Merge branch 'main' into auto-update-10.5281/zenodo.6559474

Author: FynnBe

.github/workflows/auto_update_main.yaml

@@ -48,6 +48,11 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0  # get all branches to check for pending resources by checking if auto-update-... branch exists
+    - name: checkout gh-pages for update_partner_resources.py
+      uses: actions/checkout@v2
+      with:
+        ref: gh-pages
+        path: gh-pages
     - name: install script deps
       run: pip install requests typer bioimageio.spec lxml
     - name: update external resources
@@ -67,6 +72,9 @@ jobs:
         mv tmp_download_counts.json dist/download_counts.json
     - name: update partner resources
       run: python scripts/update_partner_resources.py
+    - name: add documentation files to preview
+      if: github.event_name == 'pull_request'
+      run: python scripts/download_documentation.py
     - name: Upload preview of updated partner resources
       if: github.event_name == 'pull_request'
       uses: actions/upload-artifact@v2

.github/workflows/comment_preview.yaml

@@ -11,10 +11,6 @@ jobs:
     name: comment links to previews in pull request
     runs-on: windows-2019
     steps:
-    - name: debug pr number
-      run: echo ${{ github.event.number }}
-    - name: debug original ref
-      run: echo ${{ github.event.workflow_run.head_branch }}
 #    - uses: izhangzhihao/delete-comment@master
 #      with:
 #        github_token: ${{ secrets.PAT }}

.github/workflows/validate_resources.yaml

@@ -97,7 +97,7 @@ jobs:
     - name: dynamic validation
       shell: bash -l {0}
       timeout-minutes: 30
-      run: python scripts/dynamic_validation.py dist/dynamic_validation_artifact ${{ matrix.resource_id }} ${{ matrix.version_id }} ${{ matrix.weight_format }} --create-env-outcome ${{ steps.create_env.outcome }}
+      run: python scripts/dynamic_validation.py dist/dynamic_validation_artifact ${{ matrix.resource_id }} ${{ matrix.version_id }} ${{ matrix.weight_format }} --create-env-outcome ${{ steps.create_env.outcome }} --${{ contains(inputs.deploy_to, 'gh-pages') && 'no-ignore' || 'ignore' }}-rdf-source-field-in-validation
     - name: Upload validation summary
       uses: actions/upload-artifact@v2
       with:

collection/10.5281/zenodo.5764892/resource.yaml

@@ -1,46 +1,59 @@
 doi: 10.5281/zenodo.5764892
 id: 10.5281/zenodo.5764892
+nickname: affable-shark
+nickname_icon: 🦈
 owners:
 - 77626
 status: accepted
 type: model
 versions:
-- version_id: '6322939'
-  doi: 10.5281/zenodo.6322939
-  created: '2022-03-02 12:07:39.352008'
+- created: '2022-06-15 22:06:22.658325'
+  doi: 10.5281/zenodo.6647674
+  name: NucleiSegmentationBoundaryModel
   status: accepted
+  version_id: '6647674'
+  version_name: version 7
+  rdf_source: https://zenodo.org/api/files/61da5c68-e09b-49a6-899b-94c22cdfc4d9/rdf.yaml
+- created: '2022-03-02 12:07:39.352008'
+  doi: 10.5281/zenodo.6322939
+  links:
+  - deepimagej/deepimagej
+  - ilastik/ilastik
+  - imjoy/BioImageIO-Packager
+  - ilastik/torch-em-2d-unet-notebook
   name: NucleiSegmentationBoundaryModel
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/a3d790f1-5203-4bd3-a975-d0fff38c0d97/rdf.yaml
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  status: accepted
   training_data:
     id: ilastik/stardist_dsb_training_data
-- version_id: '6319663'
+  version_id: '6322939'
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/a3d790f1-5203-4bd3-a975-d0fff38c0d97/rdf.yaml
+- created: '2022-03-01 09:27:03.758432'
   doi: 10.5281/zenodo.6319663
-  created: '2022-03-01 09:27:03.758432'
-  status: blocked
   name: NucleiSegmentationBoundaryModel
+  status: blocked
+  version_id: '6319663'
   version_name: revision 2
   rdf_source: https://zenodo.org/api/files/1cf7ce1f-f1a1-4207-9e3e-60ee4d4a0803/rdf.yaml
-- version_id: '6287342'
+- created: '2022-02-25 20:18:26.146167'
   doi: 10.5281/zenodo.6287342
-  created: '2022-02-25 20:18:26.146167'
-  status: blocked
   name: NucleiSegmentationBoundaryModel
+  status: blocked
+  version_id: '6287342'
   version_name: revision 3
   rdf_source: https://zenodo.org/api/files/0f39fc4f-e8ea-4af5-be7d-e756b566c09f/rdf.yaml
-- version_id: '6287207'
+- created: '2022-02-25 20:10:17.778295'
   doi: 10.5281/zenodo.6287207
-  created: '2022-02-25 20:10:17.778295'
-  status: blocked
   name: NucleiSegmentationBoundaryModel
+  status: blocked
+  version_id: '6287207'
   version_name: revision 4
   rdf_source: https://zenodo.org/api/files/7d930716-b8c4-4a23-922c-91e561d237b7/rdf.yaml
-- version_id: '6028056'
+- created: '2022-02-09 20:56:44.509499'
   doi: 10.5281/zenodo.6028056
-  created: '2022-02-09 20:56:44.509499'
-  status: blocked
   name: NucleiSegmentationBoundaryModel
+  status: blocked
+  version_id: '6028056'
   version_name: revision 5
   rdf_source: https://zenodo.org/api/files/50a4c576-db4c-49a6-a691-59f9d96e6d5f/rdf.yaml
 - created: '2021-12-07 18:02:09.736653+00:00'
@@ -50,5 +63,3 @@ versions:
   version_id: '5764893'
   version_name: revision 1
   rdf_source: https://zenodo.org/api/files/8137780b-871f-4d7e-b130-a63847ece4d8/rdf.yaml
-nickname: affable-shark
-nickname_icon: 🦈

collection/10.5281/zenodo.5847355/resource.yaml

@@ -1,20 +1,33 @@
 doi: 10.5281/zenodo.5847355
 id: 10.5281/zenodo.5847355
+nickname: powerful-chipmunk
+nickname_icon: 🐿
 owners:
 - 77626
 status: accepted
 type: model
 versions:
-- version_id: '6322908'
-  doi: 10.5281/zenodo.6322908
-  created: '2022-03-02 11:57:10.309729'
+- created: '2022-06-15 22:08:13.874556'
+  doi: 10.5281/zenodo.6647683
+  name: CovidIFCellSegmentationBoundaryModel
   status: accepted
+  version_id: '6647683'
+  version_name: version 4
+  rdf_source: https://zenodo.org/api/files/67864f33-063b-43e9-a40f-0f36bf6397d4/rdf.yaml
+- created: '2022-03-02 11:57:10.309729'
+  doi: 10.5281/zenodo.6322908
+  links:
+  - deepimagej/deepimagej
+  - ilastik/ilastik
+  - imjoy/BioImageIO-Packager
+  - ilastik/torch-em-2d-unet-notebook
   name: CovidIFCellSegmentationBoundaryModel
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/be41e515-ce79-48f5-a482-35e1f11701c2/rdf.yaml
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  status: accepted
   training_data:
     id: ilastik/covid_if_training_data
+  version_id: '6322908'
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/be41e515-ce79-48f5-a482-35e1f11701c2/rdf.yaml
 - created: '2022-01-18 21:31:33.668428'
   doi: 10.5281/zenodo.5874728
   name: Cell Segmentation Immunofluorescence (Membrane Prediction)
@@ -29,5 +42,3 @@ versions:
   version_id: '5847356'
   version_name: revision 1
   rdf_source: https://zenodo.org/api/files/5b0d4c67-6d0a-462c-914c-07bebe594bd8/rdf.yaml
-nickname: powerful-chipmunk
-nickname_icon: 🐿

collection/10.5281/zenodo.5869899/resource.yaml

@@ -1,32 +1,43 @@
 doi: 10.5281/zenodo.5869899
 id: 10.5281/zenodo.5869899
+nickname: hiding-tiger
+nickname_icon: 🐅
 owners:
 - 77626
 status: accepted
 type: model
 versions:
-- version_id: '6321179'
-  doi: 10.5281/zenodo.6321179
-  created: '2022-03-01 19:53:40.554063'
+- created: '2022-06-15 22:09:35.368273'
+  doi: 10.5281/zenodo.6647688
+  name: LiveCellSegmentationBoundaryModel
   status: accepted
+  version_id: '6647688'
+  version_name: version 3
+  rdf_source: https://zenodo.org/api/files/8e1dc6e7-bdc9-412c-b06c-e79ee375989f/rdf.yaml
+- created: '2022-03-01 19:53:40.554063'
+  doi: 10.5281/zenodo.6321179
+  links:
+  - deepimagej/deepimagej
+  - ilastik/ilastik
+  - imjoy/BioImageIO-Packager
+  - ilastik/torch-em-2d-unet-notebook
   name: LiveCellSegmentationBoundaryModel
-  version_name: revision 1
-  rdf_source: https://zenodo.org/api/files/f2a796dc-27f5-43b8-aadb-981898f39b87/rdf.yaml
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-2d-unet-notebook]
+  status: accepted
   training_data:
     id: ilastik/livecell_dataset
+  version_id: '6321179'
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/f2a796dc-27f5-43b8-aadb-981898f39b87/rdf.yaml
 - created: '2022-01-18 10:03:26.939252'
   doi: 10.5281/zenodo.5869900
-  name: LiveCellSegmentationBoundaryModel
   links:
   - ilastik/live-cell-boundary-model
   - ilastik/livecell_dataset
   - ilastik/ilastik
   - deepimagej/deepimagej
   - imjoy/BioImageIO-Packager
+  name: LiveCellSegmentationBoundaryModel
   status: accepted
   version_id: '5869900'
   version_name: revision 1
   rdf_source: https://zenodo.org/api/files/a6d477fe-9412-4064-b7e6-67f057fec920/rdf.yaml
-nickname: hiding-tiger
-nickname_icon: 🐅

collection/10.5281/zenodo.5874841/resource.yaml

@@ -1,14 +1,37 @@
 doi: 10.5281/zenodo.5874841
 id: 10.5281/zenodo.5874841
-owners: [77626]
+nickname: kind-seashell
+nickname_icon: 🐚
+owners:
+- 77626
 status: accepted
 type: model
 versions:
-- {created: '2022-01-18 23:04:49.485980', doi: 10.5281/zenodo.5874842, name: Mitochondria Segmentation for EM,
-  rdf_source: 'https://zenodo.org/api/files/2d9489cd-a4dd-4730-8a71-577d0fcd0f5c/rdf.yaml',
-  tags: [3d, electron-microscopy, mitochondria, instance-segmentation, unet, brain],
-  status: accepted, version_id: '5874842', version_name: revision 1,
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook],
-  training_data: {id: ilastik/mitoem_segmentation_challenge}}
-nickname: kind-seashell
-nickname_icon: 🐚
+- created: '2022-06-10 06:22:28.465944'
+  doi: 10.5281/zenodo.6630266
+  name: MitochondriaEMSegmentationBoundaryModel
+  status: accepted
+  version_id: '6630266'
+  version_name: version 2
+  rdf_source: https://zenodo.org/api/files/ac8ecde9-bafd-4c2c-9ede-0f4a47077d31/rdf.yaml
+- created: '2022-01-18 23:04:49.485980'
+  doi: 10.5281/zenodo.5874842
+  links:
+  - deepimagej/deepimagej
+  - ilastik/ilastik
+  - imjoy/BioImageIO-Packager
+  - ilastik/torch-em-3d-unet-notebook
+  name: Mitochondria Segmentation for EM
+  status: accepted
+  tags:
+  - 3d
+  - electron-microscopy
+  - mitochondria
+  - instance-segmentation
+  - unet
+  - brain
+  training_data:
+    id: ilastik/mitoem_segmentation_challenge
+  version_id: '5874842'
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/2d9489cd-a4dd-4730-8a71-577d0fcd0f5c/rdf.yaml

collection/10.5281/zenodo.5914248/resource.yaml

@@ -1,14 +1,28 @@
 doi: 10.5281/zenodo.5914248
 id: 10.5281/zenodo.5914248
+maintainers:
+- github_user: iarganda
 nickname: discreet-rooster
 nickname_icon: 🐓
 owners:
 - 147356
 status: accepted
 type: model
-maintainers: 
-- github_user: iarganda
 versions:
+- created: '2022-06-08 00:04:57.581394'
+  doi: 10.5281/zenodo.6622089
+  name: Pancreatic Phase Contrast Cell Segmentation (U-Net)
+  status: blocked
+  version_id: '6622089'
+  version_name: version 5
+  rdf_source: https://zenodo.org/api/files/2c6aa544-1689-4cd6-a069-3061573bf1b4/rdf.yaml
+- created: '2022-05-31 08:21:25.880069'
+  doi: 10.5281/zenodo.6597361
+  name: Pancreatic Phase Contrast Cell Segmentation (U-Net)
+  status: blocked
+  version_id: '6597361'
+  version_name: version 4
+  rdf_source: https://zenodo.org/api/files/7ad26838-ca63-4330-89c6-78cfea98e620/rdf.yaml
 - created: '2022-05-03 14:50:12.368648'
   doi: 10.5281/zenodo.6514622
   name: Pancreatic Phase Contrast Cell Segmentation (U-Net)

collection/10.5281/zenodo.5940478/resource.yaml

@@ -0,0 +1,16 @@
+status: blocked
+versions:
+- version_id: '5940479'
+  doi: 10.5281/zenodo.5940479
+  created: '2022-02-01 16:27:42.327446'
+  status: blocked
+  name: 3D U-Net - ZeroCostDL4Mic
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/92c3196a-02c6-4ebe-8b5c-326737e9d9d0/rdf.yaml
+id: 10.5281/zenodo.5940478
+doi: 10.5281/zenodo.5940478
+type: model
+owners:
+- 147356
+nickname: proactive-koala
+nickname_icon: '🐨'

collection/10.5281/zenodo.6028280/resource.yaml

@@ -1,13 +1,30 @@
 doi: 10.5281/zenodo.6028280
 id: 10.5281/zenodo.6028280
-owners: [77626]
+nickname: willing-hedgehog
+nickname_icon: 🦔
+owners:
+- 77626
 status: accepted
 type: model
 versions:
-- {created: '2022-02-09 21:42:30.280535', doi: 10.5281/zenodo.6028281, name: PlatynereisEMcellsSegmentationBoundaryModel,
-  rdf_source: 'https://zenodo.org/api/files/9a4c6150-10d1-4c82-9305-8ac21bc435b5/rdf.yaml',
-  status: accepted, version_id: '6028281', version_name: revision 1,
-  links: [deepimagej/deepimagej, ilastik/ilastik, imjoy/BioImageIO-Packager, ilastik/torch-em-3d-unet-notebook],
-  training_data: {id: ilastik/platynereis_em_training_data}}
-nickname: willing-hedgehog
-nickname_icon: 🦔
+- created: '2022-06-15 22:12:29.012734'
+  doi: 10.5281/zenodo.6647695
+  name: PlatynereisEMcellsSegmentationBoundaryModel
+  status: accepted
+  version_id: '6647695'
+  version_name: version 2
+  rdf_source: https://zenodo.org/api/files/d2f261ff-8734-4ad0-a84a-6c80c05e5bd3/rdf.yaml
+- created: '2022-02-09 21:42:30.280535'
+  doi: 10.5281/zenodo.6028281
+  links:
+  - deepimagej/deepimagej
+  - ilastik/ilastik
+  - imjoy/BioImageIO-Packager
+  - ilastik/torch-em-3d-unet-notebook
+  name: PlatynereisEMcellsSegmentationBoundaryModel
+  status: accepted
+  training_data:
+    id: ilastik/platynereis_em_training_data
+  version_id: '6028281'
+  version_name: revision 1
+  rdf_source: https://zenodo.org/api/files/9a4c6150-10d1-4c82-9305-8ac21bc435b5/rdf.yaml