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## remove_git-annex_history.md

      
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              November 4, 2021 11:26
            
              
                Remove git-annex history locally and remotely
              
          
    How to remove the history from a git-annex repository.

Here we are reducing the commit log of git and git-annex branches to a single commit.
The following lines assume the repository has only a single remote 'origin', on which the history of the commits will also be reduced to a single commit.
Note: Don't change the history of publicly shared repositories as this will lead to in inconsistent histories between different local copies of the repository.
Resetting local branches to a single commit

Squashing the master branch
git reset $(git commit-tree HEAD^{tree} -m "")

  
## create_conda_env_w_gin-cli.md

      
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                / create_conda_env_w_gin-cli.md
            
            
              Created
              December 22, 2020 12:04
            
              
                create conda environment with gin-cli and git-annex
              
          
    Setting a conda environment for gin including git-annex

To set up a recent version of the gin client together with a recent version of git-annex one can set up a conda environment that contains both.
For this you need to

create the environment with git-annex

ginenv=<my-environment-name>
conda create -n "$ginenv" -c conda-forge git-annex
conda activate $ginenv


## Create PyPi release
Check tests and issues
Check docu is running
Update version number + commit
Create tag locally `git tag 1.x.x`
Push tag to remote `git push origin --tags`
Create dist `python setup.py sdist`
Test `dist/<package><version>` is pip installable
Check compatiblity with PyPi `twine check dist/<package><version>.tar.gz`
Test package on PyPiTest `twine upload --repository pypitest dist/<package><version>.tar.gz`
Test installability from PyPiTest `pip install -i https://test.pypi.org/simple/ <package> --pre --extra-index-url https://pypi.org/simple`

## spikesorters.md

      
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              March 23, 2023 20:57
            
          
    This is an (incomplete) list of spike sorting tools available for (extraction and) sorting of spiking data from electrophysiologal experiments.


Software
Reference
Method
Last Release
Documentation
Language
On/Offline
Commercial/Free
Operating System
GUI


SpikeOMatic
http://www.biomedicale.parisdescartes.fr/SpikeOMatic
Gaussian Mixture Model, Dynamic Hidden Markov Model
2010
minimal
R/C (?)
offline
free
linux / windowns
minimal


Klusta
http://klusta.readthedocs.io/en/latest
Automatic sorting ?
2016
yes
Python / Cython
offline
Free
-
yes


Phy
http://phy.readthedocs.io/en/latest/
>100.000 recording sites
2018
In progress
Python
offline
Free
-
yes


Wave_Clus
http://www2.le.ac.uk/departments/engineering/research/bioengineering/neuroengineering-lab/spike-sorting
Unsupervised, Wavelet and superparam. clustering
2009
yes
Matlab
offline
Free
-
yes


Plexon Offl
	Check tests and issues
	Check docu is running
	Update version number + commit
	Create tag locally `git tag 1.x.x`
	Push tag to remote `git push origin --tags`
	Create dist `python setup.py sdist`
	Test `dist/<package><version>` is pip installable
	Check compatiblity with PyPi `twine check dist/<package><version>.tar.gz`
	Test package on PyPiTest `twine upload --repository pypitest dist/<package><version>.tar.gz`
	Test installability from PyPiTest `pip install -i https://test.pypi.org/simple/ <package> --pre --extra-index-url https://pypi.org/simple`
Software	Reference	Method	Last Release	Documentation	Language	On/Offline	Commercial/Free	Operating System	GUI
SpikeOMatic	http://www.biomedicale.parisdescartes.fr/SpikeOMatic	Gaussian Mixture Model, Dynamic Hidden Markov Model	2010	minimal	R/C (?)	offline	free	linux / windowns	minimal
Klusta	http://klusta.readthedocs.io/en/latest	Automatic sorting ?	2016	yes	Python / Cython	offline	Free	-	yes
Phy	http://phy.readthedocs.io/en/latest/	>100.000 recording sites	2018	In progress	Python	offline	Free	-	yes
Wave_Clus	http://www2.le.ac.uk/departments/engineering/research/bioengineering/neuroengineering-lab/spike-sorting	Unsupervised, Wavelet and superparam. clustering	2009	yes	Matlab	offline	Free	-	yes
Plexon Offl