Nelpy developer notes

Best practice is to work in a Python virtual environment, and especially when doing development. However, for the lazy (or stubborn, like me) I sometimes prefer to do things a little different in the following hacky way:

Make a symlink to your code from within the Python site-packages directory:

sudo ln -s /path/to/code/directory/ /path/to/python/site-packages/nelpydev

Note that the /path/to/code/directory/ should point to the actual package directory, and not the top level dir containing README.md, setup.py, and so on.

Then, from within Python, we can always do

>>> import nelpydev as neld
>>> import nelpydev.plotting as npld

to access our bleeding-edge development code system-wide.

This also facilitates having a more stable (release) version of nelpy installed alongside the development version.

For example, nelpy (the latest release version) can be installed either by calling pip install nelpy, or by cloning the git repository and running python setup.py install from within the nelpy directory.

Then we can import nelpy and nelpydev alongside each other, using (by convention) the following imports:

>>> import nelpy as nel
>>> import nelpy.plotting as npl
>>> import nelpydev as neld
>>> import nelpydev.plotting as npld

Submitting a release to PyPi

There are some excellent guides out there; check out

http://sherifsoliman.com/2016/09/30/Python-package-with-GitHub-PyPI/#convert-readmemd-to-readmerst

http://peterdowns.com/posts/first-time-with-pypi.html

https://gist.github.com/audreyr/5990987

https://github.com/tiimgreen/github-cheat-sheet/blob/master/README.md#gists

and on git flow: http://danielkummer.github.io/git-flow-cheatsheet/index.html

and so I'll keep this part short and uninformative, except to remind myself to

git push --tags

and then

python setup.py sdist upload -r pypitest
pip install -i https://testpypi.python.org/pypi nelpy

followed by testing nelpy in the REPL, and then

python setup.py sdist upload -r pypi
pip install nelpy

and testing nelpy in the REPL again.

Also, be sure to thoroughly check out https://python-packaging.readthedocs.io/en/latest/

Nelpy package organization (preliminary)

nelpy/                          Top-level package
    __init__.py                 Initialize the nelpy package
    version.py
    utils.py
    filtering.py
    decoding.py
    ...

    core/                       Core nelpy objects as a subpackage
        __init__.py
        AnalogSignalArray.py
        EpochArray.py
        SpikeTrain.py
        Trajectory.py
        ...
    io/                         Subpackage for loading external data
        __init__.py
        hc3.py
        neuralynx.py
        trodes.py
        matlab.py
        ...
    plotting/                   Subpackage for data visualization
        __init__.py
        core.py
        scalebar.py
        aiffread.py
        utils.py
        ...
    dbs/                        Subpackage for deep brain stimulation
        __init__.py
        ...
    imaging/                    Subpackage for imaging and miniscope
        __init__.py
        ...
    hmm/                        Subpackage for hidden Markov models
        __init__.py
        ...
    neuropipes/                 Subpackage for pipelines
        __init__.py
        ...

Pruning release tags

After pruning / cleaning remote releases, run

git tag -l | xargs git tag -d
git fetch --tags

to get local tags to match those of remote.

See here.

Some useful resx

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ class DivisorTooSmallError(StandardError): def init(self, arg): self.args = arg

def divide(a, b): if b < 1: raise DivisorTooSmallError return a / b

try: divide(10, 0) except DivisorTooSmallError: print("Unable to divide these numbers!") ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++