Merge pull request #124 from EthoML/dev

Dev

.github/workflows/deploy-docs.yaml → .github/workflows/publish_docs.yaml

@@ -3,12 +3,18 @@ name: Deploy VAME Docs to GitHub Pages
 on:
   push:
     branches:
-      - docs
+      - main
+      - dev
+    paths:
+      - '.github/workflows/publush_docs.yaml'
+      - 'docs/**'
+      - 'examples/**'
+      - 'src/**'
 
 jobs:
   deploy:
     name: Deploy VAME Docs to GitHub Pages
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     permissions:
       contents: write
       pages: write
@@ -27,6 +33,10 @@ jobs:
       - name: Auto generate API Reference.
         run: cd docs && pydoc-markdown
 
+      - name: Convert Jupyter Notebooks to HTML
+        run: |
+          jupyter nbconvert --to html examples/pipeline.ipynb --embed-images --no-prompt --output-dir=docs/vame-docs-app/static/notebooks_html
+
       - uses: actions/setup-node@v3
         with:
           node-version: 18
@@ -36,6 +46,7 @@ jobs:
 
       - name: Install dependencies
         run: cd docs/vame-docs-app && yarn install --frozen-lockfile
+
       - name: Build website
         run: cd docs/vame-docs-app && yarn build
 
@@ -59,3 +70,4 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/vame-docs-app/build
+          publish_branch: gh-pages

.github/workflows/testing.yaml

@@ -5,7 +5,10 @@ on:
     branches:
       - main
       - dev
-
+    paths:
+      - '.github/workflows/testing.yaml'
+      - 'src/**'
+      - 'tests/**'
 
 jobs:
   run:
@@ -31,7 +34,7 @@ jobs:
           pip install -r tests/requirements-tests.txt --no-cache-dir
 
       - name: Run tests.
-        run: pytest --cov=src/vame --cov-report=xml --cov-report=term-missing -v
+        run: pytest --cov=src/vame --cov-report=xml --cov-report=term-missing -vx
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4.0.1

.gitignore

@@ -112,3 +112,6 @@ venv_docs/
 
 # mypy
 .mypy_cache/
+
+# Others
+**/pipeline_example/**

CHANGELOG.md

@@ -1,3 +1,21 @@
+# v0.7.0
+
+### Fixes
+
+- Egocentric alignment outputs with incorrect column order  ([Issue #96](https://github.com/EthoML/VAME/issues/96))
+- Slow align egocentrical data ([Issue #113](https://github.com/EthoML/VAME/issues/113))
+- Standardized config argument across all functions
+
+### Features
+
+- User friendly way to select reference points for alignment ([Issue #89](https://github.com/EthoML/VAME/issues/89))
+- Adopt movement Xarray data format ([Issue #111](https://github.com/EthoML/VAME/issues/111))
+- Relocate IQR cleaning into preprocessing ([Issue #22](https://github.com/EthoML/VAME/issues/22))
+- Created preprocessing module ([Issue #119](https://github.com/EthoML/VAME/issues/119))
+- Separate module for visualization of results ([Issue #127](https://github.com/EthoML/VAME/issues/127))
+- Further improvements to Pipeline
+
+
 # v0.6.0
 
 ### Fixes

VAME.yaml

@@ -9,4 +9,5 @@ dependencies:
   - python=3.11
   - pip
   - pip:
-      - -r requirements.txt
+      - -r requirements.txt
+      - .

docs/README.md

@@ -7,13 +7,17 @@ This folder contains the documentation for the VAME project. The docs are a docu
 The API Reference documentation is automatically generated from the docstrings and type annotations in the codebase using [pydoc-markdown](https://github.com/NiklasRosenstein/pydoc-markdown).
 
 1. Install pydoc-markdown:
-First install `pydoc-markdown` package following their guide [here](https://niklasrosenstein.github.io/pydoc-markdown/#installation-).
+First install `pydoc-markdown` package. For the moment, we are using a fork of the original package, so you need to install it from the forked repository:
+
+```bash
+pip install git+https://github.com/luiztauffer/pydoc-markdown.git@develop
+```
 
 2. In the `docs/` directory, run the following command to generate the API Reference documentation:
 ```bash
 pydoc-markdown
 ```
-This command will generate the API Reference documentation from the project and save it in the `docs/vame-docs-app/docs/reference/vame` folder.
+This command will generate the API Reference documentation from the project and save it in the `docs/vame-docs-app/docs/reference/` folder.
 
 
 ### Running the documentation app locally
@@ -29,3 +33,4 @@ yarn
 yarn start
 ```
 
+The Docusaurus website should be running locally at: http://localhost:3000/VAME/

docs/pydoc-markdown.yml

@@ -1,11 +1,8 @@
 loaders:
   - type: python
-    search_path: ['../src']
+    search_path: ["../src/vame"]
 processors:
-  - type: filter
-    skip_empty_modules: true
-  - type: smart
-  - type: crossref
+  - type: numpy
 renderer:
   type: docusaurus
   docs_base_path: vame-docs-app/docs

docs/requirements-docs.txt

@@ -1 +1,4 @@
-pydoc-markdown==4.8.2
+# pydoc-markdown==4.8.2
+git+https://github.com/luiztauffer/pydoc-markdown.git@develop
+nbconvert==7.16.4
+mistune==2.0.4

docs/vame-docs-app/docs/getting_started/installation.md

@@ -1,6 +1,6 @@
 ---
 title: Installation
-sidebar_position: 2
+sidebar_position: 1
 ---
 
 
@@ -19,7 +19,8 @@ pip install vame-py
 
 1. Clone the VAME repository to your local machine by running
 ```bash
-git clone https://github.com/LINCellularNeuroscience/VAME.git
+git clone https://github.com/EthoML/VAME.git
+cd VAME
 ```
 
 
@@ -29,9 +30,9 @@ git clone https://github.com/LINCellularNeuroscience/VAME.git
 ```bash
 conda env create -f VAME.yaml
 ```
+
 **Option 2:**  Installing local VAME with pip in your active virtual environment by running
 ```bash
-cd VAME
 pip install .
 ```
 
@@ -43,7 +44,7 @@ You should make sure that you have a GPU powerful enough to train deep learning
 VAME can also be trained in Google Colab or on a HPC cluster.
 :::
 
-Once you have your computing setup ready, begin using VAME by following the [demo workflow guide](/docs/getting_started/running).
+Once you have your computing setup ready, begin using VAME by following the [step-by-step guide](/docs/getting_started/step_by_step).
 
 ## References
 Original VAME publication: [Identifying Behavioral Structure from Deep Variational Embeddings of Animal Motion](https://www.biorxiv.org/content/10.1101/2020.05.14.095430v2) <br/>

docs/vame-docs-app/docs/getting_started/pipeline.mdx

@@ -0,0 +1,15 @@
+---
+id: pipeline
+title: Run Pipeline
+sidebar_position: 3
+slug: /getting_started/pipeline
+---
+
+import React from 'react';
+import useBaseUrl from '@docusaurus/useBaseUrl';
+
+import IframeResizer from '@site/src/components/IframeResizer';
+
+The notebook below is available [here](https://github.com/EthoML/VAME/blob/main/examples/pipeline.ipynb).
+
+<IframeResizer src={useBaseUrl('/notebooks_html/pipeline.html')} />