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Update master #6

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agahkarakuzu merged 4 commits intobids-bep001:entity-inv-mtfrom
bids-standard:master
Nov 23, 2020
Merged

Update master #6
agahkarakuzu merged 4 commits intobids-bep001:entity-inv-mtfrom
bids-standard:master

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Pull the latest upstream.

effigies and others added 4 commits November 17, 2020 09:55
* MNT: Relax line length limit in YAML

* MNT: Ignore pycache in tools dir

* CI: Update configuration based on Travis validator

Also bump Python version and cache pip
* Add derivatives entities.

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Differentiate derivative entities from raw entities.

* Update entities page.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
* Add part entity.

* Add self to contributors file.

* Address @yarikoptic's review.

* Fix entity table spacing.

* Add missing OPTIONAL for part under func (bold phase).

* Fix spacing again.

* Remove OPTIONAL under func (bold phase). Wasn't missing.

* Fix entity order (part goes after run).

* Fix typo.

* Incorporate part into schema.

* Update definition and examples to match BEP001.

* Fix code snippets.

* Fix filename patterns now that real/imag is supported.

* Apply suggestions from code review

- Change radians to rad.
- Treat `part` like `run`. Can only be omitted if only magnitude image is provided.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Support part with BOLD and update entity table.

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update entity table and entity definitions.

* Add link in text.

* Remove section header.

* Address review.

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

* Deprecate phase suffix.

* Fix link.

* Fix link again.

* Include deprecation in table.

* Fix table.

* Update 01-magnetic-resonance-imaging-data.md

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Add entity field.

* Fix bug and generate appendix.

* Fix table.

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Improve part definition.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
* [ENH] Add flip entity

- Modify `echo` entity respectively

* revert entities.md and update the schema

* Use schema tools

* [FIX] Format field

* Update src/schema/entities.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/schema/entities.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Wording suggestion by @tsalo

* [ENH] Add flip entity

- Modify `echo` entity respectively

* revert entities.md and update the schema

* Use schema tools

* [FIX] Format field

* Update src/schema/entities.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/schema/entities.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Wording suggestion by @tsalo

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
@agahkarakuzu agahkarakuzu merged commit 436791d into bids-bep001:entity-inv-mt Nov 23, 2020
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3 participants