Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

python3Packages.starfish: disable due to incompatible dependencies #75744

Merged
merged 1 commit into from Dec 16, 2019
Merged

python3Packages.starfish: disable due to incompatible dependencies #75744

merged 1 commit into from Dec 16, 2019

Conversation

jonringer
Copy link
Contributor

@jonringer jonringer commented Dec 16, 2019 •
edited

Motivation for this change

isn't compatible with latest python-dateutil or scikit-image

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
Notify maintainers

cc @

@jonringer
python3Packages.starfish: disable due to incompatible dependencies
bff1493 
isn't compatible with latest python-dateutil or scikit-image
@costrouc
Copy link
Member

Instead of marking it broken does pushing it to a newer version fix the issue? I see that 0.1.10 was released 3 days ago.

@jonringer
Copy link
Contributor Author

I tried that, but it does not

@jonringer
Copy link
Contributor Author

specifically, this line

scikit-image >= 0.14.0, != 0.16.0.*, != 0.16.1.*, != 0.16.2.*

from https://github.com/spacetx/starfish/blob/185faa6bcdb413cea8370a5ca84c8c0cd13d1989/REQUIREMENTS.txt#L17

@costrouc
Copy link
Member

Yeup I'm trying to build it right now had to remove the pin on scikit-image and python-dateutil. I'll keep you updated if I do/do not get it working.

@jonringer
Copy link
Contributor Author

Yea, but this line scares me:

# 0.16.[012] are excluded because https://github.com/scikit-image/scikit-image/pull/3984 introduced
# a bug into max peak finder.  0.16.3 presumably will have the fix from
# https://github.com/scikit-image/scikit-image/pull/4263.

to me it says, this package is in an invalid state until 0.16.3 is released

@costrouc
Copy link
Member

Yeah that is a good point. So brings up the question we mark broken=true and in the future when 0.16.3 is release we attempt to rebuild the package?

@jonringer
Copy link
Contributor Author

I'm thinking that is the correct course of action, it's just that starfish currently fails to build in a lot of my reviews

@jonringer
Copy link
Contributor Author

disabling until it's compatible with the rest of python-modules

python-dateutil I feel fine patching, as that seems more to be a low upper-bound issue. scikit-image, i think is a blocker for this package.

@jonringer jonringer merged commit b443abf into NixOS:master Dec 16, 2019
@costrouc
Copy link
Member

Makes sense. Since I contributed this package. Any tips for being reminded about updating these packages in the future (right now I have a ton of noise on nixpkgs and I don't have as much time as I had in the future to work on these packages)? I really appreciate all the work that you have been doing in keeping pythonPackages all compatible with one another.

@jonringer
Copy link
Contributor Author

you can put nixpkgs as mention only, when a PR is opened that you maintain, you will be mentioned as a reviewer

@jonringer jonringer deleted the disable-starfish branch December 16, 2019 21:05
@costrouc
Copy link
Member

For the future when this package is built. These are the failing tests that I got without disabling any tests. Should make it easier to disable tests later.

starfish/core/codebook/test/test_approximate_nearest_code.py .           [  0%]
starfish/core/codebook/test/test_code_length.py .                        [  0%]
starfish/core/codebook/test/test_from_code_array.py .......              [  2%]
starfish/core/codebook/test/test_metric_decode.py ..                     [  3%]
starfish/core/codebook/test/test_normalize_code_traces.py ....ss         [  4%]
starfish/core/codebook/test/test_per_round_max_decode.py ......          [  6%]
starfish/core/codebook/test/test_synthetic_one_hot_codebook.py ...       [  7%]
starfish/core/codebook/test/test_to_json.py ..                           [  7%]
starfish/core/config/test/test_config.py ...........FFF.....             [ 13%]
starfish/core/experiment/builder/test/test_inplace.py .                  [ 13%]
starfish/core/experiment/builder/test/test_orderediterator.py ..         [ 14%]
starfish/core/experiment/builder/test/test_small_axis.py ......          [ 15%]
starfish/core/experiment/builder/test/structured_formatter/test_multiple_fov.py . [ 16%]
                                                                         [ 16%]
starfish/core/experiment/builder/test/structured_formatter/test_single_fov.py . [ 16%]
....                                                                     [ 17%]
starfish/core/experiment/builder/test/structured_formatter/test_tilepath.py . [ 17%]
.                                                                        [ 18%]
starfish/core/experiment/test/test_experiment.py .F..                    [ 19%]
starfish/core/experiment/test/test_version.py ..                         [ 19%]
starfish/core/expression_matrix/test/test_concatenate.py .               [ 20%]
starfish/core/expression_matrix/test/test_serialization.py .             [ 20%]
starfish/core/image/Filter/test/test_api_contract.py .............       [ 24%]
starfish/core/image/Filter/test/test_call_bases.py ....                  [ 25%]
starfish/core/image/Filter/test/test_filter.py .......                   [ 27%]
starfish/core/image/Filter/test/test_histogram_matching.py .             [ 27%]
starfish/core/image/Filter/test/test_linear_unmixing.py .                [ 27%]
starfish/core/image/Filter/test/test_map.py .                            [ 28%]
starfish/core/image/Filter/test/test_reduce.py .......F                  [ 30%]
starfish/core/image/Filter/test/test_white_tophat.py ..                  [ 30%]
starfish/core/image/Filter/test/test_zero_by_channel_magnitude.py .      [ 31%]
starfish/core/image/_registration/ApplyTransform/test/test_warp.py F     [ 31%]
starfish/core/image/_registration/LearnTransform/test/test_translation.py F [ 31%]
F                                                                        [ 32%]
starfish/core/image/_registration/test/test_transforms_list.py F         [ 32%]
starfish/core/imagestack/test/test_apply.py .......                      [ 34%]
starfish/core/imagestack/test/test_coordinates.py ...                    [ 35%]
starfish/core/imagestack/test/test_cropped_load.py ..                    [ 35%]
starfish/core/imagestack/test/test_export.py ..                          [ 36%]
starfish/core/imagestack/test/test_from_numpy_array.py ...               [ 37%]
starfish/core/imagestack/test/test_index.py .......                      [ 39%]
starfish/core/imagestack/test/test_labeled_indices.py .....              [ 40%]
starfish/core/imagestack/test/test_max_proj.py .F                        [ 41%]
starfish/core/imagestack/test/test_metadata.py ...                       [ 42%]
starfish/core/imagestack/test/test_physical_coordinate_calculator.py .   [ 42%]
starfish/core/imagestack/test/test_slice_ops.py .......                  [ 44%]
starfish/core/imagestack/test/test_slicedimage_dtype.py .....            [ 45%]
starfish/core/intensity_table/test/test_concatenate.py .                 [ 46%]
starfish/core/intensity_table/test/test_empty_intensity_table.py ..      [ 46%]
starfish/core/intensity_table/test/test_from_imagestack.py ....          [ 47%]
starfish/core/intensity_table/test/test_from_spot_data.py ....           [ 48%]
starfish/core/intensity_table/test/test_intensity_table_coords.py ..     [ 49%]
starfish/core/intensity_table/test/test_intensity_table_serialization.py . [ 49%]
                                                                         [ 49%]
starfish/core/intensity_table/test/test_overlap.py .....                 [ 51%]
starfish/core/intensity_table/test/test_stack_intensity_table_reshaping.py . [ 51%]
                                                                         [ 51%]
starfish/core/intensity_table/test/test_synthetic_intensities.py .       [ 51%]
starfish/core/intensity_table/test/test_to_mermaid.py .                  [ 51%]
starfish/core/morphology/Binarize/test/test_threshold.py ......          [ 53%]
starfish/core/morphology/Filter/test/test_areafilter.py ...              [ 54%]
starfish/core/morphology/Filter/test/test_map.py .                       [ 54%]
starfish/core/morphology/binary_mask/test/test_binary_mask.py .......    [ 56%]
starfish/core/morphology/binary_mask/test/test_expand.py ....            [ 57%]
starfish/core/morphology/binary_mask/test/test_from_binary_arrays_and_ticks.py . [ 58%]
........                                                                 [ 60%]
starfish/core/morphology/binary_mask/test/test_from_label_array_and_ticks.py . [ 60%]
......                                                                   [ 62%]
starfish/core/morphology/label_image/test/test_label_image.py .......    [ 64%]
starfish/core/spacetx_format/test_codebook.py .....                      [ 65%]
starfish/core/spacetx_format/test_coordinates.py ........                [ 68%]
starfish/core/spacetx_format/test_experiment.py .....                    [ 69%]
starfish/core/spacetx_format/test_field_of_view.py ......                [ 71%]
starfish/core/spacetx_format/test_fov_manifest.py ..                     [ 71%]
starfish/core/spacetx_format/test_fuzz.py ...                            [ 72%]
starfish/core/spacetx_format/test/test_validate.py F                     [ 73%]
starfish/core/spots/DecodeSpots/test/test_composite_codebook.py ...      [ 73%]
starfish/core/spots/DecodeSpots/test/test_decoding_without_spots.py ..   [ 74%]
starfish/core/spots/DecodeSpots/test/test_nearest_neighbor_trace_builder.py . [ 74%]
...                                                                      [ 75%]
starfish/core/spots/DecodeSpots/test/test_trace_builders.py ............ [ 78%]
                                                                         [ 78%]
starfish/core/spots/DetectPixels/test/test_calculate_mean_pixel_traces.py F [ 79%]
                                                                         [ 79%]
starfish/core/spots/DetectPixels/test/test_create_spot_attributes.py .   [ 79%]
starfish/core/spots/DetectPixels/test/test_intensities_to_decoded_image.py . [ 79%]
.                                                                        [ 80%]
starfish/core/spots/DetectPixels/test/test_targets_map.py .              [ 80%]
starfish/core/spots/FindSpots/test/test_spot_detection.py ...........F.. [ 84%]
F..F..                                                                   [ 86%]
starfish/core/spots/FindSpots/test/test_synthetic_data.py ..             [ 86%]
starfish/core/test/test_display.py FFFFFFFF                              [ 88%]
starfish/core/test/test_multiprocessing_workflow.py .                    [ 89%]
starfish/core/test/test_synthetic_spot_creation.py ..                    [ 89%]
starfish/core/types/test/test_decoded_spots.py .                         [ 90%]
starfish/core/util/test/test_levels.py ................                  [ 94%]
starfish/core/util/test/test_preserve_float_range.py ..............      [ 98%]
starfish/test/full_pipelines/api/test_allen_smFISH.py s                  [ 98%]
starfish/test/full_pipelines/api/test_dartfish.py F                      [ 99%]
starfish/test/full_pipelines/api/test_iss_api.py F                       [ 99%]
starfish/test/full_pipelines/api/test_iss_doc_pipeline.py F              [ 99%]
starfish/test/full_pipelines/api/test_merfish.py F                       [100%]

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FRidh FRidh Awaiting requested review from FRidh

@costrouc costrouc Awaiting requested review from costrouc

Assignees
No one assigned
Labels
6.topic: python 10.rebuild-darwin: 0 10.rebuild-linux: 0
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@jonringer @costrouc