Initial pixi attempt (#14)

Moving docs and testing to pixi. Updated UPSTAGE documentation to match.

Author: JamesArruda

Diff for: .github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly # or daily, weekly
+    groups:
+      dependencies:
+        patterns:
+          - '*'

Diff for: .github/workflows/documentation.yml

@@ -10,16 +10,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: prefix-dev/setup-[email protected]
         with:
-          python-version: '3.11'
-          cache: 'pip'
-      - name: Install dependencies
-        run: pip install .[docs]
-      - name: Build autodocs
-        run: sphinx-apidoc -o ./docs/source/auto ./src/upstage_des ./src/upstage_des/test
-      - name: Sphinx build
-        run: sphinx-build -b html docs/source _build
+          manifest-path: pixi.toml
+          pixi-version: v0.39.0
+          cache: true
+      - run: pixi run -e py312 build_html_docs
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v4
         if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}

Diff for: .github/workflows/lint.yml

@@ -1,27 +1,43 @@
 name: Lint
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: ['*']
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.head_ref || github.ref_name }} 
+  cancel-in-progress: true
 
 jobs:
-  build:
+  check:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        environment: [py312]
+    steps:
+     - uses: actions/checkout@v4
+     - uses: prefix-dev/[email protected]
+       with:
+         environments: ${{ matrix.environment }}
+         manifest-path: pixi.toml
+         pixi-version: v0.39.0
+         cache: true
+     - run: pixi run -e ${{ matrix.environment }} lint-check
+
+  test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        environment: [py311, py312, py313]
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.11"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install .[lint]
-    - name: Verify pyproject format ran
-      run: pyproject-fmt --check pyproject.toml 
-    - name: Verify ssort ran
-      run: ssort --check src
-    - name: Verify Ruff Formatter ran
-      run: ruff format --check src
-    - name: Run Ruff linter
-      run: ruff check --output-format=github src
-    - name: Run mypy
-      run: mypy --show-error-codes -p upstage_des
+     - uses: actions/checkout@v4
+     - uses: prefix-dev/[email protected]
+       with:
+         environments: ${{ matrix.environment }}
+         manifest-path: pixi.toml
+         pixi-version: v0.39.0
+         cache: true
+     - run: pixi run -e ${{ matrix.environment }} test

Diff for: .github/workflows/python-app.yml

@@ -102,12 +102,13 @@ celerybeat-schedule
 # mypy
 .mypy_cache/
 
-# doit
+# automation things
 .doit*
 .env
 .report.json
 .venv
 .scripts
+.pixi
 
 # VSCode
 .vscode

Diff for: .gitignore

@@ -2,52 +2,36 @@
 
 All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome.
 
-## Bug Reports and Enhancement Requests
+## How do I report an issue?
 
-Bug reports and enhancement requests are an important part of making UPSTAGE more stable and are curated though [Github issues](https://github.com/gtri/upstage/issues). If you wish to contribute, then please be sure there is an active issue to work against and there is not then go ahead and create one.
+Using the [Github issues](https://github.com/gtri/upstage/issues) feature, please explain in as much detail as possible:
 
-## Create a Fork
+1. The Python version and environment
+2. How UPSTAGE was installed
+3. A minimum working example of the bug, along with any output/errors.
 
-You will need your own copy of UPSTAGE (aka fork) to work on the code. Go to the [UPSTAGE project page](https://github.com/gtri/upstage) and hit the `Fork` button.
-
-## Making Code Changes
-
-If you wish to contribute to UPSTAGE, we ask that you follow these steps to ensure code quality.
-
-### Development Environment Setup
-
-First, create a Python 3.11 or 3.12 environment through your preferred means (conda, mamba, venv, e.g.).
-
-```bash
-python -m venv /path/to/upstage_dev/.venv
-```
+Bug reports and enhancement requests are an important part of making UPSTAGE more stable. If you wish to contribute, then please be sure
+there is an active issue to work against. If there is not one please create one.
 
-Ensure that the pip version is >= `21.3` to allow editable installations with just `pyproject.toml`
-and the `flit` backend.
+## How do I put in a good PR?
 
-```bash
-python -m pip install --upgrade pip
-```
+### Create a Fork
 
-Next, clone the repo locally:
+You will need your own copy of UPSTAGE (aka fork) to work on the code. Go to the [UPSTAGE project page](https://github.com/gtri/upstage) and hit the `Fork` button.
 
-```bash
-cd /path/to/upstage_des
-git clone https://github.com/gtri/upstage.git
-cd upstage
-```
+### Set Up the Development Environment
 
-Install UPSTAGE to your environment with
+1. Get [`pixi`](https://pixi.sh).
+2. Use `pixi run -e dev start`
 
-```bash
-pip install -e '.[docs,lint,test]'
-```
+That will give you an editable install in to the `dev` local environment managed by `pixi`. It also runs the lint,
+tests, and builds the docs. Any errors from that command should be reported as issues.
 
-### Style Guide
+### Code Quality and Testing
 
-For style, see [STYLE_GUIDE](STYLE_GUIDE.md).
-
-### Code Quality
+1. Use `pixi r -e dev lint-fix`, and `pixi r -e dev lint-check` to run style/formatting/typing checks.
+2. Use `pixi r -e dev test` to run the tests
+3. If you modify the docs, use `pixi r -e dev build_html_docs` to ensure they build.
 
 Code quality is enforced using the following tools:
 
@@ -56,41 +40,9 @@ Code quality is enforced using the following tools:
 3. [`ruff`](https://docs.astral.sh/ruff/) - linter and code formatter
 4. [`mypy`](https://mypy-lang.org/) - static type checker
 
-These tools are run as follows, allowing for auto-fixing:
-
-```bash
-# 3 formatters, linting, then type checking
-pyproject-fmt pyproject.toml
-ssort src
-ruff format src
-ruff check --fix src
-mypy --show-error-codes -p upstage_des
-```
-
-### Testing
-
-To run the unit tests in `src/upstage_des/test`, run:
-
-```bash
-pytest
-```
-
-from the top level of the repo.
-
-Test reports will be in `./build/reports`
-
-### Building the documentation
-
-Documentation is built from autodocs first, then the source build.
-
-From the top level of the repo:
-
-```bash
-sphinx-apidoc -o ./docs/source/auto ./src/upstage_des ./src/upstage_des/test
-sphinx-build -a -E -b html ./docs/source ./build/docs
-```
+### Style Guide
 
-Then the docs can be loaded from `./build/docs/index.html`
+For style, see [STYLE_GUIDE](STYLE_GUIDE.md).
 
 ## Making Pull Requests
 

Diff for: CONTRIBUTING.md

@@ -44,40 +44,13 @@ In an environment (Python 3.11+) of your choice:
 pip install upstage-des
 ```
 
-### Installation from source
-
-Alternatively, you can download UPSTAGE and install it manually. Clone, or download the archive and extract it. From the extraction location (and within a suitable Python environment):
-
-```console
-python -m pip install .
-```
-
-(or just `pip install .`)
-
-### Installation for tests
-
-To run the tests: clone locally, install into a fresh environment, and run using:
-
-```console
-pip install -e .[test]
-pytest
-```
-
 ## Documentation
 
 See the [documentation][upstage-docs] for tutorials and additional details.
 
-## How do I report an issue?
-
-Using the issue feature, please explain in as much detail as possible:
-
-1. The Python version and environment
-2. How UPSTAGE was installed
-3. A minimum working example of the bug, along with any output/errors.
-
-## How do I contribute?
+## How do I contribute or set up a develpment environment?
 
-To set up a suitable development environment, see [CONTRIBUTING][contributing].
+See [CONTRIBUTING][contributing].
 
 For information on how to style your code, see the [Style Guide][style-guide].
 

Diff for: README.md

@@ -47,25 +47,6 @@ Alternatively, you can download UPSTAGE and install it manually. Clone, or downl
 
 (or just `pip install .`)
 
-### Installation for running tests
-
-Note that the tests include the two full examples from the documentation.
-
-```console
-(venv) $ pip install upstage-des[test]
-(venv) $ pytest
-```
-
-### Installation for building docs
-
-Unless you're adding to the codebase, you won't need to run the `sphinx-apidoc` command.
-
-```console
-(venv) $ pip install upstage-des[docs]
-(venv) $ sphinx-apidoc -o .\docs\source\auto .\src\upstage_des\ .\src\upstage_des\test\
-(venv) $ sphinx-build -b html .\docs\source\ .\docs\build\
-```
-
 ## User Guide
 
 ```{toctree}
@@ -77,7 +58,8 @@ user_guide/index
 
 ## Contributing
 
-To contribute to UPSTAGE, or to learn the steps for building documentation and running tests, see [CONTRIBUTING.MD](https://github.com/gtri/upstage/blob/main/CONTRIBUTING.md))
+To contribute to UPSTAGE, or to learn the steps for building documentation, running tests, and putting
+in PRs, see [CONTRIBUTING.MD](https://github.com/gtri/upstage/blob/main/CONTRIBUTING.md))
 
 ## License and Attribution