Revert "Initial pixi attempt"

This reverts commit 261bfe1.

.github/workflows/lint.yml

@@ -3,32 +3,25 @@ name: Lint
 on: [push, pull_request]
 
 jobs:
-  lint:
+  build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        environment: [py312]
     steps:
-     - uses: prefix-dev/setup-pixi@v0.8.1
-       with:
-         environments: ${{ matrix.environment }}
-         pixi-version: v0.39.0
-         cache: true
-         auth-host: prefix.dev
-         auth-token: ${{ secrets.PREFIX_DEV_TOKEN }}
-     - run: pixi run lint-check
-
-  test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        environment: [py311, py312, py313]
-    steps:
-     - uses: prefix-dev/setup-pixi@v0.8.1
-       with:
-         environments: ${{ matrix.environment }}
-         pixi-version: v0.39.0
-         cache: true
-         auth-host: prefix.dev
-         auth-token: ${{ secrets.PREFIX_DEV_TOKEN }}
-     - run: pixi run test
+    - 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

.github/workflows/python-app.yml

@@ -0,0 +1,32 @@
+# This workflow will install Python dependencies, run tests
+
+name: Test
+
+# on:
+#   push:
+#     branches: [ "main" ]
+#   pull_request:
+#     branches: [ "main" ]
+on: [push, pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+          python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[test]
+    - name: Test with pytest
+      run: pytest

.gitignore

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

CONTRIBUTING.md

@@ -2,36 +2,52 @@
 
 All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome.
 
-## How do I report an issue?
+## Bug Reports and Enhancement Requests
 
-Using the [Github issues](https://github.com/gtri/upstage/issues) feature, please explain in as much detail as possible:
+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.
 
-1. The Python version and environment
-2. How UPSTAGE was installed
-3. A minimum working example of the bug, along with any output/errors.
+## Create a Fork
 
-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.
+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.
 
-## How do I put in a good PR?
+## Making Code Changes
 
-### Create a Fork
+If you wish to contribute to UPSTAGE, we ask that you follow these steps to ensure code quality.
 
-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.
+### Development Environment Setup
+
+First, create a Python 3.11 or 3.12 environment through your preferred means (conda, mamba, venv, e.g.).
 
-### Set Up the Development Environment
+```bash
+python -m venv /path/to/upstage_dev/.venv
+```
 
-1. Get [`pixi`](https://pixi.sh).
-2. Use `pixi run -e dev start`
+Ensure that the pip version is >= `21.3` to allow editable installations with just `pyproject.toml`
+and the `flit` backend.
 
-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.
+```bash
+python -m pip install --upgrade pip
+```
 
-### Code Quality and Testing
+Next, clone the repo locally:
 
-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.
+```bash
+cd /path/to/upstage_des
+git clone https://github.com/gtri/upstage.git
+cd upstage
+```
+
+Install UPSTAGE to your environment with
+
+```bash
+pip install -e '.[docs,lint,test]'
+```
+
+### Style Guide
+
+For style, see [STYLE_GUIDE](STYLE_GUIDE.md).
+
+### Code Quality
 
 Code quality is enforced using the following tools:
 
@@ -40,9 +56,41 @@ 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
 
-### Style Guide
+These tools are run as follows, allowing for auto-fixing:
 
-For style, see [STYLE_GUIDE](STYLE_GUIDE.md).
+```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
+```
+
+Then the docs can be loaded from `./build/docs/index.html`
 
 ## Making Pull Requests
 

README.md

@@ -44,13 +44,40 @@ 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 contribute or set up a develpment environment?
+## 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?
 
-See [CONTRIBUTING][contributing].
+To set up a suitable development environment, see [CONTRIBUTING][contributing].
 
 For information on how to style your code, see the [Style Guide][style-guide].
 

docs/source/index.md

@@ -47,6 +47,25 @@ 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}
@@ -58,8 +77,7 @@ user_guide/index
 
 ## Contributing
 
-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))
+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))
 
 ## License and Attribution