Avoid BioImage.IO Core downloading everything from model zoo entries

[qin-yu]

From this

2025-01-24 16:29:51.676 | INFO     | bioimageio.spec._internal.io_utils:open_bioimageio_yaml:131 - loading philosophical-panda from https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/rdf.yaml
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/rdf.yaml' to file '/home/runner/.cache/bioimageio/520a69782c7dafb6478e43ebcc4679b0-rdf.yaml'.
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/README.md' to file '/home/runner/.cache/bioimageio/42620dae3e3850cefbf0475c7cf590dd-README.md'.
SHA256 hash of downloaded file: fc6e1292ca309bedaca504260cecc9a7bc9f26e9328eb7a051f82a2ceec475e3
Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_input.npy' to file '/home/runner/.cache/bioimageio/101853864f8c8e986b2819c9ac44d0f9-test_input.npy'.

computing SHA256 of 101853864f8c8e986b2819c9ac44d0f9-test_input.npy:   0%|          | 0/5529[72](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:73)8 [00:00<?, ?it/s]
computing SHA256 of 101853864f8c8e986b2819c9ac44d0f9-test_input.npy (result: 6810255f5b5260fe39153f2192bedf30d9899ec4e770976b7813116c467579f0): 100%|██████████| 5529728/5529728 [00:00<00:00, 1340501691.67it/s]
computing SHA256 of 101853864f8c8e986b2819c9ac44d0f9-test_input.npy (result: 6810255f5b5260fe39153f2192bedf30d9899ec4e770976b7813116c467579f0): 100%|██████████| 5529728/5529728 [00:00<00:00, 1267119769.96it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_output.npy' to file '/home/runner/.cache/bioimageio/57b964a123db3ff8400bcce3ef902b18-test_output.npy'.

computing SHA256 of 57b964a123db3ff8400bcce3ef902b18-test_output.npy:   0%|          | 0/8294528 [00:00<?, ?it/s]
computing SHA256 of 57b964a123db3ff8400bcce3ef902b18-test_output.npy (result: d802e3024da80bff93a9ec50fbe50b9c3946534aab1b60b911511111a8e2dbca): 100%|██████████| 8294528/8294528 [00:00<00:00, 13320[73](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:74)820.44it/s]
computing SHA256 of 57b964a123db3ff8400bcce3ef902b18-test_output.npy (result: d802e3024da80bff93a9ec50fbe50b9c3946534aab1b60b911511111a8e2dbca): 100%|██████████| 8294528/8294528 [00:00<00:00, 1282808700.90it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_style.npy' to file '/home/runner/.cache/bioimageio/0b712fa8abf8707021a71[74](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:75)7e726bf7c-test_style.npy'.

computing SHA256 of 0b712fa8abf8707021a71747e726bf7c-test_style.npy:   0%|          | 0/76928 [00:00<?, ?it/s]
computing SHA256 of 0b712fa8abf8707021a71747e726bf7c-test_style.npy (result: ab464b406f9050561b40f7d76700ab5edf3aca97e31fe9a6069a51aeeca8bc81): 100%|██████████| 76928/76928 [00:00<00:00, 517912388.62it/s]
computing SHA256 of 0b712fa8abf8707021a71747e726bf7c-test_style.npy (result: ab464b406f9050561b40f7d76700ab5edf3aca97e31fe9a6069a51aeeca8bc81): 100%|██████████| 76928/76928 [00:00<00:00, 19251[75](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:76)52.57it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_downsampled_0.npy' to file '/home/runner/.cache/bioimageio/d0abd68ef3844b0d6fbed811e0fed878-test_downsampled_0.npy'.

computing SHA256 of d0abd68ef3844b0d6fbed811e0fed878-test_downsampled_0.npy:   0%|          | 0/88473728 [00:00<?, ?it/s]
computing SHA256 of d0abd68ef3844b0d6fbed811e0fed878-test_downsampled_0.npy (result: 67df53fb440e94dbb9c8e4003dcbde158646a7975c4878cacdd251e1fcfb4225): 100%|██████████| 88473728/88473728 [00:00<00:00, 1368234468.02it/s]
computing SHA256 of d0abd68ef3844b0d6fbed811e0fed878-test_downsampled_0.npy (result: 67df53fb440e94dbb9c8e4003dcbde158646a7975c4878cacdd251e1fcfb4225): 100%|██████████| 88473728/88473728 [00:00<00:00, 136152[76](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:77)08.58it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_downsampled_1.npy' to file '/home/runner/.cache/bioimageio/3765cac1d92a49daf0d6ec949919aeb1-test_downsampled_1.npy'.

computing SHA256 of 3765cac1d92a49daf0d6ec949919aeb1-test_downsampled_1.npy:   0%|          | 0/44236928 [00:00<?, ?it/s]
computing SHA256 of 3765cac1d92a49daf0d6ec949919aeb1-test_downsampled_1.npy (result: cb4addbd763d96731ebd18ed001b87ab7195ec9198f01a753a363a06c27bfb1c): 100%|██████████| 44236928/44236928 [00:00<00:00, 1367172813.64it/s]
computing SHA256 of 3765cac1d92a49daf0d6ec949919aeb1-test_downsampled_1.npy (result: cb4addbd763d96731ebd18ed001b87ab7195ec9198f01a753a363a06c27bfb1c): 100%|██████████| 44236928/44236928 [00:00<00:00, 1354794156.08it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_downsampled_2.npy' to file '/home/runner/.cache/bioimageio/7251078a2afa8713384a3103878dd09d-test_downsampled_2.npy'.

computing SHA256 of 7251078a2afa8713384a3103878dd09d-test_downsampled_2.npy:   0%|          | 0/22118528 [00:00<?, ?it/s]
computing SHA256 of 7251078a2afa8713384a3103878dd09d-test_downsampled_2.npy (result: 9c0225b94d84fcc3adfb9a73eef1303d6adb318b57a5a801e0e2e1638b458e72): 100%|██████████| 22118528/22118528 [00:00<00:00, 1361668410.33it/s]
computing SHA256 of 7251078a2afa8713384a3103878dd09d-test_downsampled_2.npy (result: 9c0225b94d84fcc3adfb9a73eef1303d6adb318b57a5a801e0e2e1638b458e72): 100%|██████████| 22118528/22118528 [00:00<00:00, 1338930701.[77](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:78)it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/test_downsampled_3.npy' to file '/home/runner/.cache/bioimageio/e434cdc3ea3e7ecfb752cdc00161[78](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:79)75-test_downsampled_3.npy'.

computing SHA256 of e434cdc3ea3e7ecfb752cdc001617875-test_downsampled_3.npy:   0%|          | 0/11059328 [00:00<?, ?it/s]
computing SHA256 of e434cdc3ea3e7ecfb752cdc001617875-test_downsampled_3.npy (result: 1ea789ff37d47197c847b585[79](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:80)9f7d063e7592b0c5e9c3094fd0e3ac209b7fc2): 100%|██████████| 11059328/11059328 [00:00<00:00, 1373144183.65it/s]
computing SHA256 of e434cdc3ea3e7ecfb752cdc001617875-test_downsampled_3.npy (result: 1ea789ff37d47197c847b585799f7d063e7592b0c5e9c3094fd0e3ac209b7fc2): 100%|██████████| 11059328/11059328 [00:00<00:00, 1329269362.33it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/cpnet_wrapper.py' to file '/home/runner/.cache/bioimageio/00bd170d6c9de6a391d6869f59058847-cpnet_wrapper.py'.

computing SHA256 of 00bd170d6c9de6a391d6869f59058847-cpnet_wrapper.py:   0%|          | 0/11053 [00:00<?, ?it/s]
computing SHA256 of 00bd170d6c9de6a391d6869f59058847-cpnet_wrapper.py (result: b8b947cdd0ea8f5b98bd7be5f12f38bb1ea1ebe0b455c62d9a6389cd21d134bf): 100%|██████████| 11053/11053 [00:00<00:00, 147173467.02it/s]
computing SHA256 of 00bd170d6c9de6a391d6869f59058847-cpnet_wrapper.py (result: b8b947cdd0ea8f5b98bd7be5f12f38bb1ea1ebe0b455c62d9a6389cd21d134bf): 100%|██████████| 11053/11053 [00:00<00:00, 28687897.35it/s] 
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/cp_state_dict_1135_gold.pth' to file '/home/runner/.cache/bioimageio/8dbb20d5a3cb3a3dfdb5101a671861ce-cp_state_dict_1135_gold.pth'.

computing SHA256 of 8dbb20d5a3cb3a3dfdb5101a671861ce-cp_state_dict_1135_gold.pth:   0%|          | 0/26556687 [00:00<?, ?it/s]
computing SHA256 of 8dbb20d5a3cb3a3dfdb5101a671861ce-cp_state_dict_1135_gold.pth (result: 26c277f3b8f6ca5aab30b4b0a832601aea60183cbed1c2333576f4135a643eb2): 100%|██████████| 26556687/26556687 [00:00<00:00, 1385235897.41it/s]
computing SHA256 of 8dbb20d5a3cb3a3dfdb5101a671861ce-cp_state_dict_1135_gold.pth (result: 26c277f3b8f6ca5aab30b4b0a832601aea60183cbed1c2333576f4135a643eb2): 100%|██████████| 26556687/26556687 [00:00<00:00, 1366910692.51it/s]
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/cp_traced_1135_gold.pt' to file '/home/runner/.cache/bioimageio/17fee110c39ccad7c3cb36d00d2fdd2c-cp_traced_1135_gold.pt'.

computing SHA256 of 17fee110c39ccad7c3cb36d00d2fdd2c-cp_traced_1135_gold.pt:   0%|          | 0/26[81](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:82)2339 [00:00<?, ?it/s]
computing SHA256 of 17fee110c39ccad7c3cb36d00d2fdd2c-cp_traced_1135_gold.pt (result: f61bae146ab522902350eadda1d509ac1037726fe6d7fb63f6a8a314021d63e7): 100%|██████████| 26812339/26812339 [00:00<00:00, 1384043871.28it/s]
computing SHA256 of 17fee110c39ccad7c3cb36d00d2fdd2c-cp_traced_1135_gold.pt (result: f61bae146ab522902350eadda1d509ac1037726fe6d7fb63f6a8a314021d63e7): 100%|██████████| 26812339/26812339 [00:00<00:00, 136429[82](https://github.com/kreshuklab/plant-seg/actions/runs/12953461209/job/36133179407#step:12:83)01.10it/s]
tests/functionals/prediction/test_prediction_biio.py INFO: P [MainThread] 2025-01-24 16:30:48,206 plantseg.functionals.prediction.prediction - Model expects these inputs: ['raw'].
2025-01-24 16:30:48.316 | WARNING  | bioimageio.spec.model.v0_5:get_axis_size:2568 - Ignoring unexpected size increment factor (n) for fixed size axis 'channel' of tensor 'raw'.

predict sample raw with philosophical-panda:   0%|          | 0/1 [00:00<?, ?block/s]
predict sample raw with philosophical-panda: 100%|██████████| 1/1 [00:04<00:00,  4.65s/block]
predict sample raw with philosophical-panda: 100%|██████████| 1/1 [00:04<00:00,  4.65s/block]
WARNING: P [MainThread] 2025-01-24 16:30:53,024 plantseg.functionals.prediction.prediction - Model has more than one output tensor. PlantSeg does not support this yet.

to this

2025-01-27 14:21:39.538 | INFO     | bioimageio.spec._internal.io_utils:open_bioimageio_yaml:131 - loading philosophical-panda from https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/rdf.yaml
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/rdf.yaml' to file '/home/runner/.cache/bioimageio/520a69782c7dafb6478e43ebcc4679b0-rdf.yaml'.
tests/functionals/prediction/test_prediction_biio.py INFO: P [MainThread] 2025-01-27 14:21:41,092 plantseg.functionals.prediction.prediction - Model expects these inputs: ['raw'].
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/cpnet_wrapper.py' to file '/home/runner/.cache/bioimageio/00bd170d6c9de6a391d6869f59058847-cpnet_wrapper.py'.
SHA256 hash of downloaded file: b8b947cdd0ea8f5b98bd7be5f12f38bb1ea1ebe0b455c62d9a6389cd21d134bf
Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.
Downloading data from 'https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimage.io/philosophical-panda/0.0.11/files/cp_state_dict_1135_gold.pth' to file '/home/runner/.cache/bioimageio/8dbb20d5a3cb3a3dfdb5101a671861ce-cp_state_dict_1135_gold.pth'.
2025-01-27 14:22:44.008 | WARNING  | bioimageio.spec.model.v0_5:get_axis_size:2568 - Ignoring unexpected size increment factor (n) for fixed size axis 'channel' of tensor 'raw'.

predict sample raw with philosophical-panda:   0%|          | 0/1 [00:00<?, ?block/s]
predict sample raw with philosophical-panda: 100%|██████████| 1/1 [00:04<00:00,  4.62s/block]
predict sample raw with philosophical-panda: 100%|██████████| 1/1 [00:04<00:00,  4.62s/block]
WARNING: P [MainThread] 2025-01-27 14:22:48,690 plantseg.functionals.prediction.prediction - Model has more than one output tensor. PlantSeg does not support this yet.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 67.59%. Comparing base (564bfa4) to head (c4a5154).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #386   +/-   ##
=======================================
  Coverage   67.59%   67.59%           
=======================================
  Files          76       76           
  Lines        5506     5506           
=======================================
  Hits         3722     3722           
  Misses       1784     1784           

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[qin-yu]

For some reason, Fynn's official solution in bioimage-io/core-bioimage-io-python#451 doesn’t seem to work, but there is a workaround.