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Optimization modules #71

Merged
merged 46 commits into from
Apr 13, 2024
Merged

Optimization modules #71

merged 46 commits into from
Apr 13, 2024

Commits on Nov 1, 2023

  1. initial import of optimization modules

    @iraikov
    iraikov committed Nov 1, 2023
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Commits on Nov 3, 2023

  1. update to poetry lock file

    @iraikov
    iraikov committed Nov 3, 2023
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  2. factoring out click interface for optimize_network

    @iraikov
    iraikov committed Nov 3, 2023
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Commits on Nov 7, 2023

  1. added missing imports from optimization in network clamp

    @iraikov
    iraikov committed Nov 7, 2023
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  2. formatting fix

    @iraikov
    iraikov committed Nov 7, 2023
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Commits on Nov 15, 2023

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. various bug fixes in infrastructure scripts

    @iraikov
    iraikov committed Nov 16, 2023
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  2. opto stim: make expProb parameter optional and set default value to 1

    @iraikov
    iraikov committed Nov 16, 2023
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Commits on Jan 23, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Jan 23, 2024
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  2. Merge branch 'main' into feature/optimization

    @iraikov
    iraikov committed Jan 23, 2024
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  3. Merge branch 'feature/optimization' of https://github.com/GazzolaLab/… 

    …MiV-Simulator into feature/optimization
    @iraikov
    iraikov committed Jan 23, 2024
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Commits on Mar 5, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 5, 2024
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Commits on Mar 6, 2024

  1. Fix always-true network shutdown

    @frthjf
    frthjf committed Mar 6, 2024
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  2. Update poetry lock

    @frthjf
    frthjf committed Mar 6, 2024
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  3. Merge branch 'feature/optimization' of https://github.com/GazzolaLab/… 

    …MiV-Simulator into feature/optimization
    @iraikov
    iraikov committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. multiple fixes to network clamp optimization and synapse parameter up… 

    …date logic
    @iraikov
    iraikov committed Mar 7, 2024
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  2. fixes related to optimize_network

    @iraikov
    iraikov committed Mar 7, 2024
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Commits on Mar 18, 2024

  1. Apply black formatting

    @frthjf
    frthjf committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 19, 2024
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Commits on Mar 21, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 21, 2024
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Commits on Mar 22, 2024

  1. Disable MPI for non-mpi interfaces

    @frthjf
    frthjf committed Mar 22, 2024
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  2. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 22, 2024
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Commits on Mar 23, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 23, 2024
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Commits on Mar 24, 2024

  1. added missing call to subworlds in network setup; 

    some initial support for reduced cell models with layer-based morphology
    @iraikov
    iraikov committed Mar 24, 2024
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  2. Merge branch 'feature/optimization' of https://github.com/GazzolaLab/… 

    …MiV-Simulator into feature/optimization
    @iraikov
    iraikov committed Mar 24, 2024
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  3. Apply codestyle

    @frthjf
    frthjf committed Mar 24, 2024
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Commits on Mar 25, 2024

  1. Remove target_trj_rate_map_dict residuals

    @frthjf
    frthjf committed Mar 25, 2024
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  2. Add Config.clamp attribute

    @frthjf
    frthjf committed Mar 25, 2024
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  3. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Mar 25, 2024
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  4. further fixes to support for reduced cell models

    @iraikov
    iraikov committed Mar 25, 2024
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Commits on Apr 3, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Apr 3, 2024
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Commits on Apr 4, 2024

  1. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Apr 4, 2024
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  2. Apply style

    @frthjf
    frthjf committed Apr 4, 2024
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  3. bug fixes in check_synapses

    @iraikov
    iraikov committed Apr 4, 2024
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  4. Merge branch 'feature/optimization' of https://github.com/GazzolaLab/… 

    …MiV-Simulator into feature/optimization
    @iraikov
    iraikov committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. bug fixes in reposition_trees

    @iraikov
    iraikov committed Apr 5, 2024
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  2. small refactor of measure_distances to avoid use of bcast_cell_attrib… 

    …utes
    @iraikov
    iraikov committed Apr 5, 2024
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  3. generate_connections: use population dict from Env

    @iraikov
    iraikov committed Apr 5, 2024
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  4. bug fixes in generate_connections

    @iraikov
    iraikov committed Apr 5, 2024
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Commits on Apr 6, 2024

  1. Rollback hardcoded types

    @frthjf
    frthjf committed Apr 6, 2024
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  2. More type checker fixes

    @frthjf
    frthjf committed Apr 6, 2024
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  3. Ignore missing populations in make_h5types

    @frthjf
    frthjf committed Apr 6, 2024
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  4. Merge branch 'main' into feature/optimization

    @frthjf
    frthjf committed Apr 6, 2024
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Commits on Apr 9, 2024

  1. Raise more meaningful error for population defintion mismatch

    @frthjf
    frthjf committed Apr 9, 2024
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Commits on Apr 11, 2024

  1. connection generator: added chunk_size setting to append_graph calls

    @iraikov
    iraikov committed Apr 11, 2024
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  2. Merge branch 'feature/optimization' of https://github.com/GazzolaLab/… 

    …MiV-Simulator into feature/optimization
    @iraikov
    iraikov committed Apr 11, 2024
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