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@bgmeulem bgmeulem released this 20 Feb 10:44
· 1210 commits to master since this release
v0.4.0-beta
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Prerelease 0.4.0-beta

Most important features to look out for in this release: MacOS support, 100% documentation coverage

Warning

MOEA_EH will be removed in a future version in favor of the Python translation of Hay
Databases will be fully self-contained in a future version, rather than simlinking to parameter files.

Changelog

Installer:

  • use pixi installation by default
  • add MacOS installation. Note that this usess a different version of numpy and NEURON, and introduces some roundoff errors compared to the linux version.
  • barrel cortex model can now be downloaded from harvard dataverse, and doesnt need to be hosted on github anymore (058ea1b)
  • download anaconda with wget without checking for a certificate (it expired) (058ea1b)
  • No more semicolons after commands in installer, otherwise errors are hard to catch (058ea1b)
  • add cmasher

biophysics

  • evaluation can now be done with a full python translation of Hay 2011, including the step currents (d994f73)
  • hay specification values (empirical mean and std) are moved to a json config file

Documentation:

  • 100% Documentation coverage

Improve visualize

  • CMV with joinstyle argument to avoid jagged lines
  • CMV: Allow overwriting frames to re-create animations
  • CMV: allow visualizing non-simulated cell objects and export to vtk
  • VTK: Added converter for Amira lattice files (structured grid) to VTK, allowing to visualize PST density files.

data_base

  • use pandas_to_parquet dumper for the parameterfiles key in init_simrun_general (only for isf_data_base, not for model_data_base) (9edb139)
  • move dbopen to the parent package data_base to remove dependency on specific data base version
  • fix assimilate_remote_register after data_base rename

Bugfixes and improvements

  • moved cluster configuration to cluster_control repo instead of ISF
  • Synapse IDs are maintained in rerun_mdb (52a0c21)
  • Update compatibility: now does not import modules, but uses modulespec to register them
  • no more internal Interface imports
  • rename sim_trail to sim_trial
  • lazy evaluate the locking config (53606b4) to show logger output only when actually needed
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