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CHANGELOG.rst

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Changelog

Version 0.13.4

Bug Fixes

  • In soma and compartment reports, add trial number in the extracted dataframe, as in the spikes report.
  • In soma and compartment reports, make the exported time relative to the offset, as in the spikes report.

Version 0.13.3

Bug Fixes

  • Create .zenodo.json as a workaround to publish the release on Zenodo.

Version 0.13.2

  • Technical release.

Version 0.13.1

  • Technical release.

Version 0.13.0

Improvements

  • When loading the cache, do not fail if the original simulation campaign and related files are missing [NSETM-2336].

Version 0.12.1

Bug Fixes

  • Fix functional tests.

Version 0.12.0

Breaking changes

  • Ensure that some methods and functions are called with named parameters. In particular, the following public methods require named parameters:
    • blueetl.analysis.run_from_file()
    • blueetl.extract.report.ReportExtractor.from_simulations()
    • blueetl.repository.Repository.__init__()
    • blueetl.repository.FilteredRepository.__init__()

Version 0.11.4

Bug Fixes

  • Fix tests with libsonata 0.1.28.
  • Skip simulations with empty path in the simulation campaign configuration (fix regression in blueetl 0.8.0).

Version 0.11.3

Bug Fixes

  • Update expected results in functional tests, because the output of statistics.Complexity changed in elephant >= 0.13.0.
  • Fix warning when building docs, and include blueetl.analysis only.

Version 0.11.2

Bug Fixes

  • Fix version number in the analysis config created by blueetl convert-spikes.

Version 0.11.1

Bug Fixes

  • Revert raising an error if the env variable SHMDIR isn't set. Log a more detailed warning instead.

Version 0.11.0

Improvements

  • Allow to access the cache config and the output path of individual analyses with analysis_config.cache and analysis_config.output, as a shortcut to analysis_config.cache.path.
  • Raise an error if the env variable SHMDIR isn't set, instead of logging a warning.

Version 0.10.1

Bug Fixes

  • Fix link to the example configuration in the documentation.

Version 0.10.0

New Features

  • Add multi_index option to the features configuration, to decide whether reset_index() should be applied to the features DataFrames. Note: the features cache will be rebuilt, although the resulting DataFrames are unchanged (because the default value of the new option is True).

Version 0.9.1

Improvements

  • Improve performance of report extraction and features calculation by writing partial DataFrames to the shared memory (or temp directory, if shared memory is not available). Both the used memory and the execution time should be lower than before, when processing large DataFrames.
  • Use zstd compression instead of snappy when writing parquet files.
  • When repo is pickled, extract the DataFrames only if they aren't already stored in the cache.
  • Remove fastparquet extra dependency.

Version 0.9.0

New Features

  • Add cache.readonly, to be able to use an existing cache without exclusive locking [NSETM-2310].
  • Add cache.store_type, to change the file format (experimental).
  • Add cache.skip_features, to skip writing the features DataFrames [NSETM-2312].

Deprecations

  • Deprecate output, use cache.path instead.
  • Deprecate clear_cache, use cache.clear instead.

Version 0.8.3

Bug Fixes

  • Ensure that invalid cache entries are always deleted from checksums.cached.yaml.

Improvements

  • Filter features only when apply_filter is called to save some time, but ensure that repo and features are filtered when they are loaded from the cache using a more restrictive filter.
  • Improve logging in blueetl.utils.timed().
  • Improve tests coverage.
  • Split migration documentation.
  • Add --sort/--no-sort option to blueetl migrate-config to sort the root keys of the converted configuration.

Version 0.8.2

Bug Fixes

  • If node_id in the neuron_classes configuration is set to an empty list, it's now considered as an empty selection instead of selecting all the neurons.

Version 0.8.1

Improvements

  • Add configuration examples 11 and 12 to the documentation.
  • Improve tests coverage.

Bug Fixes

  • Fix method Repository.missing_simulations().

Version 0.8.0

New Features

  • Support custom node_sets_file in extraction, neuron_classes and trial_steps [NSETM-2226]

Version 0.7.1

Bug Fixes

  • Fix expected data in functional tests.

Version 0.7.0

New Features

  • Allow to specify trial_steps_label to calculate the dynamic offset of trial steps [NSETM-2281]

Version 0.6.0

New Features

  • Allow to specify trial_steps_list instead of trial_steps_value and n_trials [NSETM-2280]

Bug Fixes

  • Temporarily disable trial_steps_label [NSETM-2281]

Improvements

  • Add tests for Python 3.12.
  • Remove brion dependency in tests.

Version 0.5.0

New Features

  • Add CLI to convert and import inferred spikes in CSV format.

Version 0.4.4

Improvements

  • Support relative paths in the simulation campaign config.
  • Add a simple simulation campaign using a subsampled circuit, to run the Jupyter notebooks in the documentation.

Version 0.4.3

Improvements

  • Update DOI.

Version 0.4.2

Improvements

  • Fix docs build in rtd.
  • Update badges.
  • Conditionally skip tests requiring bluepy.

Version 0.4.1

  • First public release.

Version 0.4.0

New Features

  • Extend the API of SimulationCampaign (previously SimulationsConfig) to open simulation campaigns.

Breaking changes

  • Rename SimulationsConfig to SimulationCampaign.

Version 0.3.0

New Features

  • Support SONATA simulation campaigns, circuits, and reports using bluepysnap.

Breaking changes

  • Simulation campaigns, circuits, and reports using BlueConfig format aren't supported anymore.
  • The analysis configuration accepts population and node_set, instead of target.
  • In the neuron_classes definition, the query parameters must be moved to query, $limit must be renamed to limit, $gids to node_id.
  • The function blueetl.core.utils.safe_concat has been renamed to smart_concat.
  • The module blueetl.core has been moved to a separate package, blueetl-core.

Improvements

  • The function blueetl.core.utils.smart_concat uses copy=False by default, and accepts dictionaries as pd.concat does.
  • All the internal calls to pd.concat are redirected to smart_concat.

Version 0.2.3

Improvements

  • Improve performance of etl.add_conditions.

Version 0.2.2

Bug Fixes

  • Ensure that the package can be installed and used without optional dependencies.

Version 0.2.1

Improvements

  • Support Pandas 2.0. Changed in Pandas 2.0.0: Index can hold all numpy numeric dtypes (except float16). Previously only int64/uint64/float64 dtypes were accepted.

Version 0.2.0

New Features

  • Add MultiAnalyzer class to support multiple reports [NSETM-2015]
  • Allow to resolve windows by reference [NSETM-2015]
  • Support combination of parameters in features configuration [NSETM-2091]
  • Allow to access the concatenation of features dataframes using the basename [NSETM-2149]
  • Add analysis configuration model and validation [NSETM-2099]
  • Add blueetl CLI [NSETM-2115]
  • Add blueetl.analysis.run_from_file [NSETM-2151]
  • Improve performance of report extraction [NSETM-2116]
  • Improve performance of features calculation [NSETM-2116]
  • Process features in group when possible.
  • Add _cached and _filtered private attributes to BaseExtractor.
  • Add clear_cache parameter to run_from_file and to the configuration schema [NSETM-2150]
  • Allow etl.q to support regular expressions [NSETM-2170]
  • Allow etl.q to accept a list of query dicts [NSETM-2162]
  • Allow neuron_classes configuration to be defined as a list of query dicts [NSETM-2163]

Breaking changes

  • The previous analysis configuration format has been replaced by the version 2 to support multiple reports.
  • After applying a filter, the indices of the repo DataFrames are reset to remove any gap.
  • The function call_by_simulation has been refactored and moved into blueetl.parallel.
  • In neuron_classes configuration, gid has been renamed to $gids.
  • Require Python >= 3.9.

Version 0.1.2

Improvements

  • Raise an exception if there are multiple features dataframes with the same name.
  • Enforce the correct dtype in the features dataframes.
  • Add dtypes parameter to ETLBaseAccessor.add_conditions.
  • Add dtypes and astype methods to ETLIndexAccessor.
  • Support filtering by windows or neuron classes for each features configuration [NSETM-2085]

Bug Fixes

  • Deepcopy the params dict passed to the user func.

Version 0.1.1

New Features

  • Ignore simulations for which BlueConfig no longer exists [NSETM-1967]
  • Add optional in-memory filter [NSETM-1965]
  • Support subtargets per neuron class [NSETM-2004]

Improvements

  • Add env variable BLUEETL_SUBPROCESS_LOGGING_LEVEL to set a logging level in subprocesses.
  • Improve log of execution times.
  • Improve performances of etl.q when only a single condition is specified.
  • Lock the cache used by the Analyzer instance [NSETM-1971]
  • Make the function call_by_simulation more flexible.

Bug Fixes

Version 0.1.0

First release including:

  • Core Transformations
  • Simulation Campaign Configuration
  • Spike Analysis (Repository Extraction and Features Collection)