copier update

.copier-answers.yml

@@ -1,16 +1,23 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.1
+_commit: v2.0.1
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: Maxine West
 create_example_module: false
 custom_install: true
+enforce_style:
+- black
+- isort
+failure_notification: []
+include_benchmarks: false
 include_docs: true
-include_notebooks: true
+include_notebooks: false
 mypy_type_checking: none
 package_name: koffi
-preferred_linter: black
 project_license: BSD
 project_name: koffi
-use_gitlfs: none
-use_isort: true
+project_organization: lincc-frameworks
+python_versions:
+- '3.9'
+- '3.10'
+- '3.11'

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -0,0 +1,24 @@
+# For explanation of this file and uses see
+# https://git-scm.com/docs/gitattributes
+# https://developer.lsst.io/git/git-lfs.html#using-git-lfs-enabled-repositories
+# https://lincc-ppt.readthedocs.io/en/latest/practices/git-lfs.html
+#
+# Used by https://github.com/lsst/afwdata.git
+# *.boost filter=lfs diff=lfs merge=lfs -text
+# *.dat filter=lfs diff=lfs merge=lfs -text
+# *.fits filter=lfs diff=lfs merge=lfs -text
+# *.gz filter=lfs diff=lfs merge=lfs -text
+#
+# apache parquet files
+# *.parq	filter=lfs diff=lfs merge=lfs -text
+#
+# sqlite files
+# *.sqlite3	filter=lfs diff=lfs merge=lfs -text
+#
+# gzip files
+# *.gz	filter=lfs diff=lfs merge=lfs -text
+#
+# png image files
+# *.png	filter=lfs diff=lfs merge=lfs -text
+
+.git_archival.txt export-subst

.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

@@ -9,15 +9,19 @@ on:
   pull_request:
     branches: [ main ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies
@@ -26,9 +30,6 @@ jobs:
         python -m pip install --upgrade pip
         if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
         pip install .
-    - name: Install notebook requirements
-      run: |
-        sudo apt-get install pandoc
     - name: Build docs
       run: |
         sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

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

@@ -0,0 +1,35 @@
+# This workflow runs pre-commit hooks on pushes and pull requests to main
+# 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:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      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 .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - uses: pre-commit/[email protected]
+      with:
+        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

@@ -1,5 +1,5 @@
 # This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+# For more information see: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
@@ -19,11 +19,12 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies
@@ -33,7 +34,4 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/smoke-test.yml

@@ -6,33 +6,37 @@
 name: Unit test smoke test
 
 on:
+
+  # Runs this workflow automatically
   schedule:
     - cron: 45 6 * * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
 
 jobs:
   build:
 
     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@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       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@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       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=koffi --cov-report=xml
+        python -m pytest --cov=koffi --cov-report=xml
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -140,4 +140,15 @@ dask-worker-space/
 tmp/
 
 # Mac OS
-.DS_Store
+<<<<<<< before updating
+.DS_Store
+=======
+.DS_Store
+
+# Airspeed Velocity performance results
+_results/
+_html/
+
+# Project initialization script
+.initialize_new_project.sh
+>>>>>>> after updating