NeuroML 2.2 release #152
Merged
NeuroML 2.2 release #152
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Follows the same logic as -neuron, but also includes an additional -np flag for MPI runs that NetPyNE supports. Fixes #80
get_window_title and set_window_title have been deprecated in matplotlib version 3.4 and will be dropped in future releases. Reference: https://matplotlib.org/stable/api/prev_api_changes/api_changes_3.4.0.html#backend-deprecations Fixes #95
feat: update matplotlib usage to remove deprecated methods
enh(pynml): add -netpyne option
feat: add function to validate NeuroML2 LEMS file
exit() is a helper for the interactive shell, sys.exit() should be used in programs
Enable documentation on RTD
Make it ignore packages where type information is not available
Also update links to schema docs
The complete libNeuroML API is based on lxml.etree now, and this unfortunately cannot be pickled. So we cannot pass the NeuroMLDocument to the run_simulation function when using pp for parallel runs. Instead, we pass None and let the run_simulation method read in the template NeuroML file and create the NeuroMLDocument there as required.
- Also, printing stderr output from jnml command
* development: ci: remove `bin` from NEURON_HOME ci: export NEURON_HOME ci: add NEURON to requirements ci: also run tuning example feat: print necessary messages in the tuner chore(NeuroMLTuner): document return values for optimisation funcs
pip install modelspec version for dev
|
Something is pulling in It doesn't seem to be any of our tools---we have |
Tweaks to tuner code
Nicer to just pass a string instead of a StringIO object, and this also allows us to close the StringIO object also.
|
@sanjayankur31 It's probably because this test on master uses the master branch of libneuroml pylems, etc. which haven't been updated in a while, which probably have previous typing/py39 issues. Should be resolved when those repos have dev merged to master (next week...) |
Specifying universal_newlines so "realtime output" works correctly
- non-default arguments cannot follow default arguments
Feat/document 2stage opt
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.