Merge branch 'main' into paper/JOSS-submission

Author: Asanto32

.gitattributes

@@ -0,0 +1,2 @@
+docs/source/tutorial_data/three_nights.bin filter=lfs diff=lfs merge=lfs -text
+*.ipynb filter=lfs diff=lfs merge=lfs -text

.github/workflows/docs.yaml

@@ -13,10 +13,9 @@ on:
 
 jobs:
   build-and-publish-docs:
-    if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Fetch LFS files
       run: git lfs pull
     - uses: actions/setup-python@v5
@@ -26,10 +25,16 @@ jobs:
       run: |
         python -m pip install poetry
         poetry install --with docs
-    - name: Build docs
+    - name: Build Sphinx docs
+      working-directory: docs
       run: |
-        poetry run pdoc src/wristpy -o docs_build -t docs/pdoc-theme --docformat google
-        touch docs_build/.nojekyll
-    - uses: JamesIves/github-pages-deploy-action@6c2d9db40f9296374acc17b90404b6e8864128c8
+        poetry run make html
+        touch build/html/.nojekyll
+        ls -la build/html | sed 's/^/BUILD: /'
+    - name: Deploy to gh-pages
+      uses: JamesIves/github-pages-deploy-action@6c2d9db40f9296374acc17b90404b6e8864128c8
       with:
-        folder: docs_build
+        branch: gh-pages
+        folder: docs/build/html
+        clean: true
+        single-commit: true

.github/workflows/pypi.yaml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: ${{ github.event_name == 'pull_request' && 2 || 0 }}
     - uses: actions/setup-python@v5

.github/workflows/release.yaml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Check out the repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         lfs: true
 

.github/workflows/test.yaml

@@ -21,7 +21,7 @@ jobs:
         python_version: ['3.10', '3.11', '3.12', '3.13']
         resolution: [lowest-direct, highest]
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install poetry
       run: pipx install poetry
 
@@ -57,7 +57,7 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install poetry
       run: pipx install poetry
     - uses: actions/setup-python@v5
@@ -75,7 +75,7 @@ jobs:
   mypy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Install poetry
       run: pipx install poetry
     - uses: actions/setup-python@v5

.gitignore

@@ -76,6 +76,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/build/
+
 
 # PyBuilder
 .pybuilder/

.pre-commit-config.yaml

@@ -41,13 +41,15 @@ repos:
     - --fix=lf
   - id: trailing-whitespace
   - id: pretty-format-json
+    exclude: ^docs/source/.*\.ipynb$
     args:
     - --autofix
     - --indent=4
     - --no-sort-keys
   - id: check-merge-conflict
   - id: check-yaml
   - id: check-json
+    exclude: ^docs/source/.*\.ipynb$
   - id: check-toml
 
 - repo: local

README.md

@@ -1,6 +1,10 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13883190.svg)](https://doi.org/10.5281/zenodo.13883190)
 
-# `wristpy` <img src="https://media.githubusercontent.com/media/childmindresearch/wristpy/main/docs/wristpy_logo.png" align="right" width="25%"/>
+# `wristpy` <picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://media.githubusercontent.com/media/childmindresearch/wristpy/main/docs/source/_static/images/wristpy_logo_dark.png">
+  <source media="(prefers-color-scheme: light)" srcset="https://media.githubusercontent.com/media/childmindresearch/wristpy/main/docs/source/_static/images/wristpy_logo_light.png">
+  <img src="https://media.githubusercontent.com/media/childmindresearch/wristpy/main/docs/source/_static/images/wristpy_logo_light.png" align="right" width="25%" alt="wristpy logo"/>
+</picture>
 
  A Python package for wrist-worn accelerometer data processing.
 

docs/Makefile

@@ -0,0 +1,27 @@
+
+
+
+SPHINXOPTS    ?=
+SPHINXBUILD  ?= sphinx-build
+SOURCEDIR    = source
+BUILDDIR     = build
+
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+clean:
+	@if [ -z "$(BUILDDIR)" ]; then \
+		echo "Error: BUILDDIR is not set."; \
+		exit 1; \
+	fi
+	rm -rf $(BUILDDIR)/*
+
+livehtml:
+	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)