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

#327 - update gh actions

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

#326 - do not visit root_path

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

#325 - fix variable not defined

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

#324 - import tqdm from bioimageio.spec and update pre-commit

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

#323 - CI update: use micromamba instead of miniconda

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

#322 - TF: prevent model compilation

Pull Request - State: closed - Opened by jdeschamps over 1 year ago - 5 comments

#321 - add_weights example in model_creation notebook

Pull Request - State: closed - Opened by ivan-ea almost 2 years ago

#320 - validate (citation) dois

Issue - State: open - Opened by FynnBe almost 2 years ago

#319 - Improve TF Model Adapter

Issue - State: open - Opened by FynnBe almost 2 years ago

#318 - MyPy check

Pull Request - State: closed - Opened by FynnBe almost 2 years ago - 1 comment
Labels: ci, github_actions

#317 - Can I check if my tensorflow model is compatible

Issue - State: open - Opened by odinsbane almost 2 years ago - 12 comments

#316 - bioimageio.core.contrib

Pull Request - State: closed - Opened by FynnBe almost 2 years ago - 1 comment
Labels: ci, github_actions

#315 - fix 'None' is not iterable

Pull Request - State: closed - Opened by FynnBe almost 2 years ago - 1 comment
Labels: bug

#314 - Error if no preprocessing when adding deepimagej config

Issue - State: closed - Opened by ivan-ea almost 2 years ago - 3 comments

#313 - only warn about unknown run mode; don't raise

Pull Request - State: closed - Opened by FynnBe almost 2 years ago

#312 - Play with how a contrib module could look like

Pull Request - State: closed - Opened by FynnBe almost 2 years ago - 24 comments

#311 - Support adding multiple weights using build_model

Issue - State: open - Opened by oeway almost 2 years ago - 4 comments

#310 - Workflow RDF

Pull Request - State: open - Opened by FynnBe almost 2 years ago - 6 comments

#309 - Use map_location cpu in weight-converter

Pull Request - State: closed - Opened by constantinpape almost 2 years ago

#308 - Weight conversion error from GPU/CPU weights

Issue - State: closed - Opened by ivan-ea almost 2 years ago - 2 comments

#307 - Cuda not available when installing using the command in README

Issue - State: closed - Opened by ivan-ea almost 2 years ago - 5 comments

#306 - Update setup.py

Pull Request - State: closed - Opened by FynnBe almost 2 years ago

#305 - Update VERSION

Pull Request - State: closed - Opened by constantinpape almost 2 years ago

#304 - Add support for tensorflow 2

Pull Request - State: closed - Opened by constantinpape almost 2 years ago - 10 comments
Labels: enhancement, ci, github_actions

#303 - Validator does not run the last version of the spec written by the library

Issue - State: closed - Opened by esgomezm almost 2 years ago - 1 comment

#302 - Weight conversion for tensorflow 2 is not yet implemented.

Issue - State: closed - Opened by esgomezm almost 2 years ago - 4 comments

#301 - added model.eval() and debugged resource tests

Pull Request - State: closed - Opened by jhennies almost 2 years ago

#300 - Implement scale_mean_var

Pull Request - State: closed - Opened by FynnBe almost 2 years ago

#299 - basic support for scaling during tiled prediction

Pull Request - State: closed - Opened by pattonw almost 2 years ago - 4 comments

#298 - Read information about required number of channels for a given model

Issue - State: closed - Opened by Czaki almost 2 years ago - 4 comments

#297 - 0.5.6 contains breaking changes

Issue - State: closed - Opened by uschmidt83 about 2 years ago - 3 comments

#296 - Update VERSION

Pull Request - State: closed - Opened by FynnBe about 2 years ago

#295 - Fix tf legacy

Pull Request - State: closed - Opened by FynnBe about 2 years ago
Labels: bug, ci, github_actions

#294 - Add averaging between tiles

Issue - State: open - Opened by Buglakova about 2 years ago
Labels: enhancement

#293 - Better documentation for prediction functions

Issue - State: open - Opened by Buglakova about 2 years ago
Labels: documentation

#292 - Fix pip installation

Pull Request - State: closed - Opened by FynnBe about 2 years ago - 1 comment
Labels: bug

#291 - Incorporate czaki contribution

Pull Request - State: closed - Opened by FynnBe about 2 years ago

#290 - Fix source node checker

Pull Request - State: closed - Opened by FynnBe about 2 years ago
Labels: bug

#289 - test_model is not working

Issue - State: closed - Opened by constantinpape about 2 years ago

#288 - unable to run 'predict_with_padding' or tiling

Issue - State: closed - Opened by esgomezm about 2 years ago - 4 comments

#287 - Update pytorch dependecies

Pull Request - State: closed - Opened by Czaki about 2 years ago - 3 comments

#286 - Wrong specyfication of pytorch extra requirements are wrongly specified

Issue - State: closed - Opened by Czaki about 2 years ago - 3 comments

#285 - 'InputTensor' object has no attribute 'root_path'

Issue - State: closed - Opened by oeway about 2 years ago - 1 comment

#284 - allow to create prediction pipeline from raw_nodes.Model

Pull Request - State: closed - Opened by FynnBe about 2 years ago - 1 comment

#283 - Cache default location causes problems for shared machines

Issue - State: closed - Opened by constantinpape about 2 years ago

#282 - use numpy.ufuncs instead of xarray.ufuncs

Pull Request - State: closed - Opened by FynnBe about 2 years ago - 6 comments

#281 - Fix xarray deprecation warning

Issue - State: closed - Opened by constantinpape about 2 years ago

#280 - Report model downloading progress

Issue - State: open - Opened by oeway about 2 years ago - 1 comment

#279 - build_model should delete generated files after zipping

Issue - State: closed - Opened by tomburke-rse over 2 years ago - 1 comment

#278 - create_prediction_pipeline from RawResourceDescription

Issue - State: closed - Opened by oeway over 2 years ago - 6 comments

#277 - Update VERSION

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#276 - support progress reporting for export_resource_package

Issue - State: open - Opened by k-dominik over 2 years ago

#275 - Correct the axes that create sample tiffs

Pull Request - State: closed - Opened by carlosuc3m over 2 years ago - 3 comments

#274 - Implement TritonModelAdapter

Issue - State: open - Opened by constantinpape over 2 years ago

#273 - Promote tifffile to full dependency

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#272 - tf/keras test fails because env can't be set up

Issue - State: open - Opened by constantinpape over 2 years ago

#271 - Updates to prediction functionality etc

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#270 - Check the integrity of weights files and disable cache

Issue - State: open - Opened by oeway over 2 years ago - 2 comments

#269 - Export export_resource_package as folder

Issue - State: open - Opened by oeway over 2 years ago - 1 comment

#268 - Upgrade bioimageio.spec with the core

Issue - State: open - Opened by oeway over 2 years ago

#267 - Extend test resources

Pull Request - State: closed - Opened by FynnBe over 2 years ago - 6 comments
Labels: testing

#266 - Refactor image functionality

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 1 comment
Labels: refactoring

#265 - Update model test to handle expanded output shape and add test model

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

#264 - WIP add test_output_shape_with_offset

Pull Request - State: closed - Opened by FynnBe over 2 years ago
Labels: enhancement, testing

#263 - Error saving a tiff image

Issue - State: closed - Opened by esgomezm over 2 years ago - 4 comments

#262 - Widefield models not recognized by test validator

Issue - State: open - Opened by lmoyasans over 2 years ago - 8 comments

#261 - Expose model_adapter for the BioEngine

Pull Request - State: closed - Opened by oeway over 2 years ago - 4 comments

#260 - Issue with build_model on macOS

Issue - State: closed - Opened by uschmidt83 over 2 years ago - 7 comments

#259 - Update for resolved paths

Pull Request - State: closed - Opened by FynnBe over 2 years ago - 4 comments

#258 - Export and load didn't work for some models

Issue - State: open - Opened by oeway over 2 years ago - 7 comments

#257 - Rdf version not valid

Issue - State: closed - Opened by lmoyasans over 2 years ago - 14 comments

#256 - Add functionality to overwrite dij config

Pull Request - State: closed - Opened by constantinpape over 2 years ago
Labels: enhancement

#255 - Unzip local bioimage model zoo models

Issue - State: closed - Opened by esgomezm over 2 years ago - 13 comments

#254 - Bump post version

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#253 - Fix torch to onnx conversion

Pull Request - State: closed - Opened by constantinpape over 2 years ago
Labels: bug

#252 - bump post

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#251 - no required measures for mode=fixed

Pull Request - State: closed - Opened by FynnBe over 2 years ago
Labels: bug

#250 - Bump patch version

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#249 - Use new no-cache env var

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#248 - Bump patch

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#247 - Adapt to changes in the version object

Pull Request - State: closed - Opened by constantinpape over 2 years ago

#246 - Generate single model fixtures dynamically

Issue - State: open - Opened by constantinpape over 2 years ago

#245 - Fix computation for number of tiles

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 2 comments
Labels: bug

#244 - More fixes for predict_with_tiling

Issue - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#243 - Improve 404 errors

Issue - State: closed - Opened by FynnBe over 2 years ago - 1 comment

#242 - Improve documentation for the command line

Issue - State: open - Opened by oeway over 2 years ago - 3 comments

#241 - Dataset statistics

Pull Request - State: closed - Opened by FynnBe over 2 years ago

#240 - add test_load_remote_rdf

Pull Request - State: closed - Opened by FynnBe over 2 years ago - 2 comments
Labels: enhancement, testing

#237 - Check if inputs are valid according to input shape parametrization

Issue - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#224 - Infer `.pt` weight file as `torchscript`

Pull Request - State: closed - Opened by oeway over 2 years ago - 3 comments

#223 - How to set statistics for per_dataset processing?

Issue - State: open - Opened by constantinpape over 2 years ago - 2 comments

#210 - Save 3D, 2D+c or 2D+t test and sample images correctly

Issue - State: closed - Opened by esgomezm over 2 years ago - 15 comments

#200 - Enable tiling with different output shape WIP

Pull Request - State: closed - Opened by constantinpape over 2 years ago - 1 comment

#197 - Support out-of-core prediction_with_tiling (with dask?)

Issue - State: open - Opened by constantinpape almost 3 years ago - 1 comment

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