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[INFRA] Convert entity table to yaml #475

Merged
merged 53 commits into from
Aug 11, 2020
Merged

[INFRA] Convert entity table to yaml #475

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18a3f24
Draft entity and datatype files.
tsalo May 16, 2020
02c3403
Draft more specifications.
tsalo May 16, 2020
6ea0dfd
Add specifications for top-level files and directories.
tsalo May 16, 2020
6626368
Reorganize yaml files.
tsalo May 17, 2020
5c26565
Add inclusion for top level files.
tsalo May 19, 2020
d6601e7
Rename yaml files and add required field.
tsalo May 22, 2020
ee9535f
Convert dict to list in example file.
tsalo May 22, 2020
56a42b6
[DATALAD RUNCMD] Replace suffices with suffixes
yarikoptic May 22, 2020
596ed00
Add leading "." to extensions to match specification.
tsalo Jun 3, 2020
45fdfca
Convert dict to list.
tsalo Jun 3, 2020
9ec4e09
Fix iEEG extension based on issue.
tsalo Jun 3, 2020
d03d895
Split auxdatatypes and drop datatypes key.
tsalo Jun 3, 2020
8d3436c
Add descriptions to entities.
tsalo Jun 3, 2020
aa1ac3e
Draft metadata.
tsalo Jun 3, 2020
5791baf
ENH: top level bids.yaml to bind all separate files together
yarikoptic Jun 10, 2020
2193404
ENH: initial version of tools/bids-schema to assist with producing ma…
yarikoptic Jun 10, 2020
cc69735
RF: do not require !include - just load entire file tree!
yarikoptic Jun 10, 2020
c41a0dc
ENH: Produce entity table
yarikoptic Jun 10, 2020
797b23c
TEMP ENH: script to produce and replace the entity table inplace with…
yarikoptic Jun 11, 2020
56447c3
ENH: a few more paths for git to ignore
yarikoptic Jun 11, 2020
06429b5
[DATALAD RUNCMD] (Re)generate entity table from the schema
yarikoptic Jun 11, 2020
e58931d
Revert aa1ac3e.
tsalo Jun 13, 2020
ef49d03
Reorganize BIDS schema code.
tsalo Jun 14, 2020
69b50fe
Add modality names.
tsalo Jun 14, 2020
0673b73
Fix table header and allow run for anat.
tsalo Jun 14, 2020
b11685d
Add split entity.
tsalo Jun 14, 2020
8d0b612
Switch from click to argparse.
tsalo Jun 15, 2020
26f56ed
Merge branch 'master' into ref/json-entity
tsalo Jul 11, 2020
0bacc04
Split entity table and add docstrings.
tsalo Jul 18, 2020
e2b923b
Merge branch 'ref/json-entity' of https://github.com/tsalo/bids-speci…
tsalo Jul 18, 2020
532bb6c
Fix extra empty line.
tsalo Jul 18, 2020
4041d00
Apply suggestions from code review
tsalo Jul 22, 2020
bfac102
Remove top-level fieldmaps.
tsalo Jul 22, 2020
6ce57e1
Remove unsupported suffixes.
tsalo Jul 22, 2020
4e291e2
Fix 4d MEG suffix.
tsalo Jul 22, 2020
c9020f5
Merge branch 'master' into ref/json-entity
tsalo Jul 22, 2020
bf80162
Remove spurious trailing " in yaml paragraph
yarikoptic Jul 23, 2020
37132a4
Improve handling of multiline strings in yaml.
tsalo Jul 24, 2020
814e453
Add comments to separate groups.
tsalo Jul 24, 2020
0984f8c
Draft schema instructions in CONTRIBUTING.md.
tsalo Jul 24, 2020
cab708a
Partially address review.
tsalo Jul 26, 2020
8aa4994
Apply suggestions from code review
tsalo Jul 26, 2020
592a0db
Drop unnecessary paths from .gitignore.
tsalo Aug 2, 2020
1159d66
Try adding schema test.
tsalo Aug 2, 2020
5576c66
Use -c.
tsalo Aug 2, 2020
330e4dc
YAML isn't a builtin.
tsalo Aug 2, 2020
a233116
It's named pyyaml.
tsalo Aug 2, 2020
85ba0ca
Fix linting issues in yaml files and fix test.
tsalo Aug 2, 2020
dd4e1c1
Not a Python command.
tsalo Aug 2, 2020
125c492
Apply suggestions from code review
tsalo Aug 10, 2020
5c426b0
Implement changes from #556.
tsalo Aug 10, 2020
86650bf
Merge branch 'master' into ref/json-entity
tsalo Aug 10, 2020
177b15a
add LICENSE to top_level_files.yaml
sappelhoff Aug 11, 2020
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9 changes: 9 additions & 0 deletions src/schema/top_level_files.yml
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Original file line number Diff line number Diff line change
@@ -1,32 +1,41 @@
README:
required: True
extensions:
- md
- rst
- None
CHANGES:
required: True
extensions:
- md
- rst
- None
dataset_description:
required: True
extensions:
- json
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genetic_info:
required: False
extensions:
- json
participants:
required: True
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extensions:
- tsv
- json
phasediff:
required: False
extensions:
- json
phase1:
required: False
extensions:
- json
phase2:
required: False
extensions:
- json
fieldmap:
required: False
extensions:
- json