Brainstem client doc update

[petersenpeter]

No description provided.

[Copilot]

Pull request overview

Updates BrainSTEM documentation to reflect the current “API tools” client surface and authentication flow, aligning tutorials and endpoint references with the brainstem_api_tools BrainstemClient.

Changes:

• Replace legacy brainstem_api_client + load_model/save_model/delete_model examples with brainstem_api_tools + load/save/delete.
• Refresh auth docs to describe Personal Access Tokens and the browser-based device authorization flow (incl. headless flow).
• Replace hard-coded UUID examples with <id>-style placeholders across API reference pages.

Reviewed changes

Copilot reviewed 45 out of 45 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
docs/tutorials/two-photon-imaging-workflow.md	Updates Python snippet to use brainstem_api_tools and client.load(...) with dot-notation filters.
docs/tutorials/managing-data-storage.md	Migrates examples to client.load(...) and brainstem_api_tools; includes updated MATLAB snippet usage.
docs/tutorials/electrophysiology-workflow.md	Migrates workflow API-access snippet to client.load(...) and updates model names/filters.
docs/api/users/user.md	Switches user endpoint examples to load/save/delete.
docs/api/users/laboratory.md	Switches laboratory endpoint examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/users/group_membership_request.md	Switches group membership request examples to load and replaces concrete IDs with placeholders.
docs/api/users/group_membership_invitation.md	Switches group membership invitation examples to load and replaces concrete IDs with placeholders.
docs/api/users/group.md	Switches group endpoint examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/strain.md	Switches strain/strainapproval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/species.md	Switches species/speciesapproval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/setuptype.md	Switches setuptype/setuptypeapproval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/regulatoryauthority.md	Switches regulatoryauthority/approval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/brainregion.md	Switches brainregion examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/behavioralparadigm.md	Switches behavioralparadigm/approval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/taxonomies/behavioralcategory.md	Switches behavioralcategory/approval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/subject.md	Switches subject examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/session.md	Switches session examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/project_membership_invitation.md	Switches project membership invitation examples to load and replaces concrete IDs with placeholders.
docs/api/stem/project_group_membership_invitation.md	Switches project group membership invitation examples to load and replaces concrete IDs with placeholders.
docs/api/stem/project.md	Switches project examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/collection.md	Switches collection examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/cohort.md	Switches cohort examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/stem/breeding.md	Switches breeding examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/resources/supplier.md	Switches supplier/supplierapproval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/resources/hardwaredevice.md	Switches hardwaredevice/approval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/resources/consumable.md	Switches consumable/approval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/personal_attributes/setup.md	Switches setup examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/personal_attributes/license.md	Switches license examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/personal_attributes/inventory.md	Switches inventory examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/personal_attributes/datastorage.md	Switches datastorage examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/personal_attributes/behavioralassay.md	Switches behavioralassay examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/subjectlog.md	Switches subjectlog examples to load/save/delete (incl. options actions) and replaces concrete IDs with placeholders.
docs/api/modules/procedurelog.md	Switches procedurelog examples to load/save/delete (incl. options actions) and replaces concrete IDs with placeholders.
docs/api/modules/procedure.md	Switches procedure examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/manipulation.md	Switches manipulation examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/equipment.md	Switches equipment examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/dataacquisition.md	Switches dataacquisition examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/consumablestock.md	Switches consumablestock examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/modules/behavior.md	Switches behavior examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/dissemination/publication.md	Switches publication examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api/dissemination/journal.md	Switches journal/journalapproval examples to load/save/delete and replaces concrete IDs with placeholders.
docs/api.md	Rewrites token management docs around PATs + device auth flow; updates example URLs/placeholders.
docs/api-tools/python-api-tool.md	Updates Python tool docs for device auth, load/save/delete, pagination, and convenience loaders.
docs/api-tools/matlab-api-tool.md	Updates MATLAB tool docs for device auth, BrainstemClient usage, and convenience loaders.
docs/api-tools.md	Adds a short note about PAT + browser-based device auth across tools.

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