Merge pull request #54 from CBroz1/main

Prep for pypi publish

Author: tdincer

CHANGELOG.md

@@ -2,15 +2,17 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [0.2.0] - Unreleased
-+ Relocate module imports to the top of the files
-+ Add - Call reusable CICD
+## [0.2.0] - 2022-10-10
 + Update - Remove direct dependency (`element-interface`) for PyPI release.
 + Update - Docstring PEP257 compliance #24 
 + Update - Explicit handling of KeyboardInterrupt #26
 + Update - Streamline insert_new_params #27
++ Update - Relocate module imports to the top of the files
++ Update - Missing f for formatted string in read_yaml
 + Change - Rename datajoint-saved config to `dj_dlc_config.yaml`
-+ Fix - Missing f for formatted string in read_yaml
++ Add - Call reusable CICD
++ Add - NWB export
++ Add - mkdocs deployment with workflow API docs
 
 ## [0.1.1] - 2022-06-10
 ### Fixed
@@ -29,6 +31,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - Drafts from a collection of precursor pipelines, including [DataJoint_Demo_DeepLabCut](https://github.com/MMathisLab/DataJoint_Demo_DeepLabCut) graciously provided by the Mathis Lab.
 + Add - Support for 2d single-animal models
 
-[0.1.1]: https://github.com/datajoint/element-deeplabcut/compare/0.1.0...0.1.1
-[0.1.0]: https://github.com/datajoint/element-deeplabcut/compare/0.0.0a...0.1.0
+[0.2.0]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.0
+[0.1.1]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.1.1
+[0.1.0]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.1.0
 [0.0.0a]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.0.0a

README.md

@@ -90,6 +90,40 @@ For more detail, check the docstring of the `element-deeplabcut`:
 
 [![YouTube tutorial](https://img.youtube.com/vi/8FDjTuQ52gQ/0.jpg)](https://www.youtube.com/watch?v=8FDjTuQ52gQ)
 
+### Exporting to NWB
+
+The `export/nwb.py` module calls [DLC2NWB](https://github.com/DeepLabCut/DLC2NWB/) to
+save output generated by Element DeepLabCut as NWB files. 
+The main function, `dlc_session_to_nwb`, contains a flag to control calling a parallel 
+function in [Element Session](https://github.com/datajoint/element-session/blob/main/element_session/export/nwb.py).
+
+Before using, please install [DLC2NWB](https://github.com/DeepLabCut/DLC2NWB/)
+
+```bash
+pip install dlc2nwb
+```
+
+Then, call the export function using keys from the `PoseEstimation` table.
+
+```python
+from element_deeplabcut import model
+from element_session import session
+from element_deeplabcut.export import dlc_session_to_nwb
+
+session_key = (session.Session & CONDITION)
+pose_key = (model.PoseEstimation & session_key).fetch1('KEY')
+dlc_session_to_nwb(pose_key, use_element_session=True, session_kwargs=SESSION_KWARGS)
+```
+
+Here, `CONDITION` should uniquely identify a session and `SESSION_KWARGS` can be any of
+the items described in the docstring of `element_session.export.nwb.session_to_nwb`
+as a dictionary.
+
+As DLC2NWB does not currently offer a separate function for generating `PoseEstimation`
+objects (see [ndx-pose](https://github.com/rly/ndx-pose)), the current solution is to
+allow DLC2NWB to write to disk, and optionally rewrite this file using metadata provided
+by the export function in Element Session.
+
 ## Citation
 
 + If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.