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CHANGELOG

v0.2.2 (2024-09-26)

Fix

  • fix: suppress linter warning for undefined version variable (560c03a)

Test

  • test: update GHA semantic release and test (9c0a6d3)

Unknown

  • Merge pull request #9 from MilagrosMarin/main

fix: suppress linter warning for undefined version variable (76e7f75)

  • Merge pull request #8 from MilagrosMarin/main

test: update GHA semantic release and test (bea174b)

  • Merge remote-tracking branch 'refs/remotes/origin/main' (c7fd8ce)

  • Merge pull request #7 from MilagrosMarin/main

Update GHA (0cc7422)

  • Merge branch 'datajoint:main' into main (d0bcd00)

  • Merge pull request #6 from MilagrosMarin/main (009549f)

  • fix GHA (8df4c94)

  • add mkdocs-release-caller.yml (b039679)

v0.2.1 (2024-09-26)

Refactor

  • refactor(setup): move installation of kpms as extras_require for consistency with other elements (eb5db5d)

Unknown

  • Merge pull request #5 from MilagrosMarin/dev_docs

Fix mkdocs build issues, Refactor reader module and setup, Update docs and Dockerfile (9864376)

  • update CHANGELOG (5a58710)

  • fix reader module as package and can be imported properly (1b5c98b)

  • update markdown in docs/src (8268ea2)

  • udpate Dockerfile (ae2a596)

  • update version and changelog (b3f075b)

  • update Dockerfile with latest installation of kpms (a09325e)

  • update Dockerfile with extras_require (fd824f2)

  • Merge branch 'datajoint:main' into dev_docs (31483e6)

  • Merge pull request #4 from MilagrosMarin/main

Fix deprecated library to run KPMS + add task_mode + complete functionality of the tutorial in codespaces (62de906)

  • update image of pipeline in tutorial (f30df2f)

  • Merge remote-tracking branch 'refs/remotes/previous/main' into main_element_moseq_v2 (97d7123)

  • Update CHANGELOG.md (57d1ae3)

  • update outputs in the tutorial from testing with codespaces (0c26b41)

  • update images according to design reverted (4237479)

  • update dockerfile (82cb6dc)

  • update dockerfile (02ae743)

  • udpate dockerfile (53340e4)

  • add jupyter_bokeh for PCAPrep to use Panel interactively in VSCode notebooks (fa80df5)

  • minor update in tutorial (44bb3c5)

  • update dockerfile (7338a6e)

  • black formatting (7924359)

  • update setup.py (9b43cf3)

  • cleanup setup.py (b2c9e5a)

  • update tutorial (be44c2b)

  • update image (4106b5c)

  • minor update in docstrings (8227ef7)

  • improve docstring (91d3cac)

  • minor refactor import structure of kpms_reader (cc0a92b)

  • revert changes in PreFitTask and FullFitTask (8deb0f1)

  • fix docs (70108e4)

  • update CHANGELOG (cd3cd04)

  • black formatting (ff976e3)

  • update CHANGELOG (2de60e4)

  • Update tutorial with changes in pipeline design (01adc23)

  • Update images with changes to pipeline design (f3b9f70)

  • FullFitTask to Lookup and add fullfit_idattr (7b222eb)

  • PreFitTask to Lookup and add prefit_id (cea79f3)

  • Merge remote-tracking branch 'origin/main' (5c18720)

  • Update moseq_train.py with except FileNotFoundError (fd4f0c5)

  • Update moseq_train.py with kappa values as int (fdb08fe)

  • Update moseq_train.py (5841bf1)

  • Update moseq_infer.py (69ad231)

  • Reviewer's suggestion: task_mode='load' and make model attribute required (c60d0f7)

  • Update element_moseq/moseq_train.py

Co-authored-by: Kushal Bakshi <[email protected]> (160d29b)

  • Update element_moseq/moseq_train.py

Co-authored-by: Kushal Bakshi <[email protected]> (70050ce)

  • Update element_moseq/moseq_train.py

Co-authored-by: Kushal Bakshi <[email protected]> (14f0684)

  • Update element_moseq/moseq_infer.py

Co-authored-by: Kushal Bakshi <[email protected]> (44e0314)

  • black formatting moseq_infer (e31867d)

  • default task_mode = &#39;load&#39; (d3a1f17)

  • revert remove pip install jax == 0.3.22 (cbf7ea5)

  • update CHANGELOG (acec2e9)

  • Fix error with scipy.linalg , tril (e36ee39)

  • update plot_scree and plot_pcs for Codespace (593bf9b)

  • update changelog and version (0654c30)

  • black formatting (f112519)

  • Merge remote-tracking branch 'previous/main' (a35eaca)

  • task_mode=&#34;load&#34; updates for tutorial purposes (5302ce0)

v0.1.1 (2024-09-26)

Unknown

  • Merge pull request #3 from MilagrosMarin/main

Pipeline Architecture Refinement and Enhancement (2e87c49)

  • black formatting (83c68d5)

  • update tutorial.ipynb (1f1831c)

  • kappa type from int to float (cd2e872)

  • refactor setup_project code block (8485325)

  • added suggestions from this PR (f5b2a66)

  • black formatting moseq_train (9b36f16)

  • Merge remote-tracking branch 'origin/main' (32a8965)

  • fix env variables DevContainer (441ce35)

  • refactor PCAPrep make function (7e58ffe)

  • Update CHANGELOG.md (b04a80c)

  • Update CHANGELOG.md (9d9f8b8)

  • Update CHANGELOG.md (20a1960)

  • black formatting version (6cb9056)

  • black formatting (51bba6d)

  • update CHANGELOG (3ba3a49)

  • add cite in citation.md (edaa0a9)

  • update moseq_infer.py (6c8e707)

  • update moseq_train.py (7553b9c)

  • update images (f220165)

  • update tutorial.ipynb (3de9e01)

  • update pipeline.md with new architecture (35e6ea0)

  • update changelog (0bd5155)

  • revert mv tutorial_pipeline.py to tests (0f74e35)

  • bump version and update changelog (e0cbd7f)

  • major changes to moseq_infer (760f745)

  • major changes to moseq_train (a58389a)

  • from previous commit (4a2464f)

  • git mv tutorial_pipeline.py to tests (09d580d)

  • update tutorial notebook (761146b)

  • add import two dependencies (e555e73)

  • update images (52f6fa5)

  • from XFitting to PCAFit, PreFit & FullFit (142ad44)

  • update Dockerfile pointing to inbox and outbox (d201bc4)

  • git mv kpms_model -> moseq_infer.py (4151274)

  • revert git mv moseq_infer -> kpms_model (1dc9506)

  • suggestion pull/2#discussion_r1532927138_ (5c7dfed)

  • suggestion pull/2#discussion_r1532926679_ (0b918fb)

  • refactor make of Inference 2#disc_r1532924691_ (4889c8d)

  • suggestion pull/2#discussion_r1532921555_ (e24377f)

  • one activation for both of the modules (b8e8eac)

  • eliminate redundancy of get_kpms_x_data_dir func (96ed977)

  • move prefitting and fullfitting to moseq_train (d2064bc)

  • kpms_pca->moseq_train & kpms_model->moseq_infer (105157f)

  • update citation.md (fd94abb)

  • update IMAGING_ROOT_DATA_DIR to /example_data (4c07e50)

  • suggestion pull/2#discussion_r1532188097_ (ba450ae)

  • suggestion pull/2#discussion_r1532440194_ (db7c393)

  • suggestion pull/2#discussion_r1532435698_ (e91afcd)

  • suggestion pull/2#discussion_r1532421093_ (58ab1a3)

  • suggestion pull/2#discussion_r1532403101_ (065d014)

  • suggestion pull/2#discussion_r1532375217_ (42f3168)

  • suggestion pull/2#discussion_r1532373250_ (22a05dc)

  • suggestion pull/2#discussion_r1532339169_ (2c929a7)

  • suggestion pull/2#discussion_r1532337714_ (57ae481)

  • suggestion pull/2#discussion_r1532329205_ (961a77b)

  • suggestion pull/2#discussion_r1532363814_ (f0f60c9)

  • Suggestion pull/2#discussion_r1532363392_ (09d8009)

  • Suggestion pull/2#discussion_r1532233183_ (e77f2f2)

  • Suggestion pull/2#discussion_r1532189430_ (71d72fe)

  • Thinh's suggestion: pull/2#discussion_r1532180529 (11f97b0)

v0.1.0 (2024-09-26)

Unknown

  • Merge pull request #2 from MilagrosMarin/first_release

Initial Release for element-moseq (1dea4e4)

  • update env variables in dockerfile (9f22796)

  • update changelog (7294c80)

  • update kpms_model.py (43545d5)

  • update README (59bbeb4)

  • update docs (cf224a7)

  • update setup.py (73e62b0)

  • update .devcontainer (d6b9d93)

  • update kpms_pca.py (2a2d780)

  • update kpms_model.py (4a3a2c2)

  • update kpms_pca.py (e620922)

  • update kpms_reader.py (b0d182f)

  • tutorial black (5bb5c9f)

  • blackformatting tutorial (9a1d43b)

  • update tutorial.ipynb (90a65ac)

  • add CHANGELOG (3360062)

  • black formatting README (d57b52f)

  • add files for the element (24673ec)

  • add .github (d7743cd)

  • images:update flowchart, add new pipeline images (cb6e032)

  • update the video train logic in LoadKeypointSet (fcd8e69)

  • update kpms_pca.py (b50860e)

  • update tutorial.ipynb (WIP) (b1e2b26)

  • Update logic in GenerateResults (0ead1ea)

  • Update README (aafbc4a)

  • tutorial {WIP} (bff0c61)

  • add docs [WIP] (397a6f0)

  • Add kpms_model computation and logic (a2c2fdb)

  • blackformatting kpms_pca (87ad0f7)

  • add import dependency in kpms_pca (6a6b5b8)

  • Add docstrings in tables and make in kpms_pca (bc01778)

  • add flowchart.svg (bd4bcbd)

  • Merge remote-tracking branch 'origin/dev_mila' into dev_mila (10dc515)

  • Update flowchart.drawio (0711044)

  • update docstring of readers and black formatting (ae9acae)

  • add images (d7c8576)

  • fix markdown typo in kpms_pca.py (d42d87e)

  • Update Prefitting computation logic (aa151c2)

  • Fix attrib PreFittingTask and FullFittingTask (c55844a)

  • update PCAFitting to save data & metadata files (af6c094)

  • Update notebook after testing the newpca logics (cd27d1e)

  • Add load_dj_config function to readers (fd2ccca)

  • Update DimsExplainedVariance computation logic (8a8139d)

  • Update PCAFitting computation logic (53edbcb)

  • Update FormattedDataset logic (13e2480)

  • markdown clarification in tutorial_pipeline (d8137da)

  • delete unused dependencies in kpms_model (f9c0b5c)

  • RecordingInfo to av. metadata for one kpset_id (afd6c45)

  • project_path to project_dir for consistency (15bbe27)

  • from 'format' to 'format_method' (47087f2)

  • Merge remote-tracking branch 'origin/dev_mila' into dev_mila (5c1debb)

  • code review - pipeline restructure (dc8c153)

  • revert update on dockerfile-> will update it later (4a3294a)

  • Merge branch 'main' of github.com:MilagrosMarin/element-moseq into dev_mila (84944ed)

  • fixed import keypoint-moseq in ipython codespace (4b71c99)

  • test codespaces (848b889)

  • test modif dockerfile in codespaces (1b2362d)

  • test element-moseq[elements] in codespaces (fe6be54)

  • update testing notebook (3ee1d09)

  • first draft of element_moseq/kpms_pca.py (7d7ad37)

  • Create functions in readers/kpms_reader.py (c18000f)

  • update tutorial_pipeline.py w new schema names (8af783a)

  • from pca.py to kpms_pca.py [WIP] (a675c58)

  • from model.py to kpms_model.py [WIP] (ba85e31)

  • readers WIP (9f41ace)

  • fix RecordingInfo.populate() (e55b69d)

  • test element-moseq[elements] in codespaces (4eba566)

  • WIP: restructure model schema (b468fd4)

  • WIP: redefine schema model and connect to pca (6bc6f8d)

  • testing notebook (6bf3a03)

  • Testing notebook (69787e8)

  • WIP: test schema pca and basic structure model (9bea9d0)

  • WIP notebooks (e68c61e)

  • WIP pipeline (9080fe3)

  • add necessary dependency (97047db)

  • update setup (03f5948)

  • update description of MoSeq in README (bb8e543)

  • add jax and jaxlib to fix installation (2022f35)

  • from default to kpms_default and add mchips (45c9e1a)

  • Update README (66cddfc)

  • delete -U (2689bb8)

  • test moseq installation using https (644505d)

  • change default kpms installation (ae1cbf4)

  • test default installation (94c4dc6)

  • test with no version (36dcdc2)

  • test without version.py (d759058)

  • test container without DATA_MOUNTPOINT (d01b394)

  • test container only with element-moseq[elements] (30907d5)

  • minor change in setup.py (a3f149c)

  • add README (029501c)

  • update setup.py (d039df7)

  • fix dockerfile and devcontainer (3ca0467)

  • add DevContainers (e9d4b4b)

  • add .gitignore (4f4d05b)

  • create README.md (c7dce57)

  • first commit (d4d7430)