Ecosyste.ms: Issues

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GitHub / bioimage-io/core-bioimage-io-python issues and pull requests

#425 - Add quick links within model_usage.ipynb

Pull Request - State: closed - Opened by FynnBe about 1 month ago
Labels: enhancement, ci, github_actions

#424 - Collections abc fix

Pull Request - State: closed - Opened by FynnBe about 1 month ago
Labels: bug, ci, github_actions

#423 - Issue with predict_many in bioimageio.core using Python 3.10.12

Issue - State: closed - Opened by falibabaei about 1 month ago - 1 comment

#422 - Missed function in package

Issue - State: closed - Opened by yhfu2307 about 2 months ago - 1 comment

#421 - Model test failed

Issue - State: open - Opened by oeway 2 months ago - 2 comments

#420 - No test-model command

Pull Request - State: closed - Opened by oeway 2 months ago - 1 comment
Labels: documentation, testing

#419 - export models defined in code

Issue - State: open - Opened by FynnBe 3 months ago

#418 - Use relative and absolute tolerance for validating model outputs

Pull Request - State: closed - Opened by melisande-c 3 months ago - 1 comment

#417 - kwargs of `ArchitectureFromLibraryDescr` is restricted to `YamlValue`

Issue - State: closed - Opened by thodkatz 3 months ago - 4 comments

#416 - Validate model output with precision relative to the values of the data

Issue - State: closed - Opened by melisande-c 3 months ago - 7 comments

#415 - New predict command: tiled prediction not working for model v0.4

Issue - State: open - Opened by constantinpape 3 months ago - 3 comments

#414 - New predict command: how to pass input_block_shape?

Issue - State: open - Opened by constantinpape 3 months ago - 3 comments

#413 - New predict command: normalization not applied?

Issue - State: closed - Opened by constantinpape 3 months ago - 3 comments

#412 - New predict command: axis naming is inconsistent

Issue - State: closed - Opened by constantinpape 3 months ago - 5 comments

#411 - Create a common interface for weight conversion

Pull Request - State: open - Opened by thodkatz 3 months ago

#411 - Create a common interface for weight conversion

Pull Request - State: open - Opened by thodkatz 3 months ago

#409 - Prediction with one channel not working on format version v0.4

Issue - State: closed - Opened by IvanHCenalmor 3 months ago - 2 comments
Labels: enhancement, performance

#409 - Prediction with one channel not working on format version v0.4

Issue - State: closed - Opened by IvanHCenalmor 3 months ago - 2 comments
Labels: enhancement, performance

#408 - Update _torchscript_model_adapter.py

Pull Request - State: open - Opened by esgomezm 4 months ago - 3 comments

#408 - Update _torchscript_model_adapter.py

Pull Request - State: open - Opened by esgomezm 4 months ago - 3 comments

#407 - Update model_usage notebook

Pull Request - State: closed - Opened by thodkatz 4 months ago

#407 - Update model_usage notebook

Pull Request - State: closed - Opened by thodkatz 4 months ago

#406 - add predict command

Pull Request - State: closed - Opened by FynnBe 4 months ago - 3 comments
Labels: documentation, enhancement

#405 - How to run 'powerful-fish' on my image?

Issue - State: open - Opened by tibuch 4 months ago - 2 comments
Labels: enhancement

#404 - bump patch

Pull Request - State: closed - Opened by FynnBe 4 months ago
Labels: documentation

#404 - bump patch

Pull Request - State: closed - Opened by FynnBe 4 months ago
Labels: documentation

#403 - Make sure torchscript models run in eval mode

Pull Request - State: closed - Opened by FynnBe 4 months ago

#402 - always test all weight formats

Pull Request - State: closed - Opened by FynnBe 4 months ago
Labels: documentation, testing

#401 - Fix prediction with blocking

Pull Request - State: closed - Opened by thodkatz 4 months ago - 2 comments

#399 - Improve model adapters

Pull Request - State: closed - Opened by FynnBe 4 months ago

#398 - Further improve example notebook

Issue - State: closed - Opened by FynnBe 4 months ago

#395 - adding example bioimageio.core_usage notebook and requirements txt file

Pull Request - State: open - Opened by mariana-gferreira 5 months ago - 2 comments

#395 - adding example bioimageio.core_usage notebook and requirements txt file

Pull Request - State: closed - Opened by mariana-gferreira 5 months ago - 2 comments

#394 - Update model usage example

Pull Request - State: closed - Opened by FynnBe 5 months ago
Labels: documentation

#393 - Improve backward compatibility

Pull Request - State: closed - Opened by FynnBe 6 months ago - 1 comment
Labels: documentation

#392 - Half precision support?

Issue - State: closed - Opened by benjijamorris 6 months ago - 1 comment

#391 - How to apply a model from Python

Issue - State: open - Opened by haesleinhuepf 6 months ago - 6 comments

#390 - fix broken link

Pull Request - State: closed - Opened by haesleinhuepf 6 months ago

#389 - bump patch

Pull Request - State: closed - Opened by FynnBe 6 months ago
Labels: documentation

#388 - patch release: do not assume inputs are tileable

Pull Request - State: closed - Opened by FynnBe 7 months ago
Labels: documentation

#387 - skip simple procs if their input is not present

Pull Request - State: closed - Opened by FynnBe 7 months ago - 1 comment

#386 - Optional inputs not working

Issue - State: closed - Opened by constantinpape 7 months ago
Labels: bug

#385 - Fix data dep size

Pull Request - State: closed - Opened by FynnBe 7 months ago
Labels: bug, documentation

#384 - Prediction for a single block for SAM not working

Issue - State: closed - Opened by constantinpape 7 months ago - 1 comment

#383 - Plans for weight converter? Common interface.

Issue - State: open - Opened by constantinpape 7 months ago - 2 comments

#382 - imageio version too restrictive?

Issue - State: closed - Opened by danifranco 7 months ago - 2 comments

#381 - Update notebooks

Pull Request - State: closed - Opened by FynnBe 7 months ago
Labels: documentation

#380 - Pytorch Lightning model adaptor

Issue - State: open - Opened by jdeschamps 7 months ago
Labels: good first issue

#379 - remove singledispatch for better static typing

Pull Request - State: closed - Opened by FynnBe 7 months ago
Labels: documentation, removal

#378 - Fix pytorch_state_dict import from library

Pull Request - State: closed - Opened by jdeschamps 7 months ago - 2 comments

#377 - bump post

Pull Request - State: open - Opened by FynnBe 7 months ago - 1 comment
Labels: documentation

#375 - Previously working code has stopped to work with import error

Issue - State: closed - Opened by jhennies 7 months ago - 8 comments

#374 - add ruff to dev envs

Pull Request - State: closed - Opened by FynnBe 7 months ago
Labels: enhancement

#372 - Add Tile object to represent tiled samples

Pull Request - State: closed - Opened by FynnBe 8 months ago
Labels: enhancement

#372 - Add Tile object to represent tiled samples

Pull Request - State: open - Opened by FynnBe 8 months ago
Labels: enhancement

#371 - WIP - prediction module

Pull Request - State: closed - Opened by mese79 8 months ago - 1 comment

#370 - Fix optional inputs for pytorch

Pull Request - State: closed - Opened by constantinpape 8 months ago
Labels: bug

#370 - Fix optional inputs for pytorch

Pull Request - State: closed - Opened by constantinpape 8 months ago
Labels: bug

#369 - Error when importing

Issue - State: closed - Opened by danifranco 11 months ago - 2 comments

#368 - bug when `add_deepimagej_config=True` in `build_model`

Issue - State: open - Opened by esgomezm 11 months ago - 5 comments

#367 - Fixes conftest

Pull Request - State: closed - Opened by Tomaz-Vieira 12 months ago

#366 - Fixes typing issues in core.io

Pull Request - State: closed - Opened by Tomaz-Vieira 12 months ago

#365 - Spec v0 5 fixing pytorch conversion

Pull Request - State: closed - Opened by Tomaz-Vieira 12 months ago

#364 - Fixes some typing issues in tensor flow adapter

Pull Request - State: closed - Opened by Tomaz-Vieira 12 months ago - 1 comment

#363 - Fixes type-checking with spec v0.5 in torchscript model adapter

Pull Request - State: closed - Opened by Tomaz-Vieira 12 months ago

#362 - Improve weights conversion to ONNX

Issue - State: open - Opened by FynnBe about 1 year ago - 1 comment
Labels: good first issue

#361 - pin bioimageio.spec again to 0.4.9.*

Pull Request - State: closed - Opened by FynnBe about 1 year ago

#360 - Release 0.5.10

Pull Request - State: closed - Opened by FynnBe about 1 year ago
Labels: documentation

#359 - Fix critical bug in predict with tiling

Pull Request - State: closed - Opened by constantinpape about 1 year ago - 1 comment
Labels: bug

#357 - fixed link

Pull Request - State: closed - Opened by jo-mueller about 1 year ago

#356 - Link in example broken

Issue - State: closed - Opened by jo-mueller about 1 year ago - 1 comment

#355 - Loading model resource gives assertion error

Issue - State: open - Opened by jhennies about 1 year ago - 2 comments

#354 - Add/improve weight converters

Issue - State: open - Opened by FynnBe about 1 year ago
Labels: good first issue

#353 - Investigate integration of aicsimageio

Issue - State: open - Opened by FynnBe about 1 year ago

#352 - developer documentation

Issue - State: open - Opened by FynnBe about 1 year ago
Labels: documentation

#350 - programmatic access for datasets

Issue - State: open - Opened by FynnBe about 1 year ago
Labels: enhancement, medium-term-goal

#348 - Fix a tiny typo

Pull Request - State: closed - Opened by matuskalas about 1 year ago

#347 - Hackathon 2023/10 notes

Issue - State: closed - Opened by FynnBe about 1 year ago - 2 comments

#346 - Update to bioimageio.spec=0.5

Pull Request - State: closed - Opened by FynnBe about 1 year ago
Labels: documentation, ci, github_actions

#345 - Reproducibility test for model creation fails

Issue - State: closed - Opened by Justin-Sonneck over 1 year ago - 3 comments

#344 - validate markdown documentation

Issue - State: open - Opened by FynnBe about 2 years ago - 5 comments

#343 - Provide our CI testing environment as docker containers

Issue - State: open - Opened by oeway over 1 year ago

#342 - Image normalization causing test_model test failure

Issue - State: closed - Opened by veegalinova over 1 year ago - 3 comments

#341 - MONAI translation to BioImage format

Issue - State: open - Opened by IvanHCenalmor over 1 year ago - 1 comment
Labels: enhancement

#340 - Check file integrity with SHA256 as part of any resource test

Pull Request - State: closed - Opened by FynnBe over 1 year ago - 1 comment
Labels: testing

#339 - Bump patch version

Pull Request - State: closed - Opened by constantinpape over 1 year ago - 1 comment

#338 - Ci env caching

Pull Request - State: closed - Opened by FynnBe over 1 year ago
Labels: ci, github_actions

#337 - Fix tests

Pull Request - State: closed - Opened by FynnBe over 1 year ago - 7 comments
Labels: bug, ci, github_actions, testing

#336 - Add multichan output model to test issues in build-spec

Pull Request - State: closed - Opened by constantinpape over 1 year ago - 2 comments
Labels: enhancement, testing

#335 - Implement sha256 check for the model

Issue - State: closed - Opened by oeway over 1 year ago - 1 comment

#334 - Better default io names in build_model()

Issue - State: closed - Opened by FynnBe over 1 year ago - 13 comments
Labels: enhancement

#333 - cache downloads and mamba envs

Pull Request - State: closed - Opened by FynnBe over 1 year ago
Labels: ci, github_actions

#332 - disable tracking during testing

Pull Request - State: closed - Opened by FynnBe over 1 year ago