From ac3f334f00710c82c10a7432c2e9ce3310b6bee9 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 15:55:57 -0500
Subject: [PATCH 1/6] Update GitHub Actions

---
 .github/workflows/release.yaml                | 18 ++++++++++
 .github/workflows/test.yaml                   | 33 +++++++++++++++++++
 .../workflows/u24_element_before_release.yaml | 17 ----------
 .../workflows/u24_element_release_call.yaml   | 28 ----------------
 .../workflows/u24_element_tag_to_release.yaml | 14 --------
 CHANGELOG.md                                  |  5 +++
 element_deeplabcut/version.py                 |  2 +-
 7 files changed, 57 insertions(+), 60 deletions(-)
 create mode 100644 .github/workflows/release.yaml
 create mode 100644 .github/workflows/test.yaml
 delete mode 100644 .github/workflows/u24_element_before_release.yaml
 delete mode 100644 .github/workflows/u24_element_release_call.yaml
 delete mode 100644 .github/workflows/u24_element_tag_to_release.yaml

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..4fb78cb
--- /dev/null
+++ b/.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
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
new file mode 100644
index 0000000..ac7af16
--- /dev/null
+++ b/.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//.}
diff --git a/.github/workflows/u24_element_before_release.yaml b/.github/workflows/u24_element_before_release.yaml
deleted file mode 100644
index 692cf82..0000000
--- a/.github/workflows/u24_element_before_release.yaml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: u24_element_before_release
-on:
-  pull_request:
-  push:
-    branches:
-      - '**'
-    tags-ignore:
-      - '**'
-  workflow_dispatch:
-jobs:
-  call_context_check:
-    uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
-  call_u24_elements_build_alpine:
-    uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_build.yaml@main
-    with:
-      py_ver: 3.9
-      image: djbase
diff --git a/.github/workflows/u24_element_release_call.yaml b/.github/workflows/u24_element_release_call.yaml
deleted file mode 100644
index 4324cca..0000000
--- a/.github/workflows/u24_element_release_call.yaml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: u24_element_release_call
-on:
-  workflow_run:
-    workflows: ["u24_element_tag_to_release"]
-    types:
-      - completed
-jobs:
-  call_context_check:
-    uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
-  test_call_u24_elements_release_alpine:
-    if: >-
-      github.event.workflow_run.conclusion == 'success' && ( contains(github.event.workflow_run.head_branch, 'test') || (github.event.workflow_run.event == 'pull_request'))
-    uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_release.yaml@main
-    with:
-      py_ver: 3.9
-      twine_repo: testpypi
-    secrets:
-      TWINE_USERNAME: ${{secrets.TWINE_TEST_USERNAME}}
-      TWINE_PASSWORD: ${{secrets.TWINE_TEST_PASSWORD}}
-  call_u24_elements_release_alpine:
-    if: >-
-      github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'datajoint' && !contains(github.event.workflow_run.head_branch, 'test')
-    uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_release.yaml@main
-    with:
-      py_ver: 3.9
-    secrets:
-      TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
-      TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
diff --git a/.github/workflows/u24_element_tag_to_release.yaml b/.github/workflows/u24_element_tag_to_release.yaml
deleted file mode 100644
index 57334e9..0000000
--- a/.github/workflows/u24_element_tag_to_release.yaml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: u24_element_tag_to_release
-on:
-  push:
-    tags:
-      - '*.*.*'
-      - 'test*.*.*'
-jobs:
-  call_context_check:
-    uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
-  call_u24_elements_build_alpine:
-    uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_build.yaml@main
-    with:
-      py_ver: 3.9
-      image: djbase
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b264da9..d8d961a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,10 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.7] - 2023-08-04
+
++ Update - GitHub Actions with new reusable workflows
+
 ## [0.2.6] - 2023-05-22
 
 + Add - DeepLabCut, NWB, and DANDI citations
@@ -68,6 +72,7 @@ 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
 
+[0.2.7]: 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
 [0.2.4]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.4
diff --git a/element_deeplabcut/version.py b/element_deeplabcut/version.py
index 21ce3f8..617ac09 100644
--- a/element_deeplabcut/version.py
+++ b/element_deeplabcut/version.py
@@ -1,4 +1,4 @@
 """
 Package metadata
 """
-__version__ = "0.2.6"
+__version__ = "0.2.7"

From cc2cbfcbc79fc38da6fe2eadcad189c9732190d4 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 16:07:43 -0500
Subject: [PATCH 2/6] Rename images

---
 images/{diagram_flowchart.drawio => flowchart.drawio} | 0
 images/{diagram_flowchart.svg => flowchart.svg}       | 0
 images/{diagram_dlc.svg => pipeline.svg}              | 0
 images/{diagram_dlc_model.svg => pipeline_model.svg}  | 0
 images/{diagram_dlc_train.svg => pipeline_train.svg}  | 0
 5 files changed, 0 insertions(+), 0 deletions(-)
 rename images/{diagram_flowchart.drawio => flowchart.drawio} (100%)
 rename images/{diagram_flowchart.svg => flowchart.svg} (100%)
 rename images/{diagram_dlc.svg => pipeline.svg} (100%)
 rename images/{diagram_dlc_model.svg => pipeline_model.svg} (100%)
 rename images/{diagram_dlc_train.svg => pipeline_train.svg} (100%)

diff --git a/images/diagram_flowchart.drawio b/images/flowchart.drawio
similarity index 100%
rename from images/diagram_flowchart.drawio
rename to images/flowchart.drawio
diff --git a/images/diagram_flowchart.svg b/images/flowchart.svg
similarity index 100%
rename from images/diagram_flowchart.svg
rename to images/flowchart.svg
diff --git a/images/diagram_dlc.svg b/images/pipeline.svg
similarity index 100%
rename from images/diagram_dlc.svg
rename to images/pipeline.svg
diff --git a/images/diagram_dlc_model.svg b/images/pipeline_model.svg
similarity index 100%
rename from images/diagram_dlc_model.svg
rename to images/pipeline_model.svg
diff --git a/images/diagram_dlc_train.svg b/images/pipeline_train.svg
similarity index 100%
rename from images/diagram_dlc_train.svg
rename to images/pipeline_train.svg

From fcd026a86be2d22d74f70a5ffdd6a82de1a77626 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 16:20:11 -0500
Subject: [PATCH 3/6] Update readme

---
 README.md            | 30 ++++++++++++++++++++++++++----
 docs/src/concepts.md |  2 +-
 docs/src/index.md    |  2 +-
 3 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 3392f20..e5bd971 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-# 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
@@ -6,7 +8,27 @@ 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)
+## 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.
diff --git a/docs/src/concepts.md b/docs/src/concepts.md
index 15d055f..02000bd 100644
--- a/docs/src/concepts.md
+++ b/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))
 
diff --git a/docs/src/index.md b/docs/src/index.md
index 8e493e6..5732762 100644
--- a/docs/src/index.md
+++ b/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

From dff5b8776d12dc3c9332f60514fa926f7e3b12ae Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 16:21:57 -0500
Subject: [PATCH 4/6] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d8d961a..e3ac610 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 ## [0.2.7] - 2023-08-04
 
 + Update - GitHub Actions with new reusable workflows
++ Update - Readme instructions
 
 ## [0.2.6] - 2023-05-22
 

From f37a17f2f59bc974b82b6d4c0dffbde72be34ec1 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 16:26:21 -0500
Subject: [PATCH 5/6] Format with black

---
 element_deeplabcut/model.py |  4 +++-
 element_deeplabcut/train.py | 16 ++++++++++------
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/element_deeplabcut/model.py b/element_deeplabcut/model.py
index ef49333..097a5c8 100644
--- a/element_deeplabcut/model.py
+++ b/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:
diff --git a/element_deeplabcut/train.py b/element_deeplabcut/train.py
index ff85146..f63c756 100644
--- a/element_deeplabcut/train.py
+++ b/element_deeplabcut/train.py
@@ -241,13 +241,16 @@ class ModelTraining(dj.Computed):
     # https://github.com/DeepLabCut/DeepLabCut/issues/70
 
     def make(self, key):
-        from deeplabcut import train_network # isort:skip
+        from deeplabcut import train_network  # isort:skip
+
         try:
-            from deeplabcut.utils.auxiliaryfunctions import get_model_folder # isort:skip
+            from deeplabcut.utils.auxiliaryfunctions import (
+                get_model_folder,
+            )  # isort:skip
         except ImportError:
             from deeplabcut.utils.auxiliaryfunctions import (
-                GetModelFolder as get_model_folder
-            ) # isort:skip
+                GetModelFolder as get_model_folder,
+            )  # isort:skip
 
         """Launch training for each train.TrainingTask training_id via `.populate()`."""
         project_path, model_prefix = (TrainingTask & key).fetch1(
@@ -278,8 +281,9 @@ def make(self, key):
         # ---- Trigger DLC model training job ----
         train_network_input_args = list(inspect.signature(train_network).parameters)
         train_network_kwargs = {
-            k: int(v) if k in ("shuffle", "trainingsetindex", "maxiters") else v 
-            for k, v in dlc_config.items() if k in train_network_input_args
+            k: int(v) if k in ("shuffle", "trainingsetindex", "maxiters") else v
+            for k, v in dlc_config.items()
+            if k in train_network_input_args
         }
         for k in ["shuffle", "trainingsetindex", "maxiters"]:
             train_network_kwargs[k] = int(train_network_kwargs[k])

From b16c3861c5a4f51aaabb6300999b0fc4a0b92641 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Fri, 4 Aug 2023 16:28:19 -0500
Subject: [PATCH 6/6] Format with black

---
 element_deeplabcut/train.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/element_deeplabcut/train.py b/element_deeplabcut/train.py
index f63c756..89d1047 100644
--- a/element_deeplabcut/train.py
+++ b/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.