Merge pull request #39 from LSSTDESC/copier-update-v0.3

Updated to copier template v0.3

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: da1cc49
+_commit: v0.3
 _src_path: gh:LSSTDESC/RAIL-project-template
 author_email: [email protected]
 author_name: LSST Dark Energy Science Collaboration (DESC) Photo-z WG

.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/pull_request_template.md

@@ -1,63 +1,8 @@
-<!-- 
-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.
--->
-- [ ] 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 -->
-
+## Problem & Solution Description (including issue #)
 
 
 ## Code Quality
-- [ ] I have read the Contribution Guide
-- [ ] 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)
+- [ ] My code follows [the code style of this project](https://rail-hub.readthedocs.io/en/latest/source/contributing.html#naming-conventions)
+- [ ] I have written unit tests or justified all instances of `#pragma: no cover`; in the case of a bugfix, a new test that breaks as a result of the bug has been added
+- [ ] My code contains relevant comments and necessary documentation for future maintainers; the change is reflected in applicable demos/tutorials (with output cleared!) and added/updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
+- [ ] Any breaking changes, described above, are accompanied by backwards compatibility and deprecation warnings

.github/workflows/add-issue-to-project-tracker.yml

@@ -4,6 +4,8 @@ on:
   issues:
     types:
       - opened
+  pull_request:
+    types: [opened, reopened]
 
 jobs:
   add-to-project:

.github/workflows/linting.yml

@@ -12,16 +12,12 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10']
-
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         sudo apt-get update
@@ -32,5 +28,6 @@ jobs:
     - name: Analyze code with linter
       run: |
         pylint -rn -sn --recursive=y ./src
+        pylint -rn -sn --recursive=y ./tests
       # the following line allows the CI test to pass, even if pylint fails
       continue-on-error: true

.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
@@ -19,7 +19,8 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
@@ -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

@@ -7,13 +7,16 @@ on:
   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

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

@@ -15,7 +15,7 @@ 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

.pre-commit-config.yaml

@@ -1,16 +1,6 @@
+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.
-  - repo: https://github.com/lincc-frameworks/pre-commit-hooks
-    rev: v0.1
-    hooks:
-      - id: check-lincc-frameworks-template-version
-        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:
@@ -22,21 +12,6 @@ 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
@@ -83,4 +58,19 @@ repos:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
-          ]
+          ]
+
+    # 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

pyproject.toml

@@ -1,5 +1,6 @@
 [project]
 name = "pz-rail-bpz"
+requires-python = ">=3.9"
 license = {file = "LICENSE"}
 readme = "README.md"
 authors = [
@@ -44,11 +45,6 @@ write_to = "src/rail/bpz/_version.py"
 [tool.setuptools.package-data]
 "rail.examples.estimation.configs" = ["*.columns"]
 
-[tools.setuptools.packages.find]
-where = ["."]
-include = ["rail"]
-namespaces = true
-
 [tool.pytest.ini_options]
 testpaths = [
     "tests",