Run copier.

.copier-answers.yml

@@ -1,10 +1,12 @@
 # Changes here will be overwritten by Copier
-_commit: v1.3.4
+_commit: v1.4.2
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: lincc-frameworks-team@lists.lsst.org
 author_name: LINCC Frameworks
 create_example_module: false
 custom_install: true
+include_benchmarks: false
+include_docs: true
 include_notebooks: true
 mypy_type_checking: basic
 package_name: hipscat_import

.github/pull_request_template.md

@@ -26,7 +26,7 @@ If it fixes an open issue, please link to the issue here. If this PR closes an i
 
 
 ## Code Quality
-- [ ] I have read the [Contribution Guide](https://lincc-ppt.readthedocs.io/en/latest/source/contributing.html)
+- [ ] I have read the Contribution Guide
 - [ ] My code follows the code style of this project
 - [ ] My code builds (or compiles) cleanly without any errors or warnings
 - [ ] My code contains relevant comments and necessary documentation
@@ -50,8 +50,8 @@ If it fixes an open issue, please link to the issue here. If this PR closes an i
 - [ ] Any updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
 
 ### Build/CI Change Checklist
-- [ ] If required or optional dependencies have changed (including version numbers), I have updated the [README](https://github.com/lincc-frameworks/python-project-template/blob/main/README.md) to reflect this
-- [ ] If this is a new CI setup, I have added the associated badge to the [README](https://github.com/lincc-frameworks/python-project-template/blob/main/README.md)
+- [ ] If required or optional dependencies have changed (including version numbers), I have updated the README to reflect this
+- [ ] If this is a new CI setup, I have added the associated badge to the README
 
 <!-- ### Version Change Checklist [For Future Use] -->
 

.github/workflows/build-documentation.yml

@@ -24,9 +24,8 @@ jobs:
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
+        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
         pip install .
-        pip install .[dev]
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install notebook requirements
       run: |
         sudo apt-get install pandoc

.github/workflows/linting.yml

@@ -33,4 +33,3 @@ jobs:
 
       run: |
         pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc
-

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

@@ -36,4 +36,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/smoke-test.yml

@@ -1,5 +1,7 @@
 # This workflow will run daily at 06:45.
 # It will install Python dependencies and run tests with a variety of Python versions.
+# See documentation for help debugging smoke test issues:
+#    https://lincc-ppt.readthedocs.io/en/latest/practices/ci_testing.html#version-culprit
 
 name: Unit test smoke test
 
@@ -30,6 +32,9 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: List dependencies
+      run: |
+        pip list
     - name: Run unit tests with pytest
       run: |
         python -m pytest tests

.gitignore

@@ -138,3 +138,6 @@ dask-worker-space/
 
 # tmp directory
 tmp/
+
+# Mac OS
+.DS_Store

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     # 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: v0.1
+    rev: v0.1.1
     hooks:
       - id: check-lincc-frameworks-template-version
         name: Check template version

.prepare_project.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+echo "Initializing local git repository"
+{
+    gitversion=( $(git version | sed 's/^.* //;s/\./ /g') )
+    if let "${gitversion[0]}<2"; then
+	# manipulate directly
+	git init . && echo 'ref: refs/heads/main' >.git/HEAD
+    elif let "${gitversion[0]}==2 & ${gitversion[1]}<34"; then
+	# rename master to main
+	git init . && { git branch -m master main 2>/dev/null || true; };
+    else
+	# set the initial branch name to main
+	git init --initial-branch=main >/dev/null
+    fi
+} > /dev/null
+
+echo "Installing package and runtime dependencies in local environment"
+pip install -e . > /dev/null
+
+echo "Installing developer dependencies in local environment"
+pip install -e .'[dev]' > /dev/null
+
+echo "Installing pre-commit"
+pre-commit install > /dev/null

docs/requirements.txt

@@ -1,8 +1,7 @@
 sphinx==6.1.3
-sphinx_rtd_theme==1.2.0
+sphinx-rtd-theme==1.2.0
 sphinx-autoapi==2.0.1
 nbsphinx
-ipykernel
 ipython
 jupytext
 jupyter

pyproject.toml

@@ -37,7 +37,7 @@ dev = [
     "pytest-cov",
     "pytest-timeout",
     "sphinx==6.1.3", # Used to automatically generate documentation
-    "sphinx_rtd_theme==1.2.0", # Used to render documentation
+    "sphinx-rtd-theme==1.2.0", # Used to render documentation
     "sphinx-autoapi==2.0.1", # Used to automatically generate api documentation
     "mypy", # Used for static type checking of files
     # if you add dependencies here while experimenting in a notebook and you
@@ -53,7 +53,7 @@ dev = [
 
 [build-system]
 requires = [
-    "setuptools>=45", # Used to build and package the Python project
+    "setuptools>=62", # Used to build and package the Python project
     "setuptools_scm>=6.2", # Gets release version from git. Makes it available programmatically
 ]
 build-backend = "setuptools.build_meta"
@@ -69,6 +69,9 @@ timeout = 1
 markers = [
     "dask: mark tests as having a dask client runtime dependency",
 ]
+testpaths = [
+    "tests",
+]
 
 [tool.coverage.report]
 omit = [