conda-forge / nipype-feedstock

A conda-smithy repository for nipype.

About nipype-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/nipy/nipype

Package license: Apache-2.0

Summary: Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, AFNI, Slicer, ANTS), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Current build status

Azure

Variant Status linux_64_python3.10.____cpython linux_64_python3.8.____cpython linux_64_python3.9.____cpython osx_64_python3.10.____cpython osx_64_python3.8.____cpython osx_64_python3.9.____cpython osx_arm64_python3.10.____cpython osx_arm64_python3.8.____cpython osx_arm64_python3.9.____cpython win_64_python3.10.____cpython win_64_python3.8.____cpython win_64_python3.9.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing nipype

Installing nipype 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, nipype can be installed with conda:

conda install nipype

or with mamba:

mamba install nipype

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

conda search nipype --channel conda-forge

or with mamba:

mamba search nipype --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

# List dependencies of `nipype`:
mamba repoquery depends nipype --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-Cloud 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 nipype-feedstock

If you would like to improve the nipype 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/nipype-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

• @chrisgorgo
• @effigies
• @mgxd
• @satra

nipype-feedstock's Issues

Depend on matplotlib-base instead of matplotlib (improvement)

If possible it would be a lot cleaner to depend on matplotlib-base instead of matplotlib as this now results in a cascading of mostly unnecessary dependencies.

I'm getting permission denied error in windows 10 Anaconda

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

release 0.12(build0) tagged as both broken and main

Hi @conda-forge/core,

Please remove the main labels from the 0.12 files tagged with the broken labels. This was a result of a premature release.

Thank you!

not installable on M1

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

it seems that nipype package is arch specific according to https://anaconda.org/conda-forge/nipype . As a result -- it is not installable on M1

(heudiconv) datalad@26696 ~ % conda install -c conda-forge -y nipype   
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - nipype

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

which in case of installing downstream heudiconv project results even in worse behavior of noninformative empty message: conda/conda#10672 (comment)

So, likely just needs m1 build or announce package a noarch altogether. (in datalad we switch from noarch to arch specific only to run tests across different python versions... was that a motivation here or there are any extensions?)

attn @effigies

Installed packages

(heudiconv) datalad@26696 ~ % conda list                            
# packages in environment at /Users/datalad/miniconda-test3/envs/heudiconv:
#
# Name                    Version                   Build  Channel
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
ca-certificates           2023.7.22            hf0a4a13_0    conda-forge
dcm2niix                  1.0.20230411         h1995070_0    conda-forge
dcmstack                  0.8.0              pyhd8ed1ab_2    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
isodate                   0.6.1              pyhd8ed1ab_0    conda-forge
libblas                   3.9.0           18_osxarm64_openblas    conda-forge
libcblas                  3.9.0           18_osxarm64_openblas    conda-forge
libcxx                    16.0.6               h4653b0c_0    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_1    conda-forge
libgfortran5              13.2.0               hf226fd6_1    conda-forge
liblapack                 3.9.0           18_osxarm64_openblas    conda-forge
libopenblas               0.3.24          openmp_hd76b1f2_0    conda-forge
libsqlite                 3.43.0               hb31c410_0    conda-forge
libzlib                   1.2.13               h53f4e23_5    conda-forge
llvm-openmp               16.0.6               h1c12783_0    conda-forge
ncurses                   6.4                  h7ea286d_0    conda-forge
nibabel                   5.0.1              pyhd8ed1ab_0    conda-forge
numpy                     1.26.0          py311hb8f3215_0    conda-forge
openssl                   3.1.3                h53f4e23_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pathlib                   1.0.1                      py_1    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pydicom                   2.4.3              pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
python                    3.11.5          h47c9636_0_cpython    conda-forge
python_abi                3.11                    4_cp311    conda-forge
rdflib                    7.0.0              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge

Environment info

(heudiconv) datalad@26696 ~ % conda info

     active environment : heudiconv
    active env location : /Users/datalad/miniconda-test3/envs/heudiconv
            shell level : 1
       user config file : /Users/datalad/.condarc
 populated config files : /Users/datalad/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.18.final.0
       virtual packages : __osx=12.1=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/datalad/miniconda-test3  (writable)
      conda av data dir : /Users/datalad/miniconda-test3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/datalad/miniconda-test3/pkgs
                          /Users/datalad/.conda/pkgs
       envs directories : /Users/datalad/miniconda-test3/envs
                          /Users/datalad/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.12.0 requests/2.31.0 CPython/3.9.18 Darwin/21.2.0 OSX/12.1
                UID:GID : 502:20
             netrc file : None
           offline mode : False