feat: migrate to copier-numpy template

.copier-answers.yml

@@ -0,0 +1,18 @@
+# Changes here will be overwritten by Copier (DO NOT EDIT MANUALLY)
+_commit: v0.4.0-2-g5b15cde
+_src_path: gh:eckelsjd/copier-numpy
+author_email: eckelsjd@umich.edu
+author_name: Joshua Eckels
+copyright_license: GPL-3.0
+distribution_name: amisc
+import_name: amisc
+include_cicd: true
+include_docs: true
+init_github: true
+install_jupyter: false
+is_distributable: true
+project_description: Efficient framework for building surrogates of multidisciplinary
+    systems using the adaptive multi-index stochastic collocation (AMISC) technique.
+project_name: amisc
+repository_namespace: eckelsjd
+requires_python: '>=3.11'

.github/workflows/deploy.yml

@@ -1,28 +1,23 @@
-name: Release package
+name: Build and publish
 on:
   push:
     tags:
-      - 'v*'
-permissions:
-  contents: write
+      - 'v*.*.*'
+
 jobs:
   build:
     name: Build distribution
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Configure Git Credentials
-      run: |
-        git config user.name github-actions[bot]
-        git config user.email 41898282+github-actions[bot]@users.noreply.github.com
     - uses: pdm-project/setup-pdm@v4
     - run: pdm build
     - uses: actions/upload-artifact@v4
       with:
         name: python-package-distributions
         path: dist/
 
-  publish-pypi:
+  pypi-release:
     name: Publish to PyPI
     needs:
     - build
@@ -42,7 +37,7 @@ jobs:
   github-release:
     name: Github release
     needs:
-    - publish-pypi
+    - build
     runs-on: ubuntu-latest
     permissions:
       contents: write
@@ -52,22 +47,20 @@ jobs:
       with:
         name: python-package-distributions
         path: dist/
-    - uses: sigstore/gh-action-sigstore-python@v2
+    - uses: actions/checkout@v4
       with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
-    - name: Create Github Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release create
-        '${{ github.ref_name }}'
-        --repo '${{ github.repository }}'
-    - name: Upload artifacts
+        fetch-depth: 0
+    - uses: pdm-project/setup-pdm@v4
+      with:
+        python-version: 3.11
+        cache: true
+    - run: pdm sync -G dev --no-default
+    - name: Create release notes
+      run: pdm run cz changelog $(pdm run cz version --project) --dry-run > body.md
+    - uses: softprops/action-gh-release@v2
+      with:
+        body_path: body.md
+        tag_name: ${{ github.ref_name }}
+        files: dist/*
       env:
-        GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release upload
-        '${{ github.ref_name }}' dist/**
-        --repo '${{ github.repository }}'
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Build documentation
+name: Docs
 on:
   push:
     branches:
@@ -12,11 +12,16 @@ jobs:
     steps:
       # Checkout this repository and cd to project root, set up python/pdm and cache
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Configure Git Credentials
         run: |
           git config user.name github-actions[bot]
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
       - uses: pdm-project/setup-pdm@v4
+        with:
+          python-version: 3.11
+          cache: true
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - uses: actions/cache@v4
         with:
@@ -25,21 +30,6 @@ jobs:
           restore-keys: |
             mkdocs-material-
       # Build and push docs to gh-pages branch (triggers doc site publish action)
-      - run: pdm sync
+      - run: pdm sync -G doc -G test
+      - run: pdm run test  # to generate coverage report
       - run: pdm run mkdocs gh-deploy --force
-
-  coverage-test:
-    name: Test coverage
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up PDM
-        uses: pdm-project/setup-pdm@v4
-      - name: Install dependencies
-        run: pdm install
-      - name: Run tests
-        run: pdm run -v test
-      - name: Coveralls
-        uses: coverallsapp/github-action@v2
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

@@ -1,23 +1,38 @@
-name: Run PR test matrix
+name: Lint and test
 on:
   pull_request:
     branches: [ main ]
 permissions:
   contents: write
 jobs:
+  check-lint:
+    name: Lint check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pdm-project/setup-pdm@v4
+        with:
+          python-version: 3.11
+          cache: true
+      - run: pdm sync -G dev --no-default
+      - run: pdm run lint
+
   pr-tests:
+    name: PR tests
     runs-on: ${{ matrix.os }}
+    needs: check-lint
     strategy:
       matrix:
         python-version: ['3.11', '3.12']
-        os: [ ubuntu-latest, macOS-latest, windows-latest ]
+        os: [ ubuntu-latest, windows-latest ]
     steps:
       - uses: actions/checkout@v4
       - name: Set up PDM
         uses: pdm-project/setup-pdm@v4
         with:
+          cache: true
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pdm install
+        run: pdm sync -G test
       - name: Run tests
         run: pdm run -v test

.gitignore

@@ -54,6 +54,7 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+.pytest_status
 
 # Translations
 *.mo
@@ -163,7 +164,8 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
+
 # Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
 # Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
 

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+default_install_hook_types: [ pre-commit, commit-msg ]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # Use the latest version available
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: check-merge-conflict
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.1   # Use the desired version of ruff
+    hooks:
+      - id: ruff
+        files: ^src/|^tests/
+        args: [ --exit-non-zero-on-fix ]
+
+  - repo: local
+    hooks:
+      - id: pytest-status
+        name: pytest-status
+        description: "Make sure all tests have passed since last source code change."
+        entry: pdm run python _pre_commit_checks.py
+        args: [ --pytest-status ]
+        language: system
+        pass_filenames: false
+        require_serial: true
+
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.29.0
+    hooks:
+      - id: commitizen

CHANGELOG.md

@@ -0,0 +1 @@
+Changes should automatically show up here when using `cz bump`.

docs/CONTRIBUTING.md → CONTRIBUTING.md

@@ -1,34 +1,31 @@
-## Contributing to `amisc`
+## Contributing to amisc
 You might be here if you want to:
 
 - Report a bug
 - Discuss the current state of the code
 - Submit a fix
 - Propose a new feature
 - Write unit tests
-- Add to the documentation
+- Add to the documentation.
 
 We use [Github](https://guides.github.com/introduction/flow/index.html) to host code and documentation, to track issues and feature requests, and to accept pull requests.
 
 ## Submitting pull requests
 Pull requests are the best way to propose changes to the codebase (bug fixes, new features, docs, etc.)
 
-1. Fork the repo and create your branch from `main`. 
-3. If you are adding a feature or making major changes, first create the [issue](https://github.com/eckelsjd/amisc/issues). 
-4. If you've added code that should be tested, add to `/tests`. 
-5. If you've made major changes, update the `/docs`. 
-6. Ensure the test suite passes (`pdm run test`).
-7. Make sure your code passes lint checks (coming soon). 
-8. Follow [Conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) guidelines when adding a commit message.
-9. Issue that pull request!
+1. Fork the repo and create a branch from `main`.
+1. If you are adding a feature or making major changes, first create the issue in Github.
+1. If you've added code that should be tested, add to `/tests`.
+1. If you've made major changes, update the `/docs`.
+1. Ensure the test suite passes (`pdm run test`).
+1. Follow [Conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) guidelines when adding a commit message.
+1. Ensure all `pre-commit` checks pass. Pro tip: use `pdm lint` to help.
+1. Issue the pull request!
 
-We strongly recommend using [pdm](https://github.com/pdm-project/pdm) to set up your development environment. An example contribution workflow is shown here:
+Use [pdm](https://github.com/pdm-project/pdm) to set up your development environment. An example contribution workflow is shown here:
 
 ```shell
-pip install --user pdm
-
 # Fork the repo on Github
-
 git clone https://github.com/<your-user-name>/amisc.git
 cd amisc
 pdm install
@@ -38,38 +35,31 @@ git checkout -b <your-branch-name>
 
 pdm run test  # make sure tests pass
 git add -A
-git commit -m "Adding a bugfix or new feature"
+git commit -m "fix: adding a bugfix"
 git push -u origin <your-branch-name>
 
 # Go to Github and "Compare & Pull Request" on your fork
 # For your PR to be merged:
   # squash all your commits on your branch (interactively in an IDE most likely)
   # rebase to the top of origin/main to include new changes from others
-  
+
 git fetch
 git rebase -i main your-branch  # for example
-  
+
 # Resolve any conflicts
 # Your history now looks something like this:
 #              o your-branch
 #             /
 # ---o---o---o main
-  
-# You can delete the branch and fork when your PR has been merged
+
+# You can delete the branch and fork when your PR has been merged!
 ```
 
 You can also find a good tutorial [here](https://github.com/firstcontributions/first-contributions/tree/main).
 
-## Report bugs using [issues](https://github.com/eckelsjd/amisc/issues)
+## Report bugs using issues
 Open a new issue and describe your problem using the template. Provide screenshots where possible and example log files.
 Add labels to help categorize and describe your issue.
 
-## Community
-Start or take part in community [discussions](https://github.com/eckelsjd/amisc/discussions) for non-code related things.
-
 ## License
-By contributing, you agree that your contributions will be licensed under its GNU GPLv3 License.
-
-## Releases
-The package version is tracked at `amisc.__init__.__version__`. You should not edit this value. The version will be 
-increased on a case-by-case basis and released depending on the changes being merged.
+By contributing, you agree that your contributions will be licensed under the GPL-3.0 license.