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theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.
https://diffxpy.rtfd.io
BSD 3-Clause "New" or "Revised" License
193 stars 23 forks source link

Allow csc_matrix input for rank and ttest #175

Open ivirshup opened 4 years ago

ivirshup commented 4 years ago

As title.

I've mostly done spot checks, and have given updating the tests a shot. I'm not able to get passing tests even without the changes, so not sure what to do about that.

davidsebfischer commented 4 years ago

Thanks @ivirshup! Which unit test did not work for you?

ivirshup commented 4 years ago

Most of them seem to be failing, here's the summary from running pytest at the root of the repo:

diffxpy/unit_test/test_acc_glm_all_numpy_temp.py F                                                                      [  1%]
diffxpy/unit_test/test_backends.py .FF                                                                                  [  5%]
diffxpy/unit_test/test_constrained.py FFF                                                                               [ 10%]
diffxpy/unit_test/test_continuous_de.py .F                                                                                         [ 13%]
diffxpy/unit_test/test_continuous_null.py ...                                                                                      [ 17%]
diffxpy/unit_test/test_data_types.py FF                                                                                            [ 20%]
diffxpy/unit_test/test_enrich.py F                                                                                                 [ 22%]
diffxpy/unit_test/test_extreme_values.py FF                                                                                        [ 25%]
diffxpy/unit_test/test_fit.py FFFFFF                                                                                               [ 33%]
diffxpy/unit_test/test_numeric_covar.py .                                                                                          [ 35%]
diffxpy/unit_test/test_pairwise_null.py FFF.FF                                                                                     [ 44%]
diffxpy/unit_test/test_partition.py FFFFF                                                                                          [ 51%]
diffxpy/unit_test/test_single_de.py FFF.FF                                                                                         [ 60%]
diffxpy/unit_test/test_single_external_libs.py .F                                                                                  [ 63%]
diffxpy/unit_test/test_single_fullrank.py .                                                                                        [ 64%]
diffxpy/unit_test/test_single_null.py FFF...FFF                                                                                    [ 77%]
diffxpy/unit_test/test_single_sf_null.py FF                                                                                        [ 80%]
diffxpy/unit_test/test_stats.py .....                                                                                              [ 88%]
diffxpy/unit_test/test_twosample.py ....                                                                                           [ 94%]
diffxpy/unit_test/test_vsrest.py FFFF                                                                                              [100%]

Here's a gist with the full output.

davidsebfischer commented 4 years ago

a couple of them are failing because there is paths in there specific to my machine because i need file IO for those tests, i have only been running the unit tests locally so far, will look into getting pytest to work!