Merge pull request #86 from kabilar/main

Update GitHub Actions and Readme

.github/workflows/release.yaml

@@ -0,0 +1,18 @@
+name: Release
+on:
+  workflow_dispatch:
+jobs:
+  make_github_release:
+    uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
+  pypi_release:
+    needs: make_github_release
+    uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
+    secrets:
+      TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
+      TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
+    with:
+      UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write

.github/workflows/test.yaml

@@ -0,0 +1,33 @@
+name: Test
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 8 * * 1"
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.9", "3.10"]
+        mysql_ver: ["8.0", "5.7"]
+        include:
+          - py_ver: "3.8"
+            mysql_ver: "5.7"
+          - py_ver: "3.7"
+            mysql_ver: "5.7"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 "black[jupyter]"
+      - name: Run style tests
+        run: |
+          python_version=${{matrix.py_ver}}
+          black element_deeplabcut --check --verbose --target-version py${python_version//.}

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.8] - 2023-08-07
+
++ Update - GitHub Actions with new reusable workflows
++ Update - Readme instructions
+
 ## [0.2.7] - 2023-08-04
 
 + Fix - Update the project path in the pose config file to train the model
@@ -72,6 +77,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
   graciously provided by the Mathis Lab.
 + Add - Support for 2d single-animal models
 
+[0.2.8]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.8
 [0.2.7]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.7
 [0.2.6]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.6
 [0.2.5]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.5

README.md

@@ -1,12 +1,34 @@
-# DataJoint Element - DeepLabCut
+[![PyPI version](https://badge.fury.io/py/element-deeplabcut.svg)](http://badge.fury.io/py/element-deeplabcut)
+
+# DataJoint Element for Pose Estimation with DeepLabCut
 
 DataJoint Element for markerless pose estimation with
 [DeepLabCut](https://www.deeplabcut.org/).  DataJoint Elements collectively standardize
 and automate data collection and analysis for neuroscience experiments.  Each Element is
 a modular pipeline for data storage and processing with corresponding database
 tables that can be combined with other Elements to assemble a fully functional pipeline.
 
-![diagram](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/diagram_flowchart.svg)
+## Experiment Flowchart
+
+![flowchart](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/flowchart.svg)
+
+## Data Pipeline Diagram
+
+![pipeline](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/pipeline.svg)
+
+## Getting Started
+
++ Install from PyPI
+
+     ```bash
+     pip install element-deeplabcut
+     ```
+
++ [Interactive tutorial](https://github.com/datajoint/workflow-deeplabcut)
+
++ [Documentation](https://datajoint.com/docs/elements/element-deeplabcut)
+
+## Support
 
-Installation and usage instructions can be found at the 
-[Element documentation](https://datajoint.com/docs/elements/element-deeplabcut).
++ 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.

docs/src/concepts.md

@@ -88,7 +88,7 @@ corresponding tables in the database.  Within the workflow, Element DeepLabCut c
 to upstream Elements including Lab, Animal, and Session.  For more detailed
 documentation on each table, see the API docs for the respective schemas.
 
-![element-deeplabcut diagram](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/diagram_dlc.svg)
+![pipeline](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/pipeline.svg)
 
 ### `lab` schema ([API docs](../api/workflow_deeplabcut/pipeline/#workflow_deeplabcut.pipeline.Device))
 

docs/src/index.md

@@ -6,7 +6,7 @@ and automate data collection and analysis for neuroscience experiments.  Each El
 a modular pipeline for data storage and processing with corresponding database
 tables that can be combined with other Elements to assemble a fully functional pipeline.
 
-![diagram](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/diagram_flowchart.svg)
+![flowchart](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/flowchart.svg)
 
 Element DeepLabCut runs DeepLabCut which uses image recognition machine learning models
 to generate animal position estimates from consumer grade video equipment.  The Element

element_deeplabcut/model.py

@@ -630,7 +630,9 @@ def generate(
         """
         processed_dir = get_dlc_processed_data_dir()
         output_dir = cls.infer_output_dir(
-            {**video_recording_key, "model_name": model_name}, relative=False, mkdir=True
+            {**video_recording_key, "model_name": model_name},
+            relative=False,
+            mkdir=True,
         )
 
         if task_mode is None:

element_deeplabcut/train.py

@@ -21,7 +21,7 @@ def activate(
     *,
     create_schema: bool = True,
     create_tables: bool = True,
-    linking_module: str = None
+    linking_module: str = None,
 ):
     """Activate this schema.