Updating to the latest copier version.

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v2.0.5
+_commit: v2.1.1
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: mtauraso@uw.edu
 author_name: LINCC Frameworks
@@ -18,7 +18,8 @@ project_license: MIT
 project_name: hyrax
 project_organization: lincc-frameworks
 python_versions:
-- '3.9'
 - '3.10'
 - '3.11'
 - '3.12'
+- '3.13'
+test_lowest_version: none

.github/ISSUE_TEMPLATE/1-bug_report.md

@@ -9,9 +9,13 @@ assignees: ''
 **Bug report**
 
 
+**Environment Information**
+
+
 **Before submitting**
 Please check the following:
 
-- [ ] I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
+- [ ] I have described the situation in which the bug arose, including what code was executed, and any applicable data others will need to reproduce the problem.
+- [ ] I have included information about my environment, including the version of this package (e.g. `hyrax.__version__`)
 - [ ] I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a description of what I expected instead.
 - [ ] If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

.github/workflows/asv-main.yml

@@ -8,8 +8,8 @@ on:
     branches: [ main ]
 
 env:
-  PYTHON_VERSION: "3.10"
-  ASV_VERSION: "0.6.4"
+  PYTHON_VERSION: "3.11"
+  ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
 
 concurrency:
@@ -34,7 +34,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Install dependencies
-      run: pip install "asv[virtualenv]==${{env.ASV_VERSION}}"
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}}
     - name: Configure git
       run: |
         git config user.name "github-actions[bot]"

.github/workflows/asv-nightly.yml

@@ -9,8 +9,8 @@ on:
   workflow_dispatch:
 
 env:
-  PYTHON_VERSION: "3.10"
-  ASV_VERSION: "0.6.4"
+  PYTHON_VERSION: "3.11"
+  ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
   NIGHTLY_HASH_FILE: nightly-hash
 
@@ -30,7 +30,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Install dependencies
-      run: pip install "asv[virtualenv]==${{env.ASV_VERSION}}"
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}}
     - name: Configure git
       run: |
         git config user.name "github-actions[bot]"

.github/workflows/asv-pr.yml

@@ -15,8 +15,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  PYTHON_VERSION: "3.10"
-  ASV_VERSION: "0.6.4"
+  PYTHON_VERSION: "3.11"
+  ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
   ARTIFACTS_DIR: ${{github.workspace}}/artifacts
 
@@ -39,7 +39,7 @@ jobs:
       run: |
         echo "Workflow Run ID: ${{github.run_id}}"
     - name: Install dependencies
-      run: pip install "asv[virtualenv]==${{env.ASV_VERSION}}" lf-asv-formatter
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}} lf-asv-formatter
     - name: Make artifacts directory
       run: mkdir -p ${{env.ARTIFACTS_DIR}}
     - name: Save pull request number

.github/workflows/build-documentation.yml

@@ -21,10 +21,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         sudo apt-get update

.github/workflows/pre-commit-ci.yml

@@ -20,13 +20,14 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.11'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Install dependencies
       run: |
         sudo apt-get update
-        python -m pip install --upgrade pip
-        pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        uv pip install --system .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - uses: pre-commit/action@v3.0.1
       with:
         extra_args: --all-files --verbose

.github/workflows/publish-to-pypi.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/smoke-test.yml

@@ -20,20 +20,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Install dependencies
       run: |
         sudo apt-get update
-        python -m pip install --upgrade pip
-        pip install -e .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        uv pip install --system -e .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - name: List dependencies
       run: |
         pip list

.github/workflows/testing-and-coverage.yml

@@ -1,3 +1,4 @@
+
 # This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
@@ -15,24 +16,25 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Install dependencies
       run: |
         sudo apt-get update
-        python -m pip install --upgrade pip
-        pip install -e .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        uv pip install --system -e .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - name: Run unit tests with pytest
       run: |
         python -m pytest --cov=hyrax --cov-report=xml -m "not slow"
     - name: Upload coverage report to codecov
       uses: codecov/codecov-action@v5
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
+        token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -34,7 +34,7 @@ repos:
         args: ['--maxkb=500']
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.1
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml

.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

.setup_dev.sh

@@ -1,10 +1,19 @@
 #!/usr/bin/env bash
 
+# Bash Unofficial strict mode (http://redsymbol.net/articles/unofficial-bash-strict-mode/) 
+# and (https://disconnected.systems/blog/another-bash-strict-mode/)
+set -o nounset # Any uninitialized variable is an error
+set -o errexit # Exit the script on the failure of any command to execute without error
+set -o pipefail # Fail command pipelines on the failure of any individual step
+IFS=$'\n\t' #set internal field separator to avoid iteration errors
+# Trap all exits and output something helpful
+trap 's=$?; echo "$0: Error on line "$LINENO": $BASH_COMMAND"; exit $s' ERR
+
 # This script should be run by new developers to install this package in
 # editable mode and configure their local environment
 
 echo "Checking virtual environment"
-if [ -z "${VIRTUAL_ENV}" ] && [ -z "${CONDA_PREFIX}" ]; then
+if [ "${VIRTUAL_ENV:-missing}" = "missing" ] && [ "${CONDA_PREFIX:-missing}" = "missing" ]; then
     echo 'No virtual environment detected: none of $VIRTUAL_ENV or $CONDA_PREFIX is set.'
     echo
     echo "=== This script is going to install the project in the system python environment ==="
@@ -20,7 +29,7 @@ fi
 
 echo "Checking pip version"
 MINIMUM_PIP_VERSION=22
-pipversion=( $(python -m pip --version | awk '{print $2}' | sed 's/\./ /g') )
+pipversion=( $(python -m pip --version | awk '{print $2}' | sed 's/\./\n\t/g') )
 if let "${pipversion[0]}<${MINIMUM_PIP_VERSION}"; then
     echo "Insufficient version of pip found. Requires at least version ${MINIMUM_PIP_VERSION}."
     echo "See https://lincc-ppt.readthedocs.io/ for details."

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 LINCC Frameworks
+Copyright (c) 2025 LINCC Frameworks
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

benchmarks/asv.conf.json

@@ -37,7 +37,7 @@
     // The Pythons you'd like to test against. If not provided, defaults
     // to the current version of Python used to run `asv`.
     "pythons": [
-        "3.10"
+        "3.11"
     ],
     // The matrix of dependencies to test. Each key is the name of a
     // package (in PyPI) and the values are version numbers.  An empty

docs/conf.py

@@ -15,7 +15,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "hyrax"
-copyright = "2024, LINCC Frameworks"
+copyright = "2025, LINCC Frameworks"
 author = "LINCC Frameworks"
 release = version("hyrax")
 # for example take major/minor

pyproject.toml

@@ -1,20 +1,20 @@
 [project]
 name = "hyrax"
-license = {file = "LICENSE"}
+license = "MIT"
+license-files = ["LICENSE"]
 readme = "README.md"
 authors = [
     { name = "LINCC Frameworks", email = "mtauraso@uw.edu" }
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
-    "License :: OSI Approved :: MIT License",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
     "Programming Language :: Python",
 ]
 dynamic = ["version"]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "astropy", # Used to load fits files of sources to query HSC cutout server
     # Pin to the current version of pytorch ignite so workarounds to 
@@ -65,7 +65,7 @@ examples = [
 ]
 
 dev = [
-    "asv==0.6.5", # Used to compute performance benchmarks
+    "asv[virtualenv]==0.6.5", # Used to compute performance benchmarks
     "jupyter", # Clears output from Jupyter notebooks
     "matplotlib", # For example notebooks
     "pre-commit", # Used to run checks before finalizing a git commit
@@ -107,18 +107,9 @@ markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
 ]
 
-[tool.black]
-line-length = 110
-target-version = ["py39"]
-
-[tool.isort]
-profile = "black"
-line_length = 110
-
 [tool.ruff]
 line-length = 110
-target-version = "py39"
-
+target-version = "py310"
 [tool.ruff.lint]
 select = [
     # pycodestyle
@@ -150,7 +141,6 @@ select = [
     # Numpy v2.0 compatibility
     "NPY201",
 ]
-
 ignore = [
     "UP006", # Allow non standard library generics in type hints
     "UP007", # Allow Union in type hints
@@ -161,5 +151,6 @@ ignore = [
     "UP028", # Allow yield in for loop
 ]
 
+
 [tool.coverage.run]
 omit=["src/hyrax/_version.py"]

tests/hyrax/test_packaging.py

@@ -0,0 +1,6 @@
+import hyrax
+
+
+def test_version():
+    """Check to see that we can get the package version"""
+    assert hyrax.__version__ is not None