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[FIX] fix force false skipped when unzipping files #584

Merged
merged 1 commit into from
Jun 18, 2023
Merged

[FIX] fix force false skipped when unzipping files #584

merged 1 commit into from
Jun 18, 2023

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Remi-Gau
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fix #572

@Remi-Gau Remi-Gau linked an issue Jun 18, 2023 that may be closed by this pull request
gzipped source files interfering with 'force'=false when copying #572
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@Remi-Gau Remi-Gau merged commit d97d8df into bids-standard:dev Jun 18, 2023
@Remi-Gau Remi-Gau deleted the fix/gzip branch June 18, 2023 15:55
Remi-Gau added a commit that referenced this pull request Nov 20, 2023
@Remi-Gau @pre-commit-ci
@allcontributors @effigies @dependabot @github-actions @nbeliy
[MAINT] pre-release 0.2.0 (#647)
b2b698c 
* add transformers to label and merge identical rows

* update doc

* refactor

* add cumulative behavior to label indentical rows

* refactor

* expand behavior of label rows to support cell type for columns

* add tests for merge rows

* FCI

* FCI

* add inequality to Filter transformer

* support regex for Replace transformers

* update docs

* refactor

* add possibility to generate json version of transformers

* add demo transformers split by trials

* update help sections

* update code to adapt to new schema

* fix entity order bug

* return only one datatypes when they are duplicates

* set file modality in constructor

* get definition will look into metadata if it returns empty in colums

* rm old CI

* remove labels from dependabot config

* fix test that delete schema

* make layout more verbose

* make layout more versbose and make warning mosre useful

* only display a . for actually indexed modality

* fix octave bug

* add function to create basic participant.tsv

* silence warning test for octave

* make query warning more explicit

* add extra model validation

* revert 21a9a9e

* retry more informative error on metadata query

* remove some old copyrights

* lint

* use new copyright format

* update doc

* bring back images for contributing

* fix typo

* update demos

* update notebooks and convert to matlab scripts

* update notebooks

* add test workflow

* FCI

* FCI

* fix notebooks

* Update demos/working_with_files.m

* update doc

* FCI

* switch back to isdir to see if older octave is happier with this

* update README

* update create participants.tsv

* update image path

* fix copyright line skip

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

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

* fix spelling

* fix report tests

* update create participants

* add create session tsv

* fix test

* update test

* update bids init

* refactor create readme

* update create readme

* add extra columns sessions.tsv

* add doc arguments

* lint

* improve test and messages

* fix some test

* exclude some files from scans.tsv

* refactor tests

* fix octave warning

* silence warning test on octave

* skip bids validation with octave for now

* skip failing matlab test

* simplify test

* windows related fixes

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

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

* skip octave test

* improve error message

* fix octave test

* fix listing of trial types

* improve default stats model when no task present

* silence test for warning under octave

* fix creation of json for derivatives when entity labels are numbers

* make download more robust

* skip warning test for octave

* reformat windows path when printing to avoiding escaped characters warnings

* improve error message on query

* fix create sessions and participants tsv

* add potential datalad related hints when file writing fails

* fix typo

* improve error message

* silence codespell

* silence octave warning

* improve transformers

* add response time histogram

* add get root node method

* refactor

* use bids stats model to plot events

* fix code spell and octave bug

* fix miss hit config

* remove comment

* fix download face rep dataset

* better handle datalad datasets

* validate folder name in bids.init

* fix cell indexing

* fix cell indexing

* update doc

* add diagnostic for events

* improve figure saving

* update doc

* rename transformers tests

* refactor tests

* silence writing tranformers test definitions

* move logical operation as compute opertion

* update transformer test description

* update facerep

* add versbosity options to reports

* add flag to all figures

* add filter to layout to only index certain subjects, sessions, modalities

* use filtering of layout

* fix when no filter

* use regexp

* fix when to use regex

* improve octave support of transformers

* rm some tests skip for octave

* stop using moxunit

* refactor ci

* change action version

* use bids validator with octave

* fix octace in ci

* add JSONio to octave path

* add quotes

* fiw path

* fix path

* fix dead links

* fix links

* update download

* update precommit

* fix tests

* make transformer more tolerant when filtering variable is missing

* [DOC] update bids.layout doc and return_file_index error message (#539)

* update doc

* add more detail when error happens in return_file_index

* update precommit

* update pre-commit and run on all files

* [ENH] update warning message on return_file_index failure (#540)

* update doc

* add more detail when error happens in return_file_index

* update precommit

* update pre-commit and run on all files

* update warning

* improve error message

* update info about gunzip (#547)

* [MAINT] back merge master (#549)

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

* CI: Use PAT to submit pull requests (#534)

This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions.

* Bump peter-evans/create-pull-request from 4 to 5 (#536)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v4...v5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

* [MAINT] update schema (#548)

* update schema

* readd token$

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [FIX] failing to return file index during dependencies indexing thorw warning and not error (#546)

* no file index throws warning and not error

* silence octave warning

* update doc (#554)

* [ENH] support querying for scans.tsv and sessions.tsv  (#550)

* add querying for scans

* add querying for sessions

* count sessions and scans as suffixes

* fix tests

* [ENH] allow to query directly for tsv content (#555)

* silence some warnings

* test error

* allow  query  of  participants (#557)

* [INFRA] run tests on mac OS and windows for matlab (#560)

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

* CI: Use PAT to submit pull requests (#534)

This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions.

* Bump peter-evans/create-pull-request from 4 to 5 (#536)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v4...v5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

* [MAINT] update schema (#548)

* update schema

* readd token$

* update ci (#558)

* split workflows matlab and octave

* fix

* use shorthand for commands

* skip coverage on windows

* [FIX] remove byte order mark from tsv file (#556)

* fix bom

* add data

* octave fix

* change the way CI is detected

* fix tests

* sanitize path in error

* [DATALAD] Recorded changes

* [DATALAD] Recorded changes

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [INFRA] randomize tests order (#566)

* randomize tests

* fix doc generation and links

* skip dead links

* skip dead links

* skip dead links

* skip dead links

* use temp_dir

* [MAINT] update schema dev (#580)

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

* CI: Use PAT to submit pull requests (#534)

This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions.

* Bump peter-evans/create-pull-request from 4 to 5 (#536)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v4...v5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

* [MAINT] update schema (#548)

* update schema

* readd token$

* update ci (#558)

* [FIX] remove byte order mark from tsv file (#556)

* fix bom

* add data

* octave fix

* Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570)

Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0.
- [Release notes](https://github.com/matlab-actions/run-command/releases)
- [Commits](matlab-actions/run-command@v1.1.3...v1.2.0)

---
updated-dependencies:
- dependency-name: matlab-actions/run-command
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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

* [MAINT] update schema (#577)

* update schema

* rm token

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [ENH] give more meaningful error messsages when failing to read json (#582)

* add warning mentioning which json files could not be read

* add file not found erro

* fix force false skipped when unzipping files (#584)

* [DOC] update help of several functions (#583)

* update doc

* update example

* fixes

* [ENH] add electrodes and optodes as group dependencies (#586)

* add electrodes and optodes as dependencies

* inline function

* fix

* allow indexing of files missing session entity when schemaless (#598)

* improve wrong dir message (#601)

* [ENH] index and query phenotype (#590)

* index and query phenotype

* do not load content and metadata

* [ENH] do not add subject to layout if it is empty (#600)

* do not add subject to layout if it is empty

* subject is in structure if schemaless

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

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

* refactor

* get properties and not fields when dealing with bids.File instance

* rerun

* silence failing tests on windows

---------

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

* [MAINT] Update from main (#606)

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

* CI: Use PAT to submit pull requests (#534)

This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions.

* Bump peter-evans/create-pull-request from 4 to 5 (#536)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v4...v5)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

* [MAINT] update schema (#548)

* update schema

* readd token$

* update ci (#558)

* [FIX] remove byte order mark from tsv file (#556)

* fix bom

* add data

* octave fix

* Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570)

Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0.
- [Release notes](https://github.com/matlab-actions/run-command/releases)
- [Commits](matlab-actions/run-command@v1.1.3...v1.2.0)

---
updated-dependencies:
- dependency-name: matlab-actions/run-command
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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

* [MAINT] update schema (#577)

* update schema

* rm token

* docs: add coxroy as a contributor for bug, ideas, and userTesting (#585)

* docs: update README.md [skip ci]

* docs: update .all-contributorsrc [skip ci]

---------

Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>

* BIDS schema update (#587)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#592)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#594)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* Bump matlab-actions/run-command from 1.2.0 to 1.2.1 (#602)

Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/matlab-actions/run-command/releases)
- [Commits](matlab-actions/run-command@v1.2.0...v1.2.1)

---
updated-dependencies:
- dependency-name: matlab-actions/run-command
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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

* [FIX] handle nan and and datetimes when printing tables (#605)

* fix bugs in tables and datetimes

* skip on windows

* update schema

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* [ENH] use inheritance in get_meta_list (#609)

* use inheritance in get_meta_list

* refactor

* [ENH] improve bids schema api (#610)

* improve API

* add doc

* skip octave for test

* [FIX] better handle printing of paths in windows (#611)

* better handle printting of paths in windows

* fix more paths

* more clean up

* fix more paths

* fix bug with unsorted model (#613)

* add info about skipped tests (#614)

* Incorporating json into bids.File (issues #596 #371) (#597)

* First attempt to incorporate json into bids.File

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

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

* lint

* Added util function to update structures

* Style and tests for util/update_struct.m

* Using metadata field instead of json_struct

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

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

* Removed JSONFile subclass

* Added tests for metadata for File class

* Fixed spelling in doc

* File: Added functions that act on individual fields

* File: fixed style

* Splitted File.metadada tests into smaller ones

---------

Co-authored-by: Beliy Nikita <beliy.nikita@uliege.be>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* add id to warning

* fix bug with 2 json file for one level (#616)

* [ENH] improve performance and testing (#618)

* update timing

* try speed up test by not indexing dependencies

* run on latest and oldest matlab

* [DATALAD] Recorded changes

* [DATALAD] Recorded changes

* cancel previous runs

* speed up some tests or functions

* run slow and fast tests in parallel

* windows env var fix

* try using globals

* fix

* add more slow test

* add doc

* update demo (#621)

* update demo

* doc changes

* [ENH] remove atlas and update res and den metadata (#622)

* rm atlas and update res and den metadata

* fix

* [FIX] Fix tests after merge from master (#627)

* fix tests after merge from main

* fix test octave

* use objects for levels (#630)

* add internal function to start resolvig uri (#631)

* fix hed tags (#632)

* [MAINT] merge main in dev (#644)

* BIDS schema update (#628)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* Bump actions/checkout from 3 to 4 (#629)

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

* BIDS schema update (#633)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#634)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#635)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#636)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)

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

* BIDS schema update (#637)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#639)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* BIDS schema update (#640)

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* Bump matlab-actions/setup-matlab from 1.2.4 to 1.2.5 (#641)

Bumps [matlab-actions/setup-matlab](https://github.com/matlab-actions/setup-matlab) from 1.2.4 to 1.2.5.
- [Release notes](https://github.com/matlab-actions/setup-matlab/releases)
- [Commits](matlab-actions/setup-matlab@v1.2.4...v1.2.5)

---
updated-dependencies:
- dependency-name: matlab-actions/setup-matlab
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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

* Bump matlab-actions/run-command from 1.2.1 to 1.2.2 (#642)

Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.1 to 1.2.2.
- [Release notes](https://github.com/matlab-actions/run-command/releases)
- [Commits](matlab-actions/run-command@v1.2.1...v1.2.2)

---
updated-dependencies:
- dependency-name: matlab-actions/run-command
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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

* [FIX] update test after schema update (#643)

* fix test after schema update

* set os version for doc

* update schema

* fix typos

* update tests

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>
Co-authored-by: Nikita Beliy <beliy.nikita@outlook.com>
Co-authored-by: Beliy Nikita <beliy.nikita@uliege.be>
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gzipped source files interfering with 'force'=false when copying
1 participant
@Remi-Gau