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[Documentation]: Update parallel I/O and iterative write tutorial #1514

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oruebel opened this issue Jul 19, 2022 · 0 comments · Fixed by #1633
Closed
3 tasks done

[Documentation]: Update parallel I/O and iterative write tutorial #1514

oruebel opened this issue Jul 19, 2022 · 0 comments · Fixed by #1633
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category: enhancement improvements of code or code behavior priority: low alternative solution already working and/or relevant to only specific user(s) topic: docs issues related to documentation

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oruebel commented Jul 19, 2022 •
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What would you like changed or added to the documentation and why?

Once hdmf-dev/hdmf#747 has been released in HDMF, we should update the parallel I/O tutorial accordingly to:

  1. avoid having to create an empty DataChunkIterator and use H5DataIO instead
  2. avoid having to close and reopen the file
  3. Show how this pattern can be used to customize write in the serial case as well

We should also update the following section of the iterative write tutorial https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/iterative_write.html#alternative-approach-user-defined-dataset-write to use the new functionality and avoid writing a dataset that is too small and then resizing later.

Do you have any interest in helping write or edit the documentation?

Yes.

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@oruebel oruebel added category: enhancement improvements of code or code behavior topic: docs issues related to documentation priority: low alternative solution already working and/or relevant to only specific user(s) labels Jul 19, 2022
@oruebel oruebel self-assigned this Jul 19, 2022
@oruebel oruebel changed the title [Documentation]: Update parallel I/O tutorial [Documentation]: Update parallel I/O and iterative write tutorial Jul 26, 2022
oruebel added a commit that referenced this issue Jan 11, 2023
@oruebel
Fix #1514 Update parallel I/O tutorial to use H5DataIO instead of Dat…
07ccd73 
…aChunkIterator to setup data for parallel write
@oruebel oruebel mentioned this issue Jan 11, 2023
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oruebel added a commit that referenced this issue Jan 11, 2023
@oruebel @rly
Update iterative write and parallel I/O tutorial (#1633)
8395176 
* Update iterative write tutorial
* Update doc makefiles to clean up files created by the advanced io tutorial
* Fix #1514  Update parallel I/O tutorial to use H5DataIO instead of DataChunkIterator to setup data for parallel write
* Update changelog
* Fix flake8
* Fix broken external links
* Update make.bat
* Update CHANGELOG.md
* Update plot_iterative_write.py
* Update docs/gallery/advanced_io/plot_iterative_write.py

Co-authored-by: Ryan Ly <[email protected]>
mavaylon1 added a commit that referenced this issue Jan 17, 2023
@mavaylon1 @oruebel
@rly @dependabot @bendichter @h-mayorquin
nwb_schema_2.6.0 (#1636)
e3381a0 
* Check nwb_version on read (#1612)

* Added NWBHDF5IO.nwb_version property and check for version on NWBHDF5IO.read
* Updated icephys tests to skip version check when writing non NWBFile container
* Add tests for NWB version check on read
* Add unit tests for NWBHDF5IO.nwb_version property
* Updated changelog

Co-authored-by: Ryan Ly <[email protected]>

* Bump setuptools from 65.4.1 to 65.5.1 (#1614)

Bumps [setuptools](https://github.com/pypa/setuptools) from 65.4.1 to 65.5.1.
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/CHANGES.rst)
- [Commits](pypa/setuptools@v65.4.1...v65.5.1)

---
updated-dependencies:
- dependency-name: setuptools
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* modify export.rst to have proper links to the NWBFile API docs (#1615)

* Create project_action.yml (#1617)

* Create project_action.yml

* Update project_action.yml

* Update project_action.yml

* Update project_action.yml (#1620)

* Update project_action.yml (#1623)

* Project action (#1626)

* Create project_action.yml

* Update project_action.yml

* Update project_action.yml

* Update project_action.yml

* Show recommended usaege for hdf5plugin in tutorial (#1630)

* Show recommended usaege for hdf5plugin in tutorial

* Update docs/gallery/advanced_io/h5dataio.py

* Update docs/gallery/advanced_io/h5dataio.py

Co-authored-by: Heberto Mayorquin <[email protected]>

Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Heberto Mayorquin <[email protected]>

* Update iterative write and parallel I/O tutorial (#1633)

* Update iterative write tutorial
* Update doc makefiles to clean up files created by the advanced io tutorial
* Fix #1514  Update parallel I/O tutorial to use H5DataIO instead of DataChunkIterator to setup data for parallel write
* Update changelog
* Fix flake8
* Fix broken external links
* Update make.bat
* Update CHANGELOG.md
* Update plot_iterative_write.py
* Update docs/gallery/advanced_io/plot_iterative_write.py

Co-authored-by: Ryan Ly <[email protected]>

* Update project_action.yml (#1632)

* nwb_schema_2.6.0

* Update CHANGELOG.md

* remove

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Oliver Ruebel <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Heberto Mayorquin <[email protected]>
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Update iterative write and parallel I/O tutorial NeurodataWithoutBorders/pynwb
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