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I really just want to add nibabel and nilearn to our server_environment because they are needed for some viz functions, but then I noticed some other stuff, so this PR will:

  1. Add nibabel and nilearn
  2. Remove vtk_dev channel
  3. Remove defaults channel
  4. Remove the numpy<1.19.0 pin

Hopefully it all works but if it doesn't, hopefully I can at least get (1) in there. I'll need to double-check that the env otherwise looks the same in terms of what gets installed by looking at mne sys_info.

@larsoner
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Old:

Platform:      Linux-5.4.0-1031-azure-x86_64-with-glibc2.10
Python:        3.8.5 (default, Sep  4 2020, 07:30:14)  [GCC 7.3.0]
Executable:    /home/vsts/miniconda/bin/python3.8
CPU:           x86_64: 2 cores
Memory:        Unavailable (requires "psutil" package)
mne:           0.22.dev0
numpy:         1.18.5 {blas=openblas, lapack=openblas}
scipy:         1.5.4
matplotlib:    3.3.3 {backend=agg}

sklearn:       Not found
numba:         Not found
nibabel:       Not found
cupy:          Not found
pandas:        Not found
dipy:          Not found
mayavi:        Not found
pyvista:       0.27.4 {OpenGL 3.3 (Core Profile) Mesa 18.3.1 via llvmpipe (LLVM 7.0, 256 bits)}
vtk:           9.0.0
PyQt5:         Not found

New:

Platform:      Linux-5.4.0-1031-azure-x86_64-with-glibc2.10
Python:        3.8.5 (default, Sep  4 2020, 07:30:14)  [GCC 7.3.0]
Executable:    /home/vsts/miniconda/bin/python3.8
CPU:           x86_64: 2 cores
Memory:        Unavailable (requires "psutil" package)
mne:           0.22.dev0
numpy:         1.19.4 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy:         1.5.3
matplotlib:    3.3.3 {backend=agg}

sklearn:       0.23.2
numba:         Not found
nibabel:       3.2.1
nilearn:       0.7.0
dipy:          Not found
cupy:          Not found
pandas:        1.1.4
mayavi:        Not found
pyvista:       0.27.4 {OpenGL 3.3 (Core Profile) Mesa 18.3.1 via llvmpipe (LLVM 7.0, 256 bits)}
vtk:           9.0.0
PyQt5:         Not found

@GuillaumeFavelier I got a segfault when I tried to remove vtk_dev -- any idea why we have to use that version rather than the one provided by conda-forge?

@larsoner larsoner changed the title MAINT: Improve server env MRG, MAINT: Improve server env Dec 14, 2020
- nbclient
- mffpy>=0.5.7
- pip:
- mne
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mne and jupyter are stuck in pip because they require / pull in PyQt5, which often breaks headless servers (anything that tries to import PyQt5 will die because Qt5 throws an error)

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any idea why we have to use that version rather than the one provided by conda-forge?

To fetch the version of vtk built with osmesa. At least, it was the case when I added this conf.

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Pushed a commit for the yield_fixture business, too.

@GuillaumeFavelier you happy? If so I'll merge when green

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LGTM

@larsoner larsoner merged commit 52c4fff into mne-tools:master Dec 14, 2020
@larsoner larsoner deleted the tests branch December 14, 2020 15:47
larsoner added a commit to agramfort/mne-python that referenced this pull request Dec 16, 2020
* upstream/master: (42 commits)
  MRG, ENH: Add DICS bias tests (mne-tools#8610)
  MRG, BUG, ENH: Add window option (mne-tools#8662)
  BUG: Fix alpha for volumes (mne-tools#8663)
  MRG, BUG: Fix bugs with envcorr (mne-tools#8658)
  MRG, ENH: Progressbar for csd_morlet (mne-tools#8608)
  Render is necessary now (mne-tools#8657)
  VIZ: Fix head size (mne-tools#8651)
  MRG, MAINT: bump sphinxcontrib-bitex version (mne-tools#8653)
  MRG, MAINT: Improve server env (mne-tools#8656)
  BUG: Mayavi center (mne-tools#8644)
  VIZ, ENH: allow show/hide annotations by label (mne-tools#8624)
  Add regression test for EEGLAB data with a chanlocs struct (mne-tools#8647)
  FIX: scalar_bar (mne-tools#8643)
  MRG: Small fix to tutorial; rename plot_events ordinate label to "Event id"; improve some SSP docstrings (mne-tools#8612)
  MRG, ENH: make plot alignment use defaults for colors (mne-tools#8553)
  BUG: Fix passing of channel type (mne-tools#8638)
  FIX: fixed loop over norm PSF/CTF options (mne-tools#8636)
  MRG, BUG: Pass kwargs (mne-tools#8630)
  DOC: Clearer error message (mne-tools#8631)
  BUG: Fix number of labels (mne-tools#8629)
  ...
larsoner added a commit to wmvanvliet/mne-python that referenced this pull request Dec 16, 2020
* upstream/master: (38 commits)
  MRG, ENH: Add DICS bias tests (mne-tools#8610)
  MRG, BUG, ENH: Add window option (mne-tools#8662)
  BUG: Fix alpha for volumes (mne-tools#8663)
  MRG, BUG: Fix bugs with envcorr (mne-tools#8658)
  MRG, ENH: Progressbar for csd_morlet (mne-tools#8608)
  Render is necessary now (mne-tools#8657)
  VIZ: Fix head size (mne-tools#8651)
  MRG, MAINT: bump sphinxcontrib-bitex version (mne-tools#8653)
  MRG, MAINT: Improve server env (mne-tools#8656)
  BUG: Mayavi center (mne-tools#8644)
  VIZ, ENH: allow show/hide annotations by label (mne-tools#8624)
  Add regression test for EEGLAB data with a chanlocs struct (mne-tools#8647)
  FIX: scalar_bar (mne-tools#8643)
  MRG: Small fix to tutorial; rename plot_events ordinate label to "Event id"; improve some SSP docstrings (mne-tools#8612)
  MRG, ENH: make plot alignment use defaults for colors (mne-tools#8553)
  BUG: Fix passing of channel type (mne-tools#8638)
  FIX: fixed loop over norm PSF/CTF options (mne-tools#8636)
  MRG, BUG: Pass kwargs (mne-tools#8630)
  DOC: Clearer error message (mne-tools#8631)
  BUG: Fix number of labels (mne-tools#8629)
  ...
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2 participants