Run copier update

.copier-answers.yml

@@ -1,13 +1,14 @@
 # Changes here will be overwritten by Copier
-_commit: v1.3.3
+_commit: v1.4.1
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks
 create_example_module: false
 custom_install: true
+include_docs: true
 include_notebooks: false
-module_name: lsdb
 mypy_type_checking: basic
+package_name: lsdb
 preferred_linter: pylint
 project_license: BSD
 project_name: lsdb

.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: Build docs
       run: |
-        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

.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

.github/workflows/type-checking.yml

@@ -33,4 +33,3 @@ jobs:
 
       run: |
         mypy ./src ./tests --ignore-missing-imports
-

.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     # is out of date.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
@@ -132,7 +132,7 @@ repos:
             "-b", # Flag to select which builder to use
             "html", # Use the HTML builder
             "-d", # Flag for cached environment and doctrees
-            "docs/build/doctrees", # directory
+            "./docs/_build/doctrees", # directory
             "./docs", # Source directory of documents
-            "docs/build/html", # Output directory for rendered documents.
-          ]
+            "./_readthedocs", # Output directory for rendered documents.
+          ]

.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

.readthedocs.yml

@@ -1,6 +1,6 @@
 # .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
@@ -19,4 +19,4 @@ python:
    install:
    - requirements: docs/requirements.txt
    - method: pip
-     path: .
+     path: .

LICENSE

@@ -25,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

docs/conf.py

@@ -6,9 +6,9 @@
 
 import os
 import sys
+from importlib.metadata import version
 
 import autoapi
-from importlib.metadata import version
 
 # Define path to the code to be documented **relative to where conf.py (this file) is kept**
 sys.path.insert(0, os.path.abspath("../src/"))
@@ -31,11 +31,13 @@
 extensions.append("autoapi.extension")
 
 templates_path = []
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
 master_doc = "index"  # This assumes that sphinx-build is called from the root directory
-html_show_sourcelink = False  # Remove 'view source code' from top of page (for html, not python)
-add_module_names = False # Remove namespaces from class/method signatures
+html_show_sourcelink = (
+    False  # Remove 'view source code' from top of page (for html, not python)
+)
+add_module_names = False  # Remove namespaces from class/method signatures
 
 autoapi_type = "python"
 autoapi_dirs = ["../src"]

docs/requirements.txt

@@ -1,3 +1,3 @@
 sphinx==6.1.3
-sphinx_rtd_theme==1.2.0
-sphinx-autoapi==2.0.1
+sphinx-rtd-theme==1.2.0
+sphinx-autoapi==2.0.1

pyproject.toml

@@ -28,15 +28,23 @@ dev = [
     "pytest",
     "pytest-cov", # Used to report total code coverage
     "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
 ] 
 [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"
 
 [tool.setuptools_scm]
 write_to = "src/lsdb/_version.py"
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+]
+
+[tool.setuptools.package-data]
+lsdb = ["py.typed"]