conda-forge / mne-feedstock

A conda-smithy repository for mne.

About mne-python-feedstock

Feedstock license: BSD-3-Clause

Home: http://mne.tools

Package license: BSD-3-Clause

Summary: MNE-Python is a software for MEG and EEG data analysis.

Development: https://github.com/mne-tools/mne-python

Documentation: http://mne.tools

The main package for MNE-Python is named mne in conda-forge and should be suitable for most users. The conda recipe produces the following:

• mne: should be installed for full functionality including 3D visualization.
• mne-base: only pulls dependencies for basic functionality and 2D visualization.
• mne-installer-menus: should not be installed manually, as it is only meant to be used by the standalone installers.

Current build status

Azure

Variant Status linux_64 osx_64 osx_arm64 win_64

Current release info

Name	Downloads	Version	Platforms

Installing mne-python

Installing mne-python from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, mne, mne-base, mne-installer-menus can be installed with conda:

conda install mne mne-base mne-installer-menus

or with mamba:

mamba install mne mne-base mne-installer-menus

It is possible to list all of the versions of mne available on your platform with conda:

conda search mne --channel conda-forge

or with mamba:

mamba search mne --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search mne --channel conda-forge

# List packages depending on `mne`:
mamba repoquery whoneeds mne --channel conda-forge

# List dependencies of `mne`:
mamba repoquery depends mne --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating mne-python-feedstock

If you would like to improve the mne-python recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/mne-python-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @christianbrodbeck
• @hoechenberger
• @larsoner

mne-feedstock's Issues

Pin Python to >=3.8,<3.11

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I installed mne-base and then decided to "upgrade" to mne. But I ran into package resolution problems because during the mne-base install, I received Python 3.11, which apparently (?) doesn't want to live together with mne and its dependencies, at least on my Apple Silicon computer. I haven't done any extensive testing, though

Installed packages

...

Environment info

...

Remove cupy dependency again

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Cupy should be removed again

Installed packages

none

Environment info

none

Menu icons don't show up on Linux (.desktop files contain references to .png files we don't ship!)

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

0.20 packages

There are currently no 0.20 packages on anaconda.org. Apparently the build failed.

@conda-forge-admin, please add bot automerge

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

Expand docstrings?

This one mostly goes out to @larsoner

cc @agramfort @sappelhoff @mmagnuski

Since

• VS Code's Pylance still doesn't support the expansion of our doccer-style docstrings,
• and we're unlikely to see this feature anytime soon,
• and we once discussed that we don't want to do this expansion for sdist releases either (I think),

I just thought: Why not do it here, during the conda build? We are basically free do any modifications we like during the build stage!

It should be a rather straightforward operation, no?

And everybody following our official installation instructions (i.e., ending up with a conda-based install) would automatically have fully functional docstrings in VS Code.

WDYT?

Add menu entries on Windows

We can automatically add menu entries for … whatever … on Windows :) See discussion at https://github.com/hoechenberger/mne-installers/issues/10#issuecomment-889690408 and below

cc @rob-luke

does mayavi get installed for you?

check this out:

    conda create --name test_mne_017_conda --yes python=3.6
    conda activate test_mne_017_conda
    conda install --yes mne
    python -c "import mne; mne.sys_info()"

/home/sik/miniconda3/envs/test_mne_017_conda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
Platform:      Linux-4.15.0-34-generic-x86_64-with-debian-buster-sid
Python:        3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 02:32:25)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Executable:    /home/sik/miniconda3/envs/test_mne_017_conda/bin/python
CPU:           x86_64: 4 cores
Memory:        Unavailable (requires "psutil" package)
mne:           0.17.0
numpy:         1.15.0 {blas=mkl_rt, lapack=mkl_rt}
scipy:         1.1.0
matplotlib:    2.2.2 {backend=Qt5Agg}

sklearn:       0.19.1
nibabel:       2.3.1
mayavi:        Not found
cupy:          Not found
pandas:        Not found
dipy:          0.14.0

BUG: mne-qt-browser missing in recipe

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

When mne is installed via conda, the new browser-backend mne-qt-browser which is part of mne since version 0.24. isn't installed with it. It is probably missing in the recipe.

Code reproducing the problem:

conda create -n mne -c conda-forge mne

Expected result:

mne-qt-browser found in installed packages.