Error running tests - Githubissues

dlogan commented 4 years ago

I got this trying to run the Testing Installation (1.3) here. Note, some early tests failed. Any thoughts?

$ python3 -m pytest
============================================================================ test session starts =============================================================================
platform linux -- Python 3.6.9, pytest-5.4.1, py-1.8.1, pluggy-0.13.1 -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /home/logand05/github/DeepProfiler, inifile: setup.cfg
plugins: cov-2.8.1
collected 86 items                                                                                                                                                           

tests/deepprofiler/dataset/test_compression.py::test_init PASSED                                                                                                       [  1%]
tests/deepprofiler/dataset/test_compression.py::test_recompute_percentile PASSED                                                                                       [  2%]
tests/deepprofiler/dataset/test_compression.py::test_set_control_samples_filter PASSED                                                                                 [  3%]
tests/deepprofiler/dataset/test_compression.py::test_set_formats PASSED                                                                                                [  4%]
tests/deepprofiler/dataset/test_compression.py::test_set_scaling_factor PASSED                                                                                         [  5%]
tests/deepprofiler/dataset/test_compression.py::test_target_path PASSED                                                                                                [  6%]
tests/deepprofiler/dataset/test_compression.py::test_process_image FAILED                                                                                              [  8%]
tests/deepprofiler/dataset/test_illumination_correction.py::test_init PASSED                                                                                           [  9%]
tests/deepprofiler/dataset/test_illumination_correction.py::test_channel_function FAILED                                                                               [ 10%]
tests/deepprofiler/dataset/test_illumination_correction.py::test_apply PASSED                                                                                          [ 11%]
tests/deepprofiler/dataset/test_illumination_statistics.py::test_init PASSED                                                                                           [ 12%]
tests/deepprofiler/dataset/test_illumination_statistics.py::test_add_to_mean_no_scaling FAILED                                                                         [ 13%]
tests/deepprofiler/dataset/test_illumination_statistics.py::test_add_to_mean_with_scaling FAILED                                                                       [ 15%]
tests/deepprofiler/dataset/test_illumination_statistics.py::test_process_image FAILED                                                                                  [ 16%]
tests/deepprofiler/dataset/test_illumination_statistics.py::test_compute_stats FAILED                                                                                  [ 17%]
tests/deepprofiler/dataset/test_image_dataset.py::test_init PASSED                                                                                                     [ 18%]
tests/deepprofiler/dataset/test_image_dataset.py::test_get_image_paths PASSED                                                                                          [ 19%]
tests/deepprofiler/dataset/test_image_dataset.py::test_get_train_batch PASSED                                                                                          [ 20%]
tests/deepprofiler/dataset/test_image_dataset.py::test_scan PASSED                                                                                                     [ 22%]
tests/deepprofiler/dataset/test_image_dataset.py::test_number_of_records PASSED                                                                                        [ 23%]
tests/deepprofiler/dataset/test_image_dataset.py::test_add_target PASSED                                                                                               [ 24%]
tests/deepprofiler/dataset/test_image_dataset.py::test_read_dataset PASSED                                                                                             [ 25%]
tests/deepprofiler/dataset/test_indexing.py::test_write_compression_index PASSED                                                                                       [ 26%]
tests/deepprofiler/dataset/test_indexing.py::test_split_index PASSED                                                                                                   [ 27%]
tests/deepprofiler/dataset/test_metadata.py::test_parse_delimiter PASSED                                                                                               [ 29%]
tests/deepprofiler/dataset/test_metadata.py::test_read_plates PASSED                                                                                                   [ 30%]
tests/deepprofiler/dataset/test_metadata.py::test_load_single PASSED                                                                                                   [ 31%]
tests/deepprofiler/dataset/test_metadata.py::test_load_multiple PASSED                                                                                                 [ 32%]
tests/deepprofiler/dataset/test_metadata.py::test_filter_records PASSED                                                                                                [ 33%]
tests/deepprofiler/dataset/test_metadata.py::test_split_metadata PASSED                                                                                                [ 34%]
tests/deepprofiler/dataset/test_metadata.py::test_merge_outlines PASSED                                                                                                [ 36%]
tests/deepprofiler/dataset/test_pixels.py::test_openImage PASSED                                                                                                       [ 37%]
tests/deepprofiler/dataset/test_target.py::test_init PASSED                                                                                                            [ 38%]
tests/deepprofiler/dataset/test_target.py::test_get_values PASSED                                                                                                      [ 39%]
tests/deepprofiler/dataset/test_target.py::test_shape PASSED                                                                                                           [ 40%]
tests/deepprofiler/dataset/test_utils.py::test_print_progress PASSED                                                                                                   [ 41%]
tests/deepprofiler/dataset/test_utils.py::test_check_path PASSED                                                                                                       [ 43%]
tests/deepprofiler/dataset/test_utils.py::test_init PASSED                                                                                                             [ 44%]
tests/deepprofiler/imaging/test_augmentations.py::test_augment PASSED                                                                                                  [ 45%]
tests/deepprofiler/imaging/test_augmentations.py::test_augment_multiple PASSED                                                                                         [ 46%]
tests/deepprofiler/imaging/test_boxes.py::test_get_locations PASSED                                                                                                    [ 47%]
tests/deepprofiler/imaging/test_boxes.py::test_prepare_boxes PASSED                                                                                                    [ 48%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_graph PASSED                                                                                                    [ 50%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_init PASSED                                                                                           [ 51%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_build_input_graph PASSED                                                                              [ 52%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_build_augmentation_graph PASSED                                                                       [ 53%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_start PASSED                                                                                          [ 54%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_sample_batch PASSED                                                                                   [ 55%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_generate PASSED                                                                                       [ 56%]
tests/deepprofiler/imaging/test_cropping.py::test_crop_generator_stop PASSED                                                                                           [ 58%]
tests/deepprofiler/imaging/test_cropping.py::test_single_image_crop_generator_init PASSED                                                                              [ 59%]
tests/deepprofiler/imaging/test_cropping.py::test_single_image_crop_generator_start PASSED                                                                             [ 60%]
tests/deepprofiler/imaging/test_cropping.py::test_single_image_crop_generator_prepare_image PASSED                                                                     [ 61%]
tests/deepprofiler/imaging/test_cropping.py::test_single_image_crop_generator_generate PASSED                                                                          [ 62%]
tests/deepprofiler/learning/test_metric.py::test_init PASSED                                                                                                           [ 63%]
tests/deepprofiler/learning/test_metric.py::test_create_metric PASSED                                                                                                  [ 65%]
tests/deepprofiler/learning/test_metric.py::test_metric PASSED                                                                                                         [ 66%]
tests/deepprofiler/learning/test_model.py::test_init PASSED                                                                                                            [ 67%]
tests/deepprofiler/learning/test_model.py::test_seed PASSED                                                                                                            [ 68%]
tests/deepprofiler/learning/test_model.py::test_train PASSED                                                                                                           [ 69%]
tests/deepprofiler/learning/test_profiling.py::test_init PASSED                                                                                                        [ 70%]
tests/deepprofiler/learning/test_profiling.py::test_configure PASSED                                                                                                   [ 72%]
tests/deepprofiler/learning/test_profiling.py::test_check PASSED                                                                                                       [ 73%]
tests/deepprofiler/learning/test_profiling.py::test_extract_features PASSED                                                                                            [ 74%]
tests/deepprofiler/learning/test_profiling.py::test_profile PASSED                                                                                                     [ 75%]
tests/deepprofiler/learning/test_training.py::test_learn_model PASSED                                                                                                  [ 76%]
tests/deepprofiler/learning/test_validation.py::test_init Fatal Python error: Aborted

Thread 0x00007fe304ff9700 (most recent call first):
  File "/usr/lib/python3.6/threading.py", line 295 in wait
  File "/usr/lib/python3.6/queue.py", line 164 in get
  File "/usr/lib/python3/dist-packages/tensorflow_core/python/summary/writer/event_file_writer.py", line 159 in run
  File "/usr/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/usr/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x00007fe3057fa700 (most recent call first):
  File "/usr/lib/python3.6/threading.py", line 295 in wait
  File "/usr/lib/python3.6/queue.py", line 164 in get
  File "/usr/lib/python3/dist-packages/tensorflow_core/python/summary/writer/event_file_writer.py", line 159 in run
  File "/usr/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/usr/lib/python3.6/threading.py", line 884 in _bootstrap
...

... plus lots more failed Threads.

Here's the output of pip freeze in case that helps

$ pip freeze
absl-py==0.8.1
antlr==2.7.5rc1
appdirs==1.4.3
asn1crypto==0.24.0
astor==0.8.0
attrs==19.3.0
backports.functools-lru-cache==1.6.1
backports.shutil-get-terminal-size==1.0.0
beautifulsoup4==4.9.0
bleach==2.1.2
caffe==1.0.0
certifi==2020.4.5.1
cffi==1.11.5
chardet==3.0.4
click==7.1.2
cloudpickle==1.3.0
comet-git-pure==0.19.16
comet-ml==3.1.6
configobj==5.0.6
configparser==3.5.0
cryptography==2.1.4
cvxopt==1.1.9
cycler==0.10.0
decorator==4.4.2
-e git+https://github.com/cytomining/DeepProfiler.git@568eedd1455b3fd519382e0dfff0ff7fe668d8f3#egg=deepprofiler
enum34==1.1.6
et-xmlfile==1.0.1
everett==0.9
Flask==1.1.1
funcsigs==1.0.2
functools32==3.2.3.post2
future==0.15.2
gast==0.2.0
google-pasta==0.1.7
GPy==1.9.9
GPyOpt==1.2.6
grpcio==1.24.0
h5py==2.7.1
hpccm==19.9.0
html5lib==0.999999999
idna==2.9
ipaddress==1.0.17
ipython==5.5.0
ipython-genutils==0.2.0
itsdangerous==1.1.0
jdcal==1.0
Jinja2==2.10.3
joblib==0.11
jsonschema==3.0.2
Keras==2.3.1
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
keyring==10.6.0
keyrings.alt==3.0
kiwisolver==1.1.0
leveldb==0.1
lxml==4.5.0
Mako==1.0.7
Markdown==2.6.9
MarkupSafe==1.1.1
matplotlib==2.2.5
mock==2.0.0
netifaces==0.10.9
networkx==2.2
nose==1.3.7
nose-parameterized==0.3.4
numexpr==2.6.4
numpy==1.16.6
nvidia-ml-py==7.352.0
nvidia-ml-py3==7.352.0
olefile==0.45.1
openpyxl==2.4.9
pandas==0.24.2
paramz==0.9.5
pathlib2==2.3.0
patsy==0.4.1+dev
pbr==3.1.1
pexpect==4.2.1
pfz-gpu==0.1
pickleshare==0.7.4
Pillow==6.2.2
pluggy==0.6.0
ply==3.11
prompt-toolkit==1.0.15
protobuf==3.8.0
py==1.5.2
pycparser==2.18
pycrypto==2.6.1
pycuda==2019.1.2
pydot==1.2.3
pyflakes==1.6.0
Pygments==2.2.0
pygobject==3.26.1
pygpu==0.7.6
pyinotify==0.9.6
pyOpenSSL==17.5.0
pyparsing==2.4.7
pyrsistent==0.16.0
pytest==3.3.2
python-dateutil==2.8.1
pytools==2017.6
pytz==2020.1
PyWavelets==1.0.3
pyxdg==0.25
PyYAML==3.12
requests==2.23.0
scandir==1.7
scikit-cuda==0.5.3
scikit-image==0.14.5
scikit-learn==0.20.4
scipy==1.2.3
SecretStorage==2.3.1
selectors2==2.0.1
simplegeneric==0.8.1
simplejson==3.13.2
six==1.14.0
soupsieve==1.9.5
statsmodels==0.8.0
subprocess32==3.5.4
tables==3.4.2
tensorboard==1.15.0
tensorflow-estimator==1.15.1
tensorflow-gpu==1.15.2
tensorflow-serving-api==1.15.0
termcolor==1.1.0
Theano==1.0.4
torch==1.4.0
torchvision==0.5.0
traitlets==4.3.2
typing==3.7.4.1
typing-extensions==3.7.4.2
urllib3==1.25.9
wcwidth==0.1.7
webencodings==0.5
websocket-client==0.57.0
Werkzeug==0.16.0
wrapt==1.9.0
wurlitzer==2.0.0
xlrd==1.1.0
xlwt==0.7.5

Arkkienkeli commented 4 years ago

Hi @dlogan, thank you for reporting this. I did run all the tests with the latest DeepProfiler build and they work fine. Probably it can be fixed if you change your Keras version to 2.2.5.

jccaicedo commented 4 years ago

Interesting. @Arkkienkeli , do you think we should update the setup.py to require this Keras version exactly instead of >= ?

I also wonder if it's worth using pyenv for running DP instead of installing it as a package in the user environment. Doing this may avoid conflicts with package versions that the user already has.

dlogan commented 4 years ago

I tried to change my Keras version but pip uninstall keeps refusing. So anything you can do to force a particular version would be really helpful.

From: jccaicedo notifications@github.com Sent: Monday, May 4, 2020 7:23:16 PM To: cytomining/DeepProfiler DeepProfiler@noreply.github.com Cc: Logan, David David.J.Logan@pfizer.com; Mention mention@noreply.github.com Subject: [EXTERNAL] Re: [cytomining/DeepProfiler] Error running tests (#227)

Interesting. @Arkkienkelihttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Arkkienkeli&d=DwMCaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=zz49f3Oj1fOD_PvMjQAyrDqN1PxPPdfC8nRuTZGu3Z0&m=cTnovKbWqGBfeWJSnpd6xlHDpyQe5E3441NrGSbMt1g&s=PKPjKXmzbub4b1LVZ3sPjHA1CpZRl0_4UBeOUcKJoZA&e= , do you think we should update the setup.py to require this Keras version exactly instead of >= ?

I also wonder if it's worth using pyenv for running DP instead of installing it as a package in the user environment. Doing this may avoid conflicts with package versions that the user already has.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cytomining_DeepProfiler_issues_227-23issuecomment-2D623759233&d=DwMCaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=zz49f3Oj1fOD_PvMjQAyrDqN1PxPPdfC8nRuTZGu3Z0&m=cTnovKbWqGBfeWJSnpd6xlHDpyQe5E3441NrGSbMt1g&s=vBxnc6UGReWumxKvDl7qh59o3wvlzfnU-XELsrHkm88&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAJLG676WMNRYLSBK2Q27ELRP5E6JANCNFSM4MWZRZGQ&d=DwMCaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=zz49f3Oj1fOD_PvMjQAyrDqN1PxPPdfC8nRuTZGu3Z0&m=cTnovKbWqGBfeWJSnpd6xlHDpyQe5E3441NrGSbMt1g&s=sKHzN_hZ2znDNKisEmI9vYDJfU5Wb1tzQvcAj0E1_pQ&e=.

Arkkienkeli commented 4 years ago

@dlogan pip3 install keras==2.2.5 will do the job. I also strongly advise you to use virtual environment (virtualenv) for different python frameworks, so you won't break your system-wide packages.

dlogan commented 4 years ago

Thanks, I did create a venv, though I still had to manually pip3 install Keras==2.2.5 (not sure if that is just my environment, or if it should be added to instructions?). I ran the tests again after install, and this time it got farther, but not without a few errors:

======================================================================= short test summary info ========================================================================
FAILED tests/deepprofiler/learning/test_profiling.py::test_configure - RuntimeError: Attempted to use a closed Session.
FAILED tests/deepprofiler/learning/test_profiling.py::test_extract_features - RuntimeError: Attempted to use a closed Session.
FAILED tests/deepprofiler/learning/test_profiling.py::test_profile - RuntimeError: Attempted to use a closed Session.
======================================================== 3 failed, 83 passed, 60 warnings in 233.30s (0:03:53) ==========

Suggestions?

dlogan commented 4 years ago

In case pip freeze output helps. Thanks!

(venv) logand05@cortex:~/github/DeepProfiler$ pip freeze
absl-py==0.9.0
astor==0.8.1
attrs==19.3.0
beautifulsoup4==4.9.0
certifi==2020.4.5.1
chardet==3.0.4
click==7.1.2
comet-git-pure==0.19.16
comet-ml==3.1.6
configobj==5.0.6
coverage==5.1
cycler==0.10.0
decorator==4.4.2
-e git+https://github.com/broadinstitute/DeepProfiler.git@000b2a9d566309a2542f75d183649bd79cb15718#egg=deepprofiler
everett==1.0.2
gast==0.3.3
google-pasta==0.2.0
GPy==1.9.9
GPyOpt==1.2.6
grpcio==1.28.1
h5py==2.10.0
idna==2.9
imageio==2.8.0
importlib-metadata==1.6.0
joblib==0.14.1
jsonschema==3.0.2
Keras==2.2.5
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
kiwisolver==1.2.0
lxml==4.5.0
Markdown==3.2.1
matplotlib==3.2.1
more-itertools==8.2.0
netifaces==0.10.9
networkx==2.4
numpy==1.18.4
nvidia-ml-py3==7.352.0
packaging==20.3
pandas==1.0.3
paramz==0.9.5
Pillow==7.1.2
pkg-resources==0.0.0
pluggy==0.13.1
protobuf==3.11.3
py==1.8.1
pyparsing==2.4.7
pyrsistent==0.16.0
pytest==5.4.1
pytest-cov==2.8.1
python-dateutil==2.8.1
pytz==2020.1
PyWavelets==1.1.1
PyYAML==5.3.1
requests==2.23.0
scikit-image==0.16.2
scikit-learn==0.22.2.post1
scipy==1.4.1
six==1.14.0
soupsieve==2.0
tensorboard==1.14.0
tensorflow==1.14.0
tensorflow-estimator==1.14.0
termcolor==1.1.0
typing-extensions==3.7.4.2
urllib3==1.25.9
wcwidth==0.1.9
websocket-client==0.57.0
Werkzeug==1.0.1
wrapt==1.12.1
wurlitzer==2.0.0
zipp==3.1.0

Arkkienkeli commented 4 years ago

After reinstalling DeepProfiler I have started to have the same issue. Will investigate.

Arkkienkeli commented 4 years ago

Fixed aba4157739aa31d2a9b56d38b45088d4d91511b0

dlogan commented 4 years ago

Thanks this fix did help to get me farther and with no errors, however it hangs for me in test_profile:

tests/deepprofiler/learning/test_profiling.py::test_configure PASSED                                                       [ 72%]
tests/deepprofiler/learning/test_profiling.py::test_check PASSED                                                           [ 73%]
tests/deepprofiler/learning/test_profiling.py::test_extract_features PASSED                                                [ 74%]
tests/deepprofiler/learning/test_profiling.py::test_profile

Arkkienkeli commented 4 years ago

@dlogan Do you use GPU during executing the tests? Some tests can take quite long on the CPU. I see from yours pip freeze that you don't have tensorflow-gpu. If you have GPU with installed CUDA, you can install tensorflow-gpu. Please, have a look at compatibility list of TensorFlow and CUDA versions here: https://stackoverflow.com/questions/50622525/which-tensorflow-and-cuda-version-combinations-are-compatible We usually use tensorflow version 1.15.2, but if you have CUDA 9, then I would go for 1.12.3

dlogan commented 4 years ago

Thanks again @Arkkienkeli ! Indeed in my venv I hadn't installed tensorflow-gpu. I thought 'pip install tensorflow' was supposed to figure that out, but I needed to do 'tensorflow-gpu' explicitly. I do have 4 GPUs with CUDA.

Since then, I have made progress, but not quite there running the tests, ugh! Notes/suggestions to add to wiki:

perhaps obvious, but add 'sudo apt upgrade' after 'sudo apt update'
I needed to upgrade pip by adding 'pip3 install -U pip' before installing deepprofiler because 'imagecodecs' wasn't installing. See this https://github.com/scikit-image/scikit-image/issues/4673
I needed to add 'pip install Keras'. I believe Keras-Applications and Keras-Preprocessing were being installed with deepprofiler, but Keras wasn't. Seems odd, but I tried this more than once from a clean venv

And now running 'python3 -m pytest' I get this error/output. Thoughts?

(venv-test1) [logand05@cortex:~/github/DeepProfiler]$ python3 -m pytest
=============================================================================== test session starts ===============================================================================
platform linux -- Python 3.6.9, pytest-5.4.2, py-1.8.1, pluggy-0.13.1 -- /home/logand05/github/DeepProfiler/venv-test1/bin/python3
cachedir: .pytest_cache
rootdir: /home/logand05/github/DeepProfiler, inifile: setup.cfg
plugins: cov-2.8.1
collected 0 items / 1 error
Coverage.py warning: Couldn't parse Python file '/home/logand05/github/DeepProfiler/scripts/locations.py' (couldnt-parse)

===================================================================================== ERRORS ======================================================================================
__________________________________________________________________________ ERROR collecting test session __________________________________________________________________________
venv-test1/lib/python3.6/site-packages/_pytest/config/__init__.py:495: in _importconftest
    return self._conftestpath2mod[key]
E   KeyError: PosixPath('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py')

During handling of the above exception, another exception occurred:
venv-test1/lib/python3.6/site-packages/_pytest/config/__init__.py:501: in _importconftest
    mod = conftestpath.pyimport()
venv-test1/lib/python3.6/site-packages/py/_path/local.py:721: in pyimport
    raise self.ImportMismatchError(modname, modfile, self)
E   py._path.local.LocalPath.ImportMismatchError: ('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py'))

During handling of the above exception, another exception occurred:
venv-test1/lib/python3.6/site-packages/py/_path/common.py:383: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
venv-test1/lib/python3.6/site-packages/py/_path/common.py:435: in gen
    for p in self.gen(subdir):
venv-test1/lib/python3.6/site-packages/py/_path/common.py:435: in gen
    for p in self.gen(subdir):
venv-test1/lib/python3.6/site-packages/py/_path/common.py:424: in gen
    dirs = self.optsort([p for p in entries
venv-test1/lib/python3.6/site-packages/py/_path/common.py:425: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
venv-test1/lib/python3.6/site-packages/_pytest/nodes.py:506: in _recurse
    ihook = self._gethookproxy(dirpath)
venv-test1/lib/python3.6/site-packages/_pytest/nodes.py:487: in _gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
venv-test1/lib/python3.6/site-packages/_pytest/config/__init__.py:473: in _getconftestmodules
    mod = self._importconftest(conftestpath)
venv-test1/lib/python3.6/site-packages/_pytest/config/__init__.py:509: in _importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure: (local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py'), (<class 'py._path.local.LocalPath.ImportMismatchError'>, ImportMismatchError('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py')), <traceback object at 0x7f526ad86d08>))

----------- coverage: platform linux, python 3.6.9-final-0 -----------
Name                                                                                                       Stmts   Miss  Cover
------------------------------------------------------------------------------------------------------------------------------
deepprofiler/__init__.py                                                                                       0      0   100%
deepprofiler/__main__.py                                                                                     106    106     0%
deepprofiler/dataset/__init__.py                                                                               0      0   100%
deepprofiler/dataset/compression.py                                                                           91     91     0%
deepprofiler/dataset/illumination_correction.py                                                               25     25     0%
deepprofiler/dataset/illumination_statistics.py                                                               76     76     0%
deepprofiler/dataset/image_dataset.py                                                                        161    138    14%
deepprofiler/dataset/indexing.py                                                                              22     22     0%
deepprofiler/dataset/metadata.py                                                                              54     42    22%
deepprofiler/dataset/pixels.py                                                                                13      9    31%
deepprofiler/dataset/target.py                                                                                13      9    31%
deepprofiler/dataset/utils.py                                                                                 69     43    38%
deepprofiler/imaging/__init__.py                                                                               0      0   100%
deepprofiler/imaging/augmentations.py                                                                         18     18     0%
deepprofiler/imaging/boxes.py                                                                                 83     73    12%
deepprofiler/imaging/cropping.py                                                                             176    176     0%
deepprofiler/learning/__init__.py                                                                              1      1     0%
deepprofiler/learning/metric.py                                                                               13     13     0%
deepprofiler/learning/model.py                                                                               117    117     0%
deepprofiler/learning/profiling.py                                                                            61     61     0%
deepprofiler/learning/training.py                                                                             25     25     0%
deepprofiler/learning/validation.py                                                                           23     23     0%
plugins/__init__.py                                                                                            0      0   100%
plugins/crop_generators/__init__.py                                                                            0      0   100%
plugins/crop_generators/autoencoder_crop_generator.py                                                         14     14     0%
plugins/crop_generators/crop_generator.py                                                                      3      3     0%
plugins/crop_generators/mixup_crop_generator.py                                                               65     65     0%
plugins/crop_generators/repeat_channel_crop_generator.py                                                      29     29     0%
plugins/metrics/__init__.py                                                                                    0      0   100%
plugins/metrics/top_k.py                                                                                      12     12     0%
plugins/models/__init__.py                                                                                     0      0   100%
plugins/models/autoencoder.py                                                                                 41     41     0%
plugins/models/cnn.py                                                                                         33     33     0%
plugins/models/densenet.py                                                                                     9      9     0%
plugins/models/inception_resnet_v2.py                                                                         28     28     0%
plugins/models/resnet.py                                                                                      57     57     0%
scripts/__init__.py                                                                                            0      0   100%
scripts/create_metadata_index.py                                                                             112    112     0%
setup.py                                                                                                       2      2     0%
tests/__init__.py                                                                                              0      0   100%
tests/conftest.py                                                                                             56     38    32%
tests/deepprofiler/__init__.py                                                                                 0      0   100%
tests/deepprofiler/dataset/__init__.py                                                                         0      0   100%
tests/deepprofiler/dataset/test_compression.py                                                                75     75     0%
tests/deepprofiler/dataset/test_illumination_correction.py                                                    36     36     0%
tests/deepprofiler/dataset/test_illumination_statistics.py                                                    56     56     0%
tests/deepprofiler/dataset/test_image_dataset.py                                                              75     75     0%
tests/deepprofiler/dataset/test_indexing.py                                                                   21     21     0%
tests/deepprofiler/dataset/test_metadata.py                                                                   71     71     0%
tests/deepprofiler/dataset/test_pixels.py                                                                     18     18     0%
tests/deepprofiler/dataset/test_target.py                                                                     22     22     0%
tests/deepprofiler/dataset/test_utils.py                                                                      73     73     0%
tests/deepprofiler/imaging/__init__.py                                                                         0      0   100%
tests/deepprofiler/imaging/test_augmentations.py                                                              17     17     0%
tests/deepprofiler/imaging/test_boxes.py                                                                      38     38     0%
tests/deepprofiler/imaging/test_cropping.py                                                                  138    138     0%
tests/deepprofiler/learning/__init__.py                                                                        0      0   100%
tests/deepprofiler/learning/test_metric.py                                                                    22     22     0%
tests/deepprofiler/learning/test_model.py                                                                     51     51     0%
tests/deepprofiler/learning/test_profiling.py                                                                 51     51     0%
tests/deepprofiler/learning/test_training.py                                                                  18     18     0%
tests/deepprofiler/learning/test_validation.py                                                                37     37     0%
tests/plugins/__init__.py                                                                                      0      0   100%
tests/plugins/crop_generators/__init__.py                                                                      0      0   100%
tests/plugins/crop_generators/test_autoencoder_crop_generator.py                                              47     47     0%
tests/plugins/crop_generators/test_crop_generator.py                                                           5      5     0%
tests/plugins/crop_generators/test_mixup_crop_generator.py                                                   120    120     0%
tests/plugins/models/__init__.py                                                                               0      0   100%
tests/plugins/models/test_autoencoder.py                                                                      26     26     0%
tests/plugins/models/test_cnn.py                                                                              22     22     0%
tests/plugins/models/test_densenet.py                                                                         23     23     0%
tests/plugins/models/test_inception_resnet_v2.py                                                               0      0   100%
tests/plugins/models/test_resnet.py                                                                           22     22     0%
venv-test1/lib/python3.6/site-packages/PIL/Image.py                                                         1367   1127    18%
venv-test1/lib/python3.6/site-packages/PIL/ImageMode.py                                                       23     18    22%
venv-test1/lib/python3.6/site-packages/PIL/TiffTags.py                                                        40      2    95%
venv-test1/lib/python3.6/site-packages/PIL/__init__.py                                                        42     22    48%
venv-test1/lib/python3.6/site-packages/PIL/_binary.py                                                         25     12    52%
venv-test1/lib/python3.6/site-packages/PIL/_util.py                                                           16      6    62%
venv-test1/lib/python3.6/site-packages/PIL/_version.py                                                         1      0   100%
venv-test1/lib/python3.6/site-packages/_pytest/_argcomplete.py                                                37     36     3%
venv-test1/lib/python3.6/site-packages/_pytest/_code/code.py                                                 655    469    28%
venv-test1/lib/python3.6/site-packages/_pytest/_code/source.py                                               244    190    22%
venv-test1/lib/python3.6/site-packages/_pytest/_io/saferepr.py                                                63     48    24%
venv-test1/lib/python3.6/site-packages/_pytest/assertion/__init__.py                                          79     75     5%
venv-test1/lib/python3.6/site-packages/_pytest/assertion/rewrite.py                                          595    525    12%
venv-test1/lib/python3.6/site-packages/_pytest/cacheprovider.py                                              278    238    14%
venv-test1/lib/python3.6/site-packages/_pytest/capture.py                                                    484    466     4%
venv-test1/lib/python3.6/site-packages/_pytest/compat.py                                                     180    157    13%
venv-test1/lib/python3.6/site-packages/_pytest/config/__init__.py                                            654    527    19%
venv-test1/lib/python3.6/site-packages/_pytest/config/argparsing.py                                          244    199    18%
venv-test1/lib/python3.6/site-packages/_pytest/debugging.py                                                  194    185     5%
venv-test1/lib/python3.6/site-packages/_pytest/doctest.py                                                    332    323     3%
venv-test1/lib/python3.6/site-packages/_pytest/faulthandler.py                                                53     42    21%
venv-test1/lib/python3.6/site-packages/_pytest/fixtures.py                                                   775    672    13%
venv-test1/lib/python3.6/site-packages/_pytest/helpconfig.py                                                 120    111     8%
venv-test1/lib/python3.6/site-packages/_pytest/junitxml.py                                                   350    348     1%
venv-test1/lib/python3.6/site-packages/_pytest/logging.py                                                    359    294    18%
venv-test1/lib/python3.6/site-packages/_pytest/main.py                                                       397    269    32%
venv-test1/lib/python3.6/site-packages/_pytest/mark/__init__.py                                               84     70    17%
venv-test1/lib/python3.6/site-packages/_pytest/mark/structures.py                                            173    168     3%
venv-test1/lib/python3.6/site-packages/_pytest/monkeypatch.py                                                148    136     8%
venv-test1/lib/python3.6/site-packages/_pytest/nodes.py                                                      296    197    33%
venv-test1/lib/python3.6/site-packages/_pytest/pastebin.py                                                    64     63     2%
venv-test1/lib/python3.6/site-packages/_pytest/pathlib.py                                                    203    191     6%
venv-test1/lib/python3.6/site-packages/_pytest/python.py                                                     776    759     2%
venv-test1/lib/python3.6/site-packages/_pytest/reports.py                                                    244    236     3%
venv-test1/lib/python3.6/site-packages/_pytest/resultlog.py                                                   68     66     3%
venv-test1/lib/python3.6/site-packages/_pytest/runner.py                                                     269    229    15%
venv-test1/lib/python3.6/site-packages/_pytest/setuponly.py                                                   42     41     2%
venv-test1/lib/python3.6/site-packages/_pytest/setupplan.py                                                   13     12     8%
venv-test1/lib/python3.6/site-packages/_pytest/skipping.py                                                   101     97     4%
venv-test1/lib/python3.6/site-packages/_pytest/stepwise.py                                                    58     48    17%
venv-test1/lib/python3.6/site-packages/_pytest/store.py                                                       34     29    15%
venv-test1/lib/python3.6/site-packages/_pytest/terminal.py                                                   804    654    19%
venv-test1/lib/python3.6/site-packages/_pytest/tmpdir.py                                                      87     80     8%
venv-test1/lib/python3.6/site-packages/_pytest/warnings.py                                                    77     61    21%
venv-test1/lib/python3.6/site-packages/attr/converters.py                                                     27     25     7%
venv-test1/lib/python3.6/site-packages/coverage/collector.py                                                 200    194     3%
venv-test1/lib/python3.6/site-packages/coverage/control.py                                                   376    371     1%
venv-test1/lib/python3.6/site-packages/cycler.py                                                             175    107    39%
venv-test1/lib/python3.6/site-packages/dateutil/__init__.py                                                    5      2    60%
venv-test1/lib/python3.6/site-packages/dateutil/_common.py                                                    25     15    40%
venv-test1/lib/python3.6/site-packages/dateutil/_version.py                                                    1      0   100%
venv-test1/lib/python3.6/site-packages/dateutil/easter.py                                                     27     20    26%
venv-test1/lib/python3.6/site-packages/dateutil/parser/__init__.py                                            32      4    88%
venv-test1/lib/python3.6/site-packages/dateutil/parser/_parser.py                                            807    690    14%
venv-test1/lib/python3.6/site-packages/dateutil/parser/isoparser.py                                          176    145    18%
venv-test1/lib/python3.6/site-packages/dateutil/relativedelta.py                                             239    206    14%
venv-test1/lib/python3.6/site-packages/dateutil/rrule.py                                                     974    863    11%
venv-test1/lib/python3.6/site-packages/dateutil/tz/__init__.py                                                 4      0   100%
venv-test1/lib/python3.6/site-packages/dateutil/tz/_common.py                                                155    122    21%
venv-test1/lib/python3.6/site-packages/dateutil/tz/_factories.py                                              49     21    57%
venv-test1/lib/python3.6/site-packages/dateutil/tz/tz.py                                                     795    639    20%
venv-test1/lib/python3.6/site-packages/dateutil/tz/win.py                                                    151    147     3%
venv-test1/lib/python3.6/site-packages/imagecodecs/__init__.py                                                 5      0   100%
venv-test1/lib/python3.6/site-packages/imagecodecs/imagecodecs.py                                            300    191    36%
venv-test1/lib/python3.6/site-packages/imageio/__init__.py                                                    13      0   100%
venv-test1/lib/python3.6/site-packages/imageio/core/__init__.py                                                8      0   100%
venv-test1/lib/python3.6/site-packages/imageio/core/fetching.py                                              106     89    16%
venv-test1/lib/python3.6/site-packages/imageio/core/findlib.py                                                74     65    12%
venv-test1/lib/python3.6/site-packages/imageio/core/format.py                                                268    178    34%
venv-test1/lib/python3.6/site-packages/imageio/core/functions.py                                             157    124    21%
venv-test1/lib/python3.6/site-packages/imageio/core/request.py                                               314    274    13%
venv-test1/lib/python3.6/site-packages/imageio/core/util.py                                                  262    210    20%
venv-test1/lib/python3.6/site-packages/imageio/plugins/__init__.py                                            22      0   100%
venv-test1/lib/python3.6/site-packages/imageio/plugins/_freeimage.py                                         601    405    33%
venv-test1/lib/python3.6/site-packages/imageio/plugins/bsdf.py                                               140    113    19%
venv-test1/lib/python3.6/site-packages/imageio/plugins/dicom.py                                              146    122    16%
venv-test1/lib/python3.6/site-packages/imageio/plugins/example.py                                             43     23    47%
venv-test1/lib/python3.6/site-packages/imageio/plugins/feisem.py                                              41     32    22%
venv-test1/lib/python3.6/site-packages/imageio/plugins/ffmpeg.py                                             304    258    15%
venv-test1/lib/python3.6/site-packages/imageio/plugins/fits.py                                                40     24    40%
venv-test1/lib/python3.6/site-packages/imageio/plugins/freeimage.py                                          176    122    31%
venv-test1/lib/python3.6/site-packages/imageio/plugins/freeimagemulti.py                                     144    104    28%
venv-test1/lib/python3.6/site-packages/imageio/plugins/gdal.py                                                35     19    46%
venv-test1/lib/python3.6/site-packages/imageio/plugins/grab.py                                                63     37    41%
venv-test1/lib/python3.6/site-packages/imageio/plugins/lytro.py                                              302    225    25%
venv-test1/lib/python3.6/site-packages/imageio/plugins/npz.py                                                 37     17    54%
venv-test1/lib/python3.6/site-packages/imageio/plugins/pillow.py                                             363    284    22%
venv-test1/lib/python3.6/site-packages/imageio/plugins/pillow_info.py                                          5      1    80%
venv-test1/lib/python3.6/site-packages/imageio/plugins/pillowmulti.py                                        164    134    18%
venv-test1/lib/python3.6/site-packages/imageio/plugins/simpleitk.py                                           62     38    39%
venv-test1/lib/python3.6/site-packages/imageio/plugins/spe.py                                                126     96    24%
venv-test1/lib/python3.6/site-packages/imageio/plugins/swf.py                                                181    149    18%
venv-test1/lib/python3.6/site-packages/imageio/plugins/tifffile.py                                            91     65    29%
venv-test1/lib/python3.6/site-packages/importlib_metadata/__init__.py                                        220    215     2%
venv-test1/lib/python3.6/site-packages/importlib_metadata/_compat.py                                          29     28     3%
venv-test1/lib/python3.6/site-packages/matplotlib/__init__.py                                                649    391    40%
venv-test1/lib/python3.6/site-packages/matplotlib/_cm.py                                                     141     12    91%
venv-test1/lib/python3.6/site-packages/matplotlib/_cm_listed.py                                               10      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/_color_data.py                                               7      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/_layoutbox.py                                              408    342    16%
venv-test1/lib/python3.6/site-packages/matplotlib/_mathtext_data.py                                            7      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/_pylab_helpers.py                                           52     35    33%
venv-test1/lib/python3.6/site-packages/matplotlib/_text_layout.py                                             12     10    17%
venv-test1/lib/python3.6/site-packages/matplotlib/_version.py                                                  5      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/afm.py                                                     239    189    21%
venv-test1/lib/python3.6/site-packages/matplotlib/artist.py                                                  586    408    30%
venv-test1/lib/python3.6/site-packages/matplotlib/axes/__init__.py                                             2      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/axes/_axes.py                                             2308   2121     8%
venv-test1/lib/python3.6/site-packages/matplotlib/axes/_base.py                                             1664   1450    13%
venv-test1/lib/python3.6/site-packages/matplotlib/axes/_secondary_axes.py                                    152    128    16%
venv-test1/lib/python3.6/site-packages/matplotlib/axes/_subplots.py                                          120     80    33%
venv-test1/lib/python3.6/site-packages/matplotlib/axis.py                                                   1213    987    19%
venv-test1/lib/python3.6/site-packages/matplotlib/backend_bases.py                                          1237    966    22%
venv-test1/lib/python3.6/site-packages/matplotlib/backend_tools.py                                           570    386    32%
venv-test1/lib/python3.6/site-packages/matplotlib/bezier.py                                                  204    173    15%
venv-test1/lib/python3.6/site-packages/matplotlib/blocking_input.py                                          143    102    29%
venv-test1/lib/python3.6/site-packages/matplotlib/category.py                                                 76     48    37%
venv-test1/lib/python3.6/site-packages/matplotlib/cbook/__init__.py                                          835    660    21%
venv-test1/lib/python3.6/site-packages/matplotlib/cbook/deprecation.py                                       128     31    76%
venv-test1/lib/python3.6/site-packages/matplotlib/cm.py                                                      150    111    26%
venv-test1/lib/python3.6/site-packages/matplotlib/collections.py                                             840    696    17%
venv-test1/lib/python3.6/site-packages/matplotlib/colors.py                                                  807    585    28%
venv-test1/lib/python3.6/site-packages/matplotlib/container.py                                                44     25    43%
venv-test1/lib/python3.6/site-packages/matplotlib/contour.py                                                 732    666     9%
venv-test1/lib/python3.6/site-packages/matplotlib/dates.py                                                   735    578    21%
venv-test1/lib/python3.6/site-packages/matplotlib/docstring.py                                                40     12    70%
venv-test1/lib/python3.6/site-packages/matplotlib/dviread.py                                                 466    356    24%
venv-test1/lib/python3.6/site-packages/matplotlib/font_manager.py                                            538    418    22%
venv-test1/lib/python3.6/site-packages/matplotlib/fontconfig_pattern.py                                       70     21    70%
venv-test1/lib/python3.6/site-packages/matplotlib/gridspec.py                                                245    194    21%
venv-test1/lib/python3.6/site-packages/matplotlib/image.py                                                   707    608    14%
venv-test1/lib/python3.6/site-packages/matplotlib/legend.py                                                  448    380    15%
venv-test1/lib/python3.6/site-packages/matplotlib/legend_handler.py                                          319    240    25%
venv-test1/lib/python3.6/site-packages/matplotlib/lines.py                                                   639    536    16%
venv-test1/lib/python3.6/site-packages/matplotlib/markers.py                                                 463    372    20%
venv-test1/lib/python3.6/site-packages/matplotlib/mathtext.py                                               1668   1320    21%
venv-test1/lib/python3.6/site-packages/matplotlib/mlab.py                                                    469    421    10%
venv-test1/lib/python3.6/site-packages/matplotlib/offsetbox.py                                               708    562    21%
venv-test1/lib/python3.6/site-packages/matplotlib/patches.py                                                1662   1271    24%
venv-test1/lib/python3.6/site-packages/matplotlib/path.py                                                    350    258    26%
venv-test1/lib/python3.6/site-packages/matplotlib/quiver.py                                                  474    415    12%
venv-test1/lib/python3.6/site-packages/matplotlib/rcsetup.py                                                 487    223    54%
venv-test1/lib/python3.6/site-packages/matplotlib/scale.py                                                   322    177    45%
venv-test1/lib/python3.6/site-packages/matplotlib/spines.py                                                  303    268    12%
venv-test1/lib/python3.6/site-packages/matplotlib/stackplot.py                                                42     38    10%
venv-test1/lib/python3.6/site-packages/matplotlib/streamplot.py                                              374    331    11%
venv-test1/lib/python3.6/site-packages/matplotlib/table.py                                                   334    277    17%
venv-test1/lib/python3.6/site-packages/matplotlib/texmanager.py                                              209    164    22%
venv-test1/lib/python3.6/site-packages/matplotlib/text.py                                                    950    797    16%
venv-test1/lib/python3.6/site-packages/matplotlib/textpath.py                                                228    185    19%
venv-test1/lib/python3.6/site-packages/matplotlib/ticker.py                                                 1320   1090    17%
venv-test1/lib/python3.6/site-packages/matplotlib/tight_bbox.py                                               46     43     7%
venv-test1/lib/python3.6/site-packages/matplotlib/tight_layout.py                                            171    160     6%
venv-test1/lib/python3.6/site-packages/matplotlib/transforms.py                                             1124    810    28%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/__init__.py                                              8      0   100%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/triangulation.py                                        85     74    13%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/tricontour.py                                           59     48    19%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/trifinder.py                                            26     15    42%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/triinterpolate.py                                      548    467    15%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/tripcolor.py                                            58     52    10%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/triplot.py                                              25     22    12%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/trirefine.py                                            93     81    13%
venv-test1/lib/python3.6/site-packages/matplotlib/tri/tritools.py                                             84     73    13%
venv-test1/lib/python3.6/site-packages/matplotlib/units.py                                                    70     47    33%
venv-test1/lib/python3.6/site-packages/matplotlib/widgets.py                                                1382   1209    13%
venv-test1/lib/python3.6/site-packages/more_itertools/more.py                                                903    894     1%
venv-test1/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/__init__.py                                     4      0   100%
venv-test1/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/axes_divider.py                               350    287    18%
venv-test1/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/axes_grid.py                                  397    356    10%
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venv-test1/lib/python3.6/site-packages/scipy/optimize/_shgo_lib/sobol_seq.py                                 122    114     7%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_shgo_lib/triangulation.py                             359    321    11%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_spectral.py                                           107     94    12%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trlib/__init__.py                                       6      3    50%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion.py                                        131    114    13%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/__init__.py                          2      0   100%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/canonical_constraint.py            246    234     5%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/equality_constrained_sqp.py        105     96     9%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py     175    152    13%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/projections.py                     164    145    12%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/qp_subproblem.py                   215    201     7%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/report.py                           29     10    66%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_constr/tr_interior_point.py               149    125    16%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_dogleg.py                                  40     30    25%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_exact.py                                  140    125    11%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_krylov.py                                  11      7    36%
venv-test1/lib/python3.6/site-packages/scipy/optimize/_trustregion_ncg.py                                     52     43    17%
venv-test1/lib/python3.6/site-packages/scipy/optimize/cobyla.py                                               72     60    17%
venv-test1/lib/python3.6/site-packages/scipy/optimize/lbfgsb.py                                              137    124     9%
venv-test1/lib/python3.6/site-packages/scipy/optimize/linesearch.py                                          323    302     7%
venv-test1/lib/python3.6/site-packages/scipy/optimize/minpack.py                                             284    255    10%
venv-test1/lib/python3.6/site-packages/scipy/optimize/nnls.py                                                 21     16    24%
venv-test1/lib/python3.6/site-packages/scipy/optimize/nonlin.py                                              624    491    21%
venv-test1/lib/python3.6/site-packages/scipy/optimize/optimize.py                                           1240   1167     6%
venv-test1/lib/python3.6/site-packages/scipy/optimize/slsqp.py                                               191    179     6%
venv-test1/lib/python3.6/site-packages/scipy/optimize/tnc.py                                                 102     76    25%
venv-test1/lib/python3.6/site-packages/scipy/optimize/zeros.py                                               472    418    11%
venv-test1/lib/python3.6/site-packages/scipy/signal/__init__.py                                               44      2    95%
venv-test1/lib/python3.6/site-packages/scipy/signal/_arraytools.py                                            49     41    16%
venv-test1/lib/python3.6/site-packages/scipy/signal/_max_len_seq.py                                           31     25    19%
venv-test1/lib/python3.6/site-packages/scipy/signal/_peak_finding.py                                         225    201    11%
venv-test1/lib/python3.6/site-packages/scipy/signal/_savitzky_golay.py                                        81     70    14%
venv-test1/lib/python3.6/site-packages/scipy/signal/_upfirdn.py                                               40     30    25%
venv-test1/lib/python3.6/site-packages/scipy/signal/bsplines.py                                              202    177    12%
venv-test1/lib/python3.6/site-packages/scipy/signal/filter_design.py                                        1094   1014     7%
venv-test1/lib/python3.6/site-packages/scipy/signal/fir_filter_design.py                                     272    250     8%
venv-test1/lib/python3.6/site-packages/scipy/signal/lti_conversion.py                                        160    142    11%
venv-test1/lib/python3.6/site-packages/scipy/signal/ltisys.py                                                893    757    15%
venv-test1/lib/python3.6/site-packages/scipy/signal/signaltools.py                                          1148   1072     7%
venv-test1/lib/python3.6/site-packages/scipy/signal/spectral.py                                              363    339     7%
venv-test1/lib/python3.6/site-packages/scipy/signal/waveforms.py                                             120    107    11%
venv-test1/lib/python3.6/site-packages/scipy/signal/wavelets.py                                              136    123    10%
venv-test1/lib/python3.6/site-packages/scipy/signal/windows/__init__.py                                        2      0   100%
venv-test1/lib/python3.6/site-packages/scipy/signal/windows/windows.py                                       288    243    16%
venv-test1/lib/python3.6/site-packages/scipy/sparse/__init__.py                                               19      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/_index.py                                                221    190    14%
venv-test1/lib/python3.6/site-packages/scipy/sparse/_matrix_io.py                                             42     32    24%
venv-test1/lib/python3.6/site-packages/scipy/sparse/base.py                                                  454    344    24%
venv-test1/lib/python3.6/site-packages/scipy/sparse/bsr.py                                                   313    266    15%
venv-test1/lib/python3.6/site-packages/scipy/sparse/compressed.py                                            737    654    11%
venv-test1/lib/python3.6/site-packages/scipy/sparse/construct.py                                             232    206    11%
venv-test1/lib/python3.6/site-packages/scipy/sparse/coo.py                                                   294    251    15%
venv-test1/lib/python3.6/site-packages/scipy/sparse/csc.py                                                    87     58    33%
venv-test1/lib/python3.6/site-packages/scipy/sparse/csgraph/__init__.py                                       14      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/csgraph/_laplacian.py                                     51     44    14%
venv-test1/lib/python3.6/site-packages/scipy/sparse/csgraph/_validation.py                                    31     25    19%
venv-test1/lib/python3.6/site-packages/scipy/sparse/csr.py                                                   135    103    24%
venv-test1/lib/python3.6/site-packages/scipy/sparse/data.py                                                  184    138    25%
venv-test1/lib/python3.6/site-packages/scipy/sparse/dia.py                                                   224    188    16%
venv-test1/lib/python3.6/site-packages/scipy/sparse/dok.py                                                   275    213    23%
venv-test1/lib/python3.6/site-packages/scipy/sparse/extract.py                                                22     14    36%
venv-test1/lib/python3.6/site-packages/scipy/sparse/lil.py                                                   291    232    20%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/__init__.py                                        13      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/_expm_multiply.py                                 255    225    12%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/_norm.py                                           70     63    10%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/_onenormest.py                                    199    179    10%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/dsolve/__init__.py                                  8      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/dsolve/_add_newdocs.py                              9      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py                                197    173    12%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/eigen/__init__.py                                   7      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/eigen/arpack/__init__.py                            2      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py                            725    642    11%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/eigen/lobpcg/__init__.py                            6      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/eigen/lobpcg/lobpcg.py                            323    310     4%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/interface.py                                      345    245    29%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/__init__.py                                 11      0   100%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/_gcrotmk.py                                192    182     5%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/iterative.py                               427    392     8%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/lgmres.py                                   69     59    14%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/lsmr.py                                    185    177     4%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/lsqr.py                                    200    192     4%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/minres.py                                  203    196     3%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/isolve/utils.py                                    56     46    18%
venv-test1/lib/python3.6/site-packages/scipy/sparse/linalg/matfuncs.py                                       339    279    18%
venv-test1/lib/python3.6/site-packages/scipy/sparse/sputils.py                                               176    146    17%
venv-test1/lib/python3.6/site-packages/scipy/spatial/__init__.py                                              13      0   100%
venv-test1/lib/python3.6/site-packages/scipy/spatial/_plotutils.py                                            78     65    17%
venv-test1/lib/python3.6/site-packages/scipy/spatial/_procrustes.py                                           25     20    20%
venv-test1/lib/python3.6/site-packages/scipy/spatial/_spherical_voronoi.py                                    68     57    16%
venv-test1/lib/python3.6/site-packages/scipy/spatial/distance.py                                             633    560    12%
venv-test1/lib/python3.6/site-packages/scipy/spatial/kdtree.py                                               419    379    10%
venv-test1/lib/python3.6/site-packages/scipy/spatial/transform/__init__.py                                     7      0   100%
venv-test1/lib/python3.6/site-packages/scipy/spatial/transform/_rotation_groups.py                            56     48    14%
venv-test1/lib/python3.6/site-packages/scipy/spatial/transform/_rotation_spline.py                           176    159    10%
venv-test1/lib/python3.6/site-packages/scipy/spatial/transform/rotation.py                                   466    416    11%
venv-test1/lib/python3.6/site-packages/scipy/special/__init__.py                                              17      0   100%
venv-test1/lib/python3.6/site-packages/scipy/special/_basic.py                                               524    449    14%
venv-test1/lib/python3.6/site-packages/scipy/special/_ellip_harm.py                                           16      6    62%
venv-test1/lib/python3.6/site-packages/scipy/special/_logsumexp.py                                            34     28    18%
venv-test1/lib/python3.6/site-packages/scipy/special/_spherical_bessel.py                                     18     12    33%
venv-test1/lib/python3.6/site-packages/scipy/special/lambertw.py                                               4      1    75%
venv-test1/lib/python3.6/site-packages/scipy/special/orthogonal.py                                           525    464    12%
venv-test1/lib/python3.6/site-packages/scipy/special/sf_error.py                                               6      0   100%
venv-test1/lib/python3.6/site-packages/scipy/special/spfun_stats.py                                           14      8    43%
venv-test1/lib/python3.6/site-packages/scipy/stats/__init__.py                                                13      0   100%
venv-test1/lib/python3.6/site-packages/scipy/stats/_binned_statistic.py                                      159    145     9%
venv-test1/lib/python3.6/site-packages/scipy/stats/_constants.py                                               8      0   100%
venv-test1/lib/python3.6/site-packages/scipy/stats/_continuous_distns.py                                    2930   1970    33%
venv-test1/lib/python3.6/site-packages/scipy/stats/_discrete_distns.py                                       446    296    34%
venv-test1/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py                                 1392   1041    25%
venv-test1/lib/python3.6/site-packages/scipy/stats/_distr_params.py                                            2      0   100%
venv-test1/lib/python3.6/site-packages/scipy/stats/_hypotests.py                                              43     36    16%
venv-test1/lib/python3.6/site-packages/scipy/stats/_multivariate.py                                          967    690    29%
venv-test1/lib/python3.6/site-packages/scipy/stats/_rvs_sampling.py                                           33     28    15%
venv-test1/lib/python3.6/site-packages/scipy/stats/_stats_mstats_common.py                                   107     98     8%
venv-test1/lib/python3.6/site-packages/scipy/stats/_tukeylambda_stats.py                                      54     40    26%
venv-test1/lib/python3.6/site-packages/scipy/stats/contingency.py                                             36     28    22%
venv-test1/lib/python3.6/site-packages/scipy/stats/distributions.py                                            9      0   100%
venv-test1/lib/python3.6/site-packages/scipy/stats/kde.py                                                    181    151    17%
venv-test1/lib/python3.6/site-packages/scipy/stats/morestats.py                                              829    760     8%
venv-test1/lib/python3.6/site-packages/scipy/stats/mstats.py                                                   4      0   100%
venv-test1/lib/python3.6/site-packages/scipy/stats/mstats_basic.py                                           947    845    11%
venv-test1/lib/python3.6/site-packages/scipy/stats/mstats_extras.py                                          159    141    11%
venv-test1/lib/python3.6/site-packages/scipy/stats/stats.py                                                 1634   1486     9%
venv-test1/lib/python3.6/site-packages/scipy/version.py                                                        7      1    86%
venv-test1/lib/python3.6/site-packages/six.py                                                                490    241    51%
venv-test1/lib/python3.6/site-packages/skimage/__init__.py                                                    28      9    68%
venv-test1/lib/python3.6/site-packages/skimage/_shared/__init__.py                                             0      0   100%
venv-test1/lib/python3.6/site-packages/skimage/_shared/_warnings.py                                           52     42    19%
venv-test1/lib/python3.6/site-packages/skimage/_shared/utils.py                                              120     82    32%
venv-test1/lib/python3.6/site-packages/skimage/_shared/version_requirements.py                                59     50    15%
venv-test1/lib/python3.6/site-packages/skimage/color/__init__.py                                               4      0   100%
venv-test1/lib/python3.6/site-packages/skimage/color/adapt_rgb.py                                             24     11    54%
venv-test1/lib/python3.6/site-packages/skimage/color/colorconv.py                                            353    254    28%
venv-test1/lib/python3.6/site-packages/skimage/color/colorlabel.py                                            82     67    18%
venv-test1/lib/python3.6/site-packages/skimage/color/delta_e.py                                              100     93     7%
venv-test1/lib/python3.6/site-packages/skimage/color/rgb_colors.py                                           146      0   100%
venv-test1/lib/python3.6/site-packages/skimage/data/__init__.py                                              142     84    41%
venv-test1/lib/python3.6/site-packages/skimage/data/_binary_blobs.py                                          12     10    17%
venv-test1/lib/python3.6/site-packages/skimage/data/_registry.py                                               4      0   100%
venv-test1/lib/python3.6/site-packages/skimage/exposure/__init__.py                                            4      0   100%
venv-test1/lib/python3.6/site-packages/skimage/exposure/_adapthist.py                                        106     95    10%
venv-test1/lib/python3.6/site-packages/skimage/exposure/exposure.py                                          138    117    15%
venv-test1/lib/python3.6/site-packages/skimage/exposure/histogram_matching.py                                 20     17    15%
venv-test1/lib/python3.6/site-packages/skimage/io/__init__.py                                                 33      1    97%
venv-test1/lib/python3.6/site-packages/skimage/io/_image_stack.py                                              9      4    56%
venv-test1/lib/python3.6/site-packages/skimage/io/_io.py                                                      44     31    30%
venv-test1/lib/python3.6/site-packages/skimage/io/_plugins/__init__.py                                         0      0   100%
venv-test1/lib/python3.6/site-packages/skimage/io/_plugins/imageio_plugin.py                                   6      1    83%
venv-test1/lib/python3.6/site-packages/skimage/io/_plugins/matplotlib_plugin.py                               86     67    22%
venv-test1/lib/python3.6/site-packages/skimage/io/collection.py                                              146    116    21%
venv-test1/lib/python3.6/site-packages/skimage/io/manage_plugins.py                                          136     30    78%
venv-test1/lib/python3.6/site-packages/skimage/io/sift.py                                                     27     20    26%
venv-test1/lib/python3.6/site-packages/skimage/io/util.py                                                     26     16    38%
venv-test1/lib/python3.6/site-packages/skimage/measure/__init__.py                                            15      0   100%
venv-test1/lib/python3.6/site-packages/skimage/measure/_find_contours.py                                      60     54    10%
venv-test1/lib/python3.6/site-packages/skimage/measure/_label.py                                               3      1    67%
venv-test1/lib/python3.6/site-packages/skimage/measure/_marching_cubes_classic.py                             52     44    15%
venv-test1/lib/python3.6/site-packages/skimage/measure/_marching_cubes_lewiner.py                             70     56    20%
venv-test1/lib/python3.6/site-packages/skimage/measure/_marching_cubes_lewiner_luts.py                        48      0   100%
venv-test1/lib/python3.6/site-packages/skimage/measure/_moments.py                                            73     60    18%
venv-test1/lib/python3.6/site-packages/skimage/measure/_polygon.py                                            61     56     8%
venv-test1/lib/python3.6/site-packages/skimage/measure/_regionprops.py                                       266    167    37%
venv-test1/lib/python3.6/site-packages/skimage/measure/_structural_similarity.py                               8      2    75%
venv-test1/lib/python3.6/site-packages/skimage/measure/block.py                                               18     15    17%
venv-test1/lib/python3.6/site-packages/skimage/measure/entropy.py                                              5      2    60%
venv-test1/lib/python3.6/site-packages/skimage/measure/fit.py                                                230    204    11%
venv-test1/lib/python3.6/site-packages/skimage/measure/pnpoly.py                                               5      2    60%
venv-test1/lib/python3.6/site-packages/skimage/measure/profile.py                                             35     29    17%
venv-test1/lib/python3.6/site-packages/skimage/measure/simple_metrics.py                                      18      6    67%
venv-test1/lib/python3.6/site-packages/skimage/metrics/__init__.py                                             6      0   100%
venv-test1/lib/python3.6/site-packages/skimage/metrics/_adapted_rand_error.py                                 19     15    21%
venv-test1/lib/python3.6/site-packages/skimage/metrics/_contingency_table.py                                  15     11    27%
venv-test1/lib/python3.6/site-packages/skimage/metrics/_structural_similarity.py                             100     92     8%
venv-test1/lib/python3.6/site-packages/skimage/metrics/_variation_of_information.py                           33     24    27%
venv-test1/lib/python3.6/site-packages/skimage/metrics/simple_metrics.py                                      40     32    20%
venv-test1/lib/python3.6/site-packages/skimage/util/__init__.py                                               18      2    89%
venv-test1/lib/python3.6/site-packages/skimage/util/_invert.py                                                14     11    21%
venv-test1/lib/python3.6/site-packages/skimage/util/_map_array.py                                             69     56    19%
venv-test1/lib/python3.6/site-packages/skimage/util/_montage.py                                               32     29     9%
venv-test1/lib/python3.6/site-packages/skimage/util/_regular_grid.py                                          27     24    11%
venv-test1/lib/python3.6/site-packages/skimage/util/apply_parallel.py                                         50     46     8%
venv-test1/lib/python3.6/site-packages/skimage/util/arraycrop.py                                              17     14    18%
venv-test1/lib/python3.6/site-packages/skimage/util/compare.py                                                25     21    16%
venv-test1/lib/python3.6/site-packages/skimage/util/dtype.py                                                 147    124    16%
venv-test1/lib/python3.6/site-packages/skimage/util/lookfor.py                                                 4      1    75%
venv-test1/lib/python3.6/site-packages/skimage/util/noise.py                                                  54     50     7%
venv-test1/lib/python3.6/site-packages/skimage/util/shape.py                                                  48     41    15%
venv-test1/lib/python3.6/site-packages/skimage/util/unique.py                                                  9      7    22%
venv-test1/lib/python3.6/site-packages/tifffile/__init__.py                                                    2      0   100%
venv-test1/lib/python3.6/site-packages/tifffile/tifffile.py                                                 6208   5737     8%
------------------------------------------------------------------------------------------------------------------------------
TOTAL                                                                                                     189897 152415    20%

============================================================================= short test summary info =============================================================================
ERROR  - _pytest.config.ConftestImportFailure: (local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py'), (<class 'py._path.local.LocalPath.ImportMismatch...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================================================ 1 error in 11.99s ================================================================================

and here's my pip freeze:

(venv-test1) [logand05@cortex:~/github/DeepProfiler]$ pip freeze
absl-py==0.9.0
astor==0.8.1
attrs==19.3.0
beautifulsoup4==4.9.1
certifi==2020.4.5.1
chardet==3.0.4
click==7.1.2
comet-git-pure==0.19.16
comet-ml==3.1.7
configobj==5.0.6
coverage==5.1
cycler==0.10.0
decorator==4.4.2
-e git+https://github.com/broadinstitute/DeepProfiler.git@1a0b910cb8032808933888fb3a567ac015afa8e0#egg=deepprofiler
everett==1.0.2
gast==0.3.3
google-pasta==0.2.0
GPy==1.9.9
GPyOpt==1.2.6
grpcio==1.29.0
h5py==2.10.0
idna==2.9
imagecodecs==2020.2.18
imageio==2.8.0
importlib-metadata==1.6.0
joblib==0.15.1
jsonschema==3.0.2
Keras==2.3.1
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
kiwisolver==1.2.0
lxml==4.5.1
Markdown==3.2.2
matplotlib==3.2.1
more-itertools==8.3.0
netifaces==0.10.9
networkx==2.4
numpy==1.18.4
nvidia-ml-py3==7.352.0
packaging==20.4
pandas==1.0.3
paramz==0.9.5
Pillow==7.1.2
pkg-resources==0.0.0
pluggy==0.13.1
protobuf==3.12.0
py==1.8.1
pyparsing==2.4.7
pyrsistent==0.16.0
pytest==5.4.2
pytest-cov==2.8.1
python-dateutil==2.8.1
pytz==2020.1
PyWavelets==1.1.1
PyYAML==5.3.1
requests==2.23.0
scikit-image==0.17.2
scikit-learn==0.23.0
scipy==1.4.1
six==1.14.0
soupsieve==2.0.1
tensorboard==1.14.0
tensorflow==1.14.0
tensorflow-estimator==1.14.0
tensorflow-gpu==1.14.0
termcolor==1.1.0
threadpoolctl==2.0.0
tifffile==2020.5.11
typing-extensions==3.7.4.2
urllib3==1.25.9
wcwidth==0.1.9
websocket-client==0.57.0
Werkzeug==1.0.1
wrapt==1.12.1
wurlitzer==2.0.0
zipp==3.1.0

Arkkienkeli commented 4 years ago

Hi @dlogan, sorry for getting back late, do you still have this issue? Did you try to run pytest without coverage --no-cov? I did not face that kind of error myself, but it is also suggested to remove all .pyc files: https://stackoverflow.com/questions/48696021/pytest-error-could-not-load-path-to-conftest-py

dlogan commented 4 years ago

Thanks @Arkkienkeli , just coming back to this...

Maybe not deepprofiler's issue, per se, in my venv while trying to pip install tensorflow-gpu==1.14, I was getting bdist_wheel errors like this. I suggest adding 'wheel' to setup.py or in the wiki, since doing

pip install wheel

helped me install tensorflow-gpu==1.14 cleanly.

dlogan commented 4 years ago

And I also need to manually install Keras with this too (otherwise I get ModuleNotFoundError: No module named 'keras' when running

python3 deepprofiler

Consider adding this to setup.py or wiki too.

dlogan commented 4 years ago

I'm getting an error when I run

python3 -m pytest

Sorry for the long output:

~/github/DeepProfiler$ python3 -m pytest
================================================================================== test session starts ==================================================================================
platform linux -- Python 3.6.9, pytest-5.4.3, py-1.8.1, pluggy-0.13.1 -- /home/logand05/github/DeepProfiler/deepprofenv/bin/python3
cachedir: .pytest_cache
rootdir: /home/logand05/github/DeepProfiler, inifile: setup.cfg
plugins: cov-2.9.0
collected 0 items / 1 error
Coverage.py warning: Couldn't parse Python file '/home/logand05/github/DeepProfiler/scripts/locations.py' (couldnt-parse)

======================================================================================== ERRORS =========================================================================================
_____________________________________________________________________________ ERROR collecting test session _____________________________________________________________________________
deepprofenv/lib/python3.6/site-packages/_pytest/config/__init__.py:495: in _importconftest
    return self._conftestpath2mod[key]
E   KeyError: PosixPath('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py')

During handling of the above exception, another exception occurred:
deepprofenv/lib/python3.6/site-packages/py/_path/local.py:721: in pyimport
    raise self.ImportMismatchError(modname, modfile, self)
E   py._path.local.LocalPath.ImportMismatchError: ('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py'))

----------- coverage: platform linux, python 3.6.9-final-0 -----------
Name                                                                                                        Stmts   Miss  Cover
-------------------------------------------------------------------------------------------------------------------------------
deepprofenv/lib/python3.6/site-packages/PIL/Image.py                                                         1367   1127    18%
deepprofenv/lib/python3.6/site-packages/PIL/ImageMode.py                                                       23     18    22%
deepprofenv/lib/python3.6/site-packages/PIL/TiffTags.py                                                        40      2    95%
deepprofenv/lib/python3.6/site-packages/PIL/__init__.py                                                        42     22    48%
deepprofenv/lib/python3.6/site-packages/PIL/_binary.py                                                         25     12    52%
deepprofenv/lib/python3.6/site-packages/PIL/_util.py                                                           16      6    62%
deepprofenv/lib/python3.6/site-packages/PIL/_version.py                                                         1      0   100%
deepprofenv/lib/python3.6/site-packages/_pytest/_argcomplete.py                                                37     36     3%
deepprofenv/lib/python3.6/site-packages/_pytest/_code/code.py                                                 655    469    28%
deepprofenv/lib/python3.6/site-packages/_pytest/_code/source.py                                               244    198    19%
deepprofenv/lib/python3.6/site-packages/_pytest/_io/saferepr.py                                                63     48    24%
deepprofenv/lib/python3.6/site-packages/_pytest/assertion/__init__.py                                          79     75     5%
deepprofenv/lib/python3.6/site-packages/_pytest/assertion/rewrite.py                                          595    525    12%
deepprofenv/lib/python3.6/site-packages/_pytest/cacheprovider.py                                              278    238    14%
deepprofenv/lib/python3.6/site-packages/_pytest/capture.py                                                    484    466     4%
deepprofenv/lib/python3.6/site-packages/_pytest/compat.py                                                     180    157    13%
deepprofenv/lib/python3.6/site-packages/_pytest/config/__init__.py                                            654    527    19%
deepprofenv/lib/python3.6/site-packages/_pytest/config/argparsing.py                                          244    199    18%
deepprofenv/lib/python3.6/site-packages/_pytest/debugging.py                                                  197    188     5%
deepprofenv/lib/python3.6/site-packages/_pytest/doctest.py                                                    332    323     3%
deepprofenv/lib/python3.6/site-packages/_pytest/faulthandler.py                                                53     42    21%
deepprofenv/lib/python3.6/site-packages/_pytest/fixtures.py                                                   775    672    13%
deepprofenv/lib/python3.6/site-packages/_pytest/helpconfig.py                                                 120    111     8%
deepprofenv/lib/python3.6/site-packages/_pytest/junitxml.py                                                   350    348     1%
deepprofenv/lib/python3.6/site-packages/_pytest/logging.py                                                    359    294    18%
deepprofenv/lib/python3.6/site-packages/_pytest/main.py                                                       397    269    32%
deepprofenv/lib/python3.6/site-packages/_pytest/mark/__init__.py                                               84     70    17%
deepprofenv/lib/python3.6/site-packages/_pytest/mark/structures.py                                            173    168     3%
deepprofenv/lib/python3.6/site-packages/_pytest/monkeypatch.py                                                148    136     8%
deepprofenv/lib/python3.6/site-packages/_pytest/nodes.py                                                      298    198    34%
deepprofenv/lib/python3.6/site-packages/_pytest/pastebin.py                                                    64     63     2%
deepprofenv/lib/python3.6/site-packages/_pytest/pathlib.py                                                    218    206     6%
deepprofenv/lib/python3.6/site-packages/_pytest/python.py                                                     776    759     2%
deepprofenv/lib/python3.6/site-packages/_pytest/reports.py                                                    244    236     3%
deepprofenv/lib/python3.6/site-packages/_pytest/resultlog.py                                                   68     66     3%
deepprofenv/lib/python3.6/site-packages/_pytest/runner.py                                                     269    229    15%
deepprofenv/lib/python3.6/site-packages/_pytest/setuponly.py                                                   42     41     2%
deepprofenv/lib/python3.6/site-packages/_pytest/setupplan.py                                                   13     12     8%
deepprofenv/lib/python3.6/site-packages/_pytest/skipping.py                                                   101     97     4%
deepprofenv/lib/python3.6/site-packages/_pytest/stepwise.py                                                    58     48    17%
deepprofenv/lib/python3.6/site-packages/_pytest/store.py                                                       34     29    15%
deepprofenv/lib/python3.6/site-packages/_pytest/terminal.py                                                   804    654    19%
deepprofenv/lib/python3.6/site-packages/_pytest/tmpdir.py                                                      87     80     8%
deepprofenv/lib/python3.6/site-packages/_pytest/warnings.py                                                    77     61    21%
deepprofenv/lib/python3.6/site-packages/attr/converters.py                                                     27     25     7%
deepprofenv/lib/python3.6/site-packages/coverage/collector.py                                                 200    194     3%
deepprofenv/lib/python3.6/site-packages/coverage/control.py                                                   376    371     1%
deepprofenv/lib/python3.6/site-packages/cycler.py                                                             175    107    39%
deepprofenv/lib/python3.6/site-packages/dateutil/__init__.py                                                    5      2    60%
deepprofenv/lib/python3.6/site-packages/dateutil/_common.py                                                    25     15    40%
deepprofenv/lib/python3.6/site-packages/dateutil/_version.py                                                    1      0   100%
deepprofenv/lib/python3.6/site-packages/dateutil/easter.py                                                     27     20    26%
deepprofenv/lib/python3.6/site-packages/dateutil/parser/__init__.py                                            32      4    88%
deepprofenv/lib/python3.6/site-packages/dateutil/parser/_parser.py                                            807    690    14%
deepprofenv/lib/python3.6/site-packages/dateutil/parser/isoparser.py                                          176    145    18%
deepprofenv/lib/python3.6/site-packages/dateutil/relativedelta.py                                             239    206    14%
deepprofenv/lib/python3.6/site-packages/dateutil/rrule.py                                                     974    863    11%
deepprofenv/lib/python3.6/site-packages/dateutil/tz/__init__.py                                                 4      0   100%
deepprofenv/lib/python3.6/site-packages/dateutil/tz/_common.py                                                155    122    21%
deepprofenv/lib/python3.6/site-packages/dateutil/tz/_factories.py                                              49     21    57%
deepprofenv/lib/python3.6/site-packages/dateutil/tz/tz.py                                                     795    639    20%
deepprofenv/lib/python3.6/site-packages/dateutil/tz/win.py                                                    151    147     3%
deepprofenv/lib/python3.6/site-packages/imageio/__init__.py                                                    13      0   100%
deepprofenv/lib/python3.6/site-packages/imageio/core/__init__.py                                                8      0   100%
deepprofenv/lib/python3.6/site-packages/imageio/core/fetching.py                                              106     89    16%
deepprofenv/lib/python3.6/site-packages/imageio/core/findlib.py                                                74     65    12%
deepprofenv/lib/python3.6/site-packages/imageio/core/format.py                                                268    178    34%
deepprofenv/lib/python3.6/site-packages/imageio/core/functions.py                                             157    124    21%
deepprofenv/lib/python3.6/site-packages/imageio/core/request.py                                               314    274    13%
deepprofenv/lib/python3.6/site-packages/imageio/core/util.py                                                  262    210    20%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/__init__.py                                            22      0   100%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/_freeimage.py                                         601    405    33%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/bsdf.py                                               140    113    19%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/dicom.py                                              146    122    16%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/example.py                                             43     23    47%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/feisem.py                                              41     32    22%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/ffmpeg.py                                             304    258    15%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/fits.py                                                40     24    40%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/freeimage.py                                          176    122    31%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/freeimagemulti.py                                     144    104    28%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/gdal.py                                                35     19    46%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/grab.py                                                63     37    41%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/lytro.py                                              302    225    25%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/npz.py                                                 37     17    54%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/pillow.py                                             363    284    22%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/pillow_info.py                                          5      1    80%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/pillowmulti.py                                        164    134    18%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/simpleitk.py                                           62     38    39%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/spe.py                                                126     96    24%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/swf.py                                                181    149    18%
deepprofenv/lib/python3.6/site-packages/imageio/plugins/tifffile.py                                            91     65    29%
deepprofenv/lib/python3.6/site-packages/importlib_metadata/__init__.py                                        226    221     2%
deepprofenv/lib/python3.6/site-packages/importlib_metadata/_compat.py                                          30     29     3%
deepprofenv/lib/python3.6/site-packages/matplotlib/__init__.py                                                649    391    40%
deepprofenv/lib/python3.6/site-packages/matplotlib/_cm.py                                                     141     12    91%
deepprofenv/lib/python3.6/site-packages/matplotlib/_cm_listed.py                                               10      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/_color_data.py                                               7      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/_layoutbox.py                                              408    342    16%
deepprofenv/lib/python3.6/site-packages/matplotlib/_mathtext_data.py                                            7      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/_pylab_helpers.py                                           52     35    33%
deepprofenv/lib/python3.6/site-packages/matplotlib/_text_layout.py                                             12     10    17%
deepprofenv/lib/python3.6/site-packages/matplotlib/_version.py                                                  5      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/afm.py                                                     239    189    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/artist.py                                                  586    408    30%
deepprofenv/lib/python3.6/site-packages/matplotlib/axes/__init__.py                                             2      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/axes/_axes.py                                             2308   2121     8%
deepprofenv/lib/python3.6/site-packages/matplotlib/axes/_base.py                                             1664   1450    13%
deepprofenv/lib/python3.6/site-packages/matplotlib/axes/_secondary_axes.py                                    152    128    16%
deepprofenv/lib/python3.6/site-packages/matplotlib/axes/_subplots.py                                          120     80    33%
deepprofenv/lib/python3.6/site-packages/matplotlib/axis.py                                                   1213    987    19%
deepprofenv/lib/python3.6/site-packages/matplotlib/backend_bases.py                                          1237    966    22%
deepprofenv/lib/python3.6/site-packages/matplotlib/backend_tools.py                                           570    386    32%
deepprofenv/lib/python3.6/site-packages/matplotlib/bezier.py                                                  204    173    15%
deepprofenv/lib/python3.6/site-packages/matplotlib/blocking_input.py                                          143    102    29%
deepprofenv/lib/python3.6/site-packages/matplotlib/category.py                                                 76     48    37%
deepprofenv/lib/python3.6/site-packages/matplotlib/cbook/__init__.py                                          835    660    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/cbook/deprecation.py                                       128     31    76%
deepprofenv/lib/python3.6/site-packages/matplotlib/cm.py                                                      150    111    26%
deepprofenv/lib/python3.6/site-packages/matplotlib/collections.py                                             840    696    17%
deepprofenv/lib/python3.6/site-packages/matplotlib/colors.py                                                  807    585    28%
deepprofenv/lib/python3.6/site-packages/matplotlib/container.py                                                44     25    43%
deepprofenv/lib/python3.6/site-packages/matplotlib/contour.py                                                 732    666     9%
deepprofenv/lib/python3.6/site-packages/matplotlib/dates.py                                                   735    578    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/docstring.py                                                40     12    70%
deepprofenv/lib/python3.6/site-packages/matplotlib/dviread.py                                                 466    356    24%
deepprofenv/lib/python3.6/site-packages/matplotlib/font_manager.py                                            538    418    22%
deepprofenv/lib/python3.6/site-packages/matplotlib/fontconfig_pattern.py                                       70     21    70%
deepprofenv/lib/python3.6/site-packages/matplotlib/gridspec.py                                                245    194    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/image.py                                                   707    608    14%
deepprofenv/lib/python3.6/site-packages/matplotlib/legend.py                                                  448    380    15%
deepprofenv/lib/python3.6/site-packages/matplotlib/legend_handler.py                                          319    240    25%
deepprofenv/lib/python3.6/site-packages/matplotlib/lines.py                                                   639    536    16%
deepprofenv/lib/python3.6/site-packages/matplotlib/markers.py                                                 463    372    20%
deepprofenv/lib/python3.6/site-packages/matplotlib/mathtext.py                                               1668   1320    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/mlab.py                                                    469    421    10%
deepprofenv/lib/python3.6/site-packages/matplotlib/offsetbox.py                                               708    562    21%
deepprofenv/lib/python3.6/site-packages/matplotlib/patches.py                                                1662   1271    24%
deepprofenv/lib/python3.6/site-packages/matplotlib/path.py                                                    350    258    26%
deepprofenv/lib/python3.6/site-packages/matplotlib/quiver.py                                                  474    415    12%
deepprofenv/lib/python3.6/site-packages/matplotlib/rcsetup.py                                                 487    223    54%
deepprofenv/lib/python3.6/site-packages/matplotlib/scale.py                                                   322    177    45%
deepprofenv/lib/python3.6/site-packages/matplotlib/spines.py                                                  303    268    12%
deepprofenv/lib/python3.6/site-packages/matplotlib/stackplot.py                                                42     38    10%
deepprofenv/lib/python3.6/site-packages/matplotlib/streamplot.py                                              374    331    11%
deepprofenv/lib/python3.6/site-packages/matplotlib/table.py                                                   334    277    17%
deepprofenv/lib/python3.6/site-packages/matplotlib/texmanager.py                                              209    164    22%
deepprofenv/lib/python3.6/site-packages/matplotlib/text.py                                                    950    797    16%
deepprofenv/lib/python3.6/site-packages/matplotlib/textpath.py                                                228    185    19%
deepprofenv/lib/python3.6/site-packages/matplotlib/ticker.py                                                 1320   1090    17%
deepprofenv/lib/python3.6/site-packages/matplotlib/tight_bbox.py                                               46     43     7%
deepprofenv/lib/python3.6/site-packages/matplotlib/tight_layout.py                                            171    160     6%
deepprofenv/lib/python3.6/site-packages/matplotlib/transforms.py                                             1124    810    28%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/__init__.py                                              8      0   100%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/triangulation.py                                        85     74    13%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/tricontour.py                                           59     48    19%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/trifinder.py                                            26     15    42%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/triinterpolate.py                                      548    467    15%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/tripcolor.py                                            58     52    10%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/triplot.py                                              25     22    12%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/trirefine.py                                            93     81    13%
deepprofenv/lib/python3.6/site-packages/matplotlib/tri/tritools.py                                             84     73    13%
deepprofenv/lib/python3.6/site-packages/matplotlib/units.py                                                    70     47    33%
deepprofenv/lib/python3.6/site-packages/matplotlib/widgets.py                                                1382   1209    13%
deepprofenv/lib/python3.6/site-packages/more_itertools/more.py                                                903    894     1%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/__init__.py                                     4      0   100%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/axes_divider.py                               350    287    18%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/axes_grid.py                                  397    356    10%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/axes_size.py                                  177    125    29%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/mpl_axes.py                                    91     68    25%
deepprofenv/lib/python3.6/site-packages/mpl_toolkits/axes_grid1/parasite_axes.py                              245    185    24%
deepprofenv/lib/python3.6/site-packages/numpy/__config__.py                                                    30     16    47%
deepprofenv/lib/python3.6/site-packages/numpy/__init__.py                                                      79     19    76%
deepprofenv/lib/python3.6/site-packages/numpy/_distributor_init.py                                              0      0   100%
deepprofenv/lib/python3.6/site-packages/numpy/_globals.py                                                      20      2    90%
deepprofenv/lib/python3.6/site-packages/numpy/_pytesttester.py                                                 48     39    19%
deepprofenv/lib/python3.6/site-packages/numpy/compat/__init__.py                                                8      0   100%
deepprofenv/lib/python3.6/site-packages/numpy/compat/_inspect.py                                               68     17    75%
deepprofenv/lib/python3.6/site-packages/numpy/compat/py3k.py                                                  120     81    32%
deepprofenv/lib/python3.6/site-packages/numpy/core/__init__.py                                                 82     14    83%
deepprofenv/lib/python3.6/site-packages/numpy/core/_add_newdocs.py                                            298      2    99%
deepprofenv/lib/python3.6/site-packages/numpy/core/_asarray.py                                                 41     25    39%
deepprofenv/lib/python3.6/site-packages/numpy/core/_dtype.py                                                  162    126    22%
deepprofenv/lib/python3.6/site-packages/numpy/core/_dtype_ctypes.py                                            53     34    36%
deepprofenv/lib/python3.6/site-packages/numpy/core/_exceptions.py                                              99     58    41%
deepprofenv/lib/python3.6/site-packages/numpy/core/_internal.py                                               420    318    24%
deepprofenv/lib/python3.6/site-packages/numpy/core/_methods.py                                                138    104    25%
deepprofenv/lib/python3.6/site-packages/numpy/core/_string_helpers.py                                          15      1    93%
deepprofenv/lib/python3.6/site-packages/numpy/core/_type_aliases.py                                           152     19    88%
deepprofenv/lib/python3.6/site-packages/numpy/core/_ufunc_config.py                                            86     25    71%
deepprofenv/lib/python3.6/site-packages/numpy/core/arrayprint.py                                              535    420    21%
deepprofenv/lib/python3.6/site-packages/numpy/core/defchararray.py                                            422    250    41%
deepprofenv/lib/python3.6/site-packages/numpy/core/einsumfunc.py                                              408    386     5%
deepprofenv/lib/python3.6/site-packages/numpy/core/fromnumeric.py                                             354    205    42%
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deepprofenv/lib/python3.6/site-packages/skimage/data/_binary_blobs.py                                          12     10    17%
deepprofenv/lib/python3.6/site-packages/skimage/data/_registry.py                                               4      0   100%
deepprofenv/lib/python3.6/site-packages/skimage/exposure/__init__.py                                            4      0   100%
deepprofenv/lib/python3.6/site-packages/skimage/exposure/_adapthist.py                                        106     95    10%
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deepprofenv/lib/python3.6/site-packages/skimage/io/__init__.py                                                 33      1    97%
deepprofenv/lib/python3.6/site-packages/skimage/io/_image_stack.py                                              9      4    56%
deepprofenv/lib/python3.6/site-packages/skimage/io/_io.py                                                      44     31    30%
deepprofenv/lib/python3.6/site-packages/skimage/io/_plugins/__init__.py                                         0      0   100%
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deepprofenv/lib/python3.6/site-packages/skimage/io/collection.py                                              146    116    21%
deepprofenv/lib/python3.6/site-packages/skimage/io/manage_plugins.py                                          136     30    78%
deepprofenv/lib/python3.6/site-packages/skimage/io/sift.py                                                     27     20    26%
deepprofenv/lib/python3.6/site-packages/skimage/io/util.py                                                     26     16    38%
deepprofenv/lib/python3.6/site-packages/skimage/measure/__init__.py                                            15      0   100%
deepprofenv/lib/python3.6/site-packages/skimage/measure/_find_contours.py                                      60     54    10%
deepprofenv/lib/python3.6/site-packages/skimage/measure/_label.py                                               3      1    67%
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deepprofenv/lib/python3.6/site-packages/skimage/measure/_polygon.py                                            61     56     8%
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deepprofenv/lib/python3.6/site-packages/skimage/measure/_structural_similarity.py                               8      2    75%
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deepprofenv/lib/python3.6/site-packages/skimage/measure/entropy.py                                              5      2    60%
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deepprofenv/lib/python3.6/site-packages/skimage/measure/pnpoly.py                                               5      2    60%
deepprofenv/lib/python3.6/site-packages/skimage/measure/profile.py                                             35     29    17%
deepprofenv/lib/python3.6/site-packages/skimage/measure/simple_metrics.py                                      18      6    67%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/__init__.py                                             6      0   100%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/_adapted_rand_error.py                                 19     15    21%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/_contingency_table.py                                  15     11    27%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/_structural_similarity.py                             100     92     8%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/_variation_of_information.py                           33     24    27%
deepprofenv/lib/python3.6/site-packages/skimage/metrics/simple_metrics.py                                      40     32    20%
deepprofenv/lib/python3.6/site-packages/skimage/util/__init__.py                                               18      2    89%
deepprofenv/lib/python3.6/site-packages/skimage/util/_invert.py                                                14     11    21%
deepprofenv/lib/python3.6/site-packages/skimage/util/_map_array.py                                             69     56    19%
deepprofenv/lib/python3.6/site-packages/skimage/util/_montage.py                                               32     29     9%
deepprofenv/lib/python3.6/site-packages/skimage/util/_regular_grid.py                                          27     24    11%
deepprofenv/lib/python3.6/site-packages/skimage/util/apply_parallel.py                                         50     46     8%
deepprofenv/lib/python3.6/site-packages/skimage/util/arraycrop.py                                              17     14    18%
deepprofenv/lib/python3.6/site-packages/skimage/util/compare.py                                                25     21    16%
deepprofenv/lib/python3.6/site-packages/skimage/util/dtype.py                                                 147    124    16%
deepprofenv/lib/python3.6/site-packages/skimage/util/lookfor.py                                                 4      1    75%
deepprofenv/lib/python3.6/site-packages/skimage/util/noise.py                                                  54     50     7%
deepprofenv/lib/python3.6/site-packages/skimage/util/shape.py                                                  48     41    15%
deepprofenv/lib/python3.6/site-packages/skimage/util/unique.py                                                  9      7    22%
deepprofenv/lib/python3.6/site-packages/tifffile/__init__.py                                                    2      0   100%
deepprofenv/lib/python3.6/site-packages/tifffile/tifffile.py                                                 6242   5761     8%
deepprofiler/__init__.py                                                                                        0      0   100%
deepprofiler/__main__.py                                                                                      107    107     0%
deepprofiler/dataset/__init__.py                                                                                0      0   100%
deepprofiler/dataset/compression.py                                                                            91     91     0%
deepprofiler/dataset/illumination_correction.py                                                                25     25     0%
deepprofiler/dataset/illumination_statistics.py                                                                76     76     0%
deepprofiler/dataset/image_dataset.py                                                                         161    138    14%
deepprofiler/dataset/indexing.py                                                                               22     22     0%
deepprofiler/dataset/metadata.py                                                                               54     42    22%
deepprofiler/dataset/pixels.py                                                                                 13      9    31%
deepprofiler/dataset/target.py                                                                                 13      9    31%
deepprofiler/dataset/utils.py                                                                                  69     43    38%
deepprofiler/imaging/__init__.py                                                                                0      0   100%
deepprofiler/imaging/augmentations.py                                                                          18     18     0%
deepprofiler/imaging/boxes.py                                                                                  83     73    12%
deepprofiler/imaging/cropping.py                                                                              176    176     0%
deepprofiler/learning/__init__.py                                                                               1      1     0%
deepprofiler/learning/metric.py                                                                                13     13     0%
deepprofiler/learning/model.py                                                                                123    123     0%
deepprofiler/learning/profiling.py                                                                             61     61     0%
deepprofiler/learning/training.py                                                                              25     25     0%
deepprofiler/learning/validation.py                                                                            23     23     0%
plugins/__init__.py                                                                                             0      0   100%
plugins/crop_generators/__init__.py                                                                             0      0   100%
plugins/crop_generators/autoencoder_crop_generator.py                                                          14     14     0%
plugins/crop_generators/crop_generator.py                                                                       3      3     0%
plugins/crop_generators/mixup_crop_generator.py                                                                65     65     0%
plugins/crop_generators/repeat_channel_crop_generator.py                                                       29     29     0%
plugins/metrics/__init__.py                                                                                     0      0   100%
plugins/metrics/top_k.py                                                                                       12     12     0%
plugins/models/__init__.py                                                                                      0      0   100%
plugins/models/autoencoder.py                                                                                  41     41     0%
plugins/models/cnn.py                                                                                          33     33     0%
plugins/models/densenet.py                                                                                      9      9     0%
plugins/models/inception_resnet_v2.py                                                                          28     28     0%
plugins/models/resnet.py                                                                                       57     57     0%
scripts/__init__.py                                                                                             0      0   100%
scripts/create_metadata_index.py                                                                              112    112     0%
setup.py                                                                                                        2      2     0%
tests/__init__.py                                                                                               0      0   100%
tests/conftest.py                                                                                              56     38    32%
tests/deepprofiler/__init__.py                                                                                  0      0   100%
tests/deepprofiler/dataset/__init__.py                                                                          0      0   100%
tests/deepprofiler/dataset/test_compression.py                                                                 75     75     0%
tests/deepprofiler/dataset/test_illumination_correction.py                                                     36     36     0%
tests/deepprofiler/dataset/test_illumination_statistics.py                                                     56     56     0%
tests/deepprofiler/dataset/test_image_dataset.py                                                               75     75     0%
tests/deepprofiler/dataset/test_indexing.py                                                                    21     21     0%
tests/deepprofiler/dataset/test_metadata.py                                                                    71     71     0%
tests/deepprofiler/dataset/test_pixels.py                                                                      18     18     0%
tests/deepprofiler/dataset/test_target.py                                                                      22     22     0%
tests/deepprofiler/dataset/test_utils.py                                                                       73     73     0%
tests/deepprofiler/imaging/__init__.py                                                                          0      0   100%
tests/deepprofiler/imaging/test_augmentations.py                                                               17     17     0%
tests/deepprofiler/imaging/test_boxes.py                                                                       38     38     0%
tests/deepprofiler/imaging/test_cropping.py                                                                   138    138     0%
tests/deepprofiler/learning/__init__.py                                                                         0      0   100%
tests/deepprofiler/learning/test_metric.py                                                                     22     22     0%
tests/deepprofiler/learning/test_model.py                                                                      51     51     0%
tests/deepprofiler/learning/test_profiling.py                                                                  51     51     0%
tests/deepprofiler/learning/test_training.py                                                                   18     18     0%
tests/deepprofiler/learning/test_validation.py                                                                 37     37     0%
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tests/plugins/crop_generators/__init__.py                                                                       0      0   100%
tests/plugins/crop_generators/test_autoencoder_crop_generator.py                                               47     47     0%
tests/plugins/crop_generators/test_crop_generator.py                                                            5      5     0%
tests/plugins/crop_generators/test_mixup_crop_generator.py                                                    120    120     0%
tests/plugins/models/__init__.py                                                                                0      0   100%
tests/plugins/models/test_autoencoder.py                                                                       26     26     0%
tests/plugins/models/test_cnn.py                                                                               22     22     0%
tests/plugins/models/test_densenet.py                                                                          23     23     0%
tests/plugins/models/test_inception_resnet_v2.py                                                                0      0   100%
tests/plugins/models/test_resnet.py                                                                            22     22     0%
-------------------------------------------------------------------------------------------------------------------------------
TOTAL                                                                                                      189715 152332    20%

================================================================================ short test summary info ================================================================================
ERROR  - py._path.local.LocalPath.ImportMismatchError: ('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deeppr...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=================================================================================== 1 error in 12.05s ===================================================================================

dlogan commented 4 years ago

And when I run this without coverage, I get still get an error (this is how I should run with '--no-cov', right?):

~/github/DeepProfiler$ python3 -m pytest --no-cov
================================================================================== test session starts ==================================================================================
platform linux -- Python 3.6.9, pytest-5.4.3, py-1.8.1, pluggy-0.13.1 -- /home/logand05/github/DeepProfiler/deepprofenv/bin/python3
cachedir: .pytest_cache
rootdir: /home/logand05/github/DeepProfiler, inifile: setup.cfg
plugins: cov-2.9.0
collected 0 items / 1 error

======================================================================================== ERRORS =========================================================================================
_____________________________________________________________________________ ERROR collecting test session _____________________________________________________________________________
deepprofenv/lib/python3.6/site-packages/_pytest/config/__init__.py:495: in _importconftest
    return self._conftestpath2mod[key]
E   KeyError: PosixPath('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py')

During handling of the above exception, another exception occurred:
deepprofenv/lib/python3.6/site-packages/py/_path/local.py:721: in pyimport
    raise self.ImportMismatchError(modname, modfile, self)
E   py._path.local.LocalPath.ImportMismatchError: ('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deepprofiler/tests/conftest.py'))
WARNING: Coverage disabled via --no-cov switch!
================================================================================ short test summary info ================================================================================
ERROR  - py._path.local.LocalPath.ImportMismatchError: ('tests.conftest', '/home/logand05/github/DeepProfiler/tests/conftest.py', local('/home/logand05/github/DeepProfiler/src/deeppr...
=================================================================================== warnings summary ====================================================================================
deepprofenv/lib/python3.6/site-packages/pytest_cov/plugin.py:293
  /home/logand05/github/DeepProfiler/deepprofenv/lib/python3.6/site-packages/pytest_cov/plugin.py:293: PytestWarning: Coverage disabled via --no-cov switch!
    warnings.warn(pytest.PytestWarning(message))

-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================================================== 1 warning, 1 error in 0.17s ==============================================================================

Arkkienkeli commented 4 years ago

Hello @dlogan

Thanks @Arkkienkeli , just coming back to this...

Maybe not deepprofiler's issue, per se, in my venv while trying to pip install tensorflow-gpu==1.14, I was getting bdist_wheel errors like this. I suggest adding 'wheel' to setup.py or in the wiki, since doing
pip install wheel
helped me install tensorflow-gpu==1.14 cleanly.

That is quite akward, tensorflow-gpu generally gets installed fine on a clean envionment.

Keras in setup.cfg was fixed a while ago.

Regarding pytest, did you try to remove cache files https://stackoverflow.com/questions/48696021/pytest-error-could-not-load-path-to-conftest-py ?

Is the virtual enivronment active, while you try to run tests (sorry for the lame question, but I just see ~/github/DeepProfiler$ at the beginning of the terminal line)?

Could you please also try to pull the current version?

Thank you!

dlogan commented 4 years ago

Thanks for your help @Arkkienkeli. In reverse order:

Indeed I did a 'git pull'. I'm on commit 04d1239d8310c989e50408417d412ea067ddba99
Yup, I'm on a venv. I just didn't paste in the whole prompt before 😉 . Looks like this now
```
(deepprofenv2) [logand05@cortex:~/github/DeepProfiler]$
```
I did NOT try and remove *.pyc files recursively, so this may have been an issue. Since then I created a new venv so that should help (I assume?)
Hmm, I'm still not getting Keras installed when installing deepprofiler. I do see Keras in the setup.py, though... See this output:

(deepprofenv2) [logand05@cortex:~/github/DeepProfiler]$ pip install -e .
Obtaining file:///home/logand05/github/DeepProfiler
Requirement already satisfied: beautifulsoup4>=4.6 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (4.9.1)
Requirement already satisfied: click>=6.7 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (7.1.2)
Requirement already satisfied: comet_ml>=1.0 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (3.1.10)
Requirement already satisfied: gpyopt>=1.2keras==2.2.5 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (1.2.6)
Requirement already satisfied: lxml>=4.2 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (4.5.1)
Requirement already satisfied: numpy>=1.13 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (1.18.5)
Requirement already satisfied: pandas>=0.23.0 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (1.0.4)
Requirement already satisfied: scikit-image>=0.14.0 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (0.17.2)
Requirement already satisfied: scikit-learn>=0.19.0 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (0.23.1)
Requirement already satisfied: scipy>=1.1 in ./deepprofenv2/lib/python3.6/site-packages (from deepprofiler==0.1.0) (1.4.1)
Requirement already satisfied: soupsieve>1.2 in ./deepprofenv2/lib/python3.6/site-packages (from beautifulsoup4>=4.6->deepprofiler==0.1.0) (2.0.1)
Requirement already satisfied: jsonschema!=3.1.0,>=2.6.0 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (3.2.0)
Requirement already satisfied: wurlitzer>=1.0.2 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (2.0.0)
Requirement already satisfied: requests>=2.18.4 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (2.23.0)
Requirement already satisfied: comet-git-pure>=0.19.11 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (0.19.16)
Requirement already satisfied: six in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (1.15.0)
Requirement already satisfied: websocket-client>=0.55.0 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (0.57.0)
Requirement already satisfied: everett[ini]>=1.0.1; python_version >= "3.0" in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (1.0.2)
Requirement already satisfied: netifaces>=0.10.7 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (0.10.9)
Requirement already satisfied: nvidia-ml-py3>=7.352.0 in ./deepprofenv2/lib/python3.6/site-packages (from comet_ml>=1.0->deepprofiler==0.1.0) (7.352.0)
Requirement already satisfied: GPy>=1.8 in ./deepprofenv2/lib/python3.6/site-packages (from gpyopt>=1.2keras==2.2.5->deepprofiler==0.1.0) (1.9.9)
Requirement already satisfied: pytz>=2017.2 in ./deepprofenv2/lib/python3.6/site-packages (from pandas>=0.23.0->deepprofiler==0.1.0) (2020.1)
Requirement already satisfied: python-dateutil>=2.6.1 in ./deepprofenv2/lib/python3.6/site-packages (from pandas>=0.23.0->deepprofiler==0.1.0) (2.8.1)
Requirement already satisfied: pillow!=7.1.0,!=7.1.1,>=4.3.0 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (7.1.2)
Requirement already satisfied: imageio>=2.3.0 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (2.8.0)
Requirement already satisfied: PyWavelets>=1.1.1 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (1.1.1)
Requirement already satisfied: tifffile>=2019.7.26 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (2020.6.3)
Requirement already satisfied: networkx>=2.0 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (2.4)
Requirement already satisfied: matplotlib!=3.0.0,>=2.0.0 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-image>=0.14.0->deepprofiler==0.1.0) (3.2.1)
Requirement already satisfied: joblib>=0.11 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-learn>=0.19.0->deepprofiler==0.1.0) (0.15.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./deepprofenv2/lib/python3.6/site-packages (from scikit-learn>=0.19.0->deepprofiler==0.1.0) (2.1.0)
Requirement already satisfied: attrs>=17.4.0 in ./deepprofenv2/lib/python3.6/site-packages (from jsonschema!=3.1.0,>=2.6.0->comet_ml>=1.0->deepprofiler==0.1.0) (19.3.0)
Requirement already satisfied: setuptools in ./deepprofenv2/lib/python3.6/site-packages (from jsonschema!=3.1.0,>=2.6.0->comet_ml>=1.0->deepprofiler==0.1.0) (47.1.1)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in ./deepprofenv2/lib/python3.6/site-packages (from jsonschema!=3.1.0,>=2.6.0->comet_ml>=1.0->deepprofiler==0.1.0) (1.6.1)
Requirement already satisfied: pyrsistent>=0.14.0 in ./deepprofenv2/lib/python3.6/site-packages (from jsonschema!=3.1.0,>=2.6.0->comet_ml>=1.0->deepprofiler==0.1.0) (0.16.0)
Requirement already satisfied: certifi>=2017.4.17 in ./deepprofenv2/lib/python3.6/site-packages (from requests>=2.18.4->comet_ml>=1.0->deepprofiler==0.1.0) (2020.4.5.2)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./deepprofenv2/lib/python3.6/site-packages (from requests>=2.18.4->comet_ml>=1.0->deepprofiler==0.1.0) (1.25.9)
Requirement already satisfied: idna<3,>=2.5 in ./deepprofenv2/lib/python3.6/site-packages (from requests>=2.18.4->comet_ml>=1.0->deepprofiler==0.1.0) (2.9)
Requirement already satisfied: chardet<4,>=3.0.2 in ./deepprofenv2/lib/python3.6/site-packages (from requests>=2.18.4->comet_ml>=1.0->deepprofiler==0.1.0) (3.0.4)
Requirement already satisfied: configobj; extra == "ini" in ./deepprofenv2/lib/python3.6/site-packages (from everett[ini]>=1.0.1; python_version >= "3.0"->comet_ml>=1.0->deepprofiler==0.1.0) (5.0.6)
Requirement already satisfied: paramz>=0.9.0 in ./deepprofenv2/lib/python3.6/site-packages (from GPy>=1.8->gpyopt>=1.2keras==2.2.5->deepprofiler==0.1.0) (0.9.5)
Requirement already satisfied: decorator>=4.3.0 in ./deepprofenv2/lib/python3.6/site-packages (from networkx>=2.0->scikit-image>=0.14.0->deepprofiler==0.1.0) (4.4.2)
Requirement already satisfied: cycler>=0.10 in ./deepprofenv2/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.14.0->deepprofiler==0.1.0) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./deepprofenv2/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.14.0->deepprofiler==0.1.0) (1.2.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./deepprofenv2/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image>=0.14.0->deepprofiler==0.1.0) (2.4.7)
Requirement already satisfied: zipp>=0.5 in ./deepprofenv2/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=3.1.0,>=2.6.0->comet_ml>=1.0->deepprofiler==0.1.0) (3.1.0)
Installing collected packages: deepprofiler
  Running setup.py develop for deepprofiler
Successfully installed deepprofiler
(deepprofenv2) [logand05@cortex:~/github/DeepProfiler]$ pip list | grep Keras
Keras-Applications   1.0.8
Keras-Preprocessing  1.1.2

Arkkienkeli commented 4 years ago

Hi @dlogan

Hmm, I'm still not getting Keras installed when installing deepprofiler. I do see Keras in the setup.py, though... See this output

There was a typo in setup.py, fixed.

Any luck after with new env?

dlogan commented 4 years ago

Yes, the Keras commit fixed the install issue. I tested with a new venv and it installs Keras fine now, thanks.

I'll see about the pytest issues I was having...

jccaicedo commented 3 years ago

Thanks @dlogan for reporting and @Arkkienkeli for help with this! Closing the issue!

cytomining / DeepProfiler

Error running tests #227