Merge pull request #386 from lincc-frameworks/delucchi/copier

Upgrade to PPT 2.0.1

.copier-answers.yml

@@ -1,18 +1,22 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.5
+_commit: v2.0.1
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: Doug Branton
 create_example_module: false
 custom_install: true
+enforce_style:
+- black
+failure_notification: []
 include_benchmarks: true
 include_docs: true
 include_notebooks: true
 mypy_type_checking: none
 package_name: tape
-preferred_linter: black
 project_license: MIT
 project_name: tape
 project_organization: lincc-frameworks
-use_gitlfs: none
-use_isort: false
+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/asv-main.yml

@@ -23,13 +23,13 @@ jobs:
 
     steps:
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "${{ env.PYTHON_VERSION }}"
 
@@ -46,12 +46,12 @@ jobs:
 
     steps:
       - name: Checkout main branch of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}

.github/workflows/asv-nightly.yml

@@ -25,18 +25,18 @@ jobs:
 
     steps:
       - name: Checkout main branch of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "${{ 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@v3
+        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@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.WORKING_DIR }}
           key: nightly-results-${{ steps.nightly-dates.outputs.today }}

.github/workflows/asv-pr.yml

@@ -1,101 +1,86 @@
 # This workflow will run benchmarks with airspeed velocity (asv) for pull requests.
 # It will compare the performance of the main branch with the performance of the merge
-# with the new changes and publish a comment with this assessment.  
-
-name: Run ASV benchmarks for PR
+# with the new changes. It then publishes a comment with this assessment by triggering
+# the publish-benchmarks-pr workflow.
+# Based on https://securitylab.github.com/research/github-actions-preventing-pwn-requests/.
+name: Run benchmarks for PR
 
 on:
   pull_request:
     branches: [ main ]
-
-env:
-  PYTHON_VERSION: "3.10"
-  WORKING_DIR: ${{ github.workspace }}/benchmarks
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-jobs:
+env:
+  PYTHON_VERSION: "3.10"
+  WORKING_DIR: ${{ github.workspace }}/benchmarks
+  ARTIFACTS_DIR: ${{ github.workspace }}/artifacts
 
+jobs:
   setup-python:
     runs-on: ubuntu-latest
-
     steps:
-      - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: python-${{ env.PYTHON_VERSION }}
-
-      - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: "${{ env.PYTHON_VERSION }}"
-
+    - name: Cache Python ${{ env.PYTHON_VERSION }}
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: python-${{ env.PYTHON_VERSION }}
+    - name: Set up Python ${{ env.PYTHON_VERSION }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
   asv-pr:
     runs-on: ubuntu-latest
     needs: setup-python
-
-    permissions:
-      actions: read
-      pull-requests: write
-
     defaults:
       run:
         working-directory: ${{ env.WORKING_DIR }}
-
     steps:
-      - name: Checkout PR branch of the repository
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: python-${{ env.PYTHON_VERSION }}
-
-      - name: Install dependencies
-        run: |
-          sudo apt-get update
-          python -m pip install --upgrade pip
-          pip install asv==0.6.1 virtualenv tabulate lf-asv-formatter
-
-      - name: Get current job logs URL
-        uses: Tiryoh/gha-jobid-action@v0
-        id: jobs
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          job_name: ${{ github.job }}
-
-      - name: Create ASV machine config file
-        run: asv machine --machine gh-runner --yes
-
-      - name: Run comparison of PR against main branch
-        run: |
-          git remote add upstream https://github.com/${{ github.repository }}.git
-          git fetch upstream
-          asv continuous upstream/main HEAD --verbose || true
-          asv compare upstream/main HEAD --sort ratio --verbose | tee output
-          python -m lf_asv_formatter --asv_version "$(echo asv --version)"
-          printf "\n\nClick [here]($STEP_URL) to view all benchmarks." >> output
-        env:
-          STEP_URL: "${{ steps.jobs.outputs.html_url }}#step:8:1"
-
-      - name: Find benchmarks comment
-        uses: peter-evans/find-comment@v2
-        id: find-comment
-        with:
-          issue-number: ${{ github.event.pull_request.number }}
-          comment-author: 'github-actions[bot]'
-          body-includes: view all benchmarks
-
-      - name: Create or update benchmarks comment
-        uses: peter-evans/create-or-update-comment@v3
-        with:
-          comment-id: ${{ steps.find-comment.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body-path: ${{ env.WORKING_DIR }}/output
-          edit-mode: replace
+    - name: Checkout PR branch of the repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Display Workflow Run Information
+      run: |
+        echo "Workflow Run ID: ${{ github.run_id }}"
+    - name: Cache Python ${{ env.PYTHON_VERSION }}
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: python-${{ env.PYTHON_VERSION }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install asv==0.6.1 virtualenv tabulate lf-asv-formatter
+    - name: Make artifacts directory
+      run: mkdir -p ${{ env.ARTIFACTS_DIR }}
+    - 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@v1
+      id: jobs
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        job_name: ${{ github.job }}
+    - name: Create ASV machine config file
+      run: asv machine --machine gh-runner --yes
+    - name: Save comparison of PR against main branch
+      run: |
+        git remote add upstream https://github.com/${{ github.repository }}.git
+        git fetch upstream
+        asv continuous upstream/main HEAD --verbose || true
+        asv compare upstream/main HEAD --sort ratio --verbose | tee output
+        python -m lf_asv_formatter --asv_version "$(echo asv --version)"
+        printf "\n\nClick [here]($STEP_URL) to view all benchmarks." >> output
+        mv output ${{ env.ARTIFACTS_DIR }}
+      env:
+        STEP_URL: "${{ steps.jobs.outputs.html_url }}#step:11:1"
+    - name: Upload artifacts (PR number and benchmarks output)
+      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@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