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CHANGELOG.rst

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Changelog

Version 0.7.0

New Features

  • Support for bluepysnap
  • Analysis can be run for any edge population connecting biophysical neurons
  • Allow to define a list of patterns in the rule override_mtype.

Breaking Changes

  • BluePy no longer supported
  • target was renamed to node_set as per SONATA naming convention
  • atlas-path needs to be passed as a commandline argument if mask is used
  • edge-population needs to be defined as a commandline argument

Improvements

  • Replace Equation.

Version 0.6.3

New Features

  • Add parameter neurite_type in stats._calc_bouton_density to allow the parsing of basal dendrites or apical dendrites to compute bouton density. This parameter is added as an optional input to the estimate_bouton_reduction and estimate_individual_bouton_reduction strategies.

Bug Fixes

  • Fix tests with pytest 8.
  • Add tests with python 3.11 and 3.12.

Version 0.6.2

Bug Fixes

  • In s2f-recipe-merge, add an initial delay after submitting Slurm jobs to allow sacct to return the correct status of the submitted jobs. [NSETM-1678]
  • The initial delay can be controlled with the env variable SUBMIT_JOBS_INITIAL_SLEEP.
  • The poll frequency can be controlled with the env variable SUBMIT_JOBS_POLL_FREQUENCY.
  • Fix linting.

Improvements

  • Bump versions of submitit and jsonschema.

Version 0.6.1

New Features

  • Allow to specify the parameter slurm_srun_args to be able to execute srun --mpi=none and avoid the MPI error MPT ERROR: PMI2_Init when using spack modules.
  • Define a default value for the executor parameters.
  • Update the documentation.

Version 0.6.0

New Features

  • Update the names used in the recipe to use the new format. [NSETM-1451]
  • Allow to specify the selection attributes in the new strategy add_constraints. [NSETM-1450]
  • Add s2f-recipe-merge to run multiple s2f-recipe commands split by region and merge the results. [NSETM-1450]
  • Drop support for python 3.6 and 3.7.
  • Update the documentation.

Version 0.5.1

Improvements

  • Check for duplicate rows in .tsv files (bouton density data and nsyn). [NSETM-1512]

Bug Fixes

  • Fix section ID numbering in the function that calculates the bouton density, needed for compatibility with BluePy 2.3.0. [NSETM-1477]
  • Sum the length of all the axons to calculate the bouton density, in the unlikely case of neurons with multiple axons.

Version 0.5.0

New Features

  • Add parameter n_jobs in stats.sample_bouton_density for parallel execution.

Improvements

  • Parallelize strategy estimate_bouton_reduction in s2f-recipe. [NSETM-1435]

  • Change the parallelization of the strategy estimate_individual_bouton_reduction in s2f-recipe. [NSETM-1435]

    Now the values for each pathway are computed sequentially, but the computation of the value for a single pathway is parallelized.

    The gids are split in chunks to reduce the number of tasks submitted to the subprocesses, and it's possible to specify the minimum number of gids to be processed in a single job setting the env variable MIN_GIDS_PER_JOB (default 1).

Version 0.4.1

New Features

  • Add support for analysis of bouton density and synapse counts in projections.

Bug Fixes

  • Change the old hidden variable from bluepy _PRE_SEGMENT_ID to the new one Synapse.PRE_SEGMENT_ID

Version 0.4.0

Improvements

  • Support and require Bluepy >= 2.0.

Version 0.3.4

Improvements

  • Ensure that only one instance of s2-recipe or connectome-stats is running. [NSETM-1322]

Version 0.3.3

New Features

  • Add support for p_A and pMu_A parameters. [NSETM-1096]

Bug Fixes

  • If formula result for estimate_syns_con is NaN, it's now considered as 1.0. [NSETM-1137]

Removed Features

  • Drop support for Python 2.7.

Improvements

  • Add --jobs option to parallelize tasks. [NSETM-1102]