Apply PPT v1.5.2 (#213)

* Copier re-copy

* Fix pyproject.

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.5.0
+_commit: v1.5.2
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks

.github/workflows/asv-main.yml

@@ -23,13 +23,13 @@ jobs:
 
     steps:
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@main
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@main
+        uses: actions/setup-python@v5
         with:
           python-version: "${{ env.PYTHON_VERSION }}"
 
@@ -46,12 +46,12 @@ jobs:
 
     steps:
       - name: Checkout main branch of the repository
-        uses: actions/checkout@main
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@main
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}

.github/workflows/asv-nightly.yml

@@ -25,18 +25,18 @@ jobs:
 
     steps:
       - name: Checkout main branch of the repository
-        uses: actions/checkout@main
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@main
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@main
+        uses: actions/setup-python@v5
         with:
           python-version: "${{ env.PYTHON_VERSION }}"
 
@@ -70,7 +70,7 @@ jobs:
           echo "today=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
 
       - name: Use last nightly commit hash from cache
-        uses: actions/cache@main
+        uses: actions/cache@v4
         with:
           path: ${{ env.WORKING_DIR }}
           key: nightly-results-${{ steps.nightly-dates.outputs.yesterday }}
@@ -87,7 +87,7 @@ jobs:
           echo $CURRENT_HASH > $HASH_FILE
 
       - name: Update last nightly hash in cache
-        uses: actions/cache@main
+        uses: actions/cache@v4
         with:
           path: ${{ env.WORKING_DIR }}
           key: nightly-results-${{ steps.nightly-dates.outputs.today }}

.github/workflows/asv-pr.yml

@@ -24,12 +24,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Cache Python ${{ env.PYTHON_VERSION }}
-      uses: actions/cache@main
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: python-${{ env.PYTHON_VERSION }}
     - name: Set up Python ${{ env.PYTHON_VERSION }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ env.PYTHON_VERSION }}
   asv-pr:
@@ -40,14 +40,14 @@ jobs:
         working-directory: ${{ env.WORKING_DIR }}
     steps:
     - name: Checkout PR branch of the repository
-      uses: actions/checkout@main
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Display Workflow Run Information
       run: |
         echo "Workflow Run ID: ${{ github.run_id }}"
     - name: Cache Python ${{ env.PYTHON_VERSION }}
-      uses: actions/cache@main
+      uses: actions/cache@v4
       with:
         path: ~/.cache/pip
         key: python-${{ env.PYTHON_VERSION }}
@@ -61,7 +61,7 @@ jobs:
     - name: Save pull request number
       run: echo ${{ github.event.pull_request.number }} > ${{ env.ARTIFACTS_DIR }}/pr
     - name: Get current job logs URL
-      uses: Tiryoh/gha-jobid-action@main
+      uses: Tiryoh/gha-jobid-action@v1
       id: jobs
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -80,7 +80,7 @@ jobs:
       env:
         STEP_URL: "${{ steps.jobs.outputs.html_url }}#step:11:1"
     - name: Upload artifacts (PR number and benchmarks output)
-      uses: actions/upload-artifact@main
+      uses: actions/upload-artifact@v4
       with:
         name: benchmark-artifacts
         path: ${{ env.ARTIFACTS_DIR }}

.github/workflows/build-documentation.yml

@@ -19,9 +19,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python 3.10
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies

.github/workflows/code_style.yml

@@ -21,9 +21,9 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

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

@@ -13,11 +13,11 @@ jobs:
     env: 
       SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies
@@ -26,8 +26,8 @@ jobs:
         python -m pip install --upgrade pip
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - uses: pre-commit/action@main # Still using Node 16
+    - uses: pre-commit/action@v3.0.1
       with:
         extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
-    - uses: pre-commit-ci/lite-action@main
+    - uses: pre-commit-ci/lite-action@v1.0.2
       if: always()

.github/workflows/publish-benchmarks-pr.yml

@@ -27,7 +27,7 @@ jobs:
         echo "Conclusion: ${{ github.event.workflow_run.conclusion }}"
         echo "Event: ${{ github.event.workflow_run.event }}"
     - name: Download artifact
-      uses: dawidd6/action-download-artifact@master
+      uses: dawidd6/action-download-artifact@v3
       with:
         name: benchmark-artifacts
         run_id: ${{ github.event.workflow_run.id }}
@@ -38,14 +38,14 @@ jobs:
         printf "Output:\n$(cat output)"
         printf "pr=$(cat pr)" >> $GITHUB_OUTPUT
     - name: Find benchmarks comment
-      uses: peter-evans/find-comment@main
+      uses: peter-evans/find-comment@v3
       id: find-comment
       with:
         issue-number: ${{ steps.pr-info.outputs.pr }}
         comment-author: 'github-actions[bot]'
         body-includes: view all benchmarks
     - name: Create or update benchmarks comment
-      uses: peter-evans/create-or-update-comment@main
+      uses: peter-evans/create-or-update-comment@v4
       with:
         comment-id: ${{ steps.find-comment.outputs.comment-id }}
         issue-number: ${{ steps.pr-info.outputs.pr }}

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

@@ -22,9 +22,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies

.github/workflows/smoke-test.yml

@@ -23,9 +23,9 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -43,7 +43,7 @@ jobs:
     - name: Send status to Slack app
       if: ${{ failure() && github.event_name != 'workflow_dispatch' }} # Only post if the workflow failed and was not manually started. Customize this as necessary.
       id: slack
-      uses: slackapi/slack-github-action@main
+      uses: slackapi/slack-github-action@v1
       with:
         # For posting a rich message using Block Kit
         payload: | # The payload defined here can be customized to you liking https://api.slack.com/reference/block-kit/blocks 

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

@@ -18,9 +18,9 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@main
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@main
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -33,6 +33,6 @@ jobs:
       run: |
         python -m pytest --cov=hipscat --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@main
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -145,3 +145,6 @@ tmp/
 # Airspeed Velocity performance results
 _results/
 _html/
+
+# Project initialization script
+.initialize_new_project.sh

.setup_dev.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+# 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
+    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 $2}' | sed 's/\./ /g') )
+if let "${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
+
+echo "Installing pre-commit"
+pre-commit install > /dev/null
+
+#######################################################
+# Include any additional configurations below this line
+#######################################################

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
 # On a mac, install optional dependencies with `pip install '.[dev]'` (include the single quotes)
 [project.optional-dependencies]
 dev = [
-    "adlfs", # abfs filesytem support
+"adlfs", # abfs filesytem support
     "asv==0.6.1", # Used to compute performance benchmarks
     "black", # auto-formatter
     "ipykernel", # Support for Jupyter notebooks
@@ -50,9 +50,9 @@ dev = [
     "pytest-timeout", # Used to test for code efficiency
     "s3fs", # s3 filesystem support
     "sphinx", # Used to automatically generate documentation
-    "sphinx-autoapi", # Used to automatically generate api documentation
+        "sphinx-autoapi", # Used to automatically generate api documentation
     "sphinx-rtd-theme" # Used to render documentation
-]
+    ]
 
 [build-system]
 requires = [
@@ -80,3 +80,48 @@ target-version = ["py38"]
 [tool.isort]
 profile = "black"
 line_length = 110
+
+[tool.ruff]
+line-length = 110
+target-version = "py39"
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    "W",
+    # Pyflakes
+    "F",
+    # pep8-naming
+    "N",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # docstrings
+    "D101",
+    "D102",
+    "D103",
+    "D106",
+    "D206",
+    "D207",
+    "D208",
+    "D300",
+    "D417",
+    "D419",
+
+]
+
+ignore = [
+    "UP006", # Allow non standard library generics in type hints
+    "UP007", # Allow Union in type hints
+    "SIM114", # Allow if with same arms
+    "B028", # Allow default warning level
+    "SIM117", # Allow nested with
+    "UP015", # Allow redundant open parameters
+    "UP028", # Allow yield in for loop
+]