', 'denoising', 'image-restoration', 'image-reconstruction', " "'in-silico-labeling']}]"}}], [{'bioimageio_spec_version': '0.4.9', 'error': {'license': ['Must be one of: bzip2-1.0.6, Glulxe, Parity-7.0.0, OML, UCL-1.0, UPL-1.0, BSD-Protection, ' 'OCLC-2.0, eCos-2.0, Multics, IPL-1.0, IPA, eGenix, Glide, Entessa, FSFUL, Nunit, ' 'MPL-2.0-no-copyleft-exception, libpng-2.0, OLDAP-2.2.1, curl, ANTLR-PD, CC-BY-SA-2.0, ' 'LiLiQ-P-1.1, TCP-wrappers, Unicode-DFS-20[16](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:17), ODbL-1.0, LPPL-1.3a, CERN-OHL-1.2, ADSL, ' 'CDDL-1.0, Motosoto, BUSL-1.1, OGL-UK-1.0, xinetd, Imlib2, SNIA, OGTSL, TMate, OCCT-PL, ' 'GPL-1.0-or-later, YPL-1.1, CECILL-2.0, PHP-3.0, BlueOak-1.0.0, Zimbra-1.3, OGC-1.0, ' 'NASA-1.3, SPL-1.0, Intel-ACPI, SISSL-1.2, OGL-Canada-2.0, CC-BY-3.0-US, copyleft-next-0.3.1, ' 'GFDL-1.1-invariants-or-later, GL2PS, MS-PL, SCEA, CC-BY-ND-2.5, SSPL-1.0, Spencer-86, ' 'LPPL-1.0, GPL-3.0-only, GPL-2.0-with-autoconf-exception, Giftware, CC-BY-NC-ND-3.0, ' 'CNRI-Python, GFDL-1.2-no-invariants-or-later, Afmparse, BSD-3-Clause-LBNL, NCGL-UK-2.0, ' 'GPL-1.0+, PHP-3.01, Leptonica, 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'warnings': {'license': 'BSD-2 is not a recognized SPDX license identifier. See https://spdx.org/licenses/', 'tags': "Missing tags corresponding to bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'framework': " "['tensorflow', 'pytorch', 'tensorflow.js']}, {'network': ['unet', 'densenet', 'resnet', " "'inception', 'shufflenet']}, {'task': ['semantic-segmentation', 'instance-segmentation', " "'object-detection', 'image-classification', 'denoising', 'image-restoration', " "'image-reconstruction', 'in-silico-labeling']}]", 'weights': {'tensorflow_js': "missing 'tensorflow_version' entry for weights format tensorflow_js"}}}], 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bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'framework': " "['tensorflow', 'pytorch', 'tensorflow.js']}, {'network': ['unet', 'densenet', 'resnet', " "'inception', 'shufflenet']}, {'task': ['semantic-segmentation', 'instance-segmentation', " "'object-detection', 'image-classification', 'denoising', 'image-restoration', " "'image-reconstruction', 'in-silico-labeling']}]"}}], [{'bioimageio_spec_version': '0.4.9', 'error': {'license': ['Must be one of: bzip2-1.0.6, Glulxe, Parity-7.0.0, OML, UCL-1.0, UPL-1.0, BSD-Protection, ' 'OCLC-2.0, 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See https://spdx.org/licenses/', 'tags': "Missing tags corresponding to bioimage.io categories: [{'modality': ['electron-microscopy', " "'cryo-electron-microscopy', 'fluorescence-light-microscopy', 'transmission-light-microscopy', " "'super-resolution-microscopy', 'x-ray-microscopy', 'force-microscopy', " "'high-content-imaging', 'whole-slide-imaging', 'other']}, {'dims': ['2d', '3d', '2d-t', " "'3d-t']}, {'content': ['cells', 'nuclei', 'extracellular-vesicles', 'tissue', 'plant', " "'mitochondria', 'vasculature', 'cell-membrane', 'brain', 'whole-organism']}, {'framework': " "['tensorflow', 'pytorch', 'tensorflow.js']}, {'network': ['unet', 'densenet', 'resnet', " "'inception', 'shufflenet']}, {'task': ['semantic-segmentation', 'instance-segmentation', " "'object-detection', 'image-classification', 'denoising', 'image-restoration', " "'image-reconstruction', 'in-silico-labeling']}]"}}], ```
FynnBe commented 1 year ago

@esgomezm @ivan-ea @IvanHCenalmor could someone please take care of this. Having the failing models spam the CI logs in PRs is quite the nuisance. A first step could be to fix the model errors (in github) or remove them from the manifest.bioimage.io.yaml (then they would also disappear from the website though).

FynnBe commented 1 year ago

I fixed one model to get you started: https://github.com/deepimagej/models/pull/49

ivan-ea commented 1 year ago

@esgomezm @ivan-ea @IvanHCenalmor could someone please take care of this. Having the failing models spam the CI logs in PRs is quite the nuisance. A first step could be to fix the model errors (in github) or remove them from the manifest.bioimage.io.yaml (then they would also disappear from the website though).

I think it could be ok to remove these models from the manifest. I've also encountered this problem in the DeepImageJ CI, since I'm using the bioimageio.core library to generate the tiff files, and for some models the function load_resource_description throws error. In the future I could fix these models and try to upload them to zenodo. Nevertheless I would like to know what @esgomezm thinks about the models disappearing from the website.