Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Models still included in manifest #48

Open
FynnBe opened this issue Mar 22, 2023 · 5 comments
Open

Models still included in manifest #48

FynnBe opened this issue Mar 22, 2023 · 5 comments

Comments

@FynnBe
Copy link
Contributor

FynnBe commented Mar 22, 2023

Hi there,
there are still models in the manifest file, that should be transfered to Zenodo:

models/manifest.bioimage.io.yaml

Lines 183 to 262 in 6259f76

# ==================models====================
- id: UNet2DHeLaSegmentation
type: model
rdf_source: u-net_hela_segmentation/model.yaml
links:
- deepimagej
- imjoy/BioImageIO-Packager
download_url: https://zenodo.org/record/6827059/files/deepimagej_hela_unet_segmentation.zip
- id: UNet2DGlioblastomaSegmentation
type: model
rdf_source: u-net_glioblastoma_segmentation/model.yaml
download_url: https://zenodo.org/record/4155785/files/deepimagej_u-net_glioblastoma_segmentation.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: SMLMDensityMapEstimationDEFCoN
type: model
rdf_source: defcon_density_map_estimation/model.yaml
download_url: https://zenodo.org/record/4608442/files/SMLM_Density%20Map_Estimation_%28DEFCoN%29.bioimage.io.model.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: DeepSTORMZeroCostDL4Mic
type: model
rdf_source: deepstorm_zerocostdl4mic/model.yaml
download_url: https://sandbox.zenodo.org/record/907832/files/bioimage.io.model.zip
links:
- zero/Notebook_Deep-STORM_2D_ZeroCostDL4Mic_DeepImageJ
- deepimagej
- imjoy/BioImageIO-Packager
- id: MU-Lux_CTC_PhC-C2DL-PSC
type: model
rdf_source: mu-lux_ctc_phc-c2dl-psc/model.yaml
download_url: https://sandbox.zenodo.org/record/914413/files/mu-lux_ctc_phc-c2dl-psc.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: WidefieldTxredSuperResolution
type: model
rdf_source: widefield_txred_super-resolution/model.yaml
download_url: https://sandbox.zenodo.org/record/913992/files/widefield_txred_super-resolution.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: WidefieldDapiSuperResolution
type: model
rdf_source: widefield_dapi_super-resolution/model.yaml
download_url: https://sandbox.zenodo.org/record/914422/files/widefield_dapi_super-resolution.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: WidefieldFitcSuperResolution
type: model
rdf_source: widefield_fitc_super-resolution/model.yaml
download_url: https://sandbox.zenodo.org/record/914425/files/widefield_fitc_super-resolution.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: Mt3VirtualStaining
type: model
rdf_source: mt3_virtual_staining/model.yaml
download_url: https://sandbox.zenodo.org/record/906805/files/bioimage.io.model.zip
links:
- deepimagej
- imjoy/BioImageIO-Packager
- id: SkinLesionClassification
type: model
rdf_source: skin_lesion_classification/model.yaml
download_url: https://sandbox.zenodo.org/record/906807/files/bioimage.io.model.zip
links:
- deepimagej

@FynnBe
Copy link
Contributor Author

FynnBe commented Mar 22, 2023

related issues: #47, bioimage-io/bioimage.io#308

@FynnBe
Copy link
Contributor Author

FynnBe commented Mar 22, 2023

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+, PHP-3.01, Leptonica, bzip2-1.0.5, NIST-PD-fallback, OSL-1.0, OFL-1.1, JasPer-2.0, '
                         'Naumen, AGPL-1.0-only, C-UDA-1.0, MIT, TCL, LGPL-3.0-only, ECL-1.0, MPL-2.0, CC-BY-NC-1.0, '
                         'CC-BY-NC-ND-2.5, LPPL-1.3c, JSON, NBPL-1.0, CAL-1.0-Combined-Work-Exception, Unlicense, '
                         'CNRI-Python-GPL-Compatible, TU-Berlin-2.0, NLPL, LGPL-3.0-or-later, Beerware, NGPL, ZPL-2.1, '
                         'Saxpath, CC-BY-SA-2.0-UK, CECILL-2.1, XFree86-1.1, IBM-pibs, Zlib, StandardML-NJ, RPSL-1.0, '
                         'CECILL-1.0, OGL-UK-3.0, BSD-4-Clause-Shortened, Watcom-1.0, Wsuipa, TU-Berlin-1.0, Latex2e, '
                         'CECILL-B, EUPL-1.0, GFDL-1.2-or-later, CPL-1.0, CC-BY-ND-3.0, NTP, W3C-19980720, '
                         'GFDL-1.3-only, CC-BY-SA-4.0, EUPL-1.1, GFDL-1.1-no-invariants-only, JPNIC, AMPAS, '
                         'BSD-3-Clause, MIT-0, Intel, O-UDA-1.0, NPL-1.0, CC-BY-NC-2.5, Mup, Newsletr, PDDL-1.0, '
                         'SMLNJ, BSD-1-Clause, SimPL-2.0, OLDAP-1.2, Xnet, BSD-2-Clause, AML, GFDL-1.2-only, Info-ZIP, '
                         'DSDP, AGPL-1.0, BSD-4-Clause-UC, LGPL-2.1-only, OFL-1.0, CDL-1.0, LAL-1.3, Sendmail, '
                         'OGDL-Taiwan-1.0, Zimbra-1.4, Borceux, OSL-3.0, AMDPLPA, CC-BY-NC-SA-3.0, OLDAP-2.1, '
                         'BSD-2-Clause-FreeBSD, CPOL-1.02, MPL-1.0, blessing, Parity-6.0.0, AFL-3.0, SGI-B-1.0, '
                         'BSD-2-Clause-Patent, Artistic-1.0-cl8, CC-BY-NC-ND-4.0, Apache-1.1, ErlPL-1.1, OFL-1.0-RFN, '
                         'CC-BY-NC-3.0, CC-BY-NC-2.0, MakeIndex, Barr, CC-BY-SA-2.1-JP, GFDL-1.2-no-invariants-only, '
                         'Hippocratic-2.1, Adobe-2006, OSL-2.0, CC-BY-NC-SA-4.0, LGPL-2.1-or-later, '
                         'PolyForm-Noncommercial-1.0.0, OpenSSL, GPL-3.0-with-GCC-exception, OPL-1.0, '
                         'BSD-3-Clause-Attribution, Rdisc, MS-RL, EUDatagrid, LGPLLR, AFL-2.0, MIT-Modern-Variant, '
                         'GFDL-1.3-invariants-only, LiLiQ-R-1.1, CDLA-Permissive-1.0, DRL-1.0, BSD-Source-Code, '
                         'CC-BY-NC-ND-1.0, GLWTPL, VSL-1.0, CPAL-1.0, HaskellReport, APSL-1.1, GPL-2.0-or-later, '
                         'BSD-3-Clause-Modification, OLDAP-2.3, OFL-1.1-no-RFN, BitTorrent-1.0, NRL, GFDL-1.2, MirOS, '
                         'Sleepycat, LPPL-1.1, WTFPL, PolyForm-Small-Business-1.0.0, Caldera, HTMLTIDY, SISSL, MITNFA, '
                         '0BSD, CC0-1.0, LGPL-3.0+, CDLA-Sharing-1.0, GPL-2.0-with-bison-exception, EFL-2.0, AFL-1.1, '
                         'CC-BY-2.0, RPL-1.5, MulanPSL-1.0, GPL-3.0+, HPND-sell-variant, SSH-OpenSSH, OLDAP-1.1, '
                         'BitTorrent-1.1, Artistic-1.0, SSH-short, CC-BY-3.0-AT, MIT-CMU, '
                         'GFDL-1.3-no-invariants-or-later, TOSL, MIT-open-group, OLDAP-2.6, GFDL-1.1-only, '
                         'FreeBSD-DOC, GPL-2.0, Fair, CECILL-1.1, QPL-1.0, DOC, LAL-1.2, LPL-1.02, CERN-OHL-P-2.0, '
                         'etalab-2.0, FTL, Qhull, BSD-3-Clause-Clear, BSD-3-Clause-No-Military-License, FSFAP, '
                         'APL-1.0, OLDAP-2.8, TORQUE-1.1, Sendmail-8.23, diffmark, Frameworx-1.0, '
                         'zlib-acknowledgement, EFL-1.0, IJG, GFDL-1.3-no-invariants-only, Noweb, GFDL-1.3, LGPL-2.1, '
                         'gSOAP-1.3b, OFL-1.1-RFN, GPL-3.0-with-autoconf-exception, CERN-OHL-1.1, AFL-2.1, MIT-enna, '
                         'Adobe-Glyph, EPL-1.0, Xerox, OLDAP-2.0.1, MTLL, ImageMagick, psutils, ClArtistic, '
                         'GFDL-1.3-invariants-or-later, APSL-1.2, Apache-2.0, NIST-PD, Libpng, TAPR-OHL-1.0, ICU, '
                         'CC-BY-SA-2.5, CC-PDDC, AGPL-3.0-only, OSL-1.1, SugarCRM-1.1.3, FreeImage, W3C-20150513, '
                         'D-FSL-1.0, RSA-MD, CC-BY-ND-2.0, GPL-2.0-with-GCC-exception, AGPL-3.0-or-later, '
                         'AGPL-1.0-or-later, iMatix, Plexus, OFL-1.0-no-RFN, NAIST-2003, MIT-feh, ECL-2.0, CC-BY-2.5, '
                         'XSkat, Linux-OpenIB, Spencer-99, BSD-3-Clause-No-Nuclear-License-20[14](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:15), CC-BY-NC-ND-3.0-IGO, '
                         'CC-BY-NC-SA-1.0, GPL-2.0-with-font-exception, Crossword, OLDAP-2.2.2, BSD-2-Clause-NetBSD, '
                         'GPL-2.0+, CC-BY-4.0, OLDAP-2.0, NOSL, CDDL-1.1, APSL-1.0, EUPL-1.2, Nokia, RHeCos-1.1, '
                         'GPL-2.0-only, OLDAP-2.7, Vim, SAX-PD, BSD-3-Clause-No-Nuclear-Warranty, NetCDF, dvipdfm, '
                         'SHL-0.5, LGPL-2.0-only, AAL, Unicode-TOU, LPPL-1.2, xpp, SHL-0.51, NCSA, LGPL-2.0-or-later, '
                         'CC-BY-3.0, GPL-1.0, W3C, Aladdin, BSD-3-Clause-No-Nuclear-License, GFDL-1.1-or-later, SMPPL, '
                         'GFDL-1.1, OLDAP-1.4, Condor-1.1, GPL-1.0-only, GPL-3.0, PSF-2.0, Apache-1.0, EPL-2.0, '
                         'Python-2.0, 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, bzip2-1.0.5, NIST-PD-fallback, OSL-1.0, OFL-1.1, JasPer-2.0, '
                         'Naumen, AGPL-1.0-only, C-UDA-1.0, MIT, TCL, LGPL-3.0-only, ECL-1.0, MPL-2.0, CC-BY-NC-1.0, '
                         'CC-BY-NC-ND-2.5, LPPL-1.3c, JSON, NBPL-1.0, CAL-1.0-Combined-Work-Exception, Unlicense, '
                         'CNRI-Python-GPL-Compatible, TU-Berlin-2.0, NLPL, LGPL-3.0-or-later, Beerware, NGPL, ZPL-2.1, '
                         'Saxpath, CC-BY-SA-2.0-UK, CECILL-2.1, XFree86-1.1, IBM-pibs, Zlib, StandardML-NJ, RPSL-1.0, '
                         'CECILL-1.0, OGL-UK-3.0, BSD-4-Clause-Shortened, Watcom-1.0, Wsuipa, TU-Berlin-1.0, Latex2e, '
                         'CECILL-B, EUPL-1.0, GFDL-1.2-or-later, CPL-1.0, CC-BY-ND-3.0, NTP, W3C-[19](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:20)9807[20](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:21), '
                         'GFDL-1.3-only, CC-BY-SA-4.0, EUPL-1.1, GFDL-1.1-no-invariants-only, JPNIC, AMPAS, '
                         'BSD-3-Clause, MIT-0, Intel, O-UDA-1.0, NPL-1.0, CC-BY-NC-2.5, Mup, Newsletr, PDDL-1.0, '
                         'SMLNJ, BSD-1-Clause, SimPL-2.0, OLDAP-1.2, Xnet, BSD-2-Clause, AML, GFDL-1.2-only, Info-ZIP, '
                         'DSDP, AGPL-1.0, BSD-4-Clause-UC, LGPL-2.1-only, OFL-1.0, CDL-1.0, LAL-1.3, Sendmail, '
                         'OGDL-Taiwan-1.0, Zimbra-1.4, Borceux, OSL-3.0, AMDPLPA, CC-BY-NC-SA-3.0, OLDAP-2.1, '
                         'BSD-2-Clause-FreeBSD, CPOL-1.02, MPL-1.0, blessing, Parity-6.0.0, AFL-3.0, SGI-B-1.0, '
                         'BSD-2-Clause-Patent, Artistic-1.0-cl8, CC-BY-NC-ND-4.0, Apache-1.1, ErlPL-1.1, OFL-1.0-RFN, '
                         'CC-BY-NC-3.0, CC-BY-NC-2.0, MakeIndex, Barr, CC-BY-SA-2.1-JP, GFDL-1.2-no-invariants-only, '
                         'Hippocratic-2.1, Adobe-2006, OSL-2.0, CC-BY-NC-SA-4.0, LGPL-2.1-or-later, '
                         'PolyForm-Noncommercial-1.0.0, OpenSSL, GPL-3.0-with-GCC-exception, OPL-1.0, '
                         'BSD-3-Clause-Attribution, Rdisc, MS-RL, EUDatagrid, LGPLLR, AFL-2.0, MIT-Modern-Variant, '
                         'GFDL-1.3-invariants-only, LiLiQ-R-1.1, CDLA-Permissive-1.0, DRL-1.0, BSD-Source-Code, '
                         'CC-BY-NC-ND-1.0, GLWTPL, VSL-1.0, CPAL-1.0, HaskellReport, APSL-1.1, GPL-2.0-or-later, '
                         'BSD-3-Clause-Modification, OLDAP-2.3, OFL-1.1-no-RFN, BitTorrent-1.0, NRL, GFDL-1.2, MirOS, '
                         'Sleepycat, LPPL-1.1, WTFPL, PolyForm-Small-Business-1.0.0, Caldera, HTMLTIDY, SISSL, MITNFA, '
                         '0BSD, CC0-1.0, LGPL-3.0+, CDLA-Sharing-1.0, GPL-2.0-with-bison-exception, EFL-2.0, AFL-1.1, '
                         'CC-BY-2.0, RPL-1.5, MulanPSL-1.0, GPL-3.0+, HPND-sell-variant, SSH-OpenSSH, OLDAP-1.1, '
                         'BitTorrent-1.1, Artistic-1.0, SSH-short, CC-BY-3.0-AT, MIT-CMU, '
                         'GFDL-1.3-no-invariants-or-later, TOSL, MIT-open-group, OLDAP-2.6, GFDL-1.1-only, '
                         'FreeBSD-DOC, GPL-2.0, Fair, CECILL-1.1, QPL-1.0, DOC, LAL-1.2, LPL-1.02, CERN-OHL-P-2.0, '
                         'etalab-2.0, FTL, Qhull, BSD-3-Clause-Clear, BSD-3-Clause-No-Military-License, FSFAP, '
                         'APL-1.0, OLDAP-2.8, TORQUE-1.1, Sendmail-8.[23](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:24), diffmark, Frameworx-1.0, '
                         'zlib-acknowledgement, EFL-1.0, IJG, GFDL-1.3-no-invariants-only, Noweb, GFDL-1.3, LGPL-2.1, '
                         'gSOAP-1.3b, OFL-1.1-RFN, GPL-3.0-with-autoconf-exception, CERN-OHL-1.1, AFL-2.1, MIT-enna, '
                         'Adobe-Glyph, EPL-1.0, Xerox, OLDAP-2.0.1, MTLL, ImageMagick, psutils, ClArtistic, '
                         'GFDL-1.3-invariants-or-later, APSL-1.2, Apache-2.0, NIST-PD, Libpng, TAPR-OHL-1.0, ICU, '
                         'CC-BY-SA-2.5, CC-PDDC, AGPL-3.0-only, OSL-1.1, SugarCRM-1.1.3, FreeImage, W3C-201[50](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:51)[51](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:52)3, '
                         'D-FSL-1.0, RSA-MD, CC-BY-ND-2.0, GPL-2.0-with-GCC-exception, AGPL-3.0-or-later, '
                         'AGPL-1.0-or-later, iMatix, Plexus, OFL-1.0-no-RFN, NAIST-2003, MIT-feh, ECL-2.0, CC-BY-2.5, '
                         'XSkat, Linux-OpenIB, Spencer-99, BSD-3-Clause-No-Nuclear-License-2014, CC-BY-NC-ND-3.0-IGO, '
                         'CC-BY-NC-SA-1.0, GPL-2.0-with-font-exception, Crossword, OLDAP-2.2.2, BSD-2-Clause-NetBSD, '
                         'GPL-2.0+, CC-BY-4.0, OLDAP-2.0, NOSL, CDDL-1.1, APSL-1.0, EUPL-1.2, Nokia, RHeCos-1.1, '
                         'GPL-2.0-only, OLDAP-2.7, Vim, SAX-PD, BSD-3-Clause-No-Nuclear-Warranty, NetCDF, dvipdfm, '
                         'SHL-0.5, LGPL-2.0-only, AAL, Unicode-TOU, LPPL-1.2, xpp, SHL-0.51, NCSA, LGPL-2.0-or-later, '
                         'CC-BY-3.0, GPL-1.0, W3C, Aladdin, BSD-3-Clause-No-Nuclear-License, GFDL-1.1-or-later, SMPPL, '
                         'GFDL-1.1, OLDAP-1.4, Condor-1.1, GPL-1.0-only, GPL-3.0, PSF-2.0, Apache-1.0, EPL-2.0, '
                         'Python-2.0, 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-2015, '
                         '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/UNet2DGlioblastomaSegmentation/latest/rdf.yaml',
   'status': 'failed',
   'traceback': None,
   '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"}}}],
 [{'bioimageio_spec_version': '0.4.9',
   'error': {'_schema': ['Referenced tensor input_images with 3 dimensions does not match output tensor output_images '
                         'with 4 dimensions.']},
   '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/WidefieldDapiSuperResolution/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']}, {'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': {'_schema': ['Referenced tensor input_images with 3 dimensions does not match output tensor output_images '
                         'with 4 dimensions.']},
   '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/WidefieldFitcSuperResolution/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']}, {'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, 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+, PHP-3.01, Leptonica, bzip2-1.0.5, NIST-PD-fallback, OSL-1.0, OFL-1.1, JasPer-2.0, '
                         'Naumen, AGPL-1.0-only, C-UDA-1.0, MIT, TCL, LGPL-3.0-only, ECL-1.0, MPL-2.0, CC-BY-NC-1.0, '
                         'CC-BY-NC-ND-2.5, LPPL-1.3c, JSON, NBPL-1.0, CAL-1.0-Combined-Work-Exception, Unlicense, '
                         'CNRI-Python-GPL-Compatible, TU-Berlin-2.0, NLPL, LGPL-3.0-or-later, Beerware, NGPL, ZPL-2.1, '
                         'Saxpath, CC-BY-SA-2.0-UK, CECILL-2.1, XFree86-1.1, IBM-pibs, Zlib, StandardML-NJ, RPSL-1.0, '
                         'CECILL-1.0, OGL-UK-3.0, BSD-4-Clause-Shortened, Watcom-1.0, Wsuipa, TU-Berlin-1.0, Latex2e, '
                         'CECILL-B, EUPL-1.0, GFDL-1.2-or-later, CPL-1.0, CC-BY-ND-3.0, NTP, W3C-19980[72](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:73)0, '
                         'GFDL-1.3-only, CC-BY-SA-4.0, EUPL-1.1, GFDL-1.1-no-invariants-only, JPNIC, AMPAS, '
                         'BSD-3-Clause, MIT-0, Intel, O-UDA-1.0, NPL-1.0, CC-BY-NC-2.5, Mup, Newsletr, PDDL-1.0, '
                         'SMLNJ, BSD-1-Clause, SimPL-2.0, OLDAP-1.2, Xnet, BSD-2-Clause, AML, GFDL-1.2-only, Info-ZIP, '
                         'DSDP, AGPL-1.0, BSD-4-Clause-UC, LGPL-2.1-only, OFL-1.0, CDL-1.0, LAL-1.3, Sendmail, '
                         'OGDL-Taiwan-1.0, Zimbra-1.4, Borceux, OSL-3.0, AMDPLPA, CC-BY-NC-SA-3.0, OLDAP-2.1, '
                         'BSD-2-Clause-FreeBSD, CPOL-1.02, MPL-1.0, blessing, Parity-6.0.0, AFL-3.0, SGI-B-1.0, '
                         'BSD-2-Clause-Patent, Artistic-1.0-cl8, CC-BY-NC-ND-4.0, Apache-1.1, ErlPL-1.1, OFL-1.0-RFN, '
                         'CC-BY-NC-3.0, CC-BY-NC-2.0, MakeIndex, Barr, CC-BY-SA-2.1-JP, GFDL-1.2-no-invariants-only, '
                         'Hippocratic-2.1, Adobe-2006, OSL-2.0, CC-BY-NC-SA-4.0, LGPL-2.1-or-later, '
                         'PolyForm-Noncommercial-1.0.0, OpenSSL, GPL-3.0-with-GCC-exception, OPL-1.0, '
                         'BSD-3-Clause-Attribution, Rdisc, MS-RL, EUDatagrid, LGPLLR, AFL-2.0, MIT-Modern-Variant, '
                         'GFDL-1.3-invariants-only, LiLiQ-R-1.1, CDLA-Permissive-1.0, DRL-1.0, BSD-Source-Code, '
                         'CC-BY-NC-ND-1.0, GLWTPL, VSL-1.0, CPAL-1.0, HaskellReport, APSL-1.1, GPL-2.0-or-later, '
                         'BSD-3-Clause-Modification, OLDAP-2.3, OFL-1.1-no-RFN, BitTorrent-1.0, NRL, GFDL-1.2, MirOS, '
                         'Sleepycat, LPPL-1.1, WTFPL, PolyForm-Small-Business-1.0.0, Caldera, HTMLTIDY, SISSL, MITNFA, '
                         '0BSD, CC0-1.0, LGPL-3.0+, CDLA-Sharing-1.0, GPL-2.0-with-bison-exception, EFL-2.0, AFL-1.1, '
                         'CC-BY-2.0, RPL-1.5, MulanPSL-1.0, GPL-3.0+, HPND-sell-variant, SSH-OpenSSH, OLDAP-1.1, '
                         'BitTorrent-1.1, Artistic-1.0, SSH-short, CC-BY-3.0-AT, MIT-CMU, '
                         'GFDL-1.3-no-invariants-or-later, TOSL, MIT-open-group, OLDAP-2.6, GFDL-1.1-only, '
                         'FreeBSD-DOC, GPL-2.0, Fair, CECILL-1.1, QPL-1.0, DOC, LAL-1.2, LPL-1.02, CERN-OHL-P-2.0, '
                         'etalab-2.0, FTL, Qhull, BSD-3-Clause-Clear, BSD-3-Clause-No-Military-License, FSFAP, '
                         'APL-1.0, OLDAP-2.8, TORQUE-1.1, Sendmail-8.23, diffmark, Frameworx-1.0, '
                         'zlib-acknowledgement, EFL-1.0, IJG, GFDL-1.3-no-invariants-only, Noweb, GFDL-1.3, LGPL-2.1, '
                         'gSOAP-1.3b, OFL-1.1-RFN, GPL-3.0-with-autoconf-exception, CERN-OHL-1.1, AFL-2.1, MIT-enna, '
                         'Adobe-Glyph, EPL-1.0, Xerox, OLDAP-2.0.1, MTLL, ImageMagick, psutils, ClArtistic, '
                         'GFDL-1.3-invariants-or-later, APSL-1.2, Apache-2.0, NIST-PD, Libpng, TAPR-OHL-1.0, ICU, '
                         'CC-BY-SA-2.5, CC-PDDC, AGPL-3.0-only, OSL-1.1, SugarCRM-1.1.3, FreeImage, W3C-20150513, '
                         'D-FSL-1.0, RSA-MD, CC-BY-ND-2.0, GPL-2.0-with-GCC-exception, AGPL-3.0-or-later, '
                         'AGPL-1.0-or-later, iMatix, Plexus, OFL-1.0-no-RFN, NAIST-2003, MIT-feh, ECL-2.0, CC-BY-2.5, '
                         'XSkat, Linux-OpenIB, Spencer-99, BSD-3-Clause-No-Nuclear-License-2014, CC-BY-NC-ND-3.0-IGO, '
                         'CC-BY-NC-SA-1.0, GPL-2.0-with-font-exception, Crossword, OLDAP-2.2.2, BSD-2-Clause-NetBSD, '
                         'GPL-2.0+, CC-BY-4.0, OLDAP-2.0, NOSL, CDDL-1.1, APSL-1.0, EUPL-1.2, Nokia, RHeCos-1.1, '
                         'GPL-2.0-only, OLDAP-2.7, Vim, SAX-PD, BSD-3-Clause-No-Nuclear-Warranty, NetCDF, dvipdfm, '
                         'SHL-0.5, LGPL-2.0-only, AAL, Unicode-TOU, LPPL-1.2, xpp, SHL-0.51, NCSA, LGPL-2.0-or-later, '
                         'CC-BY-3.0, GPL-1.0, W3C, Aladdin, BSD-3-Clause-No-Nuclear-License, GFDL-1.1-or-later, SMPPL, '
                         'GFDL-1.1, OLDAP-1.4, Condor-1.1, GPL-1.0-only, GPL-3.0, PSF-2.0, Apache-1.0, EPL-2.0, '
                         'Python-2.0, 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-2015, '
                         '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](https://github.com/bioimage-io/collection-bioimage-io/actions/runs/4478480836/jobs/7874255548?pr=570#step:10:95), 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/WidefieldTxredSuperResolution/latest/rdf.yaml',
   'status': 'failed',
   'traceback': None,
   'warnings': {'license': 'CC BY 4.0 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']}]"}}],

@FynnBe FynnBe mentioned this issue Mar 22, 2023
Merged
@FynnBe
Copy link
Contributor Author

FynnBe commented Mar 23, 2023

@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
Copy link
Contributor Author

FynnBe commented Mar 23, 2023

I fixed one model to get you started: #49

@FynnBe FynnBe mentioned this issue Mar 23, 2023
Closed
@ivan-ea
Copy link
Collaborator

ivan-ea commented Mar 23, 2023

@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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@FynnBe @ivan-ea