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Add NWBIO #796

Merged
merged 90 commits into from
Jul 22, 2021
Merged

Add NWBIO #796

merged 90 commits into from
Jul 22, 2021

Commits on Oct 31, 2017

  1. Synchronisation avec le projet original

    @msenoville
    msenoville committed Oct 31, 2017
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Commits on Mar 13, 2019

  1. test nwb

    @legouee
    legouee committed Mar 13, 2019
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  2. Add NWB class

    @legouee
    legouee committed Mar 13, 2019
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  3. NWB Files names

    @legouee
    legouee committed Mar 13, 2019
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  4. nwbrawio file

    @legouee
    legouee committed Mar 13, 2019
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Commits on Mar 19, 2019

  1. remove form to adding hdmf with version pynwb=1.0.0 to pynwb=1.0.1

    @legouee
    legouee committed Mar 19, 2019
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Commits on Jul 1, 2019

  1. NWB support updates

    @legouee
    legouee committed Jul 1, 2019
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Commits on Jul 12, 2019

  1. nwbio files

    @legouee
    legouee committed Jul 12, 2019
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Commits on Jul 18, 2019

  1. Read NWB files and tests

    @legouee
    legouee committed Jul 18, 2019
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Commits on Sep 5, 2019

  1. update

    @msenoville
    msenoville committed Sep 5, 2019
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Commits on Sep 6, 2019

  1. Updates

    @legouee
    legouee committed Sep 6, 2019
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Commits on Sep 18, 2019

  1. after recent modification

    @legouee
    legouee committed Sep 18, 2019
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Commits on Sep 19, 2019

  1. Segment and AnalogSignals

    @legouee
    legouee committed Sep 19, 2019
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Commits on Sep 26, 2019

  1. Without print

    @legouee
    legouee committed Sep 26, 2019
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Commits on Oct 2, 2019

  1. Writing part

    @legouee
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Commits on Oct 14, 2019

  1. Writing part

    @legouee
    legouee committed Oct 14, 2019
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Commits on Oct 24, 2019

  1. commit before switching to another branch

    @legouee
    legouee committed Oct 24, 2019
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  2. commit for unuseful files...

    @legouee
    legouee committed Oct 24, 2019
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  3. neo udpates...

    @legouee
    legouee committed Oct 24, 2019
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Commits on Oct 31, 2019

  1. Support reading and writing a .nwb file

    @legouee
    legouee committed Oct 31, 2019
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Commits on Nov 22, 2019

  1. Several blocks and segments

    @legouee
    legouee committed Nov 22, 2019
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  2. minor modif

    @legouee
    legouee committed Nov 22, 2019
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Commits on Nov 29, 2019

  1. NWB files with several blocks

    @legouee
    legouee committed Nov 29, 2019
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Commits on Dec 2, 2019

  1. Modifications segments

    @legouee
    legouee committed Dec 2, 2019
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Commits on Dec 10, 2019

  1. Merge branch 'NWB_updated' of https://github.com/legouee/python-neo i… 

    …nto NWB_updated
    @msenoville
    msenoville committed Dec 10, 2019
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  2. save modifs

    @msenoville
    msenoville committed Dec 10, 2019
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Commits on Dec 11, 2019

  1. improvement of of reading of multiple blocks

    @msenoville
    msenoville committed Dec 11, 2019
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  2. Commit before pull

    @legouee
    legouee committed Dec 11, 2019
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  3. trying to merge

    @legouee
    legouee committed Dec 11, 2019
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  4. Several blocks

    @legouee
    legouee committed Dec 11, 2019
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Commits on Dec 12, 2019

  1. Writing function

    @legouee
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Commits on Dec 13, 2019

  1. writing part

    @legouee
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Commits on Dec 18, 2019

  1. Improvements writing several blocks - wip

    @legouee
    legouee committed Dec 18, 2019
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Commits on Jan 27, 2020

  1. Neo SpikeTrain Epoch

    @legouee
    legouee committed Jan 27, 2020
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Commits on Feb 17, 2020

  1. Calcium imaging data

    @legouee
    legouee committed Feb 17, 2020
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Commits on Feb 21, 2020

  1. Calcium imaging data test

    @legouee
    legouee committed Feb 21, 2020
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Commits on Feb 28, 2020

  1. NWB

    @legouee
    legouee committed Feb 28, 2020
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Commits on Mar 4, 2020

  1. fix 'rescale' method for Event and Epoch

    @apdavison
    apdavison committed Mar 4, 2020
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Commits on Mar 5, 2020

  1. wip

    @apdavison
    apdavison committed Mar 5, 2020
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  2. Store Neo Epochs in epochs group, Spiketrains in units group.

    @apdavison
    apdavison committed Mar 5, 2020
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  3. Store global annotations appropriately, handle "stimulus" group

    @apdavison
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  4. temporarily remove incomplete calcium image data handling code, so as… 

    … to focus on improving ephys handling
    @apdavison
    apdavison committed Mar 5, 2020
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  5. Remove unused imports

    @apdavison
    apdavison committed Mar 5, 2020
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  6. group read and write methods (and rename "_handle_X" to "_read_X" for… 

    … consistency)
    @apdavison
    apdavison committed Mar 5, 2020
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  7. wip lazy loading

    @apdavison
    apdavison committed Mar 5, 2020
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Commits on Mar 6, 2020

  1. implement lazy loading

    @apdavison
    apdavison committed Mar 6, 2020
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  2. Merge branch 'master' into nwb2

    @apdavison
    apdavison committed Mar 6, 2020
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  3. fix NWB tests to download data files, so they should work on CI system

    @apdavison
    apdavison committed Mar 6, 2020
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  4. delete some old files

    @apdavison
    apdavison committed Mar 6, 2020
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  5. Add pynwb to testing requirements

    @apdavison
    apdavison committed Mar 6, 2020
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  6. More test fixes

    @apdavison
    apdavison committed Mar 6, 2020
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  7. Python 2.7 fix

    @apdavison
    apdavison committed Mar 6, 2020
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  8. PyNWB doesn't support Python 2.7

    @apdavison
    apdavison committed Mar 6, 2020
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  9. Revert some unintentional changes

    @apdavison
    apdavison committed Mar 6, 2020
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  10. fix some pep8 warnings

    @apdavison
    apdavison committed Mar 6, 2020
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  11. Added NWBIO example

    @apdavison
    apdavison committed Mar 6, 2020
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Commits on Aug 31, 2020

  1. NWBIO: be more careful with file modes

    @apdavison
    apdavison committed Aug 31, 2020
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  2. [NWBIO] better handling of dict-valued annotations

    @apdavison
    apdavison committed Aug 31, 2020
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  3. [NWBIO] Start adding support for writing to NWB groups other than "ac… 

    …quisition"
    @apdavison
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Commits on Sep 28, 2020

  1. [nwbio] handle subclasses of TimeSeries 

    (tested with intracellular ephys subclasses)
    @apdavison
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Commits on Dec 6, 2020

  1. load now handles slices of irregularly sampled data

    @bendichter
    bendichter committed Dec 6, 2020
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  2. Merge pull request #5 from bendichter/nwb_fix 

    load now handles slices of irregularly sampled data
    @apdavison
    apdavison authored Dec 6, 2020
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  3. Merge branch 'master' into nwb2 

    # Conflicts:
#	neo/core/epoch.py
#	neo/core/event.py
#	neo/io/baseio.py
    @apdavison
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Commits on Feb 3, 2021

  1. Merge branch 'master' into nwb2

    @apdavison
    apdavison committed Feb 3, 2021
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  2. handle unexpected units, such as "n/a" !

    @apdavison
    apdavison committed Feb 3, 2021
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  3. fix shape of AnalogSignalProxy in NWBIO

    @apdavison
    apdavison committed Feb 3, 2021
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  4. Be more forgiving of weird lines when loading ascii files

    @apdavison
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Commits on Apr 19, 2021

  1. Merge branch 'master' into nwb2 

    # Conflicts:
#	neo/io/__init__.py
#	neo/io/proxyobjects.py
    @apdavison
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Commits on Jun 28, 2021

  1. replace annotation "nwb_type" with "nwb_neurodata_type" to more close… 

    …ly shadow NWB naming convention

(see discussion in NeuralEnsemble#796)
    @apdavison
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  2. update links in NWBIO docstring

    @apdavison
    apdavison committed Jun 28, 2021
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  3. fix recently appeared bug (due to changes in h5py?) where boolean ind… 

    …ex is no longer accepted, need integer index
    @apdavison
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  4. Make "session_start_time" a required block annotation for NWB 

    (see discussion in NeuralEnsemble#796)
    @apdavison
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  5. Add a "block_index" argument to NWBIO.read_block()

    @apdavison
    apdavison committed Jun 28, 2021
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  6. Validate NWB files after writing them

    @apdavison
    apdavison committed Jun 28, 2021
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Commits on Jun 29, 2021

  1. Merge branch 'master' into nwb2 

    # Conflicts:
#	requirements_testing.txt
    @apdavison
    apdavison committed Jun 29, 2021
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  2. remove deprecated ChannelIndex and Unit from NWBIO

    @apdavison
    apdavison committed Jun 29, 2021
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  3. partially integrated NWB testing into common framework

    @apdavison
    apdavison committed Jun 29, 2021
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  4. Removed example NWB notebook following discussion in NeuralEnsemble#796 

    [skip ci]
    @apdavison
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Commits on Jul 8, 2021

  1. Apply suggestions from code review 

    Co-authored-by: Ben Dichter <[email protected]>
    @apdavison @bendichter
    apdavison and bendichter authored Jul 8, 2021
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  2. PR suggestions

    @legouee
    legouee committed Jul 8, 2021
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  3. Apply suggestions from code review 

    Co-authored-by: Andrew Davison <[email protected]>
    @legouee @apdavison
    legouee and apdavison authored Jul 8, 2021
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  4. Merge pull request #7 from legouee/PR-correct 

    Implement suggestions from review of PR for nwb2 branch
    @apdavison
    apdavison authored Jul 8, 2021
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Commits on Jul 9, 2021

  1. handle differences in float precision when obtaining unit prefixes

    @apdavison
    apdavison committed Jul 9, 2021
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  2. Switch testing of NWB to use BaseTestIO

    @apdavison
    apdavison committed Jul 9, 2021
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Commits on Jul 22, 2021

  1. pep8 reformatting

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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  2. more pep8 reformatting

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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  3. [nwbio] guess fix for typo

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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  4. [nwbio] add missing docstrings

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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  5. [nwbio] more pep8

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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  6. [nwbio] remove unused import

    @JuliaSprenger
    JuliaSprenger committed Jul 22, 2021
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