Merge pull request #2 from LSSTISSC/update-ppt

Update PPT to 1.5.0

.copier-answers.yml

@@ -1,17 +1,23 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.6
+_commit: v1.5.0
 _src_path: https://github.com/lincc-frameworks/python-project-template.git
 author_email: [email protected]
 author_name: LSST ISSC
 create_example_module: true
 custom_install: true
+enforce_style:
+- ruff
+failure_notification:
+- none
 include_benchmarks: false
 include_docs: true
 include_notebooks: true
 mypy_type_checking: none
 package_name: stamps_ad
-preferred_linter: none
 project_license: MIT
 project_name: stamps-ad
-project_organization: lsstissc
-use_isort: false
+project_organization: LSSTISSC
+python_versions:
+- '3.9'
+- '3.10'
+- '3.11'

.github/ISSUE_TEMPLATE/0-general_issue.md

@@ -0,0 +1,8 @@
+---
+name: General issue
+about: Quickly create a general issue
+title: ''
+labels: ''
+assignees: ''
+
+---

.github/ISSUE_TEMPLATE/1-bug_report.md

@@ -0,0 +1,17 @@
+---
+name: Bug report
+about: Tell us about a problem to fix
+title: 'Short description'
+labels: 'bug'
+assignees: ''
+
+---
+**Bug report**
+
+
+**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 included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a descriprion 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/ISSUE_TEMPLATE/2-feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Short description'
+labels: 'enhancement'
+assignees: ''
+
+---
+
+** Feature request**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the purpose of the suggested change, specifying what I need the enhancement to accomplish, i.e. what problem it solves.
+- [ ] I have included any relevant links, screenshots, environment information, and data relevant to implementing the requested feature, as well as pseudocode for how I want to access the new functionality.
+- [ ] If I have ideas for how the new feature could be implemented, I have provided explanations and/or pseudocode and/or task lists for the steps.

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/build-documentation.yml

@@ -19,9 +19,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: '3.10'
     - name: Install dependencies

.github/workflows/code_style.yml

@@ -0,0 +1,38 @@
+# This workflow will install Python dependencies, then perform static analysis for code style and type checking.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Code Style analysis
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@main
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@main
+      with:
+        python-version: ${{ matrix.python-version }}
+    - 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
+    - name: Analyze code with ruff
+      run: |
+       ruff format --check
+       ruff check

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

@@ -0,0 +1,33 @@
+# This workflow runs pre-commit hooks on pull requests 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:
+  pull_request:
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    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
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@main
+      with:
+        python-version: '3.10'
+    - 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
+    - uses: pre-commit/action@main # Still using Node 16
+      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
+      if: always()

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

@@ -22,9 +22,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: '3.10'
     - name: Install dependencies

.github/workflows/smoke-test.yml

@@ -20,24 +20,23 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
-        pip install .
-        pip install .[dev]
+        pip install -e .[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
+        python -m pytest

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

@@ -15,23 +15,24 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@main
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
-        pip install .
-        pip install .[dev]
+        pip install -e .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Run unit tests with pytest
       run: |
-        python -m pytest tests --cov=stamps_ad --cov-report=xml
+        python -m pytest --cov=stamps_ad --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@main
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -1,6 +1,5 @@
 fail_fast: true
 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.
@@ -11,7 +10,6 @@ repos:
         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:
@@ -22,7 +20,6 @@ repos:
         stages: [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: v4.4.0
@@ -34,21 +31,20 @@ repos:
         name: Check for large files
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
-
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: v0.12.1
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
         description: Verify that pyproject.toml adheres to the established schema.
-
-
-
-
-
-
-
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.3
+    hooks:
+      - id: ruff
+        name: Format and lint code using ruff
+        types_or: [ python, pyi, jupyter ]
     # 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

.prepare_project.sh

@@ -1,8 +1,17 @@
 #!/usr/bin/env bash
 
+echo "Checking pip version"
+MINIMUM_PIP_VERSION=22
+pipversion=( $(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 "Initializing local git repository"
 {
-    gitversion=( $(git version | sed 's/^.* //;s/\./ /g') )
+    gitversion=( $(git version | git version | awk '{print $3}' | sed 's/\./ /g') )
     if let "${gitversion[0]}<2"; then
 	# manipulate directly
 	git init . && echo 'ref: refs/heads/main' >.git/HEAD