State of the BEP (Do not merge) - #6

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effigies wants to merge 1237 commits into

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Commits on Jan 13, 2021

Fix bugs in schema.
tsalo
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e990848

Commits on Jan 14, 2021

[MISC] Added full names for some contributors in .mailmap file (#705)

yarikoptic
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sappelhoff
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c7751c7

Commits on Jan 15, 2021

[ENH] Bep 005: Arterial Spin Labeling (#669)

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d794736

Commits on Jan 19, 2021

Merge branch 'master' into enh/render-schema
tsalo
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1548384
Update for ASL.
tsalo
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7bad87f

Commits on Jan 22, 2021

SCHEMA: Update entity YAML keys
effigies
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ba3aa59

Commits on Jan 27, 2021

Update src/schema/datatypes/eeg.yaml

tsalo
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sappelhoff
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fcf092c
Fix spacing.
tsalo
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cb19df3

Commits on Jan 29, 2021

Address @yarikoptic's point about wording.
tsalo
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a23aa09
Point to file instead of folder.
tsalo
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4b2fcae
Expand on the need to manually check rendered text.
tsalo
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cce5e58
mt -> mtransfer
effigies
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9e3bf9f
Merge pull request #714 from bids-standard/schema/entity_keys
tsalo
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e21c2c1
[DOC] Auto-generate changelog entry for PR #714
bids-maintenance
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2da3e7c

Commits on Feb 1, 2021

Commits on Feb 2, 2021

Commits on Feb 3, 2021

Fix entity names. (#720)
tsalo
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c426e27

Commits on Feb 5, 2021

ENH: Clarify run indexing information for MRI acquisitions (#719)

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6767e05

Commits on Feb 6, 2021

Prohibit combination of echo entity and events suffix.
tsalo
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a7f7d74
Allow ce and dir with func physio data.
tsalo
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9e0b778

Commits on Feb 9, 2021

Make flip optional for MP2RAGE.

tsalo
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effigies
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7cdeadf
Rename schema groups in comments.
tsalo
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599c5d9

Commits on Feb 10, 2021

Commits on Feb 12, 2021

Update qMRI fieldmap schema (#728)
effigies
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c8f5827

Commits on Feb 15, 2021

split files scans.tsv
examplename
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92e4029

Commits on Feb 16, 2021

style improvement
eort
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0bb4755
add contributor
eort
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26757f3
change should to must
eort
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a2678fe

Commits on Feb 17, 2021

REL: v1.5.0
franklin-feingold
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ea3a97c

Commits on Feb 21, 2021

restructure intro events.md
Remi-Gau
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4178e53
fix examples in tables
Remi-Gau
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d385527
Add heading about stimuli folder
Remi-Gau
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2d7f9d8

Commits on Feb 22, 2021

Update src/04-modality-specific-files/02-magnetoencephalography.md

eort
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sappelhoff
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f769b09
Update src/99-appendices/06-meg-file-formats.md

eort
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sappelhoff
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c037c67
Update src/schema/entities.yaml

eort
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sappelhoff
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2cf3ae4
update scans with parts
eort
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758f9ca
Merge branch 'split_in_scans' of https://github.com/eort/bids-specification into split_in_scans
eort
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88e0618
Update src/99-appendices/01-contributors.md

eort
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sappelhoff
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8a5519a
Merge branch 'split_in_scans' of https://github.com/eort/bids-specification into split_in_scans
eort
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a580998
update scans.tsv
eort
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3600e28
no-bad-latin fix
eort
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196e8f5
no-bad-latin
eort
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b5f41bf
Update src/03-modality-agnostic-files.md

eort
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tsalo
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b0065cc

Commits on Feb 23, 2021

updated TotalAcquiredVolumes into TotalACquiredPairs
patsycle
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fb7feb9
update TotalAcquiredPairs
patsycle
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7bf0d49
Merge pull request #742 from bids-standard/bep-005
franklin-feingold
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9b22cad
[DOC] Auto-generate changelog entry for PR #742
bids-maintenance
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d391a53
Merge remote-tracking branch 'upstream/master' into rel/1.5.0
effigies
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0957dec
Merge pull request #736 from bids-standard/rel/1.5.0
franklin-feingold
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0c30169
Update mkdocs.yml
franklin-feingold
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e146e0f

Commits on Feb 25, 2021

fix schema for i/eeg coordsys+elecs (#743)
sappelhoff
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9cb5612

Commits on Feb 26, 2021

fix exampel
eort
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5b18e4d
Merge branch 'master' of https://github.com/bids-standard/bids-specification into split_in_scans
eort
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ef19dfb
fix example
eort
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dea04f1
Merge branch 'split_in_scans' of https://github.com/eort/bids-specification into split_in_scans
eort
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fb1b652
fix example
eort
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df3fa3d
Update src/03-modality-agnostic-files.md

eort
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tsalo
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044c068

Commits on Mar 3, 2021

[MISC] Clarify participant_id in participants.tsv file if it exists (#738)

authored
99eec00
Update src/03-modality-agnostic-files.md

eort
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sappelhoff
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baab606
update scans.tsv desc
eort
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b86309e
update scans.tsv desc
eort
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8e58509
fix conflict
eort
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e47aa79

Commits on Mar 5, 2021

[FIX] 1) Clarify appropriate labels for space entity, 2) Clarify channels+electrodes do not have to match (#734)

sappelhoff
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effigies
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54179a1
[MISC] standardize string examples format in tables (#739)

authored
feba0fc
Update src/03-modality-agnostic-files.md

eort
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tsalo
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17b00ba
Update src/99-appendices/06-meg-file-formats.md

eort
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tsalo
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22e9be5
Update src/schema/entities.yaml

eort
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sappelhoff
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f5b34f9
split files
eort
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eaf6e62

Commits on Mar 8, 2021

[INFRA] updating remark, CIs, contributor docs (#745)

sappelhoff
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Remi-Gau
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1d7b363

Commits on Mar 11, 2021

undo revert
eort
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cf88deb
fix trailing whitespace
eort
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17e7539

Commits on Mar 13, 2021

Fix typo in EEG specification
rob-luke
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f3667fd
Merge pull request #754 from rob-luke/patch-1
sappelhoff
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4f887b8
no remark on auto CHANGES
sappelhoff
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d26176c

Commits on Mar 15, 2021

Merge pull request #755 from sappelhoff/quickfix
sappelhoff
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ac2101f

Commits on Mar 16, 2021

change parts to files
eort
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1be0ce9
Merge pull request #735 from eort/split_in_scans
sappelhoff
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537e28a

Commits on Mar 25, 2021

fix hed link
sappelhoff
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54a71ac
fix local links
sappelhoff
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9c35577
fix circleci workflow
sappelhoff
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c79dd65
Merge pull request #764 from sappelhoff/fixcirlce
sappelhoff
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1acdc20
[DOC] Auto-generate changelog entry for PR #764
bids-maintenance
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a280ae8

Commits on Mar 26, 2021

install git in linkchecker job
sappelhoff
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c063527
checkout code to use git
sappelhoff
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af4935f
try to fix artifact redirector
sappelhoff
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1215ce6
tweak file path
sappelhoff
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4d3a316
add pandoc resource-path to find ASL imgs
sappelhoff
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56e84b3
Merge pull request #767 from sappelhoff/link/git
sappelhoff
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9c4c09e
[DOC] Auto-generate changelog entry for PR #767
bids-maintenance
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7f401d4

Commits on Mar 30, 2021

move schema documnetation into the schema folder

Remi-Gau
authored and
sappelhoff
committed
fd96f19
Apply suggestions from code review

Remi-Gau
and
sappelhoff
committed
822f53b
Apply suggestions from code review

sappelhoff
and
tsalo
committed
acda419

Commits on Apr 5, 2021

enh: allow encoding the fieldmapping intent of the protocol
oesteban
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c44b926
Apply suggestions from code review

oesteban
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effigies
committed
1aec168
enh: miscellaneous changes (see below)
oesteban
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9664f8f
fix: address missing field on GE devices
oesteban
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5be9e5f
fix: remove 'e.g.'
oesteban
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702d8b9

Commits on Apr 6, 2021

Merge pull request #740 from Remi-Gau/remi-schema-doc
tsalo
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3301ac2
[DOC] Auto-generate changelog entry for PR #740
bids-maintenance
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89af312
fix: add asl instances as pointed out by @mattcieslak
oesteban
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8377588

Commits on Apr 7, 2021

[ENH] Bep 009: Positron Emission Tomography (#633)

authored
cc46934

Commits on Apr 9, 2021

FIX: typo in pet: institution -> institutional
sappelhoff
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9546adf

Commits on Apr 12, 2021

Commits on Apr 13, 2021

Rename *Unit -> *Units in PET
effigies
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ab5cd60
Merge pull request #773 from effigies/fix/unit
mnoergaard
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acedf22
[DOC] Auto-generate changelog entry for PR #773
bids-maintenance
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24a4069

Commits on Apr 14, 2021

Commits on Apr 21, 2021

FIX: Amend note about b-vecs on DWI specs
oesteban
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eb8000e

Commits on Apr 22, 2021

FIX: Typos discovered by codespell (#784)

yarikoptic
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effigies
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0900f12
CI: Update linkchecker condition
effigies
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58b6566
REL: v1.6.0
effigies
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6fd9145
Merge pull request #776 from bids-standard/rel/1.6.0
effigies
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cceb6dc
REL: 1.6.1-dev
effigies
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b687525

Commits on Apr 23, 2021

FIX remove repetition in PET figure legend
Hboni
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297473f
FIX typos Dicom tag representation
Hboni
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c057764

Commits on Apr 27, 2021

ENH: add EEGLAB as valid coordinate system for EEG
sappelhoff
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ecf37c4
linebreak lint
sappelhoff
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ac33bd7
add EEGLAB-HJ
sappelhoff
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af0e1ed
fix link
sappelhoff
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dcceb2c
DOC: add section on LPA/RPA/..., consolidate links
sappelhoff
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9b10345
linter
sappelhoff
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dba308f
add info on HED key to common principles
sappelhoff
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7c977b9
HED field in data dict can also be str
sappelhoff
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892f087
[INFRA] add CI to find trailing whitespace
sappelhoff
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548fcd0
fix ci step
sappelhoff
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fea1194
remove gh action
sappelhoff
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6bbb42f
try remark-lint-no-trailing-spaces
sappelhoff
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37e486b
forgot comma
sappelhoff
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f5f4c36
STY: remove trailing whitespace
sappelhoff
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0fe2c7b
Merge remote-tracking branch 'upstream/master' into enh/fieldmaps-refactor
effigies
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8d862e7

Commits on Apr 28, 2021

Commits on Apr 29, 2021

Commits on Apr 30, 2021

Merge pull request #775 from sappelhoff/eeglab
sappelhoff
authored
3c5a162
[DOC] Auto-generate changelog entry for PR #775
bids-maintenance
committed
4327eb7

Commits on May 3, 2021

Merge pull request #777 from sappelhoff/hed
sappelhoff
authored
6da6bd5
[DOC] Auto-generate changelog entry for PR #777
bids-maintenance
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177f980

Commits on May 7, 2021

add link to README template
sappelhoff
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22c79d4
ignore temporary pdf build output
sappelhoff
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05c5387
remove superfluous brackets in script
sappelhoff
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8ba9a5a
add pandoc metadata.yml file for easier settings
sappelhoff
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08b3893
color every other row in tables
sappelhoff
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b03d1ae
fix: exclude some MD files from pdf
sappelhoff
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714a109
remove unused listings settings PDF
sappelhoff
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cf4bba5
break table to check ci
sappelhoff
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a02292b
do not install remark and remark-lint: remark-cli should suffice
sappelhoff
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d7c32db
fix linter
sappelhoff
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8789973
try pointing to pkgs locally
sappelhoff
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fd2855a
replace travis badge with gh actions, circleci svg->shield style
sappelhoff
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055cd3c
Revert "try pointing to pkgs locally"
sappelhoff
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b35ba9f
adjustments
sappelhoff
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7abac19
go back to npx
sappelhoff
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136ce75

Commits on May 8, 2021

try to add remark-gfm
sappelhoff
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5cd000c
remove debug comment
sappelhoff
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f56518c
massive commit: fix linter
sappelhoff
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fced729

Commits on May 10, 2021

Merge pull request #791 from sappelhoff/ci
Remi-Gau
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39926d1
[DOC] Auto-generate changelog entry for PR #791
bids-maintenance
committed
9a81c47

Commits on May 14, 2021

Merge pull request #794 from sappelhoff/pdf/tables
sappelhoff
authored
4a42f0b
[DOC] Auto-generate changelog entry for PR #794
bids-maintenance
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319e83d
Merge pull request #793 from sappelhoff/readme/template
sappelhoff
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c4489cd
[DOC] Auto-generate changelog entry for PR #793
bids-maintenance
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81eebff
Merge branch 'master' into master
sappelhoff
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5822d98
STY: align table pipes
sappelhoff
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e6ba1e2
consistency: DICOM Tag \d+, \d+
sappelhoff
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8f0b46d
add ietf standard link for json, closes #748
sappelhoff
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3353736

Commits on May 19, 2021

Update src/schema/entities.yaml

sappelhoff
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effigies
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8b8fd5d
catch some missing tags w/o space
sappelhoff
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de658ea
danteev/texlive was updated and fails now. try force py3
sappelhoff
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c41c270
get pip via apt
sappelhoff
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57970a5
apt, not apt-get. whatever the difference is.
sappelhoff
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1fd068a
need to apt update before installing
sappelhoff
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39fc3cc
force install without yes/no prompt
sappelhoff
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ee9f1e1

Commits on May 20, 2021

Merge pull request #786 from Hboni/master
sappelhoff
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f7fd3c2
[DOC] Auto-generate changelog entry for PR #786
bids-maintenance
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93c7951
Update src/02-common-principles.md
sappelhoff
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db8a14c
Merge pull request #797 from sappelhoff/json
sappelhoff
authored
d46b281
[DOC] Auto-generate changelog entry for PR #797
bids-maintenance
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6812fec
ieeg: deprecate DCOffsetCorrection
sappelhoff
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40acd09
clarify that entities MUST be unique
sappelhoff
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a66e36e

Commits on May 21, 2021

events: make MRI-centric language more general
sappelhoff
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46b03a8
cont. and phys: add link
sappelhoff
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2217185
fix link
sappelhoff
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6def797
Update src/04-modality-specific-files/05-task-events.md

sappelhoff
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Remi-Gau
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c8b1100

Commits on May 22, 2021

Commits on May 25, 2021

Merge pull request #800 from sappelhoff/entities/clarify/duplication
sappelhoff
authored
afee589
[DOC] Auto-generate changelog entry for PR #800
bids-maintenance
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af00f73
STY: fix trailing whitespace
sappelhoff
authored
761ef0c
Merge pull request #463 from yarikoptic/bf-surface
sappelhoff
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2b43d5b
[DOC] Auto-generate changelog entry for PR #463
bids-maintenance
committed
c043412
move deprecated field to bottom of table
sappelhoff
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d2c28f2
Apply suggestions from code review

sappelhoff
and
effigies
authored
66133d9

Commits on May 26, 2021

Commits on May 27, 2021

Commits on May 31, 2021

fix: md style link
sappelhoff
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63db4a8

Commits on Jun 1, 2021

Change composite instance to measurement in EEG
rob-luke
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51a1fe1
Change composite instance to measurement in iEEG
rob-luke
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897e36f
Change composite instance to measurement in MEG
rob-luke
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c7f7327
Remove composite instance from phys
rob-luke
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fbda604
Fix plural
rob-luke
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01a0424
Update 04-intracranial-electroencephalography.md
rob-luke
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9d94096
Update 03-electroencephalography.md
rob-luke
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cd5833f
boldify table headers
Remi-Gau
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0987e29
fix table fences
Remi-Gau
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33ab10b
fix cell padding
Remi-Gau
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0e90497
fix cell padding
Remi-Gau
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67fc366
sty in contributor page
Remi-Gau
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094d1ed
revert change to table in contributors
Remi-Gau
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9b4dce7
Merge pull request #815 from Remi-Gau/bold_table-header
sappelhoff
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e0ad5cd
[DOC] Auto-generate changelog entry for PR #815
bids-maintenance
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168cbad

Commits on Jun 8, 2021

update datatypes in common principles: pet
sappelhoff
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ce44a13
update modalities in README
sappelhoff
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b8dcec2
mkdocs: set site_url
sappelhoff
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34186f8
append en/stable/ to site_url: will it break 'latest'?
sappelhoff
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f57daf2
add perf
sappelhoff
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632ff7f
Merge pull request #819 from sappelhoff/fix/datatypes/update
sappelhoff
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17b5444
[DOC] Auto-generate changelog entry for PR #819
bids-maintenance
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cf5d192
Update 03-electroencephalography.md
rob-luke
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0d5f92c
Update 06-physiological-and-other-continuous-recordings.md
rob-luke
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ceccad4
Merge remote-tracking branch 'upstream/master' into composite-measurement
rob-luke
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6c85be7

Commits on Jun 9, 2021

Commits on Jun 10, 2021

fix: inconsistency in ieeg table and text
sappelhoff
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78a8a66
PET: clarify that time column must be first in blood tsv
sappelhoff
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c1c3d89

Commits on Jun 11, 2021

Commits on Jun 14, 2021

Merge remote-tracking branch 'upstream/master' into bep-016
effigies
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