Merge pull request #14 from MilagrosMarin/dev-milagros

Feat: refactor with schema restructuring, new table, dependency updates, and code cleanup

Author: ttngu207

.devcontainer/devcontainer.json

@@ -27,4 +27,4 @@
 			]
 		}
 	}
-}
+}

.devcontainer/docker-compose.yaml

@@ -23,4 +23,3 @@ services:
     privileged: true # only because of dind
 volumes:
   docker_data:
-

.gitignore

@@ -112,6 +112,8 @@ dj_local_c*.json
 dj_*.y*ml
 temp*
 temp/*
+test_*
+example_*
 
 # docs
 /docs/site

.pre-commit-config.yaml

@@ -45,7 +45,7 @@ repos:
 
           # these are errors that will be ignored by flake8
           # https://www.flake8rules.com/rules/{code}.html
-          - "--ignore=E203,E501,W503,W605,E402"
+          - "--ignore=E203,E501,W503,W605,E402,F401"
           # E203 - Colons should not have any space before them.
           #        Needed for list indexing
           # E501 - Line lengths are recommended to be no greater than 79 characters.

CHANGELOG.md

@@ -1,8 +1,23 @@
 # Changelog
 
-Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+
+## [0.3.0] - 2025-06-07
+
++ Feat - Created new `SelectedFullFit` table to register selected trained models for downstream inference
++ Feat - Updated pipeline architecture by inverting dependency direction:`moseq_infer.PoseEstimationMethod` is moved from `moseq_infer` to `moseq_train` and now the new table `SelectedFullFit` is a nullable foreign key in `moseq_infer.Model`.
++ Fix - Updated imports and foreign key references across schemas to match new structure.
++ Fix - `pre-commit` hooks to exclude removal of used dependencies into the table definitions (`F401`).
++ Add - Refactored `setup.py` to organize dependencies more cleanly and into optional dependencies.
++ Add - Refactored schema activation logic.
++ Add - Adjusted `tutorial_pipeline.py` to reflect the new hierarchy
++ Add - Aligned schema design with DataJoint Element conventions to support modular reuse and testing
++ Add - Update `images` according to these changes
++ Add - Update `tutorial.ipynb` to reflect these changes.
++ Add - Style and minor bug fixes.
+
 ## [0.2.3] - 2025-04-12
 
 + Fix - `moseq_train` to import `keypoint_moseq` functions inside `trigger` mode
@@ -27,7 +42,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Update - tutorial content
 + Fix - `scipy.linalg` deprecation in latest release by adjusting version in `setup.py`
 + Update -  `pre_kappa` and `full_kappa` to integer to simplify equality comparisons
-+ Update - `images` of the pipeline 
++ Update - `images` of the pipeline
 
 ## [0.1.1] - 2024-03-21
 
@@ -41,16 +56,16 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Fix - `Dockerfile` environment variables
 + Update - Activation of one schema with two modules by updating `tutorial_pipeline.ipynb`
 + Update - remove PyPI release from `release.yml`
-+ Update - README 
++ Update - README
 
 ## [0.1.0] - 2024-03-20
 
 + Add - `CHANGELOG` and version for first release
 + Add - DevContainer configuration for GitHub Codespaces
 + Add - Updated documentation in `docs` for schemas and tutorial
 + Add - `kpms_reader` readers
-+ Add - `element_moseq` pipeline architecture and design containing `kpms_pca` and `kpms_model` modules 
-+ Add - `images` with flowchart and pipeline images 
++ Add - `element_moseq` pipeline architecture and design containing `kpms_pca` and `kpms_model` modules
++ Add - `images` with flowchart and pipeline images
 + Add - `tutorial.ipynb` consistent across DataJoint Elements that can be launched using GitHub Codespaces
 + Add - `tutorial_pipeline.py` script for notebooks to import and activate schemas
 + Add - spelling, markdown, and pre-commit config files

README.md

@@ -34,7 +34,7 @@ DataJoint Elements collectively standardize and automate data collection and ana
 
 ## Support
 
-+ If you need help getting started or run into any errors, please open a GitHub Issue 
++ If you need help getting started or run into any errors, please open a GitHub Issue
 or contact our team by email at support@datajoint.com.
 
 ## Interactive Tutorial
@@ -72,4 +72,4 @@ MYSQL_VER=8.0 docker compose -f docker-compose-db.yaml up --build -d
 
 1. We recommend you start by navigating to the `notebooks` directory on the left panel and go through the `tutorial.ipynb` Jupyter notebook. Execute the cells in the notebook to begin your walkthrough of the tutorial.
 
-2. Once you are done, see the options available to you in the menu in the bottom-left corner. For example, in Codespace you will have an option to `Stop Current Codespace` but when running Dev Container on your own machine the equivalent option is `Reopen folder locally`. By default, GitHub will also automatically stop the Codespace after 30 minutes of inactivity.  Once the Codespace is no longer being used, we recommend deleting the Codespace.
+2. Once you are done, see the options available to you in the menu in the bottom-left corner. For example, in Codespace you will have an option to `Stop Current Codespace` but when running Dev Container on your own machine the equivalent option is `Reopen folder locally`. By default, GitHub will also automatically stop the Codespace after 30 minutes of inactivity.  Once the Codespace is no longer being used, we recommend deleting the Codespace.

cspell.json

@@ -207,4 +207,4 @@
         "yticks",
         "zpix"
     ]
-}
+}

element_moseq/__init__.py

@@ -1,4 +1,5 @@
 import os
+
 import datajoint as dj
 
 if "custom" not in dj.config: