diff --git a/.github/workflows/auto_update_main.yaml b/.github/workflows/auto_update_main.yaml index 32261eb3d..44bbb9b28 100644 --- a/.github/workflows/auto_update_main.yaml +++ b/.github/workflows/auto_update_main.yaml @@ -73,7 +73,7 @@ jobs: - name: update external resources id: update_external shell: bash -l {0} - run: python scripts/update_external_resources.py --max-resource-count 20 ${{ github.event_name == 'pull_request' && '--no-ignore-status-5xx' || '--ignore-status-5xx' }} + run: python scripts/update_external_resources.py --max-resource-count 30 ${{ github.event_name == 'pull_request' && '--no-ignore-status-5xx' || '--ignore-status-5xx' }} - name: "Upload collection update" uses: actions/upload-artifact@v3 with: diff --git a/.github/workflows/validate_resources.yaml b/.github/workflows/validate_resources.yaml index f98a82e56..eba9acaaf 100644 --- a/.github/workflows/validate_resources.yaml +++ b/.github/workflows/validate_resources.yaml @@ -52,7 +52,7 @@ jobs: - conda-forge create-args: >- # script dependencies bioimageio.core - bioimageio.spec + bioimageio.spec>=0.4.9.post5 lxml packaging typer diff --git a/adjectives.txt b/adjectives.txt index 31f28f264..c2c36c976 100644 --- a/adjectives.txt +++ b/adjectives.txt @@ -143,6 +143,7 @@ shivering shy sincere smart +sneaky sociable solitary straightforward diff --git a/animals.yaml b/animals.yaml index 3e98822a2..43e0e84a4 100644 --- a/animals.yaml +++ b/animals.yaml @@ -38,7 +38,7 @@ honeybee: 🐝 horse: 🐎 kangaroo: 🦘 koala: 🐨 -lady beetle: 🐞 +ladybird: 🐞 leopard: 🐆 lion: 🦁 lizard: 🦎 diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml new file mode 100644 index 000000000..b709bf077 --- /dev/null +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -0,0 +1,28 @@ +doi: 10.5281/zenodo.10366411 +id: 10.5281/zenodo.10366411 +nickname: funny-butterfly +nickname_icon: 🦋 +owners: +- 271523 +status: accepted +type: model +versions: +- created: '2024-01-11 15:31:40.010085' + doi: 10.5281/zenodo.10492722 + name: Mitochondria TOM20 artificial labelling - pix2pix + status: accepted + version_id: '10492722' + version_name: version from 2024-01-11 + rdf_source: https://zenodo.org/api/records/10492722/files/rdf.yaml/content + weights: + torchscript: + source: latest_net_G_torchscript.pt + sha256: 86f7daa11efe1071d3d52e698d462113409ee543827e76f597a60e5a1b6dd71c + pytorch_version: '2.1' +- created: '2023-12-14 12:01:44.656032' + doi: 10.5281/zenodo.10366412 + name: Mitochondria TOM20 artificial labelling - pix2pix + status: blocked + version_id: '10366412' + version_name: version from 2023-12-12 + rdf_source: https://zenodo.org/api/records/10366412/files/rdf.yaml/content diff --git a/collection/10.5281/zenodo.5910163/resource.yaml b/collection/10.5281/zenodo.5910163/resource.yaml index ac54ea7d3..ce430f193 100644 --- a/collection/10.5281/zenodo.5910163/resource.yaml +++ b/collection/10.5281/zenodo.5910163/resource.yaml @@ -15,6 +15,12 @@ versions: status: accepted version_id: '5942853' version_name: revision 1 + weights: + onnx: + authors: + - name: Wei OUYANG + source: ./densenet_model.onnx + sha256: 0cb72ff5e414630de95674a7d523da0de19850b1cada4712201699fdd960c1b0 - {created: '2022-01-27 10:28:20.092577', doi: 10.5281/zenodo.5910164, name: HPA Bestfitting Densenet, rdf_source: 'https://zenodo.org/api/files/5be7a94a-0f23-4658-bee3-d160c6eb1c83/rdf.yaml', status: blocked, version_id: '5910164', version_name: revision 1} diff --git a/collection/10.5281/zenodo.6028097/resource.yaml b/collection/10.5281/zenodo.6028097/resource.yaml index 53c8dc9d0..4dc307580 100644 --- a/collection/10.5281/zenodo.6028097/resource.yaml +++ b/collection/10.5281/zenodo.6028097/resource.yaml @@ -15,3 +15,7 @@ versions: training_data: {id: ilastik/platynereis_em_training_data} version_id: '6028098' version_name: revision 1 + maintainers: + - github_user: constantinpape + name: Constantin Pape + diff --git a/collection/10.5281/zenodo.7274275/resource.yaml b/collection/10.5281/zenodo.7274275/resource.yaml index 321afe016..8625a85bd 100644 --- a/collection/10.5281/zenodo.7274275/resource.yaml +++ b/collection/10.5281/zenodo.7274275/resource.yaml @@ -1,40 +1,70 @@ -doi: 10.5281/zenodo.7274275 -id: 10.5281/zenodo.7274275 -nickname: joyful-deer -nickname_icon: "\U0001F98C" -owners: [432585] -status: accepted -type: model -versions: -- cite: - - {doi: 10.1101/2023.04.06.535829, text: 'Hennies et al. 2023, CebraEM: A practical - workflow to segment cellular organelles in volume SEM datasets using a transferable - CNN-based membrane prediction'} - config: - bioimageio: - test_kwargs: - pytorch_state_dict: {decimal: 2} - torchscript: {decimal: 2} - created: '2023-07-07 10:12:51.478763' - doi: 10.5281/zenodo.8123818 - name: CebraNET Cellular Membranes in Volume SEM - parent: {sha256: f19d75e9ea394fd7b0bd9c86276de41b10318245315fa4d2cc6e24e63c6371a1, - uri: 'https://doi.org/10.5281/zenodo.7274275'} - rdf_source: https://zenodo.org/api/records/8123818/files/rdf.yaml/content - status: accepted - version_id: '8123818' - version_name: version 3 -- {created: '2023-07-06 08:12:02.329226', doi: 10.5281/zenodo.8119068, name: CebraNET - Cellular Membranes in Volume SEM, rdf_source: 'https://zenodo.org/api/files/34d12fe0-da40-47f7-9795-3af0e9c1baf6/rdf.yaml', - status: blocked, version_id: '8119068', version_name: version 2} -- config: - bioimageio: - test_kwargs: - pytorch_state_dict: {decimal: 2} - created: '2022-11-02 13:52:32.578744' - doi: 10.5281/zenodo.7274276 - name: CebraNET Cellular Membranes in Volume SEM - rdf_source: https://zenodo.org/api/files/c95661ca-b06a-464f-810c-5c9804ebe982/rdf.yaml - status: accepted - version_id: '7274276' - version_name: version 1 +doi: 10.5281/zenodo.7274275 +id: 10.5281/zenodo.7274275 +nickname: joyful-deer +nickname_icon: 🦌 +owners: +- 432585 +status: accepted +type: model +versions: +- created: '2023-10-27 11:34:30.252675' + doi: 10.5281/zenodo.10047226 + name: CebraNET Cellular Membranes in Volume SEM + status: accepted + version_id: '10047226' + version_name: version from 2023-10-27 + rdf_source: https://zenodo.org/api/records/10047226/files/rdf.yaml/content + config: + bioimageio: + test_kwargs: + pytorch_state_dict: + decimal: 2 + torchscript: + decimal: 2 +- created: '2023-10-27 11:32:10.061066' + doi: 10.5281/zenodo.10047209 + name: CebraNET Cellular Membranes in Volume SEM + status: blocked + version_id: '10047209' + version_name: version from 2023-10-27 + rdf_source: https://zenodo.org/api/records/10047209/files/rdf.yaml/content +- cite: + - doi: 10.1101/2023.04.06.535829 + text: 'Hennies et al. 2023, CebraEM: A practical workflow to segment cellular + organelles in volume SEM datasets using a transferable CNN-based membrane prediction' + config: + bioimageio: + test_kwargs: + pytorch_state_dict: + decimal: 2 + torchscript: + decimal: 2 + created: '2023-07-07 10:12:51.478763' + doi: 10.5281/zenodo.8123818 + name: CebraNET Cellular Membranes in Volume SEM + parent: + sha256: f19d75e9ea394fd7b0bd9c86276de41b10318245315fa4d2cc6e24e63c6371a1 + uri: https://doi.org/10.5281/zenodo.7274275 + status: accepted + version_id: '8123818' + version_name: version 3 + rdf_source: https://zenodo.org/api/records/8123818/files/rdf.yaml/content +- created: '2023-07-06 08:12:02.329226' + doi: 10.5281/zenodo.8119068 + name: CebraNET Cellular Membranes in Volume SEM + status: blocked + version_id: '8119068' + version_name: version 2 + rdf_source: https://zenodo.org/api/files/34d12fe0-da40-47f7-9795-3af0e9c1baf6/rdf.yaml +- config: + bioimageio: + test_kwargs: + pytorch_state_dict: + decimal: 2 + created: '2022-11-02 13:52:32.578744' + doi: 10.5281/zenodo.7274276 + name: CebraNET Cellular Membranes in Volume SEM + status: accepted + version_id: '7274276' + version_name: version 1 + rdf_source: https://zenodo.org/api/files/c95661ca-b06a-464f-810c-5c9804ebe982/rdf.yaml diff --git a/collection_rdf_template.yaml b/collection_rdf_template.yaml index 5a32a5d40..f90c3b00a 100644 --- a/collection_rdf_template.yaml +++ b/collection_rdf_template.yaml @@ -39,7 +39,7 @@ config: branch: master collection_file_name: manifest.bioimage.io.yaml - id: deepimagej - repository: fynnbe/models + repository: deepimagej/models branch: master collection_file_name: manifest.bioimage.io.yaml test_summaries: @@ -82,5 +82,12 @@ config: repository: stardist/stardist-bioimage-io branch: main collection_file_name: collection.yaml - + - id: biapy + repository: BiaPyX/BiaPy-bioimage-io + branch: main + collection_file_name: collection.yaml + - id: dl4miceverywhere + repository: HenriquesLab/DL4MicEverywhere-bioimage-io + branch: main + collection_file_name: collection.yaml collection: [] diff --git a/scripts/download_documentation.py b/scripts/download_documentation.py index 48cc2b3a4..591b8fc85 100644 --- a/scripts/download_documentation.py +++ b/scripts/download_documentation.py @@ -9,7 +9,8 @@ def main( - folder: Path = Path(__file__).parent / "../dist", # nested folders with rdf.yaml files + folder: Path = Path(__file__).parent + / "../dist", # nested folders with rdf.yaml files ): """Download the documentation file for every rdf.yaml found in (subfolders of) folder""" if not folder.exists(): @@ -34,9 +35,12 @@ def main( try: resolve_source( - doc_uri, output=rdf_path.with_name(f"documentation.{type_ext}"), pbar=partial(tqdm, disable=True) + doc_uri, + output=rdf_path.with_name(f"documentation.{type_ext}"), + pbar=partial(tqdm, disable=True), ) - except ValueError: + except Exception as e: + warnings.warn(f"failed to resolve doc_ui: {e}") _ = rdf_path.with_name("documentation.md").write_text(doc_uri)