Merge pull request #26 from lincc-frameworks/update-ppt

Update PPT

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.6-38-gc8eefc6
+_commit: v1.4.6-69-g9ab5459
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks

.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 ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@main
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@main
         with:
           python-version: "${{ env.PYTHON_VERSION }}"
 
@@ -46,12 +46,12 @@ jobs:
 
     steps:
       - name: Checkout main branch of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@main
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@main
         with:
           path: ~/.cache/pip
           key: python-${{ 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@main
         with:
           fetch-depth: 0
 
       - name: Cache Python ${{ env.PYTHON_VERSION }}
-        uses: actions/cache@v3
+        uses: actions/cache@main
         with:
           path: ~/.cache/pip
           key: python-${{ env.PYTHON_VERSION }}
 
       - name: Set up Python ${{ env.PYTHON_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@main
         with:
           python-version: "${{ 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@main
         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@main
         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 ${{ env.PYTHON_VERSION }}
-      uses: actions/cache@v3
+      uses: actions/cache@main
       with:
         path: ~/.cache/pip
         key: python-${{ env.PYTHON_VERSION }}
     - name: Set up Python ${{ env.PYTHON_VERSION }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@main
       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@v3
+      uses: actions/checkout@main
       with:
         fetch-depth: 0
     - name: Display Workflow Run Information
       run: |
         echo "Workflow Run ID: ${{ github.run_id }}"
     - name: Cache Python ${{ env.PYTHON_VERSION }}
-      uses: actions/cache@v3
+      uses: actions/cache@main
       with:
         path: ~/.cache/pip
         key: python-${{ 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@v0
+      uses: Tiryoh/gha-jobid-action@main
       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@v3
+      uses: actions/upload-artifact@main
       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@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

@@ -21,16 +21,15 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     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]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Analyze code with mypy

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

@@ -13,22 +13,21 @@ 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@v3
+    - uses: actions/checkout@main
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      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 .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - uses: pre-commit/action@v3.0.0
+    - 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@v1.0.1
+    - uses: pre-commit-ci/lite-action@main
       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@v2
+      uses: dawidd6/action-download-artifact@master
       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@v2
+      uses: peter-evans/find-comment@main
       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@v3
+      uses: peter-evans/create-or-update-comment@main
       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@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

@@ -23,24 +23,20 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     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
-    - name: Send failure email
-      run: |
-        echo "NOT IMPLEMENTED IN PPT, UPDATE PPT WHEN IT IS READY"

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

@@ -18,20 +18,21 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     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 -e .
         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 --cov=pandas_ts --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
@@ -34,7 +31,6 @@ 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
@@ -54,10 +50,6 @@ repos:
         name: Lint code using ruff
         # Disable ruff for notebooks since it is too strict.
         types_or: [ python, pyi ]
-
-
-
-    # Analyze type hints and report errors.
   - repo: local
     hooks:
       - id: mypy
@@ -68,12 +60,8 @@ repos:
         files: ^(src|tests)/
         args:
           [
-
             "--ignore-missing-imports", # Ignore imports without type hints
-
           ]
-
-
     # 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