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CHANGELOG

v0.4.0 (2024-09-24)

Feature

  • feat: add plotting function to call dlc PlottingResults on PoseEstimation results (d05c664)

Fix

  • fix(dlc_plots): bugfix import errors (144c34a)

  • fix(pose_estimation): Save config to outbox as dj_dlc_config (f69c46a)

Unknown

  • Merge pull request #131 from datajoint/semantic-release-with-github-app

Semantic release with GitHub app (088a8ab)

  • Update test.yaml (3eec2bf)

  • Update semantic-release-caller.yml (61b3f65)

  • Merge pull request #129 from ttngu207/main (f7cac84)

  • Merge pull request #126 from ttngu207/main

add plotting function to call dlc PlottingResults on PoseEstimation results (af4ce80)

  • bump version (ddd5c16)

  • Merge pull request #124 from ttngu207/main

fix(pose_estimation): Save config to outbox as dj_dlc_config (a1073bb)

v0.3.1 (2024-09-16)

Chore

  • chore: explicit & consistent config_filename (129f661)

  • chore: rename dlc_model to avoid easy naming collision (bdf0ae2)

  • chore: improve imports, avoid circular dependencies (bf02c7c)

  • chore: code cleanup (6c10ac7)

  • chore: black formatting + improve Windows/Linux path robustness (c13611d)

  • chore(tests): set tear down to True (5897edd)

Documentation

  • docs: 🐛 update mkdocs.yaml (c228d8e)

Feature

  • feat: better handling for "cropping" input (fd6ba27)

  • feat(pose_estimation): use memoized_results (fe8224b)

  • feat(tests): add pytest (9133925)

Fix

  • fix: remove prototyping code (52175f4)

  • fix: minor import bug (c061e9a)

  • fix: directly implement logic of do_pose_estimation in the make (c7aba7d)

  • fix: remove "print" statement (0044441)

  • fix(tests): clean up notebook (47bbbbc)

  • fix(tests): minor bugfix in tests (9151e69)

Style

  • style: black formatting (61ee5fa)

Unknown

  • Merge pull request #121 from ttngu207/main

add new table LabeledVideo to generate/store labeled video data after PoseEstimation (117694e)

  • Revert "Update tutorial_pipeline.py"

This reverts commit 079641d45835507fcda1bf0822a4f8c025dde337. (8fff7b0)

  • Update tutorial_pipeline.py (079641d)

  • update: version, changelog (783985c)

  • Merge remote-tracking branch 'upstream/main' (70630b0)

  • Merge pull request #120 from ttngu207/main

feat(pose_estimation): use memoized_results (2833f15)

  • Merge pull request #119 from ttngu207/main

chore: improve imports, avoid circular dependencies (34a6edb)

Create semantic-release-caller.yml (c2ea14f)

  • Create semantic-release-caller.yml (e9f96d7)

  • Merge pull request #115 from datajoint/MilagrosMarin-patch-1

Update devcontainer-build-publish-caller.yml (4a954bf)

  • Update devcontainer-build-publish-caller.yml (9af7d83)

  • Merge pull request #114 from datajoint/MilagrosMarin-patch-2

Create mkdocs-release-caller.yml (b7f0842)

  • Create mkdocs-release-caller.yml (5e219cf)

  • Merge pull request #113 from datajoint/MilagrosMarin-patch-1

Update devcontainer-build-publish-caller.yml (dbec5b2)

  • Update devcontainer-build-publish-caller.yml (20b8753)

  • Merge pull request #112 from datajoint/MilagrosMarin-patch-1

Create devcontainer-build-publish-caller.yml (84db8ad)

  • Create devcontainer-build-publish-caller.yml (708d071)

  • Merge pull request #111 from MilagrosMarin/main

Fix: style tests (7f2dd68)

  • update version and changelog (2304d09)

  • black formatting (284abf6)

  • Merge branch 'datajoint:main' into main (3b68844)

  • Merge pull request #110 from datajoint/staging

Bugfix - store snapshotindex for the latest snapshot instead of the filename (1cf8347)

  • Merge remote-tracking branch 'refs/remotes/origin/main' (9cf3cef)

  • Merge pull request #108 from ttngu207/main

style: black formatting (e6944a9)

  • black formatting (a31e56f)

  • Merge remote-tracking branch 'upstream/staging' (1941bdb)

  • Merge pull request #105 from ttngu207/dev_test_dlc_training

Code cleanup + minor bugfix in cross platform paths formatting (7949f61)

  • Merge pull request #104 from sidhulyalkar/main

Update model.PoseEstimation to infer_output_dir (0f68e09)

Update snapshotindex and latest_snapshot designation (7b4e66a)

  • modify snapshot index determination (556556b)

  • modify latest snapshot determination (6278148)

  • modify snapshotindex assignment in model training (474269e)

  • Merge pull request #100 from sidhulyalkar/main

Modify training to update init_weights path (fcdb2ec)

  • update changelog (fcc7007)

  • update version (4543d08)

  • update to use deeplabcut.path (935938e)

  • update init_weights_path before training model (87e0aae)

  • Merge pull request #107 from MilagrosMarin/main

Add last PR changes to CHANGELOG, bump version, blackformatting tests (190150d)

  • add last PR to CHANGELOG and bump version (9f8b212)

  • blackformatting tests (a5ec467)

  • delete PyPI release (9762a19)

  • Merge pull request #106 from ttngu207/main

Add pytest (16c845e)

  • Merge pull request #103 from MilagrosMarin/main

Update setup dependencies + fix YAML bug + fix diagram + fix typo in docstring + tutorial setup (499d85e)

  • add YAML object as recommended in parallel PR#102 (d6fe551)

  • Refactor YAML loader instant. for consistency (abc10df)

  • update changelog and version.py (cd358eb)

  • black formatting tutorial.ipynb (fddad64)

  • black formatting dlc_reader.py (d1b86ce)

  • from safe_load to load (9b61920)

  • update outputs of the tutorial notebook (0885f48)

  • Address the bug introduced by the latest update to the YAML dependency (fbab55d)

  • fix input_dir and output_dir in the tutorial (a50836d)

  • move import os from __init__ to tutorial_pipeline (95e10df)

  • change name of flowchart.svg in notebook (a5e59e5)

  • change name of flowchart as in element-ca-imaging (8e0d9dd)

  • minor change in dependency version in setup (ebe6f2b)

  • minor update on tutorial markdowns as in array-ephys (cc0424c)

  • setup install directly from GitHub instead of PyPI (820711e)

  • move dj.config() from init to pipeline.py (28c55bc)

  • Update diagram_flowchart as in array-ephys repo (ab3370a)

  • update docstring for model_description varchar (3b635d6)

  • Revert "adjusted length of fields of varchar"

This reverts commit cc24a03684a21be82ef56e70bc159b793fe2e66d. (71af568)

  • adjusted length of fields of varchar (cc24a03)

  • Merge pull request #97 from A-Baji/main

revert: 📝 revert docs dark mode cell text color (5b12e5e)

  • revert: 📝 revert dark mode cell text color (be09507)

v0.2.10 (2023-11-20)

Unknown

  • Merge pull request #99 from sidhulyalkar/main

Update Version and Changelog (11802ff)

update setup.py to fix conflicting dependencies (fbd1ff6)

  • update setup.py to fix conflicting dependencies (1a2d262)

  • Merge pull request #96 from ttngu207/element-dlc-test

update snapshotindex after training (887b571)

  • smarter transaction logic (8a1dff2)

  • remove the project_path kwarg in insert_new_model (03c37d1)

  • update snapshotindex after training (736f4d7)

  • remove opening of new transaction for insertion into model table (09a75cb)

  • Merge pull request #95 from MilagrosMarin/element-dlc-test

minor changes to standardize the elements (ded35b3)

  • Merge pull request #3 from kushalbakshi/dev

Black formatting (b33ece9)

  • Black formatting (85e38f2)

  • minor changes to mirror PR element-array-ephys (30a1b9c)

  • Merge pull request #93 from MilagrosMarin/element-dlc-test (1314488)

  • Delete notebooks/demo.ipynb (9d5ca5a)

  • starting the demo notebook (eef6975)

  • update changelog and gitignore (741e2ce)

v0.2.9 (2023-10-26)

Unknown

  • Merge pull request #92 from MilagrosMarin/element-dlc-test

update model.py,tutorial notebook,changelog, and version (c887ab8)

  • Update element_deeplabcut/model.py

Co-authored-by: Thinh Nguyen <[email protected]> (fba8810)

Update tutorial and codespace (be8256f)

  • Merge pull request #90 from MilagrosMarin/element-dlc-test

Update the example data, environment variables, tutorial notebook and README (4a74fe4)

  • Merge pull request #89 from MilagrosMarin/element-dlc-test

Merge workflow-deeplabcut's tutorial environment (55adb0e)

  • update model.py: remove a line and update args (5e04d5f)

  • Update CHANGELOG.md (de29eef)

  • add summary section (73a1a4f)

  • Update CHANGELOG.md (e9dd1bd)

  • update tutorial with outputs included (3996ed7)

  • update the markdowns of tutorial - outputs cleared (7edff63)

  • update changelog and version (4bd81ec)

  • change in visualization plots (0fb7c05)

  • final draft with all outputs and minor changes (bb25140)

  • final draft without output (5e942b6)

  • update tutorial draft (6d5011e)

  • draft tutorial (828cd87)

  • correct the name of the pipeline figure (8ebd1f1)

  • Merge pull request #1 from ttngu207/element-dlc-test

Element dlc test (04eb7eb)

  • Merge branch 'element-dlc-test' into element-dlc-test (a2b2fd2)

  • Add a tutorial quick test (f1fad23)

  • add notebooks (94b2b17)

  • update codespace and mounting strategy (477a355)

  • Update model.py (2f41aa3)

  • use v2 example data (930c619)

  • Merge pull request #4 from MilagrosMarin/element-dlc-test

Element dlc test (299c4c1)

  • Update setup.py

Co-authored-by: Kushal Bakshi <[email protected]> (ed8de3a)

  • Update setup.py

Co-authored-by: Kushal Bakshi <[email protected]> (19dc567)

  • Update setup.py

Co-authored-by: Kushal Bakshi <[email protected]> (2e49708)

  • Update README.md

Co-authored-by: Kushal Bakshi <[email protected]> (525924d)

  • Update CONTRIBUTING.md

Co-authored-by: Kushal Bakshi <[email protected]> (1c7bec4)

  • Update .devcontainer/devcontainer.json

Co-authored-by: Kushal Bakshi <[email protected]> (61e73bf)

  • Update .devcontainer/Dockerfile

Co-authored-by: Kushal Bakshi <[email protected]> (61fbfea)

v0.2.8 (2023-08-08)

Test

  • test: environments and volumes commented in yaml (2480421)

  • test: change CaImaging image to build (e15b32f)

  • test: try with calcium imaging image (f9c8eaa)

  • test: no volumes workspaces dlc (ed8c1cc)

  • test: Revert two minor comments in dockerfile (160a32e)

  • test: from python short command in dockerfile (2a394ae)

Unknown

Update GitHub Actions and Readme (5a76c6c)

  • Update version for release (f8fde49)

  • Merge 'main' of datajoint/element-deeplabcut (8ca047d)

  • Format with black (b16c386)

  • Format with black (f37a17f)

  • Update changelog (dff5b87)

  • Update readme (fcd026a)

  • Rename images (cc2cbfc)

  • Update GitHub Actions (ac3f334)

  • update README based on ca-imaging element (cbc6e27)

  • update current_project_folder->from_top_tracking (c0b6ed2)

  • update flowchart URL (07522a7)

  • rename image names to mirror ca-imaging (0df510d)

  • Images from workflow-don't match the element (5b317a9)

  • revert model.py and train.py to add in next PR (1e6c27e)

  • Add env variables and prefix to dj database (1969e59)

  • revert removing files in element-deeplabcut (49f2b2f)

  • SCIOPS-59 & add two dependencies in setup (f30425f)

  • delete comments in dockerfile (8511b4e)

  • add s3fs postcommand in devcontainer (89df0f4)

  • update dj_public_s3_location in docker-compose (60f1a81)

  • Merge branch 'element-dlc-test' of https://github.com/MilagrosMarin/element-deeplabcut into element-dlc-test (895dbd2)

  • Update .github/ISSUE_TEMPLATE/config.yml

Co-authored-by: Kushal Bakshi <[email protected]> (80100db)

Co-authored-by: Kabilar Gunalan <[email protected]> (38587c8)

  • restore docs/ directory (735a1cb)

  • Update setup.py for DLC in M2 MacOS (84e09d9)

  • Merge branch 'element-dlc-test' of https://github.com/MilagrosMarin/element-deeplabcut into element-dlc-test (48e73e4)

  • Update setup.py (f040971)

  • Install deeplabcut (ae8ce7d)

  • updated libraries in mchips installation (3480270)

  • test minor change in dependencies in dockerfile (f5eaae4)

  • Test codespaces: #depend.reduced, lines commented (f74a497)

  • delete redundancy (9f816fb)

  • test dlc_default in Dockerfile (bd8f57c)

  • update dockerfile and setup (6359f06)

  • update .yaml files (5a01ace)

  • update .gitignore (ef0099c)

  • update code_conduct, contrib and license files (421e49d)

  • update.github directory (0eb7c3a)

  • minor change in dockerfile (c79f3f3)

  • Delete .github directory from this PR (ead5b39)

  • Delete docs directory from this PR (0b17199)

  • Major changes for PR codespace environment (842561f)

  • Merge remote-tracking branch 'origin/element-dlc-test' into element-dlc-test (6001819)

  • removed more files from git (845974a)

  • Recover files from git rm (276487b)

  • change DLC_ROOT_DATA_DIR to example_data directory (3166830)

  • removed files from git (da33fd4)

  • dockerfile new env for dlc folder (e0fb8d3)

  • uncomment env&volumes but changed to element-dlc (9354ac1)

  • from IMAGING_ROOT_DATA_DIR to DLC_ROOT_DATA_DIR (9551723)

  • setup comments deleted (da33b01)

  • use FROM with base image without digest (42fa38c)

  • test dockerfile: imaging_root_data_dir not needed (30c3dff)

  • revert dockerfile (ebfea90)

  • setup.py: delete code line about requirements.txt (a5a13f9)

  • apt-utils and apt-get in dockerfile (8901870)

  • uncomment volumes in docker config file (8a8d704)

  • add context in docker yaml as well (6133ca7)

  • use build instead of image to test the dev cont (2957160)

  • comment environment line with previous commit (d0088ed)

  • comment 'S3 location' for DLC-v1 to test dev (61aa180)

  • comment image element_dlc code line before merge (4820f75)

  • dockerfile and devcontainer files for element-dlc (0973437)

  • important change to install dlc[apple_mchips] (1ef12f9)

  • change name for clarity to get_trajectory function (18daef4)

  • add skip_duplicates to generate function (f774713)

  • Fix:generate triggers getattribute with model_name (745f5d4)

  • processed_dir can not exist - bug fixed (b0ea7d4)

  • Tutorial: major changes & network training tested (4e2a7eb)

  • Update intro tutorial notebook (3a2eba8)

  • Update name from pipeline to tutorial_pipeline (5f50b4b)

  • Merge 'main' of datajoint/element-deeplabcut (97b676a)

v0.2.7 (2023-08-04)

Unknown

  • Merge pull request #87 from MilagrosMarin/train_bug

Fix project path in the pose config file (78ac980)

  • Fix project path (81eb296)

  • [WIP] Update notebook and mac requirements (d6dad59)

  • Update requirements configuration (ca01071)

  • merge paths and pipeline files, move to notebooks (be51282)

  • Rename 03-process -> tutorial (22cb379)

  • Remove jupytext scripts and workflow version (9c123b5)

  • Move workflow pipeline files (0135a38)

  • Merge 'datajoint/workflow/main' into element (048c707)

  • Merge pull request #20 from kabilar/main

Add GitHub Actions workflows (205b5aa)

  • Update changelog (11f6773)

  • Add GitHub Actions workflows (a6b2c9f)

  • Merge pull request #19 from kabilar/main

Update requirements for released packages (299eb37)

  • Remove element-interface installation from source (e1d82b2)

  • Update command (836a4e2)

  • Update changelog (f9d56eb)

  • Update requirements (415145c)

  • Merge pull request #18 from CBroz1/main

Remove buggy EOF markers from DLC outputs in notebooks for mkdocs rendering (1f93e11)

  • 🐛 Debug mkdocs notebooks rendering 2 (3a6a635)

  • 🐛 Debug mkdocs notebooks rendering (43635d5)

  • Merge pull request #17 from tdincer/main

Update README.md (9d015e5)

  • Update README.md (32511f9)

  • Merge pull request #16 from kushalbakshi/main

Fixed typo in README (9ce9aef)

  • Fixed typo in README (5a3a1e5)

  • Merge pull request #15 from CBroz1/main

Add remaining suggestion from #14 (5e7fedd)

  • Fix typo (872d9a0)

  • Add remaining suggestion from #14 (d1dee80)

  • Merge pull request #14 from CBroz1/main

Docstrings -> Google style for mkdocs render (ba2667e)

  • Update CHANGELOG.md (a836e0a)

  • Update README.md

Co-authored-by: Kabilar Gunalan <[email protected]> (2913c86)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (3eec272)

  • Update changelog. Add attribs to Device (6584958)

  • Add class docstring for Device (b141b1e)

  • Simplify README, direct to new docs site (60997af)

  • Add typing info for mkdocs (a729432)

  • Docstrings -> Google style for mkdocs render (d7ba7e8)

  • Merge pull request #12 from CBroz1/dev

Integration tests (c6ff6d6)

  • Apply suggestion from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (edbff23)

  • WIP: Fix docker (a0a76e9)

  • WIP: add visualization notebook (698105e)

  • WIP: revise notebooks for new dataset (7fa0ddb)

  • WIP: jupysync (295df7e)

  • WIP: docker edits. notebook revamp. incomplete (6b12b85)

  • WIP: minor cleanup (af90a61)

  • WIP: all tests pass locally (c1aa455)

  • WIP: More integration tests. See details.

Currently can take MVP data and can expand. Added - More population assertions for file create time Added - Load_demo_data function for updating training config - If added to element, could continue training from prev step Modified - Device to lookup table for auto-contents Updated - str_to_bool change source due to depreciation (33e92b4)

  • WIP: Integration tests. See details.

test_ingest: add table length and content assertions test_populate: added - Not yet working user_data/*csv: add metadata from new dataset ingest.py: separate get_dlc_items by sub-function to call within tests ingest_train_params ingest_model paths.py: return none if no output dir selected pipeline.py: Equipment->Device load_demo_data.py: add functions for expanding mvp dataset generate training dataset deterministic files generate absolute paths across configs (5425bcf)

  • WIP: migrate fixtures to conftest.py (c7ffd43)

  • WIP: Remaining files from prev commit (2226891)

  • WIP. See details.

Parameterize DockerFile - move option selection to env Refactor pytests - add setup.cfg to pass default params Add Code of Conduct Refactor ingest.py to ... 1. provide subfuncs by schema 2. add verbosity flag 3. update docstrings (d2aa171)

  • Merge pull request #11 from CBroz1/dj

blackify (0e76b79)

  • Bump version (7f02a96)

  • blackify (c692fc5)

  • Merge pull request #8 from CBroz1/main

Updates for element PR #15 RecordingInfo table (4eeb86a)

  • Update workflow_deeplabcut/process.py

Co-authored-by: Kabilar Gunalan <[email protected]> (6eaf310)

  • Update workflow_deeplabcut/process.py

Co-authored-by: Kabilar Gunalan <[email protected]> (089e5a4)

  • Update workflow_deeplabcut/process.py

Co-authored-by: Kabilar Gunalan <[email protected]> (ddbd725)

  • Apply suggestion from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (345dd98)

  • Add element_interface.utils.ingest_csv_to_table (dd10089)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (ac63549)

  • Merge from cbroz1:main (b414498)

  • Apply suggestion from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (04bc842)

Update README (1df9bf0)

  • Update format (fdd12ac)

  • Fix format (0253e7e)

  • Add link to element.datajoint.org (8584969)

  • Update text (e60d017)

  • Fix format (11991b1)

  • Add links (2417a4b)

  • Remove upstream element images to shorten readme (0e19c7f)

  • Add links to elements.datajoint.org (886d3f4)

  • Add citation section (4317fd7)

  • updates corresponding to element-deeplabcut PR #15 (2259f3a)

  • Merge pull request #6 from kabilar/main

Add issue templates (bcc4eb9)

  • Add issue templates (3c4fe47)

  • Merge pull request #5 from CBroz1/main

minor README updates (9a5a1d8)

  • Update README.md from code review suggestion

Co-authored-by: Kabilar Gunalan <[email protected]> (20e0f06)

  • minor README updates (2003826)

  • Merge pull request #2 from CBroz1/main

Pushing from cbroz1:dev discussion to datajoint:main (981415c)

  • Merge pull request #2 from CBroz1/dev

Update schema split: train, model (8095081)

  • add Session = session.Session to pipeline.py, from code review (ff7cf58)

  • Update notebooks for separate video tables across schemas (d0d94b6)

  • revise version info (4338899)

  • See details. Docker, Notebooks, JupyText, ingest.py

Update docker Update NBs for 2 schema split Add jupytext py files Update ingest to reflect VideoRecording in pipeline Add ingest feature for train.VideoSet (4bbdfc0)

  • Split dlc schema (21f7494)

  • update NBs 0 - 3 (bbf2d5d)

  • Draft notebooks. WIP Integration Tests (4c9cae1)

  • See Details

  • README - add install instructions
  • Notebook/1_Explore - major revision demonstrating new helper functions
  • user_data - revise per table redesign
  • ingest.py revise for paramset redesign
  • paths.py
    • remove get_session_directory
    • remove arg from get_dlc_processed_dir
  • pipeline.py minor change per paths change above (365a090)

  • recordings.csv edit for new dev (4daf262)

  • new notebook for modeling use (598b0e2)

  • draft ingest edits (3a3ba77)

  • Merge from CBroz1/dev

Recent work (99859a6)

  • README+CHANGELOG clarity (8e7ca78)

  • Cleanup: README, versioning, add ToDo notes (9b368cb)

  • Refactor readme, remove images, add docker. See details

Docker: add dev and test environments/dockerfiles changelog/version.py: revise version number remove images: lab, session, subject diagrams README: refactor with links to images. Direct to central install.md for instructions 1_Explore_Workflow: update to show new functionality requirements: pinn versions tests: Minor edits to supress linter errors user_data: move config parameters to new csv ingest: update for config parameters paths.py: update for cross-element consistency pipeline.py: Minor edits to supress linter errors (3494447)

  • new dev branch (87a1f49)

  • minor: remove debug notebook cell (a580a4c)

  • Example ingestion in notebook 01 (8350d39)

  • repo standard items - changelog, contrib (eb3ba17)

  • remove ds_stores (5550ed8)

  • Delete .DS_Store (4ddf02f)

  • delete notes file (aa01866)

  • Initial structure (1f324c1)

  • add gitignore (cfac635)

  • Create README.md (94546b1)

  • [WIP] Update project path in pose config (4afc063)

  • paths,pipeline moved; train and dlc_reader modif (b566184)

  • Merge pull request #80 from kabilar/main

Add DeepLabCut, NWB, and DANDI citations (4046d89)

Fix dark mode and CI/CD issues (5f8a327)

v0.2.5 (2023-05-11)

Unknown

  • Fix dark mode and CI/CD issues (bf8bde4)

  • Merge pull request #78 from kushalbakshi/main

Fix docs tutorials in dark mode (c91090d)

v0.2.4 (2023-04-28)

Unknown

  • Fix docs tutorials in dark mode (3294eaa)

v0.2.3 (2023-04-05)

Unknown

  • Merge pull request #76 from sidhulyalkar/main

update changelog and version (88f9fcf)

  • update year to 2023 (63daae5)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (bd92c94)

  • update changelog releases (a21a471)

  • update changelog and version (8f355dd)

  • Update docs (bde3edb)

  • Remove Google Analytics key (e6037e0)

  • Remove Google Analytics key (c8c72f0)

  • Merge pull request #75 from ttngu207/main

fix bug (40503d7)

  • fix bug (37a100c)

  • Merge pull request #74 from sidhulyalkar/main

DLC bugfix (1627433)

Add interface to requirements (1b78339)

  • Merge branch 'main' into main (5201430)

  • Add interface to requirements (63af644)

  • fix torch version (5f8594c)

v0.2.2 (2023-01-17)

Unknown

  • Merge pull request #72 from sidhulyalkar/main

Move Rest of DLC imports into make functions (802eb0a)

  • Update CHANGELOG.md

Co-authored-by: Chris Brozdowski <[email protected]> (44607f2)

  • update changelog and version (65cd9cf)

  • add isort:skip to moved imports (88a402d)

  • move DLC imports into make functions where they are used (2654b7d)

  • Merge pull request #71 from sidhulyalkar/main

Move evaluate_network import into make function in model.py (bee89bf)

  • Merge branch 'datajoint:main' into main (2f2a9a1)

  • Merge pull request #70 from sidhulyalkar/main

Move import into make function (3f83619)

Add # isort:skip to moved import

Co-authored-by: Chris Brozdowski <[email protected]> (aeb8808)

  • move evaluate_network import into make function (25d6524)

  • Merge branch 'datajoint:main' into main (3d54566)

  • Merge pull request #69 from ttngu207/main

improve "insert_estimation_task"; loading DLC results handles multiple DLC output files (cb2b4cd)

  • Apply suggestions from code review

Co-authored-by: Chris Brozdowski <[email protected]> (a3a70bc)

  • raise FileNotFound error instead of Assertion error (7b990c7)

  • bugfix - address PR comments (ef69e6c)

  • insert_estimation_task as alias for generate (f1ea3f9)

  • Update CHANGELOG.md (1391f7a)

  • DLC reader allowing for loading dlc output in multi-file format (486fdaf)

  • improve "insert_estimation_task", renamed to "generate" (7d15fbe)

  • Merge branch 'main' of https://github.com/datajoint/element-deeplabcut (7ce878a)

  • code cleanup (2dce4a0)

  • clean up - grouping of "trigger" specific steps (0c9cc13)

  • move train_network import into make function where it is used (e8fe0d7)

  • Merge pull request #68 from kabilar/main

Update tutorial page (13cc3ea)

v0.2.1 (2022-12-16)

Fix

  • fix: 🐛 docs docker issue (3a5c5f6)

Refactor

  • refactor(CICD): 🔥 clean up dev CICD for docs (f14e9b2)

Test

Unknown

  • Merge pull request #67 from sidhulyalkar/main

Fix requirements for DLC setting tensorflow to be a subpackage (7fe2ad6)

  • Update CHANGELOG.md

Co-authored-by: Kabilar Gunalan <[email protected]> (49f51af)

  • Update element_deeplabcut/version.py

Co-authored-by: Kabilar Gunalan <[email protected]> (1fc8949)

  • fixed markdown linting (82762ee)

  • remove space (93b626b)

  • update changelog (f75aba0)

  • updated version to 0.2.2 (618a63d)

  • remove space (22fbefa)

  • Fixed requirements to handle DLC package change, fixed typo in docstring (54d2307)

  • Merge pull request #66 from CBroz1/main

[bugfix] Render notebooks as tutorials (e8fc1da)

  • uncomment docker compose (889f7df)

  • 🐛 notebook render bugfix (8943325)

  • Minor fixes (eaecf59)

  • Merge pull request #65 from CBroz1/docs-tutorial

[bugfix] Remove gitignore item for mkdocs notebook deployment (5264f2d)

  • Remove gitignore item for mkdocs notebook deployment (a97f998)

  • Merge pull request #55 from CBroz1/docs-tutorial

Tutorials folder with rendered notebooks (c628e32)

  • Update docs/src/tutorials/index.md

Co-authored-by: Tolga Dincer <[email protected]> (204436a)

  • Fetch from cbroz1:main (55422b3)

  • Add notebooks to docs; Add markdown linting (d306b34)

  • Merge pull request #64 from kabilar/main

Fix changelog for CICD (128f66d)

  • Fix changelog for CICD (dbd8c49)

  • Merge pull request #63 from kabilar/main

Update styling for docs launch (411225b)

Fix typos (dbb2245)

  • Revise docstrings (eacf864)

  • Merge pull request #60 from sidhulyalkar/main

change nframes from smallint to int data type (e07dc77)

  • change nframes from smallint to int data type (f54e054)

  • Merge pull request #59 from JaerongA/docs

fix minor typos & data types (6bb2861)

  • fix typo & data type in models.py (ccdf1ec)

  • fixed minor typos (04965e2)

  • fix typos (d0a80ca)

  • Merge pull request #58 from CBroz1/main

Version as env variable (0db4ba8)

  • Render API in source order (17af889)

  • Fix URL (1f9c277)

  • Fix typo (11c1a55)

  • Version as env variable (352c44f)

  • Merge pull request #57 from CBroz1/main

Add 404, chatbot. Remove extra CICD items (11b627d)

Add docs (99894bc)

  • Element API docs -> https urls (b7c5122)

  • Fix links in concepts (157d545)

  • Version bump (2d7c588)

  • See details.

Readme: add https:// Changelog: remove subheading docs/mkdocs.yaml: changelog new path, revise contributor notes docs/src/api/make_pages.py: - revert URL to main - add logic to exclude init.py docs/src/changelog: move docs/src/concepts.md: - move architecture after features - add dlc_session_to_nwb - rephrase language for model training - hard wrap on pgfs added in code review docs/src/index.md: add spacing for linebreaks element_deeplabcut/model and train: Add attributes to docstrings (4394572)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (5436db8)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (bc05121)

  • Add full tutorial draft (d00a1f7)

  • Remove Tutorials content, replace with ComingSoon (2397f4c)

  • Concepts.md: Move partnerships above architecture (395537e)

  • Change title on index.md (fcc4c0c)

  • Add analytics key to docker compose (90682c1)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (285dfa1)

Co-authored-by: Kabilar Gunalan <[email protected]> (7b40fe0)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (f991cbe)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (b410b55)

  • Revert docker compose edits (8e36f5b)

  • test with mkdocs instead of mike (eac8be4)

  • Add global safe config hack (14485be)

  • Remove workflow-dispatch trigger from mkdocs-build workflow (dc90bd1)

  • Remove tag check from mkdocs-build (4016d49)

  • Add staging CICD, Add element-generic mkdocs publish (bc3fbf0)

  • Mention DANDI upload (77a0629)

  • Add codebook mention. Revise changelog symbolic link (6d9125d)

  • Add codebook mention to tutorials#notebooks (7e0be4e)

  • Home nav to docs/elements/ (0f6f550)

  • Hard wrap; Concepts#data-export (ae75dae)

  • Apply suggestions from code review 3

Co-authored-by: Kabilar Gunalan <[email protected]> (7110b72)

  • Apply suggestions from code review 2

Co-authored-by: Kabilar Gunalan <[email protected]> (9b4ce4d)

  • Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]> (276526b)

  • Edits to make_pages to handle edge cases (c34289a)

  • Misc extra contributor notes (061f39f)

  • Revise doc structure (4fe5fc0)

  • Docstrings -> Google style; edit css style for blue main (afd4602)

  • Merge pull request #10 from guzman-raphael/docs

Include workflow API docs (6fff4ab)

v0.2.0 (2022-10-10)

Feature

  • feat(CICD): ♻️ clean up old CICD, deploy update in Prod (35310a9)

  • feat(CICD): ✨ calling reusable context check (ce8409d)

  • feat(CICD): ✨ use workflow_run (22d0959)

Fix

  • fix(CICD): 🐛 CICD trigger fixed (4bd38ac)

  • fix(CICD): 🐛 before_release workflow not triggerred by push with tag (90e7d6c)

  • fix(CICD): 🐛 trigger logic update (b4970e6)

  • fix(CICD): 🐛 fix context_check ref (6ba53de)

  • fix(CICD): ✨ pause auto trigger old CI (94b0b92)

  • fix(CICD): 🐛 missing py_ver input (f2d3bf3)

  • fix(CICD): 🐛 multiline (7ac7cbb)

  • fix(CICD): 🐛 typo (04f2d7e)

  • fix(CICD): 🐛 if syntax (47fc868)

  • fix(CICD): 🧪 test release ci (f0a4dc8)

  • fix(CICD): 🐛 if syntax (a4568b6)

  • fix(CICD): 🐛 fix inputs (28a2203)

  • fix(CICD): 🐛 update logic (70c2bab)

  • fix(CICD): 🐛 update reference (9c4dcaf)

  • fix(CICD): 🐛 simplify logic (6b3d2e7)

  • fix(CICD): 🐛 trigger (629022a)

  • fix(CICD): 🐛 typo (e2cb051)

Test

Unknown

  • Merge pull request #54 from CBroz1/main

Prep for pypi publish (1fa6984)

  • Prep for pypi publish (346e164)

  • Merge pull request #46 from CBroz1/dev

Add NWB export function (d2e4286)

  • Update element_deeplabcut/export/nwb.py (b9580de)

  • Update element_deeplabcut/export/nwb.py

Co-authored-by: Tolga Dincer <[email protected]> (a8acb6b)

  • Apply suggestion from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (e65f14f)

add opencv-python-headless in requirements (2143d20)

  • add opencv-python-headless in requirements (6624728)

  • Merge pull request #51 from tdincer/main

bug fix: missing f for formatted string (cf08e3e)

relocate imports (2d96b92)

  • Update CHANGELOG.md

Co-authored-by: Chris Brozdowski <[email protected]> (ddb32b1)

  • Update element_deeplabcut/version.py

Co-authored-by: Chris Brozdowski <[email protected]> (009fcc8)

  • bug fix: missing f for formatted string (68be599)

  • relocate module imports to the top of the file (bfd8624)

  • relocate imports (82a5a79)

  • Merge pull request #49 from tdincer/main

Decrease model_description char length (96c2a9b)

Increase model description attr's size (3acc964)

fix(CICD): 🐛 CICD trigger fixed (02a57f8)

  • fix conflict (7219118)

  • Merge pull request #40 from CBroz1/main

Changes to parallel workflow integration tests (8a63b19)

Include updated CICD (fabbb75)

Co-authored-by: Tolga Dincer <[email protected]> (8e1f72c)

  • Merge branch 'main' into main (5a7a3e4)

  • Version bump (4bbb209)

  • WIP #36 (6f193c1)

  • WIP: pin DLC version, rename saved yaml (b4cfe57)

  • Apply suggestions from code review

Co-authored-by: Dimitri Yatsenko <[email protected]> (bf62231)

  • WIP: minor fix for save_yaml, permit file ext (f1b9b2d)

  • WIP: revert videotype, see DeepLabCut #1900 (1fe2fd6)

  • WIP: error workaround for analyze_videos videotypes param (614f02b)

  • WIP: change config pointers to our fully managed dict (425714d)

  • WIP: minor bugfixes to output_dir and trainingsetindex as int (e630454)

  • WIP: #24, #26, #27 (8e58549)

  • increase model_description char (2af9d74)

  • Merge pull request #43 from tdincer/main

fix videotype (631d7d5)

  • Update requirements.txt

Co-authored-by: Chris Brozdowski <[email protected]> (68134cf)

v0.1.1 (2022-07-06)

Documentation

  • docs: 🐛 changelog remove unreleased and 'v' in the tag (e194858)

  • docs(CICD): 🔖 (cc95c5b)

Feature

  • feat(CICD): 🔖 call reusable cicd with test release (32d01ca)

  • feat(CICD): ✨ add pypi (db5fdd8)

  • feat(CICD): 🔖 point to prod CI (d6b2aa3)

  • feat(CICD): ✨ include debian image build (6ba5e73)

  • feat(CICD): ✨ refer centralized Dockerfile and docker-compose-build.yaml (c685dc4)

  • feat(CICD): 🐛 add build docker-compose yaml (103252f)

  • feat(CICD): ✨ calling reusable workflow (c7152b0)

Fix

  • fix(CICD): 🐛 have to pass secrets in (7ac4d79)

  • fix(CICD): 🐛 only one call is needed, otherwise conflict when create release (79223cd)

  • fix(CICD): 🐛 fix typo (e7fde40)

  • fix(CICD): 🐛 fix typo (381f89f)

  • fix(CICD): 🐛 fix typo (e0af5ca)

  • fix(CICD): 🐛 update changelog to unrelease (80c2f59)

  • fix(CICD): 🐛 rollback changelog (ccde295)

  • fix(CICD): 🐛 fix DISTRO to DIST (ef00305)

  • fix(CICD): 🐛 add Dockerfile (02d3a95)

  • fix(CICD): 🐛 add docker-compose-build.yaml (a77db0c)

  • fix(CICD): 🐛 fix push trigger (9bd44fb)

  • fix(CICD): 🐛 refer dev fork CI (5610b32)

Test

Unknown

  • Merge pull request #35 from yambottle/main

changelog fix type | add test release cicd (66802d6)

  • resolve conflict (31bfde5)

  • Merge pull request #37 from kabilar/main

Remove direct dependency for PyPI release (6ee17ef)

  • Update changelog (0ded37e)

  • Remove dependency for PyPI release (6ced597)

  • Merge pull request #33 from yambottle/main

Enable reusable CICD (b5fc591)

modify do_pose_estimation to write config.yaml in dlc_project_path (9bcb177)

  • modify do_pose_estimation to write config.yaml in dlc_project_path (9b5aeef)

  • Merge pull request #31 from tdincer/main

revert path find (7cc275a)

  • add optional project name (682f67a)

  • Equipment -> Device (664cec2)

  • revert path find (5a22175)

  • Merge pull request #29 from tdincer/main

add yaml and cv2 imports (d5b1858)

move to 'Device' upstream table. (8b4d910)

Co-authored-by: Dimitri Yatsenko <[email protected]> (be07c8b)

  • move imports back to the make functions (02a4f64)

  • Equipment -> Device (bbf2dcc)

  • remove version check from scorer_legacy (c3fe727)

  • put back the reference (1ed1043)

  • bug fix (d2d7bd5)

  • fix terminology (2040e37)

  • improved training data handling (b7dc27b)

  • Merge pull request #23 from CBroz1/dj

blackify (699a217)

  • Bump version in changelog (993377e)

  • Bump version in changelog (a4ccd34)

v0.1.0 (2022-05-10)

Unknown

  • Bump version (ca2738f)

  • blackify (8db4a54)

  • Merge pull request #22 from CBroz1/main

Device -> Equipment (b88c8dd)

  • Device -> Equipment (c6519c9)

  • Merge pull request #19 from CBroz1/main

Update diagrams and YT link in README (5a9595d)

  • add element_interface Issue #21 (7f2eddd)

  • Diagrams: +subject. Link: YouTube thumbnail (f3bbd7f)

  • Update diagrams and YT link in README (141230d)

  • Merge pull request #18 from ttngu207/main

minor update in File table for consistency (0c71ecb)

  • Update element_deeplabcut/model.py

Co-authored-by: Chris Brozdowski <[email protected]> (55e3040)

  • non-nullable recording duration (4eb8a26)

  • minor update in File table for consistency (1e6a8f0)

  • Merge pull request #16 from kabilar/main

Update README (1062b4b)

  • Update README.md

Co-authored-by: Chris Brozdowski <[email protected]> (e5dde7a)

  • Update README.md

Co-authored-by: Chris Brozdowski <[email protected]> (1f53b68)

  • Update format (f631195)

  • Fix format (9f39af4)

  • Fix typo (c7300eb)

  • Add links to elements.datajoint.org (e46c666)

  • Add citation section (edf2aef)

  • Merge pull request #15 from ttngu207/main

add RecordingInfo (705f154)

  • Update element_deeplabcut/model.py

Co-authored-by: Chris Brozdowski <[email protected]> (c4ee40a)

  • add RecordingInfo (537c2ce)

  • Merge pull request #8 from CBroz1/main

model.Model.BodyPart insertion fix; README updates (6086009)

  • Apply suggestion from code review

Co-authored-by: Thinh Nguyen <[email protected]> (9f67d08)

Missing 0 on numpy requirement (e8961ff)

  • Missing 0 on numpy requirement (df3c337)

  • Merge pull request #12 from kabilar/main

Minor text fix (9199a80)

  • Minor text fix (a2bd409)

  • Merge pull request #5 from CBroz1/main

Pushing from cbroz1:dev discussion to datajoint:main (b8b5137)

  • minor README updates (32524e2)

  • Merge pull request #5 from CBroz1/dev

Update schema split: train, model (b067e9f)

  • remove version info from init.py (9104105)

  • Apply suggestions from code review

Co-authored-by: Thinh Nguyen <[email protected]> (db6ecfb)

  • See Details. Update functions for separate video tables across schemas

helper funcs: fixed bug where root_dir[0] would get appended to root_dirs whenever get_processed_dir was called. extract_new_bodyparts: added verbose arg to prevent duplicate print when calling model.Model.insert_new_model insert_new_model: because BodyPart.extract_new_body_parts returns a list, checking the truth value is ambiguous. Changed to 'is not None' infer_ouput_dir: remove _linking_module for VideoRecording table insert_new_params: Enforce int type on paramset_idx input. Previously failed to return when attempting to insert a duplicate bc str(x)!=int(x) (26e6b44)

MVP here we come (015843a)

  • Merge branch 'main' into dev (b9fd1c9)

  • rename LabeledFrame -> File - to be more genelizable (8e4d7ce)

  • draft - using TrainingVideo table for training instead of VideoRecording (0e8cb2a)

  • edit README (2585ef3)

  • Rebasing

PEP8 README: add note on dependency conflict numpy==1.2 /images/: update diagram dlc schema:

  • remove arg for get_dlc_processed_dir
  • Add note on scorer_legacy
  • add docstrings
  • add note on continue from prev snapshot
  • add set shuffle/trainindex/maxiters to int for model training make
  • add TrainingVideo table for training instead of VideoRecording
    • LabeledFrame -> File generalizable part table
  • BodyPart.insert_new
    • refactor logic for yaml type check
    • separate BodyPart functions - return list then insert
  • Model.insert_new_model - refactor config yaml type check
    • Add scorer legacy check
    • add dlc version insertion
  • ModelEvaluation - make items nullable bc saw eval that didn't return some value
    • refactor config yaml type check
  • PoseEstimationTask - permit estimation paramset to pass to analyze_videos
    • Type set to string for concatenating output dir
    • add insert helper function
  • PoseEstimation - permit output_dir as fullpath, per 'relative' arg in task table
    • permit passing analyze_videos params
    • permit null analyze_video_param dlc_reader:
  • prev had separate output dir and project dir... removing
  • do_pose_estimation - permit args passed from PoseEstimationTask.params
  • adjust yml_path in reader to remove dlc_dir.parent Apply suggestions from code review (3c8ff44)

  • separate BodyPart functions - return list then insert (fb72d8c)

  • null analyze_video_param handling (fbf3b7e)

  • additional code review suggestions (84f0d84)

  • Apply suggestion from code review

Co-authored-by: Thinh Nguyen <[email protected]> (540ba06)

  • update diagram (88eb82f)

  • See details - long list

README: add note on dependency conflict numpy==1.2

dlc schema:

  • remove arg for get_dlc_processed_dir
  • Add note on scorer_legacy
  • add docstrings
  • add note on continue from prev snapshot
  • add set shuffle/trainindex/maxiters to int for model training make
  • BodyPart.insert_new - refactor logic for yaml type check
  • Model.insert_new_model - refactor config yaml type check
    • Add scorer legacy check
    • add dlc version insertion
    • add body part description arg
  • ModelEvaluation - make items nullable bc saw eval that didn't return some value
    • refactor config yaml type check
  • PoseEstimationTask - permit estimation paramset to pass to analyze_videos
    • Type set to string for concatenating output dir
    • add insert helper function
  • PoseEstimation - permit output_dir as fullpath, per 'relative' arg in task table
    • permit passing analyze_videos params

dlc_reader:

  • add conditional logic for if passed the output dir instead of project dir
  • assumes output dir is under project dir
  • do_pose_estimation - permit args passed from PoseEstimationTask.params (cef65ed)

  • PEP8 (aa4961e)

  • Merge pull request #4 from ttngu207/main

prototype revision no 2 (1d990db)

Add functions to link tables (b498a02)

  • Update element_deeplabcut/dlc.py

Co-authored-by: Thinh Nguyen <[email protected]> (046064d)

  • update diagram, readme (f264c6d)

  • debug trajectory func (aa22fe6)

  • Rebase. See Details

rename, restructure Update dlc_draft.py Ingest function drafts (adf3e3f)

  • add make for pose estimation (294a3e8)

  • add dlc loader (3c8ace2)

  • revised draft dlc (340bdee)

  • Merge pull request #2 from ttngu207/main

Proposed schema design (1dd0f1e)

  • dlc_draft (f44efef)

  • Merge pull request #1 from CBroz1/dev

Dev (6f2b9e0)

  • minor table structure edits with Thinh (6029422)

  • Merge from CBroz1/dev

Recent work (738999d)

  • add diagram, README+CHANGELOG clarity (7ebdfc3)

  • NotImplementedError for multi-animal (1668f8f)

  • Cleanup: rm README notes and incomplete files (07977ab)

  • Revise ingestion. Add 2d return trajectory. See details

dlc.py:

  • limit imports of DLC proper to only needed funcs
  • separate schema activation
  • config parameters to separate table following element-array-ephys
  • load fps from model files
  • remove user choice points
  • use DLC functions to load and pick between multiple files

changelog/version.py: revise version number .github/ISSUES: add bug_report and feature request (44dbe9c)