Integrate audit

.github/workflows/install_package.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
       - name: Checkout glowtracker
@@ -27,30 +27,9 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Debug action..
-        run: |
-          echo "runner os: ${{ runner.os }}"
-          echo "matrix os: ${{ matrix.os }}"
       - name: Update pip
-        run: |
-          # The newest pip version (25.3) force support of PEP 517 and will cause error in pip-tools.
-          # Have to wait for a newer than version 7.5.1 piptools 
-          python -m pip install --upgrade "pip<25.3"
-          python -m pip install --upgrade setuptools wheel pip-tools
-      - name: Compile requirements
-        # Generate the requirements.txt file listed in pyproject.toml
-        # NOTE: This step overwrites any previously existing requirements.txt file
-        run:
-          python -m piptools compile -o requirements.txt ${{ github.workspace }}/pyproject.toml --upgrade
-      - name: Install dependencies Linux/macOS
-        if: runner.os == 'Linux' || runner.os == 'macOS'
-        run:
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Install dependencies Windows
-        if: runner.os == 'Windows'
-        # Windows runner defaults to PowerShell (pwsh)
-        run:
-          if (Test-Path -Path requirements.txt) { pip install -r requirements.txt }
-      - name: Install glowtracker
-        run:
-          python -m pip install -e .
+        run: python -m pip install --upgrade pip
+      - name: Install glowtracker and test dependencies
+        run: python -m pip install -e ".[test]"
+      - name: Run tests
+        run: python -m pytest -q

.github/workflows/publish_package.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       # Updating pip and installing 'build'.
       - name: Install dependencies
         run: |
@@ -48,4 +48,4 @@ jobs:
       # Publish to PyPI using Trusted Publisher (GitHub)
       # REF: https://docs.pypi.org/trusted-publishers/using-a-publisher/
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,13 +1,36 @@
-# VSCode 
 .vscode/
+.idea/
+*.swp
+*~
+
+.DS_Store
+._*
+Thumbs.db
+
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.pytype/
+.coverage
+.coverage.*
+htmlcov/
+
+.venv/
+.venv-*/
+*.venv/
+venv/
+env/
 
-# Package building related
 build/
 dist/
-glowtracker.egg-info/
-
-# Python cache
-__pycache__/*
+*.egg-info/
+pip-wheel-metadata/
+/requirements.txt
 
-# Convenience
-*.log
+*.log
+*.part.tiff
+*-basler_*.tiff
+*-coords.txt

.python-version

@@ -0,0 +1 @@
+3.12

BUILD.md

@@ -9,19 +9,19 @@ or
 ```bash
 uv build
 ```
-The resulting packages will be in `dist/`, `glowtracker-[version].tar.gz` and `glowtracker-[version]-py3-none-any.why`.
+The resulting packages will be in `dist/` as `glowtracker-[version].tar.gz` and `glowtracker-[version]-py3-none-any.whl`.
 **Don't forget** to change the version accordingly. Following the convention of Major.Minor.Patch.
 
 # Testing installing the package
-We can test the package by install directly and locally form
+Test the package by installing the local source distribution:
 ```bash
 python -m pip install dist/glowtracker-[version].tar.gz
 ```
 or
 ```bash
 uv pip install dist/glowtracker-[version].tar.gz
 ```
-Add `--python 3.10` to select a specific python version e.g. 3.10
+Add `--python 3.12` to select the recommended Python version.
 
 
 # Running
@@ -32,4 +32,4 @@ python -m glowtracker
 or running the executable wrapper by simply type
 ```bash
 glowtracker
-```
+```

README.md

@@ -18,61 +18,50 @@
 
 ## Getting started
 ### Software Setup
-1. Create a Python environment using **uv** (recommend) or **venv**.
-    - Using **uv** (Recommend)
-        1. Install uv [[Link]](https://docs.astral.sh/uv/getting-started/installation/).
-        2. Create a virtual environment
-            ```bash
-            uv venv glowtracker.venv
-            ```
-    - Using **venv**
-        1. Create the environment
-            ```bash
-            python -m venv glowtracker.venv
-            ```
-
-2. Activate the environment
+GlowTracker supports Python 3.11 through 3.13. Python 3.12 is the recommended version.
+
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/).
+
+2. Install GlowTracker from PyPI:
+
     ```bash
-    source glowtracker.venv/Scripts/activate
+    uv venv --python 3.12
+    uv pip install glowtracker
     ```
 
-3. Install GlowTracker
-    You can choose to either install GlowTracker from a distributed Python package from PyPI or clone the git repository and run them locally.
+    Or install a development checkout using the locked dependencies:
 
-    - Using `pip` to install from PyPI repository:
-        ```bash
-        uv pip install glowtracker
-        ```
-    - Or clone and run the package locally.
-        1. Clone the pository
-            ```bash
-            git clone https://github.com/scholz-lab/GlowTracker.git
-            ```
-        2. Update the conda environment to download the dependencies
-            ```bash
-            cd Glowtracker;
-            uv pip install -r pyproject.toml;
-            ```
-
-
-4. Install the **BASLER** pylon software and runtime library [[Link]](https://www.baslerweb.com/en/software/pylon/)
+    ```bash
+    git clone https://github.com/scholz-lab/GlowTracker.git
+    cd GlowTracker
+    uv sync --extra test
+    uv run pytest -q
+    ```
+
+3. Install the **BASLER** pylon software and runtime library [[Link]](https://www.baslerweb.com/en/software/pylon/)
     - pylon Camera Software Suite
     - pylon runtime library
 
-5. (Optional) Install **Zaber Launcher** for inspecting and updating stage firmware [[Link]](https://software.zaber.com/zaber-launcher/download)
+4. (Optional) Install **Zaber Launcher** for inspecting and updating stage firmware [[Link]](https://software.zaber.com/zaber-launcher/download)
+
+5. Start the application.
+
+    - From an activated environment:
 
-6. After finished installation, the software can be started in several ways
-    - If you have installed it via pip
         ```bash
         python -m glowtracker
         ```
-        or simply
+
+        or:
+
         ```bash
         glowtracker
         ```
-    - If you have installed it by cloning the package and running them locally
+
+    - From a development checkout without activating the environment:
+
         ```bash
-        python glowtracker/__main__.py
+        uv run glowtracker
         ```
 
 ### Device Setup