Fix conservation tracking tests

[btbest]

The six tests in testConservationTrackingHeadless.py have been xfailing for quite a while because file paths were broken. Having fixed that, it turned out also the main function import didn't work as implemented.

[btbest]

(see these six tests xfailing e.g. in this run: https://github.com/ilastik/ilastik/actions/runs/4698963212/jobs/8331947378 or most recently in https://app.circleci.com/pipelines/github/ilastik/ilastik/1340/workflows/130b9cc3-3761-43b7-bd3a-ea7609e32c4e/jobs/5647)

[btbest]

Draft because (a) there's more tests with the same problem and (b) these shouldn't xfail when they can't find their input files, they should plain old fail.

But the first six are green now 🎉

[codecov]

Codecov Report

Patch coverage: 26.55% and project coverage change: +0.23 🎉

Comparison is base (fe83334) 54.35% compared to head (999d3ec) 54.59%.

❗ Current head 999d3ec differs from pull request most recent head 025785c. Consider uploading reports for the commit 025785c to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2716      +/-   ##
==========================================
+ Coverage   54.35%   54.59%   +0.23%     
==========================================
  Files         519      530      +11     
  Lines       60863    61425     +562     
  Branches     8398     8453      +55     
==========================================
+ Hits        33081    33532     +451     
- Misses      26105    26140      +35     
- Partials     1677     1753      +76     

Impacted Files	Coverage Δ
ilastik/applets/neuralNetwork/modelStateControl.py	0.00% <0.00%> (ø)
ilastik/applets/neuralNetwork/nnClassGui.py	0.00% <0.00%> (ø)
...lets/neuralNetwork/opNNClassificationDataExport.py	90.00% <ø> (ø)
...ets/trainableDomainAdaptation/modelStateControl.py	0.00% <0.00%> (ø)
...lets/trainableDomainAdaptation/tdaDataExportGui.py	0.00% <0.00%> (ø)
...leDomainAdaptation/trainableDomainAdaptationGui.py	0.00% <0.00%> (ø)
ilastik/shell/gui/ilastikShell.py	50.66% <ø> (ø)
lazyflow/operators/__init__.py	100.00% <ø> (ø)
lazyflow/operators/opCompressedUserLabelArray.py	90.32% <ø> (ø)
...ptation/_localTrainableDomainAdaptationWorkflow.py	27.11% <27.11%> (ø)
... and 15 more

... and 44 files with indirect coverage changes

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[emilmelnikov]

A small tip: Github now supports draft pull requests, so it's not necessary to add [DRAFT] or Draft: to PR name.

[btbest]

I've found and fixed the remaining tests that had the same file path issues, but those tests suffer from their own additional problem: They contained a switch that would pass all tests if they are unable to import either multiHypoTracking_with_cplex or multiHypoTracking_with_gurobi; and that's why they were passing locally for me.

I changed the pass-if-missing to xfail-if-missing, and now all of the structuredLearning tests are xfailing on CI 😄

[emilmelnikov]

I've found and fixed the remaining tests that had the same file path issues, but those tests suffer from their own additional problem: They contained a switch that would pass all tests if they are unable to import either multiHypoTracking_with_cplex or multiHypoTracking_with_gurobi; and that's why they were passing locally for me.

Instead of xfailing, we probably should conditionally skip those tests if a module cannot be imported.

[btbest]

I managed to create a new input .ilp that passes (with Gurobi 9.5.2 on my system)

Turns out the GUI gives you no way to actually see all existing track labels that have been put in Training, and I only found the ones that weren't visible when I inspected the h5 manually.

On CI the tests will be skipped because no Gurobi there :)

[k-dominik]

Hi @btbest,

sorry this took longer as I had to build the tracking with learning dependencies on apple silicon first (was pushing this off, so thanks for the nudge).

Two tests fail for me:

tests/test_ilastik/test_applets/structuredLearningTracking/testStructuredLearningTrackingHytraWithMergers.py::TestStructuredLearningTrackingHeadless::testStructuredLearningTrackingHeadless FAILED [ 50%]
tests/test_ilastik/test_applets/structuredLearningTracking/testStructuredLearningTrackingHytraWithMergers.py::TestStructuredLearningTrackingHeadless::testCSVExport FAILED                        [100%]

it appears that the outputs cannot be found, can you double check that in a clean repo, you can run these tests on windows?

e.g. I get an error wrt to not being able to find the following file:

ilastik/tests/test_ilastik/test_applets/structuredLearningTracking/../../data/inputdata/mitocheck_2d+t/mitocheck_small_2D+t_mergers-crop_data_Tracking-Result.h5

[btbest]

🤦 I had "updated" the expected output file names to what seemed to be new default file names with -crop_data in the file name.

I have no idea how I obtained output files with that name pattern at any point, but anyway I've reverted the name change.

[k-dominik]

test success confirmed on my machine, too :) sooo good to have this running again!