[MRG] Replac conda with pip in CI setup #2141

kchawla-pi · 2019-09-25T14:17:48Z

Conda has become unreliable for use with CIs. Replacing it with alternatives such as pip and apt seems a prudent long term solution.

…install

codecov · 2019-10-02T11:55:33Z

Codecov Report

Merging #2141 into master will increase coverage by 0.16%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2141      +/-   ##
==========================================
+ Coverage   92.21%   92.38%   +0.16%     
==========================================
  Files         149      149              
  Lines       18752    18752              
  Branches     2277     2277              
==========================================
+ Hits        17293    17324      +31     
+ Misses        944      917      -27     
+ Partials      515      511       -4

Impacted Files	Coverage Δ
nilearn/tests/test_signal.py	`99.23% <0%> (-0.77%)`	⬇️
nilearn/_utils/testing.py	`78.76% <0%> (ø)`	⬆️
nilearn/image/resampling.py	`93.75% <0%> (+0.89%)`	⬆️
nilearn/image/tests/test_image.py	`99.45% <0%> (+1.09%)`	⬆️
nilearn/regions/parcellations.py	`96.19% <0%> (+1.9%)`	⬆️
nilearn/_utils/cache_mixin.py	`83.65% <0%> (+1.92%)`	⬆️
nilearn/decoding/fista.py	`90.12% <0%> (+2.46%)`	⬆️
nilearn/__init__.py	`71.42% <0%> (+2.85%)`	⬆️
nilearn/input_data/nifti_masker.py	`92.56% <0%> (+4.95%)`	⬆️
nilearn/plotting/__init__.py	`95.65% <0%> (+17.39%)`	⬆️
... and 1 more

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continuous_integration/install.sh

jeromedockes · 2019-10-02T12:43:53Z

thanks! apart from the small question above +1 for merge

kchawla-pi · 2019-10-02T12:47:09Z

Thanks. I will unpin conda==4.6 next and then test these changes in AppveyorCI. Only then can we merge this.

kchawla-pi · 2019-10-02T12:50:29Z

I just remembered conda 4.7 was glitching for python3.5 installation so maybe not unpin it then.

jeromedockes · 2019-10-02T12:53:11Z

I just remembered conda 4.7 was glitching for python3.5 installation so maybe not unpin it then.

I think you can leave it pinned for now

kchawla-pi · 2019-10-02T13:47:14Z

That would make this PR very easy, but it will still leave older version of conda in play, which kind of defeats the purpose of the PR. If we were gonna rely on a pinned conda, then we don't need pip anyway. I'll use TravisCIs automatic virtualenvs. Then we'll see.

… Conda

…uild

…e builds - Removed unused code.

kchawla-pi · 2019-10-02T17:20:07Z

Appveyor manages its own conda installation as part of its images for Python 3.5 so we don't need to change that and CircleCI uses the latest packages so Between the 2 of them Conda is covered.

This is ready for a review.
But don't merge it yet, I want to induce a failure and see the traceback from that.

kchawla-pi · 2019-10-04T11:52:39Z

@jeromedockes Second review?

bthirion

Note that I'm not an expert in Circelci configs...

jeromedockes · 2019-10-07T07:50:27Z

.travis.yml


-virtualenv:
-  system_site_packages: true
+#virtualenv:


you can remove the commented-out lines

.travis.yml

jeromedockes · 2019-10-07T07:54:07Z

continuous_integration/install.sh

@@ -25,7 +25,7 @@ create_new_venv() {
    pip install nose pytest
 }

-print_conda_requirements() {
+echo_requirements_string() {
    # Echo a conda requirement string for example


this comment is slightly outdated

@emdupre

…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 ...

@emdupre

…stats * 'master' of github.com:nilearn/nilearn: 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)

@emdupre

…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

@emdupre

…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

@emdupre

…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 ...

@emdupre

…_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 ...

@emdupre

…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

@emdupre

…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

@emdupre

…smooth-image * 'master' of https://github.com/nilearn/nilearn: (114 commits) [DOC] Update whats_new to reference nilearn#2013 (Merging of several examples) (nilearn#2183) Removed sub-example due to unfit for lasso dataset - unstable float values (nilearn#2177) Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167) [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) ...

@emdupre

…te-req-dev * 'master' of https://github.com/nilearn/nilearn: (336 commits) Release Nilearn 0.6.0 alpha (nilearn#2164) Making fetch_localizer_button_task backwards compatibile (nilearn#2182) [DOC] Update whats_new to reference nilearn#2013 (Merging of several examples) (nilearn#2183) Removed sub-example due to unfit for lasso dataset - unstable float values (nilearn#2177) Fix Flake8 errors overlooked when merging PR nilearn#2028 (Plot connectome strength) (nilearn#2174) ENH: add connectome strength plot (nilearn#2028) Fix cache mixin tests (nilearn#2161) Do not fail if metadata cannot be updated for an image (nilearn#2167) [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) ...

Replaced conda with pip in CI setup

78b979d

kchawla-pi changed the title ~~Replac conda with pip in CI setup~~ [WIP] Replac conda with pip in CI setup Sep 25, 2019

kchawla-pi added 7 commits October 1, 2019 16:17

Removed conda related commands & conditions

a357b20

Simpler adaptation of existing script - conda to create venv, pip to …

cc59ca3

…install

Fix: Failure de to conflict between conda's python & pip's python

05550b8

Removed --quiet fag to aid debugging

3230c24

Corrected order of args for conda create

f29afe9

Changed package version specifier syntax to be pip compatible

9a1b6aa

Addressed pip does not handle "*" in package version spec

8e4e366

jeromedockes reviewed Oct 2, 2019

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continuous_integration/install.sh Show resolved Hide resolved

kchawla-pi added 6 commits October 2, 2019 16:09

Using TravisCI's multiple Python version to move completely away from…

f81ad88

… Conda

Bypassing conda download & installation

95f0ff4

Removing system site packages use since using virtual envs for each b…

ff090b1

…uild

Corrected allow_failures, joblib min & latest installed in appropriat…

b67c99e

…e builds - Removed unused code.

Corrected Joblib version spec string in a build

701d1df

Removed references to conda in symbols

89defe6

Changed [] to [[]], $VAR to $(VAR)

1008db7

kchawla-pi changed the title ~~[WIP] Replac conda with pip in CI setup~~ [MRG] Replac conda with pip in CI setup Oct 3, 2019

kchawla-pi mentioned this pull request Oct 4, 2019

Revert PR #2078 & change the min library versions back #2148

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bthirion approved these changes Oct 6, 2019

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jeromedockes reviewed Oct 7, 2019

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Remove unnecessary comments, add a useful one

48499bc

kchawla-pi force-pushed the pip-not-conda branch from 920b285 to 48499bc Compare October 8, 2019 13:49

kchawla-pi merged commit e0d6b6e into nilearn:master Oct 8, 2019

kchawla-pi deleted the pip-not-conda branch October 8, 2019 16:47

kchawla-pi mentioned this pull request Oct 9, 2019

[WIP] TravisCI : allowed_failures failing #2159

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[MRG] Replac conda with pip in CI setup #2141

[MRG] Replac conda with pip in CI setup #2141

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[MRG] Replac conda with pip in CI setup #2141

[MRG] Replac conda with pip in CI setup #2141

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