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@michellewang michellewang commented Oct 21, 2024

Changes proposed in this pull request:

  • Update figure

Checklist (for reviewers)

This section is for the PR reviewer

  • PR has an interpretable title with a prefix (e.g. [BUG], [DOC], [ENH], [MAINT])
    Refer to NumPy Development Guide for a full list
  • PR links to GitHub issue with mention Closes #XXXX
  • Tests pass
  • Checks pass

For new features:

  • Tests have been added

For bug fixes:

  • There is at least one test that would fail under the original bug conditions

@github-actions github-actions bot added the T.3 - Documentation Improvements or additions to documentation label Oct 21, 2024
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codecov bot commented Oct 21, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

@michellewang michellewang added this to the Release 0.3.0 milestone Oct 23, 2024
@michellewang michellewang linked an issue Oct 23, 2024 that may be closed by this pull request
@michellewang michellewang requested review from nikhil153 and removed request for nikhil153 October 25, 2024 19:31
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minor notes:
image
the two colors are pretty similar

I like the different shape for files vs directories. Maybe adding a trailing / at the end of directories would help clarify it even more.

Re-ordering looks cool!

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michellewang commented Oct 29, 2024

TODO:

  • Change orange to blue (and change back transparency of red)
  • Remove trailing slash in directories
  • Rename idps -> idp (and double-check that layout hasn't been changed yet)
  • Fix crooked lines :'(

@michellewang michellewang merged commit 7c2a4bf into nipoppy:Release-0.3.0 Oct 30, 2024
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@michellewang michellewang deleted the 396/layout_figure branch October 30, 2024 18:08
mathdugre added a commit that referenced this pull request Oct 31, 2024
* [ENH] Add `_id` suffix to `bids_participant` and `bids_session` (#382)

* rename bids_participant -> bids_participant_id

* rename bids_session -> bids_session_id

* [ENH] Make `TRACKER_CONFIG_FILE` part of pipeline step config instead of pipeline config (#352)

* set default step name

* put tracker config file under PipelineStepConfig instead of PipelineConfig (no longer a list)

* add pipeline_step column to bagel

* use pipeline step config attributes directly instead of getters

* improve pipeline step type annotation and refactor validation

* update CLI

* update tracking-related docs

* Revert "improve pipeline step type annotation and refactor validation"

This reverts commit aa2e621.

* Revert "use pipeline step config attributes directly instead of getters"

This reverts commit 6b2821f.

* remove pipeline_step_config and check_pipeline_step

* move redundant change

* fix tests after merge

* only allow tracking at participant-session level

* address PR review comment

* [API] make --dataset-root and positional arg. (#390)

* [API] make --dataset-root and positional arg.

* [MAINT] Only move PRs to pending review. (#389)

* [MAINT] Only move PRs to pending review.

The PR states is then handled by the project workflows.

* cleanup file from removed workflow.

* positional arg should not hae hyphen. Fixed to pass tests.

* [ENH] Update pipeline config layout (#383)

* move descriptors

* move sample invocations

* move tracker files

* move sample_pipelines inside examples

* update layout

* update sample global configs

* update dataset init and tests

* rename proc -> pipelines in layout

* fix docs

* [ENH] Use TSV instead of CSV for tabular files (#381)

* update JSON files

* update loading/saving function calls

* rename CSV files to TSV

* convert to TSV

* fix tests

* rename remaining csv file

* complete CSV -> TSV conversion

* update docs

* renamed "comma-separated" to "tab-separated" in docs

* add check for CSV input and update tests

* fix failing test

* explicitly set separator as '\t' in BaseTabular instead of relying on default

* [ENH] Update layout (#379)

* remove releases and demographics directories

* rename bids directory

* Revert "rename bids directory"

This reverts commit 0ff17c9.

* move logs directory

* rename sourcedata -> to_bidsify

* rename raw_imaging -> to_reorg

* change fpath_doughnut

* move pybids_db file

* move pybids_ignore_patterns directory

* move downloads under sourcedata/imaging

* add new paths for sourcedata directories

* add code directory

* move containers directory directly under root

* add demographics.csv file to layout

* move working directories under scratch/work

* rename to_reorg -> pre_reorg

* rename to_bidsify -> post_reorg

* address PR comments

* forgot to save before committing

* remove missed mentions of "raw"...

* rename bagel.tsv -> imaging_bagel.tsv

* [ENH] Rename doughnut columns (#404)

rename in_raw_imaging -> in_pre_reorg and in_sourcedata -> in_post_reorg

* [DOC] Update file trees in user guide page for DICOM reorg (#408)

update file trees

* [DOC] Update dataset layout figure (#412)

* update layout in figure

* update figure based on feedback

* remove subdirectories/files under pre-/post-reorg

* remove trailing slashes, rename idps, etc.

* [ENH] Update bagel columns (#354)

* remove `pipeline_starttime` column

* rename `session` -> `bids_session`

* make tracker robust to bad/incompatible existing bagel

* rename bids_session -> bids_session_id

* fix MRIQC bagel example and add tests for valid/invalid bagels

* csv -> tsv

* make bids_participant_id and bids_session_id required by the schema

* address comment for test

---------

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

* [REL] Fix merge conflict for REL 0.3.0 (#417)

* [MAINT] Only move PRs to pending review. (#389)

* [MAINT] Only move PRs to pending review.

The PR states is then handled by the project workflows.

* cleanup file from removed workflow.

* [BUG] keep working directory on failed run / flag to keep pipeline working directory on success (#345)

* added method / test for flag to clear working directory

* added --keep_workdir argument to parser; fixed bad spacing in test

* removed dev comments

* added pipeline runner arg to parser / cli invocation

* added logic to run_cleanup for keeping intermediary files from failed runs - TODO write test

* finalized cleanup fix and unit test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* added unit test for codecov, addressed log feedback

* added pre-commit to env

* added config saving to test from new api; renamed fail to success in test variable for clarity

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#398)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [BUG] Do not pool BIDS and PROC pipelines together when searching pipeline configs (#391)

* refactor get_pipeline_version to take a list of pipeline configs

* refactor get_pipeline_config to take a list of pipeline configs

* add tests for BidsConversionWorkflow

* fix sphinx xref warning

* remove old nitpick-ignores

* [ENH] make fmriprep `--fs-no-reconall` value-key and id more intuitive. (#406)

---------

Co-authored-by: Brent McPherson <bcmcpher@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Michelle Wang <tomichellewang@gmail.com>

---------

Co-authored-by: Michelle Wang <tomichellewang@gmail.com>
Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>
Co-authored-by: Brent McPherson <bcmcpher@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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[DOC] Update layout figure in README
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