… _acq-

…t was missing

otherwise "Electrophysiology" is too broad. Thanks @dorahermes for the note

…yout not BEP032

…ext menu

I think this is what might have freaked out `schemacode_ci / windows-latest with Python 3 (pull_request) ` (windows only!) fails with a bunch of

```
2024-04-19T19:13:44.2815607Z self = <encodings.cp1252.IncrementalDecoder object at 0x0000028D6A14D850>
2024-04-19T19:13:44.2818292Z input = b'---\nHED:\n  name: HED\n  display_name: HED Tag\n  description: |\n    Hierarchical Event Descriptor (HED) Tag.\n   ...ed or ideal position along the z axis.\n  anyOf:\n    - type: number\n    - type: string\n      enum:\n        - n/a\n'
2024-04-19T19:13:44.2820386Z final = True
2024-04-19T19:13:44.2820609Z
2024-04-19T19:13:44.2820821Z     def decode(self, input, final=False):
2024-04-19T19:13:44.2821664Z >       return codecs.charmap_decode(input,self.errors,decoding_table)[0]
2024-04-19T19:13:44.2823260Z E       UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 2105: character maps to <undefined>
2024-04-19T19:13:44.2824229Z
2024-04-19T19:13:44.2824768Z C:\hostedtoolcache\windows\Python\3.12.3\x64\Lib\encodings\cp1252.py:23: UnicodeDecodeError
```

…w others

…es (#1806)

* RF: to have "microephys" (Microelectrode physiology) for modality and icephys and ecephys for suffixes and datatypes

* Reflecting decision of having two separate datatypes under the Microelectrode Electrophysiology

#1800 (comment)

Consensus reached during working group meeting on 2024-05-15:

- modality = "Microelectrode Electrophysiology"
- datatypes = "icephys" and "ecephys"
- suffixes = "_icephys" and "_ecephys"

* Adjust wording to Horea's recommendation

* Various fixups and tune ups to wording from code review

…ctrode Electrophysiology

* test

* MACROS___make_suffix_table

* markdown

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

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* undoing changes to yaml files

* adding chanell

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

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* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/modality-specific-files/microelectrode-electrophysiology.md

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* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/modality-specific-files/microelectrode-electrophysiology.md

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* adding General ephys metadata

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

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* Examples of real datasets

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

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* Minor tuneups to formatting

---------

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* [FIX] Minor YAML formatting

* [ENH] Added additional birthdate column for participants.tsv

* [ENH] Added age_category, age_type and corresponding enums

* [ENH] Added surgery_date column

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

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* Reverted changes that better suit in a PR against master

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

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* [ENH] Added tabular_data file and columns for _probes.tsv

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

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* [ENH] Added tabular_data rules and columns for _electrodes.tsv

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

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* [ENH] Added tabular_data rules for _electrodes.tsv

* [ENH] Added tabular_data rules and columns for _channels.tsv

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

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

* [FIX] Fixed pre-commit errors

* [ENH] Added additional ephys columns for events.tsv

* [ENH] Added tabular data rules for events.tsv to include ephys related columns

* [ENH] Added metadata entities for ephys setup metadata

* [ENH] Created sidecar rule file for ephys metadata and added data origin and setup fields

* Made schema changes to match microephys data type

* Renamed rule files from ephys to microephys

* Made schema changes to match microephys data type

* [ENH] Added objects and rules for coordinate system sidecar file

* [ENH] Added processing microephys metadata field in rules

* [ENH] Added pharmaceuticals microephys metadata field in rules

* [ENH] Added supplementary  microephys metadata field and rules

* [ENH] Added sample microephys metadata rules

* [ENH] Added task microephys metadata rules

* Fixed example language convention

* Added microephys in schema rule modality

* Corrected SampleThickness to SliceThickness

* Add yaml document separator for microephys rules file

It is optional, and adding does not solve anything but makes it
consistent with the other files in the folder

* BF: should be a dict, not a list of dicts

---------

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

* origin/master: (288 commits)
  chore(deps): bump codecov/codecov-action from 4 to 5 (#1989)
  chore: Bump schema post-dev version
  schema-0.11.3.post3
  chore(ci): Fix pytest call for make_archive
  chore: Remove excess test data from bidsschematools installation directories (#1985)
  feat(cli): Add tool for filename validation for use in pre-receive hooks (#1986)
  rm COC (#1979)
  chore: Bump schema post-dev version
  schema-0.11.3.post2
  Update CONTRIBUTING.md (#1978)
  fix(schema): Check SliceTiming length against SliceEncodingDirection
  fix(schema): Do not warn about missing events for task-noise
  fix(schema): Check for existence of stim_files in beh.tsv
  chore: Use GITHUB_REF(_NAME) correctly
  chore: Debug environment
  chore: Bump schema post-dev version
  schema-0.11.3.post1
  chore: Output version, set correct env var
  chore: Update publish_schema to publish post-releases
  fix(schema): Include changes to schema that do not modify spec
  ...

 Conflicts:
	mkdocs.yml
	src/schema/objects/columns.yaml
	src/schema/objects/metadata.yaml
	src/schema/objects/modalities.yaml
	src/schema/objects/suffixes.yaml
	src/schema/rules/modalities.yaml

* origin/master: (26 commits)
  Update tools/schemacode/src/bidsschematools/types/namespace.py
  fail build on macro fails
  graceful error when failing to load invalid yml
  fix
  Update mkdocs.yml
  fix
  more seg
  Update src/modality-specific-files/electroencephalography.md
  fix channel, elec, sim recording
  fix key value and in-out
  fix tabular and seg
  reset
  fix internal links
  enh: Link all DICOM tags following standard pattern
  chore(links): Fix http -> https 301 redirects
  Update Release_Protocol.md (#1997)
  schema-1.0.1-dev
  schema-1.0.0
  [SCHEMA] Allow physio files for anat datatype (#1961)
  FIX: Add 1.10.0 to known versions list (#1994)
  ...

…tion

Co-authored-by: Peyman Najafi <najafe.peyman@gmail.com>

* cutting line lenghts

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

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* marking json examples

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

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* microephysChannels

---------

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Co-authored-by: Thomas Wachtler <wachtler@bio.lmu.de>

Co-authored-by: Thomas Wachtler <wachtler@bio.lmu.de>

…ze probe_name

…es.tsv file

…trophysiology documentation

…croelectrode electrophysiology documentation

…ication into bep032

Co-authored-by: Thomas Wachtler <wachtler@bio.lmu.de>

Co-authored-by: Thomas Wachtler <wachtler@bio.lmu.de>

Add electrode_name column to the extracellular electrophysiology
channels.tsv example to show the mapping between channels and
their corresponding electrodes.

…s schema

…al Coordinates appendix to markdown

…for consistency

- Fix WaxholmSpace species from rat to mouse and update DOI reference
- Remove RRID links from SwansonRat, CHARM, D99, and MarmosetBrainAtlas
- Add DOI link for SwansonRat reference
- Correct PaxinosRhesusMonkey author list (Toga AW -> Evrard, H)