# Neuro-SIG package re-think

**When orphaning packages, please remember to first remove neuro-sig from them.**

Please scroll to the bottom of the page to see orphaned/dropped packages.

## To keep

### Not pure python/need building

1. COPASI
1. dlib
1. dolfin
1. getdp
1. smoldyn
1. python-pygiftiio (pure Python, but not on PyPi: not been updated in years, but keeping it for the moment as it is low effort)

### Not leaf

1. python-scipy-doctest

### GUI

1. pyplane: @ankursinha
1. python-ephyviewer: @gui1ty
1. python-fsleyes: @ankursinha
1. python-spyking-circus (circus-artefacts, circus-folders, circus-gui-matlab, circus-gui-python, circus-multi, spyking-circus, spyking-circus-launcher, spyking-circus-subtask): @ankursinha
1. shybrid: @music

### Snakemake stack

1. python-irodsclient @music : packaged as a dependency for a future python-snakemake-storage-plugin-irods
1. python-snakemake-executor-plugin-azure-batch
1. python-snakemake-executor-plugin-flux
1. python-snakemake-executor-plugin-kubernetes
1. python-snakemake-executor-plugin-slurm
1. python-snakemake-executor-plugin-tes
1. python-snakemake-storage-plugin-azure
1. python-snakemake-storage-plugin-ftp
1. python-snakemake-storage-plugin-gcs
1. python-snakemake-storage-plugin-webdav
1. python-snakemake-storage-plugin-xrootd
1. python-snakemake-storage-plugin-zenodo

## Leave up to maintiners

### CLI, but easily installable from PyPi

Let primary maintainers decide. If they want to keep them, we request to drop neuro-sig

1. cffconvert: @iztokf
1. pydeps: @lbazan
1. spec2nii: @music : would also be required if we finish packaging bidscoin, https://pagure.io/neuro-sig/NeuroFedora/issue/500

Note: iztokf and lbazan have not been very active with packaging recently

### Libraries with CLI

Leave up to maintainers, remove neuro-sig if required

1. python-SALib (salib) @ankursinha
1. python-bioread (acq2hdf5, acq2mat, acq2txt, acq_info, acq_layout, acq_markers) @music
1. python-git-changelog (git-changelog) @topazus
1. python-gradunwarp (gradient_unwarp: when run from PyPI, gradient_unwarp.py) @ankursinha
1. python-grip (grip) @gui1ty
1. python-mne-bids (mne_bids) @ankursinha
1. python-multiecho (mecombine) @music : would also be required if we finish packaging bidscoin, https://pagure.io/neuro-sig/NeuroFedora/issue/500
1. python-nipype (nipypecli) @ankursinha
1. python-pynetdicom (echoscp, echoscu, findscu, getscu, movescu, qrscp, storescp, storescu) @alciregi
1. python-pynsgr (nsgr_job, nsgr_submit) @ankursinha
1. python-pysb (pysb_export) @zbyszek
1. python-vascpy (vascpy) @gui1ty

#### CLIs potentially difficult to use from PyPi

1. python-glymur (jp2dump, jpeg2jp2, tiff2jp2) @music
1. python-hdfs (hdfscli, hdfscli-avro) @ankursinha
1. python-klusta (klusta) @ankursinha
1. python-moss (check_mni_reg, recon_status, recon_movie, recon_process_stats, ts_movie, warp_qc) @ankursinha This package last released upstream in 2017, and the spec file needs significant attention if we want to keep it in Fedora.
1. python-nixio (nixio) @ankursinha
1. python-pyxdf (pure Python), @music : This only “kind of” offers a CLI: python3-pyxdf-examples includes a couple of tools that can be run with e.g. python3 -m pyxdf.cli.print_metadata, and this usage is documented in the readme. I have included it in this category because these can be run from a virtualenv, but aren’t a good fit for pipx/uvx.

### Misc

1. python-exdir @ankursinha : Jupyter Notebook extension that is installed system-wide

## Potentially can be dropped

But, of course, left up to maintainers to individually decide

### Easily installable from PyPi

1. python-annarchy (C++/Cython), @gui1ty
1. python-autograd (pure Python), @gui1ty
1. python-bioframe (pure Python), @gui1ty
1. python-chaospy (pure Python), @lbazan
1. python-cro (pure Python), @iztokf
1. python-cyipopt (C++/Cython), @music
1. python-dandischema (pure Python), @mithunveluri
1. python-glfw (pure Python + ctypes), @gui1ty
1. python-imbalanced-learn (pure Python), @iztokf
1. python-intern (pure Python), @music ; originally packaged for https://pagure.io/neuro-sig/NeuroFedora/issue/542
1. python-missingno (pure Python), @lbazan
1. python-niaclass (pure Python), @iztokf
1. python-palettable (pure Python), @gui1ty
1. python-plotnine (pure Python), @gui1ty
1. python-probeinterface (pure Python), @music
1. python-pyABF (pure Python), @gui1ty
1. python-pycatch22 (includes C), @music
1. python-pydapsys (pure Python), @gui1ty
1. python-pyopengltk (pure Python with ctypes), @gui1ty
1. python-pysdl2 (pure Python with ctypes), @gui1ty
1. python-pyspike (Cython), @ankursinha
1. python-pytest-lazy-fixture (pure Python), @ankursinha
1. python-resumable-urlretrieve (pure Python), @lbazan
1. python-simframe (pure Python), @iztokf
1. python-sklearn-genetic (pure Python), @iztokf
1. python-sklearn-genetic-opt (pure Python), @gui1ty
1. python-sklearn-nature-inspired-algorithms (pure Python), @iztokf @ankursinha
1. python-steps (C++/Cython), @ankursinha: NOTE, not recently being released on PyPi, so perhaps worth keeping: https://github.com/CNS-OIST/STEPS/releases
1. python-tvb-data (pure Python), @ankursinha
1. python-tvb-gdist (C++/Cython), @ankursinha

## Dropped/intend to drop

Orphaning message: "Dropped as per neuro-sig strategy to not maintain packages that are easily pip installable"

### ankursinha

#### 2025-07-07

1. python-nilearn
2. neuron
3. python-netpyne
4. python-bluepyopt
5. python-lfpy
6. python-neatdend
7. python-neurotune
8. python-pynn

#### 2025-07-08

1. python-mne
2. python-mne-bids

#### 2025-07-16

1. python-pybids
2. python-formulaic
3. iv
4. neurom

#### 2025-07-22

1. python-sciunit
2. python-airspeed
3. python-PyLink (archived upstream)
4. python-elephant
5. python-hdf5storage
6. python-lazy-ops (unmaintained upstream, fails tests)
7. python-lqrt (unmaintained, but passes tests)
8. python-outdated
9. python-pingouin
10. python-pyactivetwo (unmaintained upstream)
11. python-pydotplus (unmaintained upstream)

#### 2025-08-07

1. python-PyLEMS
2. python-ratinabox @music
3. python-pyfim (Cython)
4. python-pylatex
5. python-pyriemann
6. python-pyunicorn (Cython)
1. python-pyxid (pure Python): unmaintained upstream
1. python-read-roi