From f54a86e046e39e89b4e4d0da68456d9c87c07b0e Mon Sep 17 00:00:00 2001 From: "bioimage.io Bot" Date: Mon, 30 Oct 2023 10:19:47 +0000 Subject: [PATCH 01/19] Update 10.5281/zenodo.7274275 --- .../10.5281/zenodo.7274275/resource.yaml | 103 +++++++++++------- 1 file changed, 63 insertions(+), 40 deletions(-) diff --git a/collection/10.5281/zenodo.7274275/resource.yaml b/collection/10.5281/zenodo.7274275/resource.yaml index 321afe016..f9ae10c4f 100644 --- a/collection/10.5281/zenodo.7274275/resource.yaml +++ b/collection/10.5281/zenodo.7274275/resource.yaml @@ -1,40 +1,63 @@ -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 +- created: '2023-10-27 11:32:10.061066' + doi: 10.5281/zenodo.10047209 + name: CebraNET Cellular Membranes in Volume SEM + status: accepted + 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 From a0ff0727ab1cea5830f569c4d439ef92c5eed912 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Tue, 31 Oct 2023 14:31:05 +0100 Subject: [PATCH 02/19] Update resource.yaml --- collection/10.5281/zenodo.7274275/resource.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/collection/10.5281/zenodo.7274275/resource.yaml b/collection/10.5281/zenodo.7274275/resource.yaml index f9ae10c4f..9c941c675 100644 --- a/collection/10.5281/zenodo.7274275/resource.yaml +++ b/collection/10.5281/zenodo.7274275/resource.yaml @@ -17,7 +17,7 @@ versions: - created: '2023-10-27 11:32:10.061066' doi: 10.5281/zenodo.10047209 name: CebraNET Cellular Membranes in Volume SEM - status: accepted + status: blocked version_id: '10047209' version_name: version from 2023-10-27 rdf_source: https://zenodo.org/api/records/10047209/files/rdf.yaml/content From a1ded50fd61f78753be5624b8c3e93fecbd4e364 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Mon, 13 Nov 2023 14:18:03 +0100 Subject: [PATCH 03/19] Update sha256 --- collection/10.5281/zenodo.5910163/resource.yaml | 6 ++++++ 1 file changed, 6 insertions(+) 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} From 5226f0ba013d03d30a2cd8a9eeb5eda395444ca4 Mon Sep 17 00:00:00 2001 From: Daniel Franco Date: Thu, 30 Nov 2023 20:07:18 +0100 Subject: [PATCH 04/19] Add BiaPy as a community partner --- collection_rdf_template.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/collection_rdf_template.yaml b/collection_rdf_template.yaml index 5a32a5d40..1bff06375 100644 --- a/collection_rdf_template.yaml +++ b/collection_rdf_template.yaml @@ -82,5 +82,8 @@ config: repository: stardist/stardist-bioimage-io branch: main collection_file_name: collection.yaml - + - id: biapy + repository: danifranco/BiaPy-bioimage-io + branch: main + collection_file_name: collection.yaml collection: [] From fdb111370b096590767e83b9517486f7934ec573 Mon Sep 17 00:00:00 2001 From: fynnbe Date: Sat, 2 Dec 2023 17:10:55 +0100 Subject: [PATCH 05/19] don't fail on unresolvable doc_uri --- scripts/download_documentation.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) 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) From ee7d7ce6113a8fe4189e1249a1349d2c0b642e3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Wed, 6 Dec 2023 18:52:22 +0100 Subject: [PATCH 06/19] switch back to official deepimagej collection repo --- collection_rdf_template.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/collection_rdf_template.yaml b/collection_rdf_template.yaml index 1bff06375..178ab4ed6 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: From 4b7b0e15b823da96783bdc36eba8129f9ce798ae Mon Sep 17 00:00:00 2001 From: "bioimage.io Bot" Date: Thu, 14 Dec 2023 16:49:26 +0000 Subject: [PATCH 07/19] Update 10.5281/zenodo.10366411 --- collection/10.5281/zenodo.10366411/resource.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 collection/10.5281/zenodo.10366411/resource.yaml diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml new file mode 100644 index 000000000..75ca1542d --- /dev/null +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -0,0 +1,16 @@ +doi: 10.5281/zenodo.10366411 +id: 10.5281/zenodo.10366411 +nickname: funny-butterfly +nickname_icon: 🦋 +owners: +- 271523 +status: accepted +type: model +versions: +- created: '2023-12-14 12:01:44.656032' + doi: 10.5281/zenodo.10366412 + name: Mitochondria TOM20 artificial labelling - pix2pix + status: accepted + version_id: '10366412' + version_name: version from 2023-12-12 + rdf_source: https://zenodo.org/api/records/10366412/files/rdf.yaml/content From c3842b0d3ccfde4b42afa4aaf15286fa15c2146d Mon Sep 17 00:00:00 2001 From: fynnbe Date: Sat, 23 Dec 2023 02:20:56 +0100 Subject: [PATCH 08/19] ensure static validation uses latest spec with zendo API fixes --- .github/workflows/validate_resources.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 632563622216643327f4beebda3282482d899e6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Tue, 9 Jan 2024 22:40:45 +0100 Subject: [PATCH 09/19] reduce test decimals --- collection/10.5281/zenodo.7274275/resource.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/collection/10.5281/zenodo.7274275/resource.yaml b/collection/10.5281/zenodo.7274275/resource.yaml index 9c941c675..8625a85bd 100644 --- a/collection/10.5281/zenodo.7274275/resource.yaml +++ b/collection/10.5281/zenodo.7274275/resource.yaml @@ -14,6 +14,13 @@ versions: 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 From 333de393e62b61d533104a7d7e014791178b340f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Thu, 11 Jan 2024 08:23:25 +0100 Subject: [PATCH 10/19] fix gh user name --- collection/10.5281/zenodo.6028097/resource.yaml | 4 ++++ 1 file changed, 4 insertions(+) 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 + From 1a7c0992ea65c304adeb34753ea571819449f3c4 Mon Sep 17 00:00:00 2001 From: esgomezm <43643518+esgomezm@users.noreply.github.com> Date: Thu, 11 Jan 2024 15:23:38 +0000 Subject: [PATCH 11/19] Update resource.yaml --- collection/10.5281/zenodo.10366411/resource.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml index 75ca1542d..4fb23272c 100644 --- a/collection/10.5281/zenodo.10366411/resource.yaml +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -10,7 +10,7 @@ versions: - created: '2023-12-14 12:01:44.656032' doi: 10.5281/zenodo.10366412 name: Mitochondria TOM20 artificial labelling - pix2pix - status: accepted + status: blocked version_id: '10366412' version_name: version from 2023-12-12 rdf_source: https://zenodo.org/api/records/10366412/files/rdf.yaml/content From 5f8954b60a468dd23fe3b6872fb251d9f17e8b88 Mon Sep 17 00:00:00 2001 From: "bioimage.io Bot" Date: Fri, 12 Jan 2024 03:23:04 +0000 Subject: [PATCH 12/19] Update 10.5281/zenodo.10366411 --- collection/10.5281/zenodo.10366411/resource.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml index 4fb23272c..53aed0bee 100644 --- a/collection/10.5281/zenodo.10366411/resource.yaml +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -7,6 +7,13 @@ owners: 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 - created: '2023-12-14 12:01:44.656032' doi: 10.5281/zenodo.10366412 name: Mitochondria TOM20 artificial labelling - pix2pix From 7439ec6f095de12a09cae2fa41320af3ecb1442c Mon Sep 17 00:00:00 2001 From: esgomezm <43643518+esgomezm@users.noreply.github.com> Date: Tue, 16 Jan 2024 13:34:11 +0000 Subject: [PATCH 13/19] add dl4miceverywhere as community partner --- collection_rdf_template.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/collection_rdf_template.yaml b/collection_rdf_template.yaml index 178ab4ed6..752e90146 100644 --- a/collection_rdf_template.yaml +++ b/collection_rdf_template.yaml @@ -86,4 +86,8 @@ config: repository: danifranco/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: [] From 9e5ddb830930bf43cfaeddfe2c16111482167d8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Tue, 23 Jan 2024 11:23:25 +0100 Subject: [PATCH 14/19] add pytoch_version --- collection/10.5281/zenodo.10366411/resource.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml index 53aed0bee..85bd1dd1c 100644 --- a/collection/10.5281/zenodo.10366411/resource.yaml +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -14,6 +14,11 @@ versions: 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 From 691e1c2b53af4268804103e99b18329f09ee19b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Tue, 23 Jan 2024 11:44:14 +0100 Subject: [PATCH 15/19] fix adding pytorch_version --- collection/10.5281/zenodo.10366411/resource.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/collection/10.5281/zenodo.10366411/resource.yaml b/collection/10.5281/zenodo.10366411/resource.yaml index 85bd1dd1c..b709bf077 100644 --- a/collection/10.5281/zenodo.10366411/resource.yaml +++ b/collection/10.5281/zenodo.10366411/resource.yaml @@ -15,10 +15,10 @@ versions: 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' + 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 From d4e706a7f4ba8c11c67afae5c2caf89b08d6fbf9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Wed, 24 Jan 2024 19:50:25 +0100 Subject: [PATCH 16/19] lady beetle -> ladybird use common British name --- animals.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: 🦎 From a05571a4d8c2731cfa8532c45c751325234c0738 Mon Sep 17 00:00:00 2001 From: Daniel Franco Date: Thu, 25 Jan 2024 08:38:49 +0100 Subject: [PATCH 17/19] Change BiaPy repo to BiaPyX --- collection_rdf_template.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/collection_rdf_template.yaml b/collection_rdf_template.yaml index 1bff06375..60df37d29 100644 --- a/collection_rdf_template.yaml +++ b/collection_rdf_template.yaml @@ -83,7 +83,7 @@ config: branch: main collection_file_name: collection.yaml - id: biapy - repository: danifranco/BiaPy-bioimage-io + repository: BiaPyX/BiaPy-bioimage-io branch: main collection_file_name: collection.yaml collection: [] From d5184c95c5a112504b335c75fc9caa84a85f80b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Fri, 9 Feb 2024 14:19:16 +0100 Subject: [PATCH 18/19] add sneaky --- adjectives.txt | 1 + 1 file changed, 1 insertion(+) 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 From 057a9fddca0170b2bd3e89ca442e39681fee86a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fynn=20Beuttenm=C3=BCller?= Date: Tue, 13 Feb 2024 14:51:34 +0100 Subject: [PATCH 19/19] increaset PR limit from 20 to 30 --- .github/workflows/auto_update_main.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: