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MAINT: Future-compatible cmap reversal #2131

Merged
merged 3 commits into from
Sep 25, 2019
Merged

MAINT: Future-compatible cmap reversal #2131

merged 3 commits into from
Sep 25, 2019

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larsoner
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Without this change I get warnings of the form:

/home/larsoner/python/nilearn/nilearn/plotting/cm.py:159: MatplotlibDeprecationWarning: 
The revcmap function was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use Colormap.reversed() instead.
  _cmaps_data[_cmapname_r] = _cm.revcmap(_cmapspec)

The suggested fix of .reversed() is not immediately usable because that wouldn't give us the data to put in _cmaps_data, so just take the (simple) mpl code to do the reversal knowing they're all dict and not callable.

@jeromedockes
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thanks!
the travis failure is unrelated

@jeromedockes
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how did you trigger the warning? running the tests?
and I guess this is starting from matplotlib 3.2?

@larsoner
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Any nilearn.plotting import should do it if you are on latest matplotilb dev

@larsoner
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(I based the 3.2 in the comments on the deprecation warning I got from MPL)

@jeromedockes
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sorry for the delay @larsoner
would you mind rebasing or merging master? that should fix the travis failure

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codecov bot commented Sep 24, 2019 •
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Codecov Report

Merging #2131 into master will decrease coverage by <.01%.
The diff coverage is 89.47%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master   #2131      +/-   ##
=========================================
- Coverage    92.3%   92.3%   -0.01%     
=========================================
  Files         142     142              
  Lines       18508   18515       +7     
  Branches     2255    2255              
=========================================
+ Hits        17084   17090       +6     
- Misses        920     921       +1     
  Partials      504     504
Impacted Files Coverage Δ
nilearn/plotting/cm.py 86.13% <89.47%> (-0.03%) ⬇️

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@larsoner
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My editor removed trailing whitespace (arguably a good thing), which caused CIs to flag PEP8 errors on those lines (arguably a good thing), so I'm going to fix the PEP8 errors in those vicinities (could be a good or bad thing). There are a ton in the file and I don't want to touch everything, so I'll try to stay localized.

Or if you prefer I can revert the whitespace changes and just keep the relevant ones for MPL deprecation.

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jeromedockes commented Sep 24, 2019 via email

jeromedockes
jeromedockes approved these changes Sep 24, 2019
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LGTM. thanks a lot!

@kchawla-pi
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Add this under fixes in what's new.

@larsoner
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Done

@GaelVaroquaux
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LGTM. Merging.

@GaelVaroquaux GaelVaroquaux merged commit bf65253 into nilearn:master Sep 25, 2019
@larsoner larsoner deleted the dep branch September 25, 2019 18:41
kchawla-pi added a commit to AlexandreAbraham/nilearn that referenced this pull request Sep 30, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into fix_…
eda8bd1 
…clean

* 'master' of https://github.com/nilearn/nilearn: (2100 commits)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  added whats_new
  Added test for labels=None
  More explicit doc string
  Test for right length of labels
  Added tests for empty list case and labels as ndarray
  ensure labels is a list, not an ndarray
  Change such that empty lists are recognized as False
  Undid some documentation changes as their reason is not understood
  Replaced conda latest version with 4.6.* pending replacement
  Removed omit sections (nothing to omit, it would seem)
  Corrected docstring for bg_img in plot_stat_map
  Removed omit=*test* to fix error during coverage reporting
  ...

# Conflicts:
#	nilearn/tests/test_signal.py
kchawla-pi added a commit to kchawla-pi/nilearn that referenced this pull request Oct 8, 2019
@kchawla-pi
Merge branch 'master' of github.com:nilearn/nilearn into rm-dep-warn-…
d627227 
…encoding

* 'master' of github.com:nilearn/nilearn: (228 commits)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  added whats_new
  Added test for labels=None
  More explicit doc string
  Test for right length of labels
  Added tests for empty list case and labels as ndarray
  ensure labels is a list, not an ndarray
  ...
kchawla-pi added a commit to KamalakerDadi/nilearn that referenced this pull request Oct 9, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into glas…
98345d6 
…s_brain_orientation

* 'master' of https://github.com/nilearn/nilearn: (116 commits)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  added whats_new
  ...

# Conflicts:
#	doc/whats_new.rst
kchawla-pi added a commit to glemaitre/nilearn that referenced this pull request Oct 9, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into is/p…
ee46da0 
…lot_connectome_strength

* 'master' of https://github.com/nilearn/nilearn: (272 commits)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  ...

# Conflicts:
#	examples/03_connectivity/plot_sphere_based_connectome.py
kchawla-pi added a commit to KamalakerDadi/nilearn that referenced this pull request Oct 9, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into conf…
16d718b 
…ounds_for_connectome

* 'master' of https://github.com/nilearn/nilearn: (227 commits)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  ...
kchawla-pi added a commit to KamalakerDadi/nilearn that referenced this pull request Oct 9, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into plot…
f183965 
…_roi_contours

* 'master' of https://github.com/nilearn/nilearn: (227 commits)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  ...
kchawla-pi added a commit to illdopejake/nilearn that referenced this pull request Oct 12, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into spri…
1bcfdba 
…nt_modify_fetch_dev

* 'master' of https://github.com/nilearn/nilearn: (228 commits)
  [MRG] Nans in view connectome (nilearn#2166)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  ...

# Conflicts:
#	nilearn/datasets/func.py
kchawla-pi added a commit to KamalakerDadi/nilearn that referenced this pull request Oct 14, 2019
@kchawla-pi
Merge branch 'master' of https://github.com/nilearn/nilearn into ev_d…
259783f 
…ecomposition

* 'master' of https://github.com/nilearn/nilearn: (348 commits)
  [MRG] FIX: orientation problem with plot_glass_brain (nilearn#1888)
  Import HTMLDocument in its original module to preserve backwards compatibility (nilearn#2162)
  Fixing malfunctioning allowed-failure section in Travis (nilearn#2160)
  Update Brainomics fetcher (nilearn#2097)
  Remove inplace modification in signal.clean (nilearn#2125)
  Iter age group prediction example (nilearn#2063)
  Expose bg_img, vmin and vmax in plot_img signature (nilearn#2157)
  Replac conda with pip in TravisCI setup (nilearn#2141)
  Core devs doc and add @emdupre (nilearn#2151)
  Add check for vmin, vmax in plot_surf_roi (nilearn#2052)
  [ENH] Initial visual reports (nilearn#2019)
  Renamed test to deduplicate name (nilearn#2144)
  Fixes nilearn#2029 Handle gzip files without extensions (nilearn#2126)
  Update Schaefer parcelation to v0.14.3 (nilearn#2138)
  MAINT: Future-compatible cmap reversal (nilearn#2131)
  fix openmp crash (nilearn#2140)
  change nose to pytest on appveyor (nilearn#2130)
  adding fix to whatsnew
  fix wrong urls in nki dataset
  Made Flake8 happy
  ...

# Conflicts:
#	doc/connectivity/resting_state_networks.rst
#	doc/whats_new.rst
#	examples/03_connectivity/plot_canica_analysis.py
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@larsoner @jeromedockes @kchawla-pi @GaelVaroquaux