Open mwatts15 opened 6 years ago
@mwatts15 I've updated https://github.com/openworm/c302/blob/master/c302/OpenWormReader.py to be runnable with:
python c302/OpenWormReader.py
similarly to
python c302/UpdatedSpreadsheetDataReader.py
which reads directly from the latest spreadsheet. This works with the version of PyOpenWorm we use in the Docker installation: https://github.com/openworm/OpenWorm/blob/development/Dockerfile#L105, but not the latest in the dev branch...
There are a couple things to update:
@mwatts15 I've taken out all of those references to the files in the other CElegansNeuroML repo in the latest commit, which doesn't seem to have been merged into your branch: https://github.com/openworm/c302/commit/a80499738067f2a9b0256003cc9c9ddcd44c32f2#diff-4dca74f5e9f27a6180a8aa5606bf514cL25.
Not sure what you mean by "The database has to be explicitly cloned now". Can't this be a step integrated in an updated setup.py for PyOpenWorm?
@mwatts15 I've taken out all of those references to the files in the other CElegansNeuroML repo in the latest commit, which doesn't seem to have been merged into your branch: a804997#diff-4dca74f5e9f27a6180a8aa5606bf514cL25.
Thanks. Why not use the logging module in the initializer? When I use OpenWormReader outside of that script, wouldn't I generally want the option to quiet its output?
Not sure what you mean by "The database has to be explicitly cloned now". Can't this be a step integrated in an updated setup.py for PyOpenWorm?
You run a command pow clone <github-repo>
which creates a .pow
directory under your current working directory. Not doing that as part of the PyOpenWorm setup.py
script is a design decision that we can chat about, but I don't think comment thread is the place.
I've just used the simpler print_() statement to make it easier to follow logs across c302/pyNeuroML/libNeuroML etc. e.g.
...
c302 >>> Generating plots for: Membrane potentials of 14 neuron(s) (Oscillator C0)
pyNeuroML >>> Generating plot: Membrane potentials of 14 neuron(s) (Oscillator C0)
c302 >>> Plotting neuron activities ([Ca2+])
...
I know they could all be updated to use logger, but hope you can live with it for now...
Re the database, will try that. I assume pow is an executable created when PyOpenWorm is installed? Any issue with this overwriting a system command pow for calculating powers?
Yes, pow
is installed with PyOpenWorm. I don't know of any GNU or Unix utility called pow
, but probably users can resolve any namespace conflicts themselves.
As a first approximation, can just hard-code
<http://openworm.org/entities/bio#worm0>
as the context to query against (it's sort of the 'top-level' context produced by insert_worm.py into the OpenWormData repo). Will be modified in owupd1 to its final form.