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MPI iclamp fix #332

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MPI iclamp fix #332

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Commits on Feb 7, 2023

  1. Initial draft auditory filternet

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Commits on Feb 10, 2023

  1. Trying different temporal envelope

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Commits on Feb 11, 2023

  1. Work on spectral modulation filters

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Commits on Feb 26, 2023

  1. Auditory filternet refinement

    @xpliu16
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Commits on Mar 2, 2023

  1. Padding and other adjustments to auditory filters

    @xpliu16
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  2. Merge pull request AllenInstitute#288 from xpliu16/aud_filternet 

    Aud filternet
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Commits on Mar 14, 2023

  1. Handling delay, better documentation of filters, passing of threshold

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  2. Merge pull request AllenInstitute#290 from xpliu16/aud_filternet 

    Handling delay, better documentation of filters, passing of threshold
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Commits on Mar 29, 2023

  1. Miscellaneous updates

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  2. Merge pull request AllenInstitute#295 from xpliu16/aud_filternet 

    Miscellaneous updates
    @xpliu16
    xpliu16 authored Mar 29, 2023
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Commits on Jun 2, 2023

  1. Aud filternet b_t now variable

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  2. Merge branch 'develop' into aud_filternet

    @xpliu16
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  3. Merge pull request AllenInstitute#304 from xpliu16/aud_filternet 

    Aud filternet
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Commits on Jun 28, 2023

  1. Fixed psi and direction reading bug

    @xpliu16
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  2. Merge branch 'develop' of https://github.com/xpliu16/bmtk into aud_fi… 

    …lternet
    @xpliu16
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  3. Merge pull request AllenInstitute#310 from xpliu16/aud_filternet 

    Aud filternet
    @xpliu16
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  4. Fixed bug on "delay"

    @xpliu16
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  5. Merge pull request AllenInstitute#311 from xpliu16/aud_filternet 

    Fixed bug on "delay"
    @xpliu16
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Commits on Sep 19, 2023

  1. update comsol module

    @nilsvanrompaey
    nilsvanrompaey committed Sep 19, 2023
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  2. update bio_comsol example

    @nilsvanrompaey
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  3. add comsol .mph file (without saved results)

    @nilsvanrompaey
    nilsvanrompaey committed Sep 19, 2023
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  4. small changes

    @nilsvanrompaey
    nilsvanrompaey committed Sep 19, 2023
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  5. add dir structure and probe image

    @nilsvanrompaey
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Commits on Sep 28, 2023

  1. fix small inconsistency

    @nilsvanrompaey
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Commits on Sep 29, 2023

  1. fix small errors

    @nilsvanrompaey
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Commits on Oct 4, 2023

  1. mpi iclamp fix

    @tjbanks
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Commits on Oct 5, 2023

  1. Adding example with instructions for using NSG with BioNet

    @kaeldai
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  2. Merge pull request AllenInstitute#333 from kaeldai/examples/nsg 

    Adding example with instructions for using NSG with BioNet
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Commits on Nov 1, 2023

  1. Enabling numba speedup on non-separable FilterNet

    @shixnya
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  2. Revert "Enabling numba speedup on non-separable FilterNet" 

    This reverts commit 1fe1d04.
    @shixnya
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  3. Making non-separable FilterNet faster (AllenInstitute#335) 

    * Enabling numba speedup on non-separable FilterNet

* minor change to reduce characters per line

* Adding numba as a requirement

* making MPI optional.
    @shixnya
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Commits on Nov 8, 2023

  1. Fixing FilterNet bug (ON/OFF offset, issue AllenInstitute#339) (Allen… 

    …Institute#340)

Before the fix, spatial filters for ON and OFF receptive fields were pointing to the same object. Resolved by creating filter objects separately.
    @shixnya
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Commits on Nov 14, 2023

  1. Made use of numba optional to prevent conflicts with NEST simulator

    @kaeldai
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  2. adding some minor alterations to bionet to run more robustly

    @kaeldai
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  3. Merge pull request AllenInstitute#341 from kaeldai/fix/numba_tests_nest 

    * Made use of numba optional to prevent conflicts with NEST simulator. 
* Fixed conftest imports which was having some issues when AllenSDK is also installed (AllenSDK install conftest as a module).
* Issue with bionet unit tests still running despite not having vecstim module compiled (test_virtualcell)
    @kaeldai
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Commits on Dec 27, 2023

  1. adding PointNet module to insert NEST synapse weight_recorder

    @kaeldai
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  2. Adding PointNet example with plastic synapses (and recordings)

    @kaeldai
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  3. Adding weight_recorder module documentation

    @kaeldai
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  4. Merge pull request AllenInstitute#345 from kaeldai/feature/nest_weigh… 

    …t_recorder

Feature/nest weight recorder
    @kaeldai
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Commits on Feb 21, 2024

  1. add init files to fix pytest

    @kaeldai
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  2. Merge pull request AllenInstitute#347 from kaeldai/fix/pytest_issues 

    add init files to fix pytest
    @kaeldai
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  3. Making physical spacing optional for drifting gratings + faster separ… 

    …able FilterNet (AllenInstitute#346)


* Making physical_spacing of moving gratings optional + faster separable FilterNet by ignoring zeros in the kernel.

* Changing the variable name + adding documentation
'physical_spacing' to 'degrees_per_pixel'.
    @shixnya
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Commits on Feb 23, 2024

  1. Including forgotten docstring (AllenInstitute#348) 

    Just adding one docstring for the new parameter
    @shixnya
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Commits on Feb 26, 2024

  1. Adding example for running all-active cell simulation with full axon

    @kaeldai
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  2. Merge pull request AllenInstitute#349 from kaeldai/example/bio_all_ac… 

    …tive_sweep

Adding example for running all-active cell simulation with full axon
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Commits on Feb 27, 2024

  1. fixing issue with writing to nwb with mpi and adding some extra docum… 

    …entation
    @kaeldai
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  2. Merge pull request AllenInstitute#350 from kaeldai/documentation/nwb_… 

    …update

fixing issue with writing to nwb with mpi and adding some extra docum…
    @kaeldai
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Commits on Mar 13, 2024

  1. Use inspect module in add_movie for GratingMovie 

    Previously, if 'phase' was added as a parameter to add_movie it would
not be passed to GratingMovie.create_movie and would be ignored.
By using the inspect module, we can ensure that any arguments to
GratingMovie.__init__ and GratingMovie.create_movie are automatically
supported by FilterSimulator.add_movie.

We also created a test case, the setup of which can be reused to test
a variety of functionality of FilterSimulator.
    @HDictus
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  2. resolving merge conflicts

    @kaeldai
    kaeldai committed Mar 13, 2024
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  3. fixing issue with spatial_filter

    @kaeldai
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Commits on Mar 18, 2024

  1. Merge pull request AllenInstitute#352 from HDictus/movie-phase 

    Use inspect.signature in add_movie for GratingMovie
    @kaeldai
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Commits on Mar 20, 2024

  1. fixing one last issue

    @kaeldai
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  2. fixing merge

    @kaeldai
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  3. merge was not fully saved

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  4. fixing import issue

    @kaeldai
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  5. Merge pull request AllenInstitute#351 from AllenInstitute/aud_filternet 

    Aud filternet
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Commits on Mar 21, 2024

  1. Fixing issue if model_template column is missing

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  2. Merge pull request AllenInstitute#353 from AllenInstitute/aud_filternet 

    Fixing issue if model_template column is missing
    @kaeldai
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  3. Including forgotten docstring (AllenInstitute#354)

    @shixnya
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Commits on Mar 29, 2024

  1. Auditory filternet tutorial draft

    @xpliu16
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  2. Merge pull request AllenInstitute#355 from xpliu16/develop 

    Auditory filternet tutorial draft
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  3. Auditory filternet tutorial update

    @xpliu16
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  4. Merge branch 'AllenInstitute:develop' into develop

    @xpliu16
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  5. Merge pull request AllenInstitute#356 from xpliu16/develop 

    Auditory filternet tutorial update
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Commits on Apr 1, 2024

  1. Merge pull request AllenInstitute#330 from nilsvanrompaey/develop 

    Add functionality to BioNet's comsol module and update bio_comsol example
    @kaeldai
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  2. minor changes to bio_comsol example

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  3. Merge pull request AllenInstitute#357 from kaeldai/updates/comsol_exa… 

    …mple

minor changes to bio_comsol example
    @kaeldai
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  4. updating version number

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  5. Merge pull request AllenInstitute#358 from kaeldai/feature/ver_bump_1… 

    ….1.0

updating version number
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Commits on Apr 16, 2024

  1. updated aud filternet

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  2. Merge branch 'develop' of https://github.com/xpliu16/bmtk into develop

    @xpliu16
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  3. Merge pull request AllenInstitute#359 from xpliu16/develop 

    Aud_filternet update
    @xpliu16
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Commits on Apr 20, 2024

  1. Fix error that random seed is not set when using SpikeGenerator(seed=0)

    @chenziao
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Commits on Apr 23, 2024

  1. Merge pull request AllenInstitute#360 from chenziao/develop 

    Fix error that random seed is not set when using SpikeGenerator(seed=0)
    @kaeldai
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  2. fixing minor bug with spike-trains unit test

    @kaeldai
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  3. Merge pull request AllenInstitute#361 from kaeldai/fix/test_psg_variable 

    fixing minor bug with spike-trains unit test
    @kaeldai
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Commits on Apr 24, 2024

  1. adding tutorial assests

    @kaeldai
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Commits on Apr 30, 2024

  1. Making changes to automatically support ModelDB Hay model HOC Template

    @kaeldai
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  2. Fixing filter_movie/ example

    @kaeldai
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  3. Merge pull request AllenInstitute#364 from kaeldai/fix/lgn_movies_exa… 

    …mples

Fixing filter_movie/ example
    @kaeldai
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Commits on May 1, 2024

  1. small change to morphology to fix how sections are parsed

    @kaeldai
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Commits on May 2, 2024

  1. Found Hoc models that would fail calls to hobj.soma[0] since it cell … 

    …had only one soma section and hobj.soma was not an iteratble list. Added Cell.soma property that can handle this case
    @kaeldai
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Commits on May 3, 2024

  1. adding ability for pointnet to use cell_model decorator when loading … 

    …cells in batch
    @kaeldai
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Commits on May 4, 2024

  1. making updates to spontaneous syns inputs

    @kaeldai
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  2. adding ability in bionet and pointnet to handle custom spikes-train f… 

    …unctions inputs
    @kaeldai
    kaeldai committed May 4, 2024
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Commits on May 5, 2024

  1. bionet iclamps can now support ranged section selection

    @kaeldai
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  2. Adding ctdb download utils

    @kaeldai
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Commits on May 7, 2024

  1. Updating ECP Plotting function

    @kaeldai
    kaeldai committed May 7, 2024
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  2. Adding fix for when running current clamps across multiple cores

    @kaeldai
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  3. Merge pull request AllenInstitute#366 from kaeldai/fix/multicore_iclamp 

    Adding fix for when running current clamps across multiple cores
    @kaeldai
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Commits on May 8, 2024

  1. Merge pull request AllenInstitute#362 from kaeldai/fix/aud_filternet_tut 

    adding tutorial assests
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Commits on May 12, 2024

  1. Fixing compartment reports to include magic statement when running mu… 

    …lti-cores
    @kaeldai
    kaeldai committed May 12, 2024
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  2. Merge pull request AllenInstitute#367 from kaeldai/fix/add_membrane_m… 

    …agic

Fixing compartment reports to include magic statement when running mu…
    @kaeldai
    kaeldai authored May 12, 2024
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Commits on May 20, 2024

  1. Enabling to run run.sim() more than once (AllenInstitute#368) 

    * SpikesMod now initialize the SpikeTrain with 'initialize()' so that sim.run() can be run more than once without an error.

Thanks, Kael!
    @shixnya
    shixnya authored May 20, 2024
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  2. NESTML example network

    @xpliu16
    xpliu16 committed May 20, 2024
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Commits on May 22, 2024

  1. Merge pull request AllenInstitute#369 from xpliu16/develop 

    NESTML example network
    @kaeldai
    kaeldai authored May 22, 2024
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  2. updating way templates can be loaded to fix an ordering bug

    @kaeldai
    kaeldai committed May 22, 2024
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Commits on Jun 14, 2024

  1. fixing issues with unit tests

    @kaeldai
    kaeldai committed Jun 14, 2024
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  2. Merge branch 'update/workshop-2024' of https://github.com/AllenInstit… 

    …ute/bmtk into update/workshop-2024
    @kaeldai
    kaeldai committed Jun 14, 2024
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  3. Merge pull request AllenInstitute#372 from AllenInstitute/update/work… 

    …shop-2024

Update/workshop 2024
    @kaeldai
    kaeldai authored Jun 14, 2024
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Commits on Jun 16, 2024

  1. fixes for Ch5 of workshop tutorial; remove dt attribute in filternet … 

    …in create_environment, automatic support for npz movies, fix issue with separable kernel when kernel is empty
    @kaeldai
    kaeldai committed Jun 16, 2024
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Commits on Jun 25, 2024

  1. small fix to xstim and larger update of SEClamp module

    @kaeldai
    kaeldai committed Jun 25, 2024
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  2. Adding fix to make using NESTML a bit more robust + another NESTML ex… 

    …ample
    @kaeldai
    kaeldai committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Fixing FilterNet behavior for frame_rate != 1000.0

    @shixnya
    shixnya committed Jun 26, 2024
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Commits on Jul 6, 2024

  1. some minor fixes

    @kaeldai
    kaeldai committed Jul 6, 2024
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  2. Merge pull request AllenInstitute#377 from kaeldai/update/workshop-2024 

    some minor fixes
    @kaeldai
    kaeldai authored Jul 6, 2024
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  3. Merge pull request AllenInstitute#378 from AllenInstitute/update/work… 

    …shop-2024

Update/workshop 2024
    @kaeldai
    kaeldai authored Jul 6, 2024
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Commits on Jul 8, 2024

  1. Merge branch 'AllenInstitute:develop' into develop

    @shixnya
    shixnya authored Jul 8, 2024
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  2. Update version to 1.1.1 

    Updating for a new release
    @kaeldai
    kaeldai authored Jul 8, 2024
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  3. Merge pull request AllenInstitute#379 from AllenInstitute/version-upd… 

    …ate-1.1.1

Update version to 1.1.1
    @kaeldai
    kaeldai authored Jul 8, 2024
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Commits on Aug 29, 2024

  1. Update version to 1.1.1 

    Updating for a new release
    @kaeldai @shixnya
    kaeldai authored and shixnya committed Aug 29, 2024
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  2. Allowing grating contrast to be 0.

    @shixnya
    shixnya committed Aug 29, 2024
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  3. Merge branch 'AllenInstitute:develop' into develop

    @shixnya
    shixnya authored Aug 29, 2024
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  4. Merge pull request AllenInstitute#375 from shixnya/develop 

    Fixing FilterNet behavior for frame_rate != 1000.0
    @kaeldai
    kaeldai authored Aug 29, 2024
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Commits on Sep 11, 2024

  1. mpi iclamp fix

    @tjbanks
    tjbanks committed Sep 11, 2024
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  2. changes

    @tjbanks
    tjbanks committed Sep 11, 2024
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  3. fix

    @tjbanks
    tjbanks committed Sep 11, 2024
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  4. fix

    @tjbanks
    tjbanks committed Sep 11, 2024
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