Merge pull request #24 from lincc-frameworks/update-template

Update template to consolidate pre-commit logic

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.6-59-g4c84e58
+_commit: v1.5.1-11-g34358f1
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: Sandro Campos

.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

@@ -18,9 +18,9 @@ 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/pre-commit-ci.yml

@@ -5,30 +5,32 @@
 name: Run pre-commit hooks
 
 on:
+  push:
+    branches: [ main ]
   pull_request:
+    branches: [ main ]
 
 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
+    - 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
       run: |
         sudo apt-get update
         python -m pip install --upgrade pip
-        pip install .
         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
-      if: always()
+        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/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

.prepare_project.sh → .initialize_new_project.sh

@@ -1,8 +1,23 @@
 #!/usr/bin/env bash
 
+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=( $(pip --version | awk '{print $2}' | sed 's/\./ /g') )
+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."
@@ -25,10 +40,13 @@ echo "Initializing local git repository"
 } > /dev/null
 
 echo "Installing package and runtime dependencies in local environment"
-pip install -e . > /dev/null
+python -m pip install -e . > /dev/null
 
 echo "Installing developer dependencies in local environment"
-pip install -e .'[dev]' > /dev/null
+python -m pip install -e .'[dev]' > /dev/null
 
 echo "Installing pre-commit"
 pre-commit install > /dev/null
+
+echo "Committing initial files"
+git add . && SKIP="no-commit-to-branch" git commit -m "Initial commit"

.pre-commit-config.yaml

@@ -1,4 +1,3 @@
-fail_fast: true
 repos:
 
     # Compare the local template version to the latest remote template version
@@ -23,21 +22,6 @@ repos:
         language: system
         entry: jupyter nbconvert --clear-output
 
-    # 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
-    # and uploaded to Codecov by calling pytest like so:
-    # `python -m pytest --cov=<package_name> --cov-report=xml`
-  - repo: local
-    hooks:
-      - id: pytest-check
-        name: Run unit tests
-        description: Run unit tests with pytest.
-        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
-        language: system
-        pass_filenames: false
-        always_run: true
-
     # Prevents committing directly branches named 'main' and 'master'.
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
@@ -128,3 +112,18 @@ repos:
             "-D", # Flag to override settings in conf.py
             "exclude_patterns=notebooks/*", # Exclude our notebooks from pre-commit
           ]
+
+    # 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
+    # and uploaded to Codecov by calling pytest like so:
+    # `python -m pytest --cov=<package_name> --cov-report=xml`
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: Run unit tests
+        description: Run unit tests with pytest.
+        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
+        language: system
+        pass_filenames: false
+        always_run: true

.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
+#######################################################

benchmarks/asv.conf.json

@@ -32,7 +32,7 @@
     // variable.
     "environment_type": "virtualenv",
     // the base URL to show a commit for the project.
-    "show_commit_url": "https://github.com/lincc-frameworks/benchmarking-asv/commit",
+    "show_commit_url": "https://github.com/lincc-frameworks/benchmarking-asv/commit/",
     // The Pythons you'd like to test against. If not provided, defaults
     // to the current version of Python used to run `asv`.
     "pythons": [

docs/notebooks/intro_notebook.ipynb

@@ -67,6 +67,14 @@
    "source": [
     "sierpinsky(4)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3a7bb740",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -77,6 +85,18 @@
    "display_name": "Python 3",
    "language": "python",
    "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,