Merge branch 'main' into mitch-experimental

.github/workflows/build-docs.yml

@@ -0,0 +1,41 @@
+# REF: https://coderefinery.github.io/documentation/gh_workflow/
+
+name: Build documentation
+
+
+on: [push, pull_request, workflow_dispatch]
+
+env: 
+  PYTHON_VERSION: '3.10'
+  POETRY_VERSION: '1.8.3'
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Local action that tries to cache as much of python & poetry as possible
+      - name: Setup environment
+        uses: ./.github/workflows/setup-python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          poetry-version: ${{ env.POETRY_VERSION }}
+
+      - name: Sphinx build
+        run: |
+          poetry run sphinx-apidoc -f -o docs/source/generated client &&
+          cd docs &&
+          poetry run make html
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build/
+          force_orphan: true

.github/workflows/run-checks.yml

@@ -0,0 +1,50 @@
+# REF: https://github.com/UQComputingSociety/uqcsbot-discord/blob/main/.github/workflows/setup-python/action.yml
+
+name: Run code checks
+
+on:
+  push:
+    branches: [ main ]
+  pull_request: []
+
+env: 
+  PYTHON_VERSION: '3.10'
+  POETRY_VERSION: '1.8.3'
+
+jobs:
+  tests:
+    name: Run tests
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+        # Local action that tries to cache as much of python & poetry as possible
+      - name: Setup environment
+        uses: ./.github/workflows/setup-python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          poetry-version: ${{ env.POETRY_VERSION }}
+
+      - name: Check with pytest
+        run: poetry run pytest
+
+  styling:
+    name: Run code styling
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+        # Local action that tries to cache as much of python & poetry as possible
+      - name: Setup environment
+        uses: ./.github/workflows/setup-python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          poetry-version: ${{ env.POETRY_VERSION }}
+
+      - name: Check with black
+        run: poetry run black .
+

.github/workflows/setup-python/action.yml

@@ -0,0 +1,71 @@
+# REF: https://github.com/UQComputingSociety/uqcsbot-discord/blob/main/.github/workflows/setup-python/action.yml
+
+name: Setup environment
+description: Setup python & poetry for running tests & typechecking
+
+inputs:
+  python-version:
+    description: Version of python to use
+    required: true
+  poetry-version:
+    description: Version of poetry to use
+    required: true
+
+runs: 
+  using: "composite"
+  steps:
+    # ------
+    # Get python
+    # ------
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    # ------
+    # Get poetry (hopefully from cache)
+    # ------
+    - name: Check for cached poetry binary
+      id: cached-poetry-binary
+      uses: actions/cache@v4
+      with:
+        path: ~/.local
+        # poetry depends on OS, python version, and poetry version
+        key: poetry-${{ runner.os }}-${{ inputs.python-version }}-${{ inputs.poetry-version }}
+
+    - name: Install poetry on cache miss
+      # we don't need an `if:` here because poetry checks if it's already installed
+      uses: snok/install-poetry@v1
+      with:
+        version: ${{ inputs.poetry-version }}
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+        virtualenvs-path: '**/.venv'
+        installer-parallel: true
+
+    - name: Ensure poetry is on PATH
+      run: echo "$HOME/.poetry/bin" >> $GITHUB_PATH
+      shell: bash
+
+    # ------
+    # Get library dependencies (hopefully from cache)
+    # ------
+    - name: Check for cached dependencies
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: '**/.venv'
+        # poetry dependencies depend on OS, python version, poetry version, and repository lockfile
+        key: poetry-deps-${{ runner.os }}-${{ inputs.python-version }}-${{ inputs.poetry-version }}-${{ hashFiles('**/poetry.lock') }}
+
+    - name: Install dependencies on cache miss
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction --no-root
+      shell: bash
+
+    # ------
+    # Finalise install
+    # ------
+    - name: Install main project
+      run: poetry install --no-interaction
+      shell: bash

.gitignore

@@ -1,4 +1,6 @@
-client/models/resources
+client/data/resources/*
+client/models/resources/*
+!client/data/resources/database.dbml
 __pycache__/
 *.task
 *.egg-info

README.md

@@ -84,6 +84,18 @@ To style individual files, you can use
 poetry run black client/models/pose_detection/classification.py
 ```
 
+## Documentation
+
+To build the docs locally, run from the root of the repo:
+
+```bash
+poetry run sphinx-apidoc -f -o docs/source/generated client &&
+cd docs &&
+poetry run make html
+```
+
+The documentation is generated automatically from the source code, so it isn't stored in the repo (hence why we need to run `sphinx-apidoc`).
+
 ## Downloading ML Models
 From top-level directory.
 ```bash

client/data/resources/database.dbml

@@ -0,0 +1,18 @@
+Project sitting_desktop_garden {
+    database_type: "SQLite"
+} 
+
+Table user {
+    id INTEGER [primary key, unique, increment]
+}
+
+Table posture {
+    id INTEGER [primary key, unique, increment]
+    user_id INTEGER [ref: > user.id]
+
+    // Proportion of time that posture is good within period 
+    prop_good REAL
+
+    period_start DATETIME
+    period_end DATETIME
+}

client/data/routines.py

@@ -0,0 +1,52 @@
+"""Data routines that can be integrated into main control flow."""
+
+import sqlite3
+from typing import Any
+from importlib import resources
+from pydbml import PyDBML
+
+DATABASE_DEFINITION = resources.files("data.resources").joinpath("database.dbml")
+DATABASE_RESOURCE = resources.files("data.resources").joinpath("database.db")
+
+
+def init_database() -> None:
+    """Initialise SQLite database if it does not already exist"""
+    # Open connection with database
+    with resources.as_file(DATABASE_RESOURCE) as database_file:
+        if database_file.is_file():
+            return
+
+        parsed = PyDBML(DATABASE_DEFINITION)
+        init_script = parsed.sql
+
+        connection = sqlite3.connect(database_file)
+
+    # Run init script
+    with connection:
+        cursor = connection.cursor()
+        cursor.executescript(init_script)
+        connection.commit()
+
+
+def get_schema_info() -> list[list[tuple[Any]]]:
+    """Column information on all tables in database.
+
+    Returns:
+        (list[list[tuple[Any]]]): Outer list contains table information, inner list contains column
+            information tuples.
+    """
+    with resources.as_file(DATABASE_RESOURCE) as database_file:
+        connection = sqlite3.connect(database_file)
+
+    with connection:
+        cursor = connection.cursor()
+        result = cursor.execute("SELECT name FROM sqlite_schema WHERE type='table'")
+        tables = result.fetchall()
+
+        table_schemas = []
+        for table in tables:
+            result = cursor.execute(f"PRAGMA table_info({table[0]})")
+            table_schema = result.fetchall()
+            table_schemas.append(table_schema)
+
+    return table_schemas

client/models/__init__.py

@@ -0,0 +1,3 @@
+"""
+Machine learning models (pose detection and face recognition)
+"""

client/models/pose_detection/__init__.py

@@ -1,6 +1,3 @@
 """
 Pose detection module
 """
-
-from .camera import is_camera_aligned
-from .classification import posture_classify

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,34 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "sitting-desktop-garden"
+copyright = (
+    "2024, Limao Chang, Mitchell Clark, Gabriel Field, Iain Jensen, David Ramsay"
+)
+author = "Limao Chang, Mitchell Clark, Gabriel Field, Iain Jensen, David Ramsay"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+
+html_theme = "alabaster"
+html_static_path = ["_static"]

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. sitting-desktop-garden documentation master file, created by
+   sphinx-quickstart on Fri Aug 16 11:14:38 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Sitting Desktop Garden Documentation
+====================================
+
+this is a description
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+Contents
+--------
+
+.. toctree::
+
+   generated/modules