Merge pull request #5 from MilagrosMarin/dev_docs

Fix `mkdocs` build issues, Refactor `reader` module and `setup`, Update docs and Dockerfile

Author: ttngu207

.devcontainer/Dockerfile

@@ -34,12 +34,12 @@ RUN \
     apt-get update && \
     apt-get install -y gcc ffmpeg graphviz && \
     pip install ipywidgets && \
-    pip install --no-cache-dir -e /tmp/element-moseq[elements,tests] && \
+    pip install --no-cache-dir -e /tmp/element-moseq[kpms,elements,tests] && \
     # clean up
     rm -rf /tmp/element-moseq/ && \
     apt-get clean
 
-# Install Keypoint-MoSeq (CPU version)
+# Install CPU version for KPMS
 RUN pip install "jax[cpu]==0.3.22" -f https://storage.googleapis.com/jax-releases/jax_releases.html
 
 ENV DJ_HOST fakeservices.datajoint.io

CHANGELOG.md

@@ -3,6 +3,13 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.1] - 2024-08-30
++ Fix - `mkdocs` build issues
++ Fix - `reader` module imports by adding `__init__.py`
++ Fix - Move KPMS installation to `extras_require` in `setup` for consistency with other Elements
++ Update - markdown files in `mkdocs`
++ Update- Dockerfile
+
 ## [0.2.0] - 2024-08-16
 + Add - `load` functions and new secondary attributes for tutorial purposes
 + Add - `outbox` results in the public s3 bucket to be mounted in Codespaces

docs/mkdocs.yaml

@@ -28,7 +28,7 @@ nav:
 # 02. Instead of designating codeblocks with bash, use console. For example..
 #     ```console
 #     cd ../my_dir
-#     ``` 
+#     ```
 # 03. Links across docs should ...
 #     A. Not involve line breaks.
 #     B. Use relative paths to docs in the same repo
@@ -48,15 +48,15 @@ nav:
 #     HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 #     ```
 # 02. The API section will pull docstrings.
-#     A. Follow google styleguide e.g., 
+#     A. Follow google styleguide e.g.,
 #        https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
 #        With typing suggestions: https://docs.python.org/3/library/typing.html
 #     B. To pull a specific workflow fork, change ./docs/src/api/make_pages.py#L19
 # 03. To see your fork of the workflow-{element} in this render, change the
 #     URL in ./docs/src/api/make_pages.py#L19 to your fork.
-# 04. To deploy this site on your fork, 
+# 04. To deploy this site on your fork,
 #     A. declare a branch called gh-pages
-#     B. go to the your fork > settings > pages 
+#     B. go to the your fork > settings > pages
 #     C. direct pages to render from the gh-pages branch at root
 #     D. push a tag to your fork with the format test*.*.*
 #
@@ -93,13 +93,14 @@ plugins:
       default_handler: python
       handlers:
         python:
+          paths: [../]
           options:
             members_order: source
             group_by_category: false
             line_length: 88
   - gen-files:
       scripts:
-      - ./src/api/make_pages.py
+        - ./src/api/make_pages.py
   - literate-nav:
       nav_file: navigation.md
   - exclude-search:
@@ -172,7 +173,7 @@ extra_css:
   - assets/stylesheets/extra.css
 
 extra_javascript:
-  - https://js-na1.hs-scripts.com/23133402.js  # HubSpot chatbot
+  - https://js-na1.hs-scripts.com/23133402.js # HubSpot chatbot
   - javascripts/mathjax.js
   - https://polyfill.io/v3/polyfill.min.js?features=es6
   - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

docs/src/citation.md

@@ -13,6 +13,4 @@ If your work uses the following resources, please cite the respective manuscript
   + Weinreb C, Pearl J, Lin S, Osman MAM, Zhang L, Annapragada S, Conlin E, Hoffman R, 
   Makowska S, Gillis WF and Jay M. Keypoint-MoSeq: parsing behavior by linking point 
   tracking to pose dynamics. BioRxiv. 2023 Dec 23. doi: https://doi.org/10.1101/2023.03.16.532307
-  + Wiltschko AB, Johnson MJ, Iurilli G, Peterson RE, Katon JM, Pashkovski SL, Abraira VE, 
-  Adams RP, Datta SR. Mapping sub-second structure in mouse behavior. Neuron. 2015 Dec 16;
-  88(6):1121-35.
+  + Wiltschko AB, Johnson MJ, Iurilli G, Peterson RE, Katon JM, Pashkovski SL, Abraira VE, Adams RP, Datta SR. Mapping sub-second structure in mouse behavior. Neuron. 2015 Dec 16;88(6):1121-35.

docs/src/index.md

@@ -29,7 +29,7 @@ combined with other Elements to assemble a fully functional pipeline.
 + Install with `pip`
 
   ```bash
-  pip install -e .
+  pip install .
   ```
 
 + [Data Pipeline](./pipeline.md) - Pipeline and table descriptions

docs/src/partnerships.md

@@ -1,3 +1,3 @@
 # Key partnerships
 
-Element MoSeq was developed in collaboration with the [Keypoint-MoSeq developers](https://github.com/dattalab/keypoint-moseq), particularly with Kai Fox from Datta's Lab at Harvard Medical School, to foster integration and interoperability between Keypoint-MoSeq and the DataJoint Element MoSeq.
+Element MoSeq was developed in collaboration with the [Keypoint-MoSeq developers](https://github.com/dattalab/keypoint-moseq), particularly with Kai Fox from Datta's Lab at Harvard Medical School, to foster integration and interoperability between Keypoint-MoSeq and the DataJoint Element-MoSeq.

docs/src/pipeline.md

@@ -49,9 +49,9 @@ The Element is composed of two main schemas, `moseq_train` and `moseq_infer`. Th
 | --- | --- |
 | Session | Unique experimental session identifier |
 
-### `model_train` schema
+### `moseq_train` schema
 
-- For further details see the [`model_train` schema API docs](https://datajoint.com/docs/elements/element-moseq/latest/api/element_moseq/model_train/)
+- For further details see the [`moseq_train` schema API docs](https://datajoint.com/docs/elements/element-moseq/latest/api/element_moseq/moseq_train/)
 
 | Table | Description |
 | --- | --- |

element_moseq/readers/__init__.py

@@ -2,4 +2,4 @@
 Package metadata
 """
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"

element_moseq/version.py

@@ -29,11 +29,12 @@
         "ipykernel>=6.0.1",
         "opencv-python",
         "scipy<1.12.0",
-        "pydot==2.0",
         "element-interface @ git+https://github.com/datajoint/element-interface.git",
-        "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git",
     ],
     extras_require={
+        "kpms": [
+            "keypoint-moseq @ git+https://github.com/dattalab/keypoint-moseq.git",
+        ],
         "elements": [
             "element-animal @ git+https://github.com/datajoint/element-animal.git",
             "element-event @ git+https://github.com/datajoint/element-event.git",