What happens if we apply the template to the template.

.copier-answers.yml

@@ -0,0 +1,30 @@
+# Changes here will be overwritten by Copier
+_commit: v2.2.0
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: [email protected]
+author_name: LINCC Frameworks
+create_example_module: false
+custom_install: custom
+enforce_style:
+- pylint
+- black
+- isort
+failure_notification: []
+include_benchmarks: false
+include_docs: true
+include_notebooks: false
+mypy_type_checking: none
+package_name: python_project_template
+project_description: LINCC-Framework's best practices for python code organization,
+    testing, documentation, and automation.
+project_license: BSD
+project_name: python-project-template
+project_organization: lincc-frameworks
+python_versions:
+- '3.9'
+- '3.10'
+- '3.11'
+- '3.12'
+- '3.13'
+- '3.14'
+test_lowest_version: none

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1,24 @@
+# For explanation of this file and uses see
+# https://git-scm.com/docs/gitattributes
+# https://developer.lsst.io/git/git-lfs.html#using-git-lfs-enabled-repositories
+# https://lincc-ppt.readthedocs.io/en/latest/practices/git-lfs.html
+#
+# Used by https://github.com/lsst/afwdata.git
+# *.boost filter=lfs diff=lfs merge=lfs -text
+# *.dat filter=lfs diff=lfs merge=lfs -text
+# *.fits filter=lfs diff=lfs merge=lfs -text
+# *.gz filter=lfs diff=lfs merge=lfs -text
+#
+# apache parquet files
+# *.parq	filter=lfs diff=lfs merge=lfs -text
+#
+# sqlite files
+# *.sqlite3	filter=lfs diff=lfs merge=lfs -text
+#
+# gzip files
+# *.gz	filter=lfs diff=lfs merge=lfs -text
+#
+# png image files
+# *.png	filter=lfs diff=lfs merge=lfs -text
+
+.git_archival.txt export-subst

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

@@ -0,0 +1,37 @@
+
+# This workflow runs pre-commit hooks on pushes and pull requests to main
+# to enforce coding style. To ensure correct configuration, please refer to:
+#  https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
+name: Run pre-commit hooks
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        uv pip install --system .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: --all-files --verbose
+      env:
+        SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
+    - uses: pre-commit-ci/[email protected]
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

.github/workflows/smoke-test.yml

@@ -23,9 +23,9 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install uv
@@ -34,6 +34,7 @@ jobs:
       run: |
         sudo apt-get update
         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/ci.yml → .github/workflows/testing-and-coverage.yml

@@ -1,4 +1,8 @@
-name: CI for Template
+
+# 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
+
+name: Unit test and code coverage
 
 on:
   push:
@@ -15,11 +19,11 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install uv
@@ -28,6 +32,7 @@ jobs:
       run: |
         sudo apt-get update
         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 /  pytest-copie
       run: |
         git config --global init.defaultBranch main

.gitignore

@@ -133,9 +133,18 @@ dmypy.json
 # vscode
 .vscode/
 
+# dask
+dask-worker-space/
+
+# tmp directory
+tmp/
+
 # Mac OS
 .DS_Store
 
 # Airspeed Velocity performance results
 _results/
-_html/
+_html/
+
+# Project initialization script
+.initialize_new_project.sh

.pre-commit-config.yaml

@@ -1,4 +1,26 @@
+
 repos:
+    # Compare the local template version to the latest remote template version
+    # This hook should always pass. It will print a message if the local version 
+    # is out of date.
+  - repo: https://github.com/lincc-frameworks/pre-commit-hooks
+    rev: v0.2.2
+    hooks:
+      - id: check-lincc-frameworks-template-version
+        name: Check template version
+        description: Compare current template version against latest
+        verbose: true
+    # Clear output from jupyter notebooks so that only the input cells are committed.
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: Clear output from Jupyter notebooks
+        description: Clear output from Jupyter notebooks.
+        files: \.ipynb$
+        exclude: ^docs/pre_executed
+        stages: [pre-commit]
+        language: system
+        entry: jupyter nbconvert --clear-output
     # Prevents committing directly branches named 'main' and 'master'.
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
@@ -44,7 +66,7 @@ repos:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
-            "--max-line-length=120",
+            "--rcfile=tests/.pylintrc",
           ]
     # Analyze the code style and report code that doesn't adhere.
   - repo: https://github.com/psf/black
@@ -57,7 +79,7 @@ repos:
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.12
+        language_version: python3.11
     # Run unit tests, verify that they pass. Note that coverage is run against
     # the ./src directory here because that is what will be committed. In the
     # github workflow script, the coverage is run against the installed package

.readthedocs.yml

@@ -1,14 +1,15 @@
+
 # .readthedocs.yml
 # Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# See  https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -18,5 +19,6 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
+   - requirements: requirements.txt
    - method: pip
-     path: .
+     path: .

.setup_dev.sh

@@ -0,0 +1,51 @@
+#!/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 $s' ERR
+
+# This script should be run by new developers to install this package in
+# editable mode and configure their local environment
+
+echo "Checking virtual environment"
+if [ "${VIRTUAL_ENV:-missing}" = "missing" ] && [ "${CONDA_PREFIX:-missing}" = "missing" ]; then
+    echo 'No virtual environment detected: none of $VIRTUAL_ENV or $CONDA_PREFIX is set.'
+    echo
+    echo "=== This script is going to install the project in the system python environment ==="
+    echo "Proceed? [y/N]"
+    read -r RESPONCE
+    if [ "${RESPONCE}" != "y" ]; then
+        echo "See https://lincc-ppt.readthedocs.io/ for details."
+        echo "Exiting."
+        exit 1
+    fi
+
+fi
+
+echo "Checking pip version"
+MINIMUM_PIP_VERSION=22
+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."
+    exit 1
+fi
+
+echo "Installing package and runtime dependencies in local environment"
+python -m pip install -e . > /dev/null
+
+echo "Installing developer dependencies in local environment"
+python -m pip install -e .'[dev]' > /dev/null
+if [ -f docs/requirements.txt ]; then python -m pip install -r docs/requirements.txt > /dev/null; fi
+
+echo "Installing pre-commit"
+pre-commit install > /dev/null
+
+#######################################################
+# Include any additional configurations below this line
+#######################################################

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, LINCC Frameworks Team
+Copyright (c) 2025, LINCC Frameworks
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

docs/Makefile

@@ -1,4 +1,4 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line, and also
@@ -8,11 +8,16 @@ SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = ../_readthedocs/
 
+.PHONY: help clean Makefile 
+
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+# Cleans up files generated by the build process
+clean:
+	rm -r "_build/doctrees"
+	rm -r "$(BUILDDIR)"
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/requirements.txt

@@ -1,3 +1,5 @@
+
 sphinx
-sphinx-rtd-theme>=3.0
+sphinx-autoapi
 sphinx-copybutton
+sphinx-rtd-theme>=3.0

pyproject.toml

@@ -1,3 +1,4 @@
+
 [project]
 name = "python-project-template"
 license = "BSD-3-Clause"
@@ -6,6 +7,7 @@ readme = "README.md"
 authors = [
     { name = "LINCC Frameworks", email = "[email protected]" }
 ]
+description = "LINCC-Framework's best practices for python code organization, testing, documentation, and automation."
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
@@ -14,16 +16,16 @@ classifiers = [
     "Programming Language :: Python",
 ]
 dynamic = ["version"]
-
+requires-python = ">=3.9"
 dependencies = [
     "setuptools_scm",
-    "sphinx", # Used to automatically generate documentation
-    "sphinx-rtd-theme>=3.0", # Used to render documentation
-    "sphinx-copybutton",
     "pyyaml-include<3.0",
 ]
-requires-python = ">=3.9"
 
+[project.urls]
+"Source Code" = "https://github.com/lincc-frameworks/python-project-template"
+
+# On a mac, install optional dependencies with `pip install '.[dev]'` (include the single quotes)
 [project.optional-dependencies]
 dev = [
     "black", # Used to format code