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Refactor package for unified data and device API - #5

Merged

glopesdev merged 280 commits into

mainfrom

refactor-unified-api

Jul 24, 2026

Merged

Refactor package for unified data and device API#5
glopesdev merged 280 commits into
mainfrom
refactor-unified-api

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 12, 2025
- remove unused import
  patricklatimer
  committed
  0d993bb
- undo formatting change
  patricklatimer
  committed
  583a270
- remove python-versions pin
  patricklatimer
  committed
  556e512
Commits on Feb 13, 2025
- add future import for list annotations
  patricklatimer
  committed
  efdefc5
- fix future import
  patricklatimer
  committed
  0a15ab2
- Merge pull request #4 from AllenNeuralDynamics/feat/threading
  Poofjunior
  authored
  7281aca
Commits on Feb 21, 2025
- update wait-for-events example
  Poofjunior
  committed
  c68f87b
- remove extraneous call
  Poofjunior
  committed
  de151be
Commits on Feb 22, 2025
- Merge pull request #5 from AllenNeuralDynamics/feat/example_update
  Poofjunior
  authored
  e3c338d
Commits on Mar 19, 2025
- Convert project to uv
  MicBoucinha
  committed
  e86eb29
- Define docstyle convention
  MicBoucinha
  committed
  0163e17
- Update default vscode settings
  ZegCricket
  committed
  15ac05e
- Add docs to the project
  ZegCricket
  committed
  efceffd
- Delete poetry.lock
  ZegCricket
  committed
  627b1db
- Update .gitignore and README
  ZegCricket
  committed
  23a2c08
Commits on Mar 20, 2025
- Merge pull request #1 from fchampalimaud/feature/docs_init
  MicBoucinha
  authored
  c9a1615
Commits on Mar 24, 2025
- Chore: remove shebangs from example scripts
  ZegCricket
  committed
  b121ab1
Commits on Mar 25, 2025
- Cleanup unused code
  MicBoucinha
  committed
  3f1b5f8
- Remove ReadXXHarpMessage classes
  MicBoucinha
  committed
  2e4f216
- Move base classes
  MicBoucinha
  committed
  00217d4
- Formatting
  MicBoucinha
  committed
  2716ce8
- Update protocol link
  MicBoucinha
  committed
  0f57b08
- Convert usage of ReadXX classes to device related methods
  MicBoucinha
  committed
  9b86a45
- Remove ReadXX methods from HarpMessage
  MicBoucinha
  committed
  bcfcf3c
- Extract unrelated Enum members
  MicBoucinha
  committed
  f474503
- Add read_S64 and read_U64 methods to Device
  MicBoucinha
  committed
  ab0a7da
- Create write_XXX methods on Device
  MicBoucinha
  committed
  0859612
- Merge branch 'feature/refactor_messages' into develop
  MicBoucinha
  committed
  a7f595c
Commits on Apr 2, 2025
- Add dump parameter to Device's write methods
  MicBoucinha
  committed
  472e1a5
- Change default name and changed visibility of control registers methods
  MicBoucinha
  committed
  904040d
- Refactor timeout assignment and correct payload string formatting
  MicBoucinha
  committed
  4af5567
- Update current_device_names
  MicBoucinha
  committed
  a2b8cc0
- Add support for device's serial number
  MicBoucinha
  committed
  45ee965
- Remove unused method
  MicBoucinha
  committed
  20c2c59
- Update README
  MicBoucinha
  committed
  1aecf2a
- Update documentation dependencies
  MicBoucinha
  committed
  b9819aa
- Update mkdocs configuration
  MicBoucinha
  committed
  2ca3e4f
- Move examples to documentation folder
  MicBoucinha
  committed
  fb78b31
- Update documentation
  MicBoucinha
  committed
  4dd42e8
- Add context manager support to Device class
  MicBoucinha
  committed
  8cd50ad
Commits on Apr 4, 2025
- Chore: add pytest configs to vscode workspace settings
  ZegCricket
  committed
  13924db
- Docs: separate examples in different pages
  ZegCricket
  committed
  413f36c
- Docs: modify documentation organizational, functional and visual aspects
  ZegCricket
  committed
  f0266cc
- Docs: modify home page
  ZegCricket
  committed
  53b41a4
- Test: comment incorrect tests to fix in the future
  ZegCricket
  committed
  b80d79b
- Docs: add documentation to HarpMessage and Device classes
  ZegCricket
  committed
  d87c1ae
- Refactor: change base.py enums to IntEnums
  ZegCricket
  committed
  56b9df3
- Refactor: rename functions to follow a consistent naming pattern
  ZegCricket
  committed
  c677429
- Refactor: move DeviceMode to base.py
  ZegCricket
  committed
  74dd5c4
- Refactor: make some class members private
  ZegCricket
  committed
  df43bde
- Refactor: modify way of sending write harp messages
  ZegCricket
  committed
  27dc1c8
- Refactor: misc changes
  ZegCricket
  committed
  355e90c
Commits on Apr 6, 2025
- Feature: add HarpMessage.create static method
  ZegCricket
  committed
  2adbdc3
- Docs: add comments to the remaining code
  ZegCricket
  committed
  152a28d
- Feature: add classes in base.py to root pyharp namespace
  ZegCricket
  committed
  09e0dd6
- Feature: remove read_xx and write_xx Device methods
  ZegCricket
  committed
  c7fea61
- Docs: reorganize examples section
  ZegCricket
  committed
  8f52e90
- Docs: add olfactometer example
  ZegCricket
  committed
  c853f05
- Docs: add pyharp core API to documentation
  ZegCricket
  committed
  5c77aa6
Commits on Apr 9, 2025
- Merge branch 'feature/update_docs' into develop
  MicBoucinha
  committed
  70d4bbf
- Change dump file usage convention
  MicBoucinha
  committed
  299b4d0
- Change DeviceMode to OperationMode for official Harp documentation coherence
  MicBoucinha
  committed
  b924837
- Change return type of Device's send method
  MicBoucinha
  committed
  1d12633
- Update and add missing OperationControl methods
  MicBoucinha
  committed
  98046e6
- Update docs links
  MicBoucinha
  committed
  9959cdd
- Fix doc link
  MicBoucinha
  committed
  61c2562
- Comment device tests
  MicBoucinha
  committed
  d1ef6e0
- Add pytest-cov dev dependency
  MicBoucinha
  committed
  4398024
- Add is_error to HarpMessage
  MicBoucinha
  committed
  9c04d72
Commits on Apr 16, 2025
- Read Timestamp entry for PayloadType
  MicBoucinha
  committed
  960ce9c
- Handle HarpMessage with arrays and timestamps
  
  MicBoucinha
  and
  ZegCricket
  committed
  bfcb9ec
Commits on Apr 23, 2025
- Restore read and write methods from Device
  
  MicBoucinha
  and
  ZegCricket
  committed
  7223e0c
- Remove dump from send method
  
  MicBoucinha
  and
  ZegCricket
  committed
  3f7922f
- Add ClockConfig and TimestampOffset
  
  MicBoucinha
  and
  ZegCricket
  committed
  924997b
- Add OperationCtrl and ResetMode
  
  MicBoucinha
  and
  ZegCricket
  committed
  3c21927
- Allow Port control
  
  MicBoucinha
  and
  ZegCricket
  committed
  ec85295
- Fix issue with payload property
  
  MicBoucinha
  and
  ZegCricket
  committed
  be6f11c
- Update payload_as_string
  
  MicBoucinha
  and
  ZegCricket
  committed
  de5a799
- Update CommonRegisters members name
  
  MicBoucinha
  and
  ZegCricket
  committed
  542de32
- Update send method to receive HarpMessage
  
  MicBoucinha
  and
  ZegCricket
  committed
  5796621
- Remove unused methods
  
  MicBoucinha
  and
  ZegCricket
  committed
  6b69b65
- Fix bug with uninitialized fields and wrong property call
  
  MicBoucinha
  and
  ZegCricket
  committed
  897ffd3
Commits on Apr 30, 2025
- Fix bug on Device's send method
  
  MicBoucinha
  and
  ZegCricket
  committed
  9dfcf15
- Handle empty replies
  
  MicBoucinha
  and
  ZegCricket
  committed
  2fd965f
- Fix bug with str method
  
  MicBoucinha
  and
  ZegCricket
  committed
  4e3ee84
Commits on May 20, 2025
- Reformat
  MicBoucinha
  committed
  f310406
- Update pre-commit config
  MicBoucinha
  committed
  721fcb4
- Add monorepo-plugin to mkdocs
  MicBoucinha
  committed
  d6a886a
- Fix typo
  MicBoucinha
  committed
  0f7bb9f
Commits on May 22, 2025
- Test new module structure
  
  MicBoucinha
  and
  ZegCricket
  committed
  b977d7d
- Update project
  
  MicBoucinha
  and
  ZegCricket
  committed
  9e9a95a
- Merge branch 'feature/pyharp_namespace' into develop
  MicBoucinha
  committed
  47c3feb
- Delete behavior driver
  MicBoucinha
  committed
  b8e4bed
- Move device.py and harp_serial.py to communication folder
  MicBoucinha
  committed
  9aedecf
- Move core from docs to protocol
  MicBoucinha
  committed
  2ff6bc2
- Update docs links with correct namespaces
  MicBoucinha
  committed
  1ae9aee
- Remove duplicated extension from mkdocs config
  MicBoucinha
  committed
  55f38d3
- Minor fix on example
  MicBoucinha
  committed
  c1d1a59
Commits on May 23, 2025
- Update files to prevent circular imports
  MicBoucinha
  committed
  deef783
Commits on Jun 12, 2025
- Update project related information for pushing it to PyPI
  
  MicBoucinha
  and
  ZegCricket
  committed
  74daef6
Commits on Jun 30, 2025
- Change namespace to "harp"
  
  MicBoucinha
  and
  ZegCricket
  committed
  60bff12
- Update minimum Python version
  
  MicBoucinha
  and
  ZegCricket
  committed
  f50be32
- Add "include markdown plugin" to docs
  
  MicBoucinha
  and
  ZegCricket
  committed
  3cf6d12
- Update version
  
  MicBoucinha
  and
  ZegCricket
  committed
  c8af5a1
Commits on Jul 1, 2025
- Add dependency to handle dataclasses on documentation generation
  MicBoucinha
  committed
  01b42cf
- Update mkdocs config
  MicBoucinha
  committed
  7ec5518
Commits on Jul 2, 2025
- Update docs
  
  MicBoucinha
  and
  ZegCricket
  committed
  a97fd0a
- Add CurrentDriver to known device names
  
  MicBoucinha
  and
  ZegCricket
  committed
  d760086
- Reorder docs' TOC
  
  MicBoucinha
  and
  ZegCricket
  committed
  aca830a
- Remove type annotation on Enum
  
  MicBoucinha
  and
  ZegCricket
  committed
  2113d59
- Update version
  MicBoucinha
  committed
  ece40f7
Commits on Jul 3, 2025
- Add github action to build and deploy docs
  MicBoucinha
  committed
  3515020
Commits on Jul 18, 2025
- Update LICENSE
  
  MicBoucinha
  and
  ZegCricket
  committed
  47cfb1d
Commits on Aug 5, 2025
- Rename communication namespace to 'serial'
  MicBoucinha
  committed
  39e3ca3
- Remove unnecessary devices folder
  MicBoucinha
  committed
  4d9a3a4
Commits on Aug 27, 2025
- Fix issue with Visual_en flag
  
  MicBoucinha
  and
  ZegCricket
  committed
  efa5e04
- Fix documentation path for Device
  
  MicBoucinha
  and
  ZegCricket
  committed
  d27c226
- Implement a Timeout handling strategy
  
  MicBoucinha
  and
  ZegCricket
  committed
  77607ae
- Update payload handling taking into account the timeout strategy in send method
  
  MicBoucinha
  and
  ZegCricket
  committed
  11c47df
- Reorganize project directory structure
  
  MicBoucinha
  and
  ZegCricket
  committed
  a0be5e2
- Create workspaces for harp-protocol and harp-serial
  
  MicBoucinha
  and
  ZegCricket
  committed
  87a8b14
- Update docs
  
  MicBoucinha
  and
  ZegCricket
  committed
  9073f4c
- Chore: add pyrefly extension to `extensions.json`
  ZegCricket
  committed
  8c07844
- Chore: add script to run docs locally on Windows
  ZegCricket
  committed
  ee5aa32
- Add harp reference epoch constant
  ZegCricket
  committed
  594399a
- Fix issues with types
  ZegCricket
  committed
  93aa50c
- Docs: fix imports from examples to take the new project structure into account
  ZegCricket
  committed
  2481ec1
Commits on Sep 16, 2025
- Refactor: simplify WriteHarpMessage handling of PayloadType
  ZegCricket
  committed
  ea50e70
- Chore: add VSCode setting that enables pyrefly to display type errors
  ZegCricket
  committed
  713c934
- Removed custom message from exceptions
  MicBoucinha
  committed
  36ec9ad
- Pin harp-protocol version on harp-serial
  MicBoucinha
  committed
  3272e10
- Fix: raise HarpReadException for missing timestamp in ReplyHarpMessage
  
  MicBoucinha
  and
  ZegCricket
  committed
  34de54d
- Add LaserDriverController to device_names
  
  MicBoucinha
  and
  ZegCricket
  committed
  a107ebb
- Refactor payload handling in HarpMessage to properly support Python 3.9
  
  MicBoucinha
  and
  ZegCricket
  committed
  ed7388a
Commits on Sep 18, 2025
- Add operation_ctrl methods to device
  
  MicBoucinha
  and
  ZegCricket
  committed
  fbd7d64
- Update documentation
  
  MicBoucinha
  and
  ZegCricket
  committed
  af7e79f
- Fix tests
  
  MicBoucinha
  and
  ZegCricket
  committed
  5ea52bb
- Merge branch 'feature/workspaces' into develop
  MicBoucinha
  committed
  25f0445
Commits on Oct 8, 2025
- Remove unnecessary udev rules file
  
  MicBoucinha
  and
  ZegCricket
  committed
  d7a6a63
- Refactor HARP_VERSION to CORE_VERSION
  
  MicBoucinha
  and
  ZegCricket
  committed
  d454897
- Update documentation
  
  MicBoucinha
  and
  ZegCricket
  committed
  4162bff
- Refactor base.py enums for consistency and clarity
  
  MicBoucinha
  and
  ZegCricket
  committed
  6e714ec
Commits on Oct 9, 2025
- Refactor HarpMessage to consolidate message creation
  
  MicBoucinha
  and
  ZegCricket
  committed
  9a440b2
- Remove HarpMessage.create static method
  
  MicBoucinha
  and
  ZegCricket
  committed
  ed8fca5
Commits on Oct 17, 2025
- Refactor HarpMessage to remove ReplyHarpMessage
  
  MicBoucinha
  and
  ZegCricket
  committed
  78cce0e
- Refactor timeout variables
  
  MicBoucinha
  and
  ZegCricket
  committed
  6f97c92
- Rename HarpTimeoutError to HarpTimeoutException and add context to it
  
  MicBoucinha
  and
  ZegCricket
  committed
  1f24190
- Update comment
  
  MicBoucinha
  and
  ZegCricket
  committed
  36a8363
Commits on Oct 22, 2025
- Add HarpMessage context to Harp exceptions
  
  MicBoucinha
  and
  ZegCricket
  committed
  e97480c
- Remove constraint when creating HarpMessage
  
  MicBoucinha
  and
  ZegCricket
  committed
  8e84b3a
- Change build system
  
  MicBoucinha
  and
  ZegCricket
  committed
  aa564c7
- Remove device_names
  
  MicBoucinha
  and
  ZegCricket
  committed
  3d8d10d
- Handle potential serial connection errors
  
  MicBoucinha
  and
  ZegCricket
  committed
  ccdef2a
- Update minimum Python version
  
  MicBoucinha
  and
  ZegCricket
  committed
  c24c51f
Commits on Oct 23, 2025
- Fix: write events to dump file
  ZegCricket
  committed
  e1025d5
- Merge remote-tracking branch 'origin/feature/dump_events_to_file' into feature/pr_review_changes
  MicBoucinha
  committed
  5676d38
Commits on Oct 24, 2025
- Refactor to improve message reading and timeout handling in Device
  
  MicBoucinha
  and
  ZegCricket
  committed
  1fbfb2d
- Separate docs from dev dependencies
  
  MicBoucinha
  and
  ZegCricket
  committed
  5f62673
- Bump version of packages
  
  MicBoucinha
  and
  ZegCricket
  committed
  c61184b
- Update documentation
  
  MicBoucinha
  and
  ZegCricket
  committed
  7523b47
- Merge branch 'feature/pr_review_changes' into develop
  MicBoucinha
  committed
  ede6aa4
Commits on Nov 5, 2025
- Update docs
  
  MicBoucinha
  and
  ZegCricket
  committed
  6f5cde3
Commits on Apr 26, 2026
- Linting
  bruno-f-cruz
  committed
  bbe437d
- Replace serial by device package
  bruno-f-cruz
  committed
  1e7986e
- Refactor protocol and register api
  bruno-f-cruz
  committed
  4662050
- Add tests for protocol
  
  bruno-f-cruz
  and
  Copilot
  committed
  39f97ab
- Add unit tests for register api
  
  bruno-f-cruz
  and
  Copilot
  committed
  20e5317
Commits on Apr 27, 2026
- Improve string visualization for Payload
  
  bruno-f-cruz
  and
  Copilot
  committed
  1a70a59
- Add small integration test
  bruno-f-cruz
  committed
  39b9904
- Remove data type inference
  
  bruno-f-cruz
  and
  Copilot
  committed
  c070cf8
- Ignore .vscode folder
  
  bruno-f-cruz
  and
  Copilot
  committed
  92cf83d
- Linting
  
  bruno-f-cruz
  and
  Copilot
  committed
  66987d1
- Remove unused type checking guards
  
  bruno-f-cruz
  and
  Copilot
  committed
  3d4cbd4
- Improve type hinting
  
  bruno-f-cruz
  and
  Copilot
  committed
  53c4e73
- Avoid accessing private attribute
  
  bruno-f-cruz
  and
  Copilot
  committed
  bc1c0ea
- Make the mess uniform for now
  
  bruno-f-cruz
  and
  Copilot
  committed
  8e6f8dd
Commits on Apr 29, 2026
- Delete unused file
  bruno-f-cruz
  committed
  b622b71
- Raise error on returned messages with error bit flag
  bruno-f-cruz
  committed
  2f8aec9
Commits on Apr 30, 2026
- Add timestamp to format
  
  bruno-f-cruz
  and
  Copilot
  committed
  ed599b3
- Add example script and refactor payload classes for clarity and consistency
  bruno-f-cruz
  committed
  2e6f5ed
Commits on May 9, 2026
- Add BitField types
  bruno-f-cruz
  committed
  a66372d
- Linting
  bruno-f-cruz
  committed
  5040c55
Commits on May 10, 2026
- Move scripts and add benchmark
  bruno-f-cruz
  committed
  3a282c6
- Structured arrays can convert directly
  bruno-f-cruz
  committed
  9a9832d
- Pre-compute group-mask enums as a lookup table
  bruno-f-cruz
  committed
  1b0b7dc
- Refactor backend to allow twin classes for Scalar and Bulk types
  bruno-f-cruz
  committed
  2aa8235
Commits on May 11, 2026
Commits on May 12, 2026
- Split scalar/array/struct payloads and type parse() return
  bruno-f-cruz
  committed
  2882178
Commits on May 17, 2026
- Add example of heterogenous register
  bruno-f-cruz
  committed
  f5c4536
- Raise proper error
  bruno-f-cruz
  committed
  00bf9c7
- Drop redundant code path
  bruno-f-cruz
  committed
  ca4ec5d
- Raise error if timestamp is explicitly requested
  bruno-f-cruz
  committed
  40c4000
- Cache bit-field definition
  bruno-f-cruz
  committed
  de96c17
- Create constants module and move tick value
  bruno-f-cruz
  committed
  ed9ddc5
- Refactor to use sentinel type
  bruno-f-cruz
  committed
  8acfdf0
- Streamline checksum calculation
  bruno-f-cruz
  committed
  ee05e7b
- Be opinionated on format typing
  bruno-f-cruz
  committed
  d7dad55
- Update register syntax
  bruno-f-cruz
  committed
  9273314
Commits on May 18, 2026
- Use `dataclass_transform` for free type hint
  bruno-f-cruz
  committed
  05a2187
- Test defaults
  bruno-f-cruz
  committed
  b437bdd
- Cleanup public api members
  bruno-f-cruz
  committed
  3bcab95
Commits on Jun 14, 2026
- Generalize payload construction for all interface types
  bruno-f-cruz
  committed
  6a17323
- Linting
  bruno-f-cruz
  committed
  afa9288
Commits on Jun 16, 2026
- Fix type errors and examples
  bruno-f-cruz
  committed
  9425aba
Commits on Jun 23, 2026
- Simplify repr field collection
  bruno-f-cruz
  committed
  653e98f
- Allow fields to also define a masked value
  bruno-f-cruz
  committed
  959e717
Commits on Jun 24, 2026
- Deprecate converter_registry
  bruno-f-cruz
  committed
  473844d
- Deprecate converter_registry
  bruno-f-cruz
  committed
  3db7518
- Add support for converters in AnonymousPayload
  bruno-f-cruz
  committed
  1d2e8e5
- Export `AnonymousPayload` from te public module
  bruno-f-cruz
  committed
  c84f93e
Commits on Jun 25, 2026
- Add support for HarpVersion and HarpVersionConverter
  bruno-f-cruz
  committed
  2589295
- Refactor device class to include core registers and decoupled from serial transport
  bruno-f-cruz
  committed
  a1f9a7a
- Decouple transport from device
  bruno-f-cruz
  committed
  4ad9343
- Use automatically generated core register definition
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  committed
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Commits on Jun 26, 2026
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Commits on Jun 28, 2026
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Commits on Jun 29, 2026
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Commits on Jul 1, 2026
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Commits on Jul 2, 2026
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Commits on Jul 17, 2026
- Fix stale references
  
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Commits on Jul 24, 2026
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