stable setup with modern dependencies

.github/workflows/python-app.yml

@@ -1,40 +1,122 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python application
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip install .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        python -m pytest
+  #This workflow will install Python dependencies, run tests and lint with
+  #  multiple versions of Python
+  # For more information see:
+  # (https://help.github.com/actions/language-and-framework-guides/
+  #  using-python-with-github-actions)
+
+  name: Python application
+
+  on:
+    push:
+      branches: [ "main" ]
+    pull_request:
+      branches: [ "main" ]
+
+  permissions:
+    contents: read
+
+  jobs:
+    build:
+      runs-on: ubuntu-latest
+      env:
+        STARBUG_TEST_DIR: ${{ github.workspace }}/tests/dat/
+        WEBBPSF_PATH: ${{ github.workspace }}/webbpsf_cache
+        STARBUG_DATDIR: ${{ github.workspace }}/starbug_data
+
+      strategy:
+        matrix:
+          # Run across multiple modern versions to ensure starbug2 handles
+          # updates smoothly
+          python-version: ["3.12", "3.13"]
+
+      steps:
+        # Upgraded to v4 for speed and security
+        - uses: actions/checkout@v4
+
+        # create directories for these dependency folders in envs
+        - name: Create DAta and Cache Directories
+          run: |
+            mkdir -p ${{ github.workspace }}/webbpsf_cache
+            mkdir -p ${{ github.workspace }}/starbug_data
+
+        # Upgraded to v5 and added automatic pip caching to speed up builds
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v5
+          with:
+            python-version: ${{ matrix.python-version }}
+            cache: 'pip'
+
+        # Standardised dependency installation using modern pyproject.toml
+        # configuration
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install flake8 pytest
+            # Install your core pipeline dependencies from the 
+            # requirements.txt file
+            if [ -f requirements.txt ]; then \
+              pip install -r requirements.txt; fi
+
+            # Install starbug2 itself in editable mode
+            pip install -e .
+
+        - name: Cache FITS test data
+          id: cache-fits
+          uses: actions/cache@v4
+          with:
+            path: |
+              tests/dat/ngc6822_F770W_i2d.fits
+              tests/dat/image.fits
+              tests/dat/psf.fits
+            key: ${{ runner.os }}-fits-cache-v1
+
+        - name: Download FITS files from Private Draft Release if cache missed
+          if: steps.cache-fits.outputs.cache-hit != 'true'
+          env:
+            GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          run: gh release download TEST_DATA --repo "${{ github.repository }}" --pattern "*.fits" --dir "tests/dat"
+
+
+        - name: Lint with flake8
+          run: |
+            # stop the build if there are Python syntax errors or undefined
+            # names
+            flake8 . --count --show-source --statistics --max-line-length=79
+            # exit-zero treats all errors as warnings. The GitHub editor is
+            # 127 chars wide
+            flake8 . --count --exit-zero --max-complexity=10 \
+              --max-line-length=127 --statistics
+
+        # --- LIGHTWEIGHT RAT LICENSE HEADER CHECK ---
+        - name: Verify License Headers (RAT Check)
+          run: |
+            echo "Checking for license headers in starbug2 source files..."
+            missing_headers=0
+
+            # Find all .py files in your source directory, ignoring 
+            # environment folders
+            for file in $(find starbug2 -name "*.py"); do
+              if ! grep -q "Copyright (C) 2026 UKATC" "$file"; then
+                echo "❌ Missing license header in: $file"
+                missing_headers=$((missing_headers + 1))
+              fi
+            done
+
+            if [ $missing_headers -gt 0 ]; then
+              echo "Error: $missing_headers file(s) are missing the" \
+                " mandatory copyright header block."
+              exit 1
+            else
+              echo "✅ All source files contain valid copyright headers."
+            fi
+
+
+        - name: Pre-test Filter PSF setup
+          run: |
+            echo "Starting pre test filter psf setup"
+            starbug2 --init -s FILTER=F444W
+            echo "Command completed successfully!"
+
+        - name: Test with pytest
+          run: |
+            python -m pytest

.github/workflows/python-publish.yml

@@ -21,9 +21,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

.gitignore

@@ -121,6 +121,9 @@ ENV/
 env.bak/
 venv.bak/
 
+# env
+/star_bug_env/
+
 # Spyder project settings
 .spyderproject
 .spyproject
@@ -138,3 +141,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# remove test files
+/tests/dat/*.fits

README.md

@@ -12,7 +12,7 @@
   • Powerful modular and simple GNU Linux standard command line interface
 
 
-<br clear="left"/>
+<br clear="left">
 
 [![Python application](https://github.com/conornally/starbug2/actions/workflows/python-app.yml/badge.svg)](https://github.com/conornally/starbug2/actions/workflows/python-app.yml)
 [![PyPI version fury.io](https://badge.fury.io/py/starbug2.svg)](https://pypi.python.org/pypi/starbug2/)
@@ -27,21 +27,60 @@
 
 ```bash
 $~ pip install starbug2
+```
+
+NOTE::
+At this point star bug is fully functional for telescopes which are not JWST.
+To bring into line for use with JWST, the "JWST initialization" section
+needs to be followed, which can be done using the following command line.
+```
 $~ starbug2 --init
 ```
-</br>
+
+NOTE:: I found the stpsf stuff to fail due to outdated dependnecy. needed to 
+do the following:
+```
+ pip install --upgrade pysiaf
+
+```
+
+### From source
+
+If installing starbugII from source, the following commands are used to ensure
+current dependencies are required. The venv name is not essential to the install
+but was set up for consistency.
+
+- ```python3 -m venv star_bug_env```
+- ```./star_bug_env/bin/pip install --upgrade stpsf==2.2.0```
+- ```./star_bug_env/bin/pip install numpy==2.3.5 photutils==2.0.1 --force```
+- ```./star_bug_env/bin/pip install parse==1.22.0```
+- ```./star_bug_env/bin/pip install setuptools==82.0.1```
+- ```./star_bug_env/bin/pip install scikit-image==0.26.0```
+- ```./star_bug_env/bin/pip install webbpsf==2.0.0```
+- ```./star_bug_env/bin/pip install pytest==9.0.3```
+- ```./star_bug_env/bin/python -m pip install build```
+
+instead of:
+- ```pip install .```
+I used the following command to ensure live development.
+- ```./star_bug_env/bin/python -m pip install -e . --no-deps```
+
+For generating the doc images. graphviz is needed. To isntall that , run 
+the following commands:
+``` pip isntall graphviz```
 
 > [!IMPORTANT]
-> If you make use of *StarbugII* in any published or presented work, please include a [citation](https://ui.adsabs.harvard.edu/abs/2023ascl.soft09012N/abstract).
+> If you make use of *StarbugII* in any published or presented work,
+> please include a [citation](https://ui.adsabs.harvard.edu/abs/2023ascl.soft09012N/abstract).
 > 
-> *StarbugII* uses methods and datatypes from [astropy](https://docs.astropy.org/en/stable/) and [photutils](https://photutils.readthedocs.io/en/stable), please acknowledge them accordingly.
-
-</br>
+> *StarbugII* uses methods and datatypes from [astropy](https://docs.astropy.org/en/stable/) and 
+> [photutils](https://photutils.readthedocs.io/en/stable), please acknowledge them accordingly.
 
 ## Documentation
 
-See the [full documentation](https://starbug2.readthedocs.io/en/latest/?badge=latest) for the complete installation and detailed guides to using the photometric routines.
-Basic usage information is produced by running:
+See the [full documentation](https://starbug2.readthedocs.io/en/latest/?badge=latest) for the complete installation and detailed 
+guides to using the photometric routines. Basic usage information is 
+produced by running:
 
 ```txt
 StarbugII - JWST PSF photometry
@@ -73,9 +112,6 @@ usage: starbug2 [-ABDfGhMPSv] [-b bgdfile] [-d apfile] [-n ncores] [-o ouput] [-
        --generate-run      *.fits : Generate a simple run script
        --version                  : Print starbug2 version
 
-       --apply-zeropint    a.fits : Apply a zeropoint (-s ZP_MAG=1.0) to a.fits
-       --calc-instr-zp     a.fits : Calculate and apply an instrumental zero point onto a.fits
-
    --> typical runs
       $~ starbug2 -vD -p file.param image.fits      //Source detect on image with a parameter file
       $~ starbug2 -vDM -n4 images*.fits             //Source detect and match outputs of a list of images

docs/source/_static/image_scripts/flow.py

@@ -0,0 +1,94 @@
+import graphviz
+
+# Initialize the directed graph
+dot = graphviz.Digraph(
+    'starbug_pipeline',
+    comment='Starbug2 Pipeline Flow',
+    format='png'
+)
+
+# Global Graph attributes
+dot.attr(rankdir='TB')
+dot.attr(splines='ortho')
+dot.attr(nodesep='0.6')
+dot.attr(ranksep='0.4')
+dot.attr(bgcolor='transparent')
+
+# Global Node attributes (Light blue fill, dark blue border, black text)
+dot.attr('node',
+         fontname='Courier New, monospace',
+         fontsize='12',
+         fontcolor='#000000',
+         style='filled',
+         fillcolor='#E3F2FD',
+         color='#1565C0',
+         penwidth='1.5')
+
+# Global Edge attributes (Solid black arrows)
+dot.attr('edge',
+         fontname='Courier New, monospace',
+         fontsize='10',
+         color='#000000',
+         arrowsize='1.0',
+         penwidth='1.5')
+
+# --- Define Nodes ---
+# Terminals / Commands (Pill-shaped/Rounded boxes)
+dot.node('init_param', '$~ starbug2 --local-param', shape='box',
+         style='filled,rounded')
+dot.node('cmd_D', '$~ starbug2 -D', shape='box', style='filled,rounded')
+dot.node('cmd_B', '$~ starbug2 -B', shape='box', style='filled,rounded')
+dot.node('cmd_P', '$~ starbug2 -P', shape='box', style='filled,rounded')
+
+# Files (Document/Note shaped icons)
+dot.node('image_fits', 'image.fits', shape='note')
+dot.node('starbug_param', 'starbug.param', shape='note')
+dot.node('image_ap', 'image-ap.fits\n(TABLE)', shape='note')
+dot.node('image_bg', 'image-bg.fits\n(IMAGE)', shape='note')
+dot.node('image_res', 'image-res.fits\n(IMAGE)', shape='note')
+dot.node('image_psf', 'image-psf.fits\n(TABLE)', shape='note')
+
+# --- Structural Positioning & Constraints ---
+# Force horizontal alignments for row uniformity
+with dot.subgraph() as s:
+    s.attr(rank='same')
+    s.node('image_fits')
+    s.node('starbug_param')
+
+with dot.subgraph() as s:
+    s.attr(rank='same')
+    s.node('cmd_D')
+    s.node('image_ap')
+
+with dot.subgraph() as s:
+    s.attr(rank='same')
+    s.node('cmd_B')
+    s.node('image_bg')
+
+with dot.subgraph() as s:
+    s.attr(rank='same')
+    s.node('cmd_P')
+    s.node('image_res')
+
+# --- Define Connections ---
+# Parameter branch
+dot.edge('init_param', 'starbug_param')
+
+
+dot.edge('starbug_param', 'cmd_D')
+
+# Main data flow
+dot.edge('image_fits', 'cmd_D')
+dot.edge('cmd_D', 'image_ap')
+
+dot.edge('cmd_D', 'cmd_B')
+dot.edge('cmd_B', 'image_bg')
+
+dot.edge('cmd_B', 'cmd_P')
+dot.edge('cmd_P', 'image_res')
+
+dot.edge('cmd_P', 'image_psf')
+
+# Save and compile to disk
+dot.render('../images/flow', cleanup=True)
+print("Pipeline chart compiled successfully as flow.png!")

docs/source/conf.py

@@ -52,7 +52,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 
 html_static_path = ['_static']
-html_favicon="_static/images/starbug.ico"
+html_favicon = "_static/images/starbug.ico"
 html_logo = "_static/images/starbug.png"
 
 html_css_files = [

docs/source/install.rst

@@ -15,9 +15,12 @@ Installing the development version::
     $~ pip install .
 
 
+NOTE::
+    At this point star bug is fully functional for telescopes which are not JWST.
+    To bring into line for use with JWST, the "JWST initialization" section
+    needs to be followed.
 
-
-Initialising
+JWST Initialization
     After the package is installed, there are a few steps required to initialise *starbug2*:
 
     `WEBBPSF <https://github.com/spacetelescope/webbpsf>`_ is a dependency of *starbug* that has its own installation process which is not done automatically. This process is documented `here <https://webbpsf.readthedocs.io/en/latest/installation.html>`_ but requires two main steps. Download the data file on the website, named something like webbpsf-data-X.X.X.tar.gz and expand it into a directory, then append to your .bashrc (or equivalent)::