Update the intrinsic image generation branch with all the multi-mission changes added to main

.github/workflows/publish_to_pypi.yml

@@ -23,14 +23,15 @@ jobs:
 
     # This job has several steps
     steps:
-      # Checks out the master branch (what we want to build and publish - hopefully with the VCS info that versioneer needs), then 
-      #  activates a relatively recent version of Python
+      # Checks out the master branch (what we want to build and publish - including the VCS info
+      #  that setuptools-scm needs to calculate the version), then activates a relatively
+      #  recent version of Python
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         fetch-tags: true
     - name: Setup the Python install
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.12
 

.github/workflows/publish_to_test_pypi.yml

@@ -28,14 +28,15 @@ jobs:
 
     # This job has several steps
     steps:
-      # Checks out the master branch (what we want to build and publish - hopefully with the VCS info that versioneer needs), then 
-      #  activates a relatively recent version of Python
+      # Checks out the master branch (what we want to build and publish - including the VCS info
+      #  that setuptools-scm needs to calculate the version), then activates a relatively
+      #  recent version of Python
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         fetch-tags: true
     - name: Setup the Python install
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.12
 

.github/workflows/test_build.yml

@@ -0,0 +1,57 @@
+# Large parts of this are directly copied or adapted from 
+#  https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+
+# This action triggers the first stage of publishing this module. When a new tag is created and pushed to the remote repository, this action
+#  will begin. It builds the module, just as it would for an actual PyPI release, then uploads it to the Test PyPI index. That way I can test install
+#  the package from the test PyPI and not expose the real PyPI index to a potentially buggered version. When I verify that it works, a real publishing can
+#  be triggered by releasing the module.
+
+# As a reminder to myself, the installation from test PyPI has to be done using this command, to make sure the dependancies are installed from the real
+#  PyPI index. PIP also seems to have issues with fitsio and regions v0.4 - but conda installing them works:
+# pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple xga
+
+# The overall name of the action
+name: Test build of sdist and wheel, triggered by tag
+
+# This action triggers when there is a push to the repo
+on: push
+
+# Now the actual jobs we want the action to do are setup
+jobs:
+  # The only job in this action, building and publishing the XGA Python module
+  build:
+    name: Build and publish XGA
+    # I actually only want to run this one if the pushed commit has a tag - I will only do this for new versions of the module
+    if: startsWith(github.ref, 'refs/tags')
+    # The build/publishing process runs on the latest version of Ubuntu - not super important what this is for this use case, so long as its not Windows
+    runs-on: ubuntu-latest
+
+    # This job has several steps
+    steps:
+      # Checks out the master branch (what we want to build and publish - hopefully with the VCS info that versioneer needs), then
+      #  activates a relatively recent version of Python
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
+    - name: Setup the Python install
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.12
+
+    # The next two chunks set up PIP properly and build the module
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+
+    - name: Build a binary wheel and source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .

.gitignore

@@ -1,9 +1,23 @@
+CLAUDE.md
 /docs/source/notebooks/tutorials/whole_sample.csv
 /docs/source/notebooks/advanced_tutorials/random_brightness_profile.xga
 .coverage
 .pytest_cache
 xga_output
+daxa_output
+*census*
+*blacklist*
+.idea
 .ipynb_checkpoints
+.vscode
+/xga.egg-info/
+*__pycache__*
 /docs/build
-*__pycache__
-xga.egg-info/
+*noupload*
+.DS_Store
+/xga/__pycache__
+*.pyc
+xga/__pycache__/__init__.cpython-39.pyc
+claude_context/
+htmlcov
+xga/_version.py

.readthedocs.yaml

@@ -10,10 +10,11 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
+  jobs:
+    post_checkout:
+      # Ensure tags are fetched so setuptools_scm can find the version
+      - git fetch --unshallow || true
+      - git fetch --tags || true
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -23,7 +24,9 @@ sphinx:
 formats:
     - pdf
 
-# Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
+     extra_requirements:
+       - docs

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, David J Turner and the Contributors
+Copyright (c) 2026, David J Turner and the Contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -37,15 +37,15 @@ XGA is available on the popular Python Package Index (PyPI), and can be installe
 pip install xga
 ```
 
-You can also fetch the current working version from the git repository, and install it (this method has replaced 'python setup.py install'):
+You can also fetch the current working version from the git repository, and install it:
 
 ```shell script
 git clone https://github.com/DavidT3/XGA
 cd XGA
 python -m pip install .
 ```
 
-Alternatively you could use the 'editable' option (this has replaced running setup.py and passing 'develop') so that any changes you pull from the remote repository are reflected without having to reinstall XGA.
+Alternatively you could use the 'editable' option so that any changes you pull from the remote repository are reflected without having to reinstall XGA.
 
 ```shell script
 git clone https://github.com/DavidT3/XGA
@@ -61,6 +61,9 @@ conda activate <YOUR ENVIRONMENT NAME GOES HERE>
 pip install pyabel==0.9
 ```
 
+> [!IMPORTANT]
+> For Python 3.10 and earlier, the optional dependency [contextlib-chdir](https://pypi.org/project/contextlib-chdir/) must be installed.
+
 ## Required Dependencies
 XGA depends on two non-Python pieces of software:
 * XMM's Science Analysis System (SAS) - Version 17.0.0, but other versions should be largely compatible with the
@@ -90,8 +93,9 @@ Before XGA can be used you must fill out a configuration file (a completed examp
 
 Follow these steps to fill out the configuration file:
 1. Import XGA to generate the initial, incomplete, configuration file.
-2. Navigate to ~/.config/xga and open xga.cfg in a text editor. The .config directory is usually hidden, so it is 
+2. Navigate to ~/.config/xga and open xga.cfg in a text editor. The .config directory is usually hidden, so it is
 probably easier to navigate via the terminal.
+   * Note: The location of the configuration directory can be overridden by setting the ``XGA_CONFIG_DIR`` environment variable. If set, XGA will look for its configuration and store its census files in exactly that directory.
 3. Take note of the entries that currently have /this/is/required at the beginning, without these entries the 
 module will not function.
 4. Set the directory where you wish XGA to save the products and files it generates. I just set it to xga_output,
@@ -136,7 +140,7 @@ If you encounter a bug, or would like to make a feature request, please use the
 [issues](https://github.com/DavidT3/XGA/issues) page, it really helps to keep track of everything.
 
 However, if you have further questions, or just want to make doubly sure I notice the issue, feel free to send
-me an email at turne540@msu.edu
+me an email at djturner@umbc.edu
 
 
 

docs/example_config/xga.cfg

@@ -18,3 +18,11 @@ mos1_expmap = {obs_id}/images/{obs_id}-{lo_en}-{hi_en}keV-mos1_merged_expmap.fit
 mos2_expmap = {obs_id}/images/{obs_id}-{lo_en}-{hi_en}keV-mos2_merged_expmap.fits
 region_file = /home/dt237/apollo_mnt/xmm_obs/code/xapa/id_results/{obs_id}/final_class_regions_REDO.reg
 
+[EROSITA_FILES]
+root_erosita_dir = /home/dt237/apollo_mnt/erosita_obs/data/
+clean_erosita_evts = {obs_id}/clean_evts.fits
+lo_en = ['0.5']
+hi_en = ['2.0']
+erosita_image = {obs_id}/images/{obs_id}_combined_{lo_en}-{hi_en}keVimg.fits
+erosita_expmap = {obs_id}/images/{obs_id}_combined_{lo_en}-{hi_en}keVexpmap.fits
+region_file = /home/dt237/apollo_mnt/erosita_obs/regions/{obs_id}.reg

docs/requirements.txt

@@ -6,7 +6,7 @@ docutils
 ipympl
 urllib3
 jinja2
-versioneer>=0.29
+setuptools-scm>=8.0.0
 setuptools>=71.0.4
 numpy>=1.26.4
 astropy>=6.1.2
@@ -21,7 +21,6 @@ corner>=2.2.2
 emcee>=3.1.6
 tabulate>=0.9.0
 getdist>=1.4.7
-pytest>=6.2.5
 cycler>=0.11.0
 exceptiongroup>=1.0.4
 importlib_resources~=6.5.2

docs/source/conf.py

@@ -1,5 +1,5 @@
-#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
-#  Last modified by David J Turner (turne540@msu.edu) 20/02/2023, 14:04. Copyright (c) The Contributors
+#  This code is part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (djturner@umbc.edu) 6/26/26, 11:29 AM. Copyright (c) The Contributors.
 
 # Configuration file for the Sphinx documentation builder.
 #
@@ -16,8 +16,6 @@
 import os
 import sys
 sys.path.insert(0, os.path.abspath('../..'))
-import shutil
-
 
 # -- Extra Setup for XGA -----------------------------------------------------
 
@@ -38,35 +36,21 @@
     # As this file lives in the docs/source folder, we go two levels up for the absolute path the XGA repo folder
     xga_path = '/'.join(current_path.split('/')[:-2])
 
-    # The test data includes a mostly complete config file, and census
-    test_cfg_path = os.path.join(xga_path, 'tests', 'test_data', 'xga.cfg')
-    test_census_path = os.path.join(xga_path, 'tests', 'test_data', 'census.csv')
-    test_data_path = os.path.join(xga_path, 'tests', 'test_data')
-
-    # Copy the config and census over to the place they should be on whatever system is building this
-    shutil.copy(test_cfg_path, config_file_path)
-    shutil.copy(test_census_path, census_file_path)
-
-    with open(config_file_path, 'r') as cfg:
-        lines = cfg.readlines()
-
-    lines = [line.replace('root_xmm_dir = ./', 'root_xmm_dir = {}'.format(test_data_path)) for line in lines]
-
-    with open(config_file_path, 'w') as cfg:
-        cfg.write(''.join(lines))
-
-# I don't like to import in the code itself, but it has to be here so we can be sure a valid config file exists
-# from xga import utils
-# utils.XGA_MODE = "DOCS"
-
 # -- Project information -----------------------------------------------------
 
 project = 'X-ray: Generate and Analyse (XGA)'
-copyright = '2022, David J Turner'
-author = 'David J Turner'
+copyright = '2026, The Contributors'
+author = 'David J Turner, XGA Team'
 
 # The full version, including alpha/beta/rc tags
-# release = '0.1'
+try:
+    from importlib.metadata import version as get_version
+    release = get_version("xga")
+    # The short X.Y version
+    version = '.'.join(release.split('.')[:2])
+except Exception:
+    version = '0.0.0'
+    release = '0.0.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/future.rst

@@ -1,20 +1,15 @@
 Planned XGA Features
 ========================
 
-* **Upper Limit X-ray Luminosities** - These luminosities are measured from photometric products when there are not sufficient X-ray counts to generate a spectrum. This will involve integrating a tool that I have already written for XCS into the structure of XGA, though rather than measuring upper limit luminosities from a single image, I intend to measure them from the combined data.
+* **Support for other X-ray telescopes** - XGA's purpose is to facilitate the exploitation of the complete public X-ray archive, hence the aim is to support all X-ray telescopes eventually. Currently XMM and eROSITA are supported, and the software is setup so that integrating new telescope-specific softwares should not be an arduous task. If you are interested in integrating a telescope into XGA please reach out to the development team (:doc:`support`). 
 
-* **Source Finder** - It is likely that I will extend my Hierarchical Clustering Peak Finder into a full source finder, as well as completing the implementation of a convolutional peak finder/source finder, which was inspired by my friend and colleague Lucas Porth.
+* **Creating a Docker image for users to download** - Creating a Docker environment with all relevant software already installed.
 
-* **More XSPEC Models** - Including a two temperature APEC model, and support for custom user defined models.
+* **More XSPEC Models** - Support for custom user defined models.
 
-* **Implement emcee scaling relation fitter** - What it says on the tin really. Implement an emcee fitter for the scaling relations so that there is an MCMC option that doesn't require the installation of a bunch of optional dependencies.
+* **Upper Limit X-ray Luminosities** - These luminosities are measured from photometric products when there are not sufficient X-ray counts to generate a spectrum. This will support measurements from combined data, as well as single images. 
 
-* **Ability to save ScalingRelation objects** - The ability to save ScalingRelation objects to disk in some way, so that code to generate them doesn't need to be run multiple times.
-
-* **Support for other X-ray telescopes** - Support for generation and analysis of data products from other telescopes.
-
-* **Creating a Docker image for users to download** - Creating a Docker environment with SAS and HEASoft already installed, for ease of use.
+* **Implement emcee scaling relation fitter** - Implement an emcee fitter for the scaling relations so that there is an MCMC option that doesn't require the installation of optional dependencies.
 
 * **Method for finding poorly removed point sources** - An attempt to mitigate occasional mistakes by source finders that produce regions that don't necessarily remove the entire point source.
 
-* **Overdensity radius measurement** - Using HydrostaticMass profiles to measure the overdensity radius of a cluster.