PPT v2.2

.copier-answers.yml

@@ -1,10 +1,10 @@
 # Changes here will be overwritten by Copier
-_commit: v2.1.0
+_commit: v2.2.0
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: malanchev@cmu.edu
 author_name: Konstantin Malanchev
 create_example_module: false
-custom_install: true
+custom_install: custom
 enforce_style:
 - ruff_lint
 - ruff_format
@@ -14,11 +14,13 @@ include_docs: true
 include_notebooks: true
 mypy_type_checking: none
 package_name: uncle_val
+project_description: Uncertainty validation for large time-domain datasets
 project_license: MIT
 project_name: uncle-val
 project_organization: lincc-frameworks
 python_versions:
 - '3.11'
 - '3.12'
 - '3.13'
+- '3.14'
 test_lowest_version: none

.github/ISSUE_TEMPLATE/1-bug_report.md

@@ -12,6 +12,13 @@ assignees: ''
 **Environment Information**
 
 
+<details>
+<summary>Traceback</summary>
+
+FILL IN YOUR STACK TRACE HERE
+
+</details>
+
 **Before submitting**
 Please check the following:
 

.github/pull_request_template.md

@@ -1,63 +1,13 @@
-<!-- 
-Thank you for your contribution to the repo :)
-
-Pull Request (PR) Instructions:
-Provide a general summary of your changes in the Title above. Fill out each section of the template, and replace the space with an `x` in all the boxes that apply. If you're unsure about any of these, don't hesitate to ask. We're here to help! Once you are satisfied with the pull request, click the "Create pull request" button to submit it for review.
-
-Before submitting this PR, please ensure that your input and responses are entered in the designated space provided below each section to keep all project-related information organized and easily accessible.
-
-How to link to a PR:
-https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue 
--->
-
 ## Change Description
 <!--- 
-Describe your changes in detail. In your description, you should answer questions like "Why is this change required? What problem does it solve?".
-
-If it fixes an open issue, please link to the issue here. If this PR closes an issue, put the word 'closes' before the issue link to auto-close the issue when the PR is merged.
+Closes #???
 -->
-- [ ] My PR includes a link to the issue that I am addressing
-
-
 
 ## Solution Description
-<!-- Please explain the technical solution that I have provided and how it addresses the issue or feature being implemented -->
-
 
 
 ## Code Quality
-- [ ] I have read the Contribution Guide
+- [ ] I have read the Contribution Guide and agree to the Code of Conduct
 - [ ] My code follows the code style of this project
 - [ ] My code builds (or compiles) cleanly without any errors or warnings
 - [ ] My code contains relevant comments and necessary documentation
-
-## Project-Specific Pull Request Checklists
-<!--- Please only use the checklist that apply to your change type(s) -->
-
-### Bug Fix Checklist
-- [ ] My fix includes a new test that breaks as a result of the bug (if possible)
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
-
-### New Feature Checklist
-- [ ] I have added or updated the docstrings associated with my feature using the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
-- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
-- [ ] I have added unit/End-to-End (E2E) test cases to cover my new feature
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
-
-### Documentation Change Checklist
-- [ ] Any updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
-
-### Build/CI Change Checklist
-- [ ] If required or optional dependencies have changed (including version numbers), I have updated the README to reflect this
-- [ ] If this is a new CI setup, I have added the associated badge to the README
-
-<!-- ### Version Change Checklist [For Future Use] -->
-
-### Other Change Checklist
-- [ ] Any new or updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
-- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
-- [ ] I have added unit/End-to-End (E2E) test cases to cover any changes
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)

.github/workflows/build-documentation.yml

@@ -22,15 +22,17 @@ jobs:
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python 3.12
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.12'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
     - name: Install dependencies
       run: |
         sudo apt-get update
-        python -m pip install --upgrade pip
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
-        pip install .
+        uv pip install --system -e .
+        if [ -f docs/requirements.txt ]; then uv pip install --system -r docs/requirements.txt; fi
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - name: Install notebook requirements
       run: |
         sudo apt-get install pandoc

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

@@ -18,7 +18,7 @@ jobs:
       with:
         fetch-depth: 0 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.12'
     - name: Install uv

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

@@ -25,7 +25,7 @@ jobs:
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.12'
     - name: Install dependencies

.github/workflows/smoke-test.yml

@@ -20,19 +20,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
     - uses: actions/checkout@v6
-    - name: Cache JAX compilation cache
-      uses: actions/cache@v5
-      with:
-        path: /tmp/jax_cache
-        key: jax-cache-${{ runner.os }}
-        restore-keys: |
-          jax-cache-
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install uv

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

@@ -16,12 +16,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install uv

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     # This hook should always pass. It will print a message if the local version 
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
-    rev: v0.1.2
+    rev: v0.2.2
     hooks:
       - id: check-lincc-frameworks-template-version
         name: Check template version
@@ -60,32 +60,15 @@ repos:
       - id: ruff-format
         name: Format code using ruff
         types_or: [ python, pyi, jupyter ]
-    # Make sure Sphinx can build the documentation while explicitly omitting 
-    # notebooks from the docs, so users don't have to wait through the execution 
-    # of each notebook or each commit. By default, these will be checked in the 
-    # GitHub workflows.
-  - repo: local
+  - repo: https://github.com/lincc-frameworks/pre-commit-hooks
+    rev: v0.2.2
     hooks:
-      - id: sphinx-build
-        name: Build documentation with Sphinx
-        entry: sphinx-build
-        language: system
-        always_run: true
-        exclude_types: [file, symlink]
+      - id: pre-executed-nb-never-execute
+        name: Check pre-executed notebooks
+        files: ^docs/pre_executed/.*\.ipynb$
+        verbose: true
         args:
-          [
-            "-M", # Run sphinx in make mode, so we can use -D flag later
-                  # Note: -M requires next 3 args to be builder, source, output
-            "html", # Specify builder
-            "./docs", # Source directory of documents
-            "./_readthedocs", # Output directory for rendered documents
-            "-T", # Show full trace back on exception
-            "-E", # Don't use saved env; always read all files
-            "-d", # Flag for cached environment and doctrees
-            "./docs/_build/doctrees", # Directory
-            "-D", # Flag to override settings in conf.py
-            "exclude_patterns=notebooks/*,_build", # Exclude notebooks and build dir from pre-commit
-          ]
+          ["docs/pre_executed/"]
     # 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

.readthedocs.yml

@@ -19,5 +19,6 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
+   - requirements: requirements.txt
    - method: pip
      path: .

docs/index.rst

@@ -6,6 +6,8 @@
 Welcome to uncle_val's documentation!
 ========================================================================================
 
+Uncertainty validation for large time-domain datasets
+
 Dev Guide - Getting Started
 ---------------------------