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JNB:BUG: Updated Suite2P example workflow for new Suite2p API and multiprocessing bug #181

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JNB:BUG: Updated Suite2P example workflow for new Suite2p API and multiprocessing bug #181

wants to merge 164 commits into from

Commits on Jun 16, 2021

  1. JNB:BUG: Updated Suite2p notebook to handle multiprocessing and updat… 

    …ed Suite2p API
    @swkeemink
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Commits on Jun 28, 2021

  1. DOC: Add elastic search on readthedocs

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  2. DOC: Change theme to pydata 

    pydata is the theme developed by pandas and now also used by numpy,
scipy and bokeh.

As the pydata theme is only available for Python 3.5+, and only
working for us with Python 3.6+, we are still using the
readthedocs theme when deploying the documentation on Python 2.7
and 3.5.
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  3. DOC: Add a redirect from gh-pages base to readthedocs

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  4. DEV: nbstripout needs to be before large file check

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  5. DEV: Add black_nbconvert to pre-commit

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  6. JNB:STY: Blacken notebooks

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  7. JNB:STY: Blacken code in comments

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  8. JNB:STY: Fix formatting after cell magic, not caught by black

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  9. TST: Test for experiment.means shape

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  10. TST: Change default test to be w/o pre-existing dir

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  11. RF: Save to multiple arrays to .npz file instead of .npy

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  12. TST: Change bad-cache tests to write .npy -> .npz file

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  13. TST: Test writing to a subfolder

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  14. TST: Test cache dir deletion between steps

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  15. TST: Test whether caching can be done into pwd

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  16. BUG: Make directory before saving cache files if needed

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  17. BUG: Don't try to make empty directory

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  18. TST: Don't write to cache for initial core tests

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  19. TST: Don't test output for initial cache test

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  20. TST: Check code actually loads/runs as appropriate

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  21. DOC: Add comments in core tests

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  22. TST:MNT: Deeper subdir test

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  23. BUG: Need to cast self.nCell as int

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  24. MNT: Reset self.means before setting it

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  25. MNT: Append to means list instead of making new list

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  26. ENH: Save means to cache

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  27. MNT: Initialise with list of list, not of 0s

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  28. TST: Add tests for manual saving .npz

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  29. MNT: Save deltaf to separate.npz cache

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  30. RF: Move _wipe into clear methods

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  31. MNT: Clear just before prep/separation begins

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  32. RF: Move load operations into its own method

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  33. RF: Use list comprehension

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  34. TST:MNT: Explicit actual, desired args to make order clear

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  35. TST:MNT: Change order in custom assertions to be actual, desired

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  36. ENH:TST: Add assert_allclose_ragged

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  37. TST: Add manual loading tests

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  38. ENH: Support specifying directory to load

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  39. TST:MNT: py3.5 compatible shutil.copytree w/o dirs_exist_ok 

    The `dirs_exist_ok` argument was added to shutil.copytree
in python 3.6.

We just delete the target directory instead, so it is compatible
with python 3.5.
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  40. MNT:TST: Use common variables for image_path and roi_path across expe… 

    …riments in same test
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  41. TST: Test with empty cache files

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  42. TST: Add tests for DataHandlerTifffileLazy

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  43. ENH: Add DataHandlerTifffileLazy datahandler

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  44. MNT: Add dimension warnings to DataHandlerTifffileLazy

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  45. MNT: Change lowmemory_mode datahandler to DataHandlerTifffileLazy

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  46. TST: Test all three datahandlers manually

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  47. TST:DOC: Fix bad class references

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  48. TST:MNT: kw -> kwargs

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  49. TST:RF: Move temporary dirname definition to BaseTestCase

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  50. TST:BUG: NamedTemporaryFile not working on Windows 

    Use a custom temporary path that we manually tear down instead
of using /tmp/
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  51. TST:MNT: Write temp files to temp dir instead of our tests dir 

    Write to /tmp on Unix and C:\TEMP on Windows.
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  52. REL: Rename dev extras to test extras

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  53. REL: Add dev requirements, containing pre-commit

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  54. CI: Add .codecov.yml to allow small decreases in coverage 

    Adapted from sklearn's .codecov.yml config file.
https://github.com/scikit-learn/scikit-learn/blob/617ff6e/.codecov.yml
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  55. MNT: Change separator _ to - in requirement.txt filenames

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  56. RF:TST: Change to using a Mixin class for Rois2MasksTest

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  57. RF:TST: Use setUp instead of mixture of setup_class/setUp

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  58. TST:DOC: Fix docstring

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  59. MNT: Can't call empty super() on python 2.7

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  60. MNT: Use parent Rois2MasksTestMixin.setUp

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  61. CI: Editable install

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  62. CI: Install sima before fissa

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  63. CI: Report nb-smoke coverage

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  64. DOC: Update intersphinx mappings

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  65. DOC: Graceful degradation of sphinx theme

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  66. CI:GHA: Always run tests, don't skip based on content 

    This is because we always need to run on pushes to the master
branch. We would like to skip running the tests on pushes to other
branches which don't affect the codebase, but it is not clear to
me if this is actually possible using just the github workflow event
triggers.
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  67. MNT: Don't initialise list with empty strings

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  68. MNT: Use list comprehension

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  69. TST: Test matfile output

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  70. TST: Test saving to matfile when results loaded from cache

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  71. BUG: Load np.array(None) as None

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  72. MNT: Don't save attributes which are None to npz files

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  73. TST:STY: Remove empty comment

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  74. TST: Check well behavioured when loading None

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  75. TST:MNT: Use assertIs to compare with None

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  76. TST:MNT: assert_allclose_ragged accept list(s) in desired

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  77. TST:MNT: assert_allclose_ragged accept None as desired value

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  78. TST:RF: Move comparisons in core to helper methods

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  79. TST:ENH: Test shape of raw as well as result

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  80. TST:RF: Move deltaf comparisons into compare_output

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  81. ENH: Add functional interface to FISSA

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  82. TST: Test functional interface

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  83. ENH: Add deltaf_across_trials argument to functional interface

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  84. DOC: Add example scripts for working with functional interface

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  85. JNB: Updates to Basic usage source

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  86. JNB: Add notebook for functional interface

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  87. DOC: Fix typo

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  88. DOC: Capitalise Jupyter

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  89. DOC: Add functional interface notebook and scripts to table

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  90. DOC: Change concise example to be run_fissa

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  91. JNB: Change to using datetime for the output directory

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  92. REL: Change bleeding-edge version to 1.0.dev0

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  93. [pre-commit.ci] pre-commit autoupdate 

    updates:
- [github.com/pre-commit/pygrep-hooks: v1.7.0 → v1.9.0](pre-commit/pygrep-hooks@v1.7.0...v1.9.0)
- [github.com/pre-commit/pre-commit-hooks: v3.3.0 → v4.0.1](pre-commit/pre-commit-hooks@v3.3.0...v4.0.1)
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  94. TST:BUG: datahandler moved to extraction

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  95. TST:ENH: Expand outputs of resource downsampler

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  96. TST:ENH: Add parser for generate_downsampled_resources

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  97. TST:RF: Move Core tests into a Mixin class

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  98. TST: Add ExperimentA resource a/expected.npz

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  99. TST: Expand core tests, comparing attributes against expected.npz fil… 

    …e contents
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  100. TST: Add ExperimentB resources, with 2 ROIs and 3 TIFFs

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  101. TST: Add core tests on Experiment B, with 2 ROIs and 3 TIFFs

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  102. TST: Remove ExperimentA tests and resources 

    We only use the (larger) ExperimentB tests instead, since these
are better. It takes a lot longer to run both ExperimentA and
ExperimentB, so we just run ExperimentB.
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  103. JNB: OO Don't overwrite output_folder from datetime one

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  104. DOC: Move Experiment parameter doc from __init__ docstring to class d… 

    …ocstring
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  105. DOC: Add versionadded to clear, save, and load methods

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  106. MNT: Use UTF-8 encoding for core so we can use greek letters in docst… 

    …rings on Py2.7
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  107. DOC: Improve core docstrings

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  108. DOC: Add attributes section to Experiment

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  109. DOC: Fix Experiment.separate docstring

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  110. DOC: Add link to paper in Experiment

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  111. DOC: Use numpydoc instead of napoleon

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  112. DOC: Add see also from run_fissa to Experiment

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  113. DOC: Add see also to skimage.measure.find_contours

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  114. DOC: Add see also to NMF and FastICA

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  115. DOC: Manually declare mapping for unicode Delta symbol

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  116. DOC: Mark docstrings which make contain unicode as raw strings

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  117. DOC: Add source_encoding for sphinx

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  118. TST: Check error raised when lowmemory_mode and datahandler both set

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  119. MNT: Raise error when both lowmemory_mode and datahandler are set

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  120. DOC: Add note about deltaf_result baseline

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  121. MNT: Move self.clear to top of init

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  122. ENH: Add __str__ and __repr__ to Experiment

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  123. ENH: Add repr to DataHandler classes

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  124. TST: Test repr for DataHandler classes

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  125. TST: Test str and repr for Experiment

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  126. TST: Test parameters are set correctly when comparing experiments

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  127. RF: Move duplicated rois2mask code into roitools

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  128. TST: Test roitools.rois2masks

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  129. RF: Add get_frame_size method to use for DataHandler.rois2masks

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  130. DOC: Fix npil.separate docstring

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  131. RF: Refactor npil.separate

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  132. ENH: Work with uppercase sep_method

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  133. RF: Import all of sklearn.decomposition

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  134. ENH: Allow arbitrary sklearn.decomposition classes

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  135. ENH: Accept "nnmf" input as alias for "nmf"

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  136. DOC: Improve npil.separate documentation

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  137. MNT: Tidy up code

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  138. TST: Test npil.separate with FactorAnalysis

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  139. STY: Blacken neuropil

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  140. MNT: Print estimator name as per sklearn class name

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  141. TST:RF: Use a Mixin class for neuropil tests

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  142. TST:MNT: Ignore ConvergenceWarning when intentionally not converging

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  143. DOC+BUG: Require sphinx>2 with numpydoc and pydata-sphinx-theme

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  144. DOC: Specify minimum numpydoc version

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  145. RF: Use kwargs for extract_func and separate_func set with functools

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  146. MNT: Pool -> multiprocessing.Pool

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  147. API: Rename extract_func, separate_func -> extract, separate

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  148. MNT: Rename results -> outputs to disambiguate from Experiment.result

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  149. MNT: Move trial unravelling from separate method to separate function

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  150. API: Rename core.separate -> core.separate_trials 

    Too many functions and methods named "separate".
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  151. TST: Add tests for separate_trials

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  152. TST:MNT: Ignore ConvergenceWarning when intentionally not converging … 

    …(fix 78385ee)
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  153. MNT: Init arrays with np.empty, dtype=object instead lists of None

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  154. MNT: np.float -> np.float64

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  155. DOC: Fix links to extraction classes

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  156. DOC: Fix name of default save_prep output

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  157. DOC: Change self.attr to experiment.attr in docstrings

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  158. ENH: updated binder environment for Python 3.9, and updated suite2p 

    We no longer support the SIMA notebook on Binder, as it requires Python
3.6.
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  159. DOC: removed binder link to sima notebook, and explained why

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  160. JNB: updated SIMA notebook to specify that it will not run in Binder

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  161. JNB:STY: Blacken notebooks

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  162. TST: Test all three datahandlers manually

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  163. TST:RF: Move temporary dirname definition to BaseTestCase

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