Clean up dependencies, + Update StochKv3 file for NEURON 9 compatibility#14
Open
darshanmandge wants to merge 1 commit into
Open
Clean up dependencies, + Update StochKv3 file for NEURON 9 compatibility#14darshanmandge wants to merge 1 commit into
darshanmandge wants to merge 1 commit into
Conversation
ilkilic
previously approved these changes
Jun 11, 2026
Codecov Report❌ Patch coverage is
🚀 New features to boost your workflow:
|
Comment on lines
+58
to
+61
| "scipy>=1.16.1", | ||
| "neurom>=3.0", | ||
| "morph_tool>=2.8", | ||
| "morphio", |
There was a problem hiding this comment.
Are these needed for optimization?
Restructure pyproject.toml so 'pip install bluepyemodel' gives a fully working local pipeline (extraction, optimisation, validation, export) without requiring any extras. Core dependencies (always installed): - numpy, scipy, bluepyopt, bluepyefe, neurom, efel, neuron, morph_tool, morphio, fasteners, jinja2, h5py, matplotlib, currentscape Optional extras: - [parallel]: ipyparallel (for HPC parallel evaluation) - [luigi]: luigi, luigi-tools (for Luigi workflow orchestration) - [nexus]: nexusforge, entity_management, pyJWT, pandas - [test]: pytest, dictdiffer - [docs]: sphinx, graphviz, etc. - [all]: everything above Removed dead/unused core dependencies: - pyyaml, gitpython, tqdm, configparser (not imported anywhere) - ipyparallel (lazy import, moved to [parallel]) - pandas (only used in nexus access point, moved to [nexus]) Fixed forge_access_point import leak: - emodel_pipeline.py and tasks/config.py no longer import from forge_access_point.py (which requires jwt/nexusforge/entity_management) - DEFAULT_NEXUS_ENDPOINT is now defined locally where needed NEURON 9 mechanism compatibility: - Updated StochKv3.mod with latest version from nbS1 OBI circuit models (BBCOREPOINTER, NRN_VERSION_GTEQ_8_2_0 guards, RANGE for thread safety) - Removed unused StochKv2.mod
darshanmandge
force-pushed
the
refactor/split-dependencies-by-pipeline-step
branch
from
e4e544b to
5c2a09b
Compare
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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.
Restructure pyproject.toml so 'pip install bluepyemodel' gives a fully working local pipeline (extraction, optimisation, validation, export) without requiring any extras.
Core dependencies (always installed):
Optional extras:
Removed dead/unused core dependencies:
Fixed forge_access_point import leak:
NEURON 9 mechanism compatibility: