chore: switch to pixi and install all deps except for gdal from pypi.

.github/workflows/test.yml

@@ -17,45 +17,23 @@ concurrency:
 
 jobs:
   test:
-    name: python ${{ matrix.python-version }}, ${{ matrix.os }}
+    name: python ${{ matrix.environment }}, ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
-    env:
-      REPO_NAME: ${{ github.event.repository.name }}
-    defaults:
-      run:
-        shell: bash -l {0}
     strategy:
       matrix:
-        python-version: [3.9, '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
+        environment: [test39, test313]
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set environment variables
-      run: |-
-        echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-    - name: Setup micromamba
-      uses: mamba-org/setup-micromamba@v2
-      env:
-        DATE: ${{ steps.date.outputs.time }}
+    - uses: prefix-dev/[email protected]
       with:
-        environment-file: ci/requirements/environment.yml
-        environment-name: ${{ env.REPO_NAME }}-tests
-        create-args: >-
-          python=${{ matrix.python-version }}
-        post-cleanup: all
-        cache-environment: true
-        cache-environment-key: ${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.DATE}}
-    - name: Install error reporter
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
-      run: |
-        python -m pip install pytest-github-actions-annotate-failures
-    - name: Install the package
-      run: |-
-        python -m pip install --no-deps .
-    - name: Run pytest
-      run: |-
-        pytest --cov --cov-append --cov-branch --cov-report=xml --junitxml=junit.xml
+        pixi-version: v0.39.5
+        environments: ${{ matrix.environment }}
+        activate-environment: ${{ matrix.environment }}
+    - name: Run pixi
+      run: pixi r test
+
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       with:

.pre-commit-config.yaml

@@ -34,7 +34,7 @@ repos:
     name: Sort top level statements with ssort
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.6
+  rev: v0.9.0
   hooks:
   - id: ruff
     name: Linting with Ruff

CONTRIBUTING.md

@@ -119,14 +119,11 @@ Ready to contribute? Here's how to set up Seamless3DEP for local development.
     git remote add upstream [email protected]:hyriver/seamless-3dep.git
     ```
 
-1. Install your local copy into a virtualenv. Assuming you have `micromamba` installed,
-    this is how you can set up your fork for local development:
+1. Install [Pixi](https://pixi.sh/latest/) then install the development environments:
 
     ```console
     cd seamless-3dep/
-    mamba env create -f ci/requirements/environment-dev.yml
-    mamba activate seamless-3dep-dev
-    python -m pip install . --no-deps
+    pixi install -e dev
     ```
 
 1. Create a branch for local development:
@@ -136,7 +133,12 @@ Ready to contribute? Here's how to set up Seamless3DEP for local development.
     git push
     ```
 
-1. Now you can make your changes locally, make sure to add a description of the changes to `HISTORY.rst` file and add extra tests, if applicable, to `tests` folder. Also, make sure to give yourself credit by adding your name at the end of the item(s) that you add in the history like this `By Taher Chegini <https://github.com/hyriver>`. Then, fetch the latest updates from the remote and resolve any merge conflicts:
+1. Now you can make your changes locally, make sure to add a description of the changes
+    to `CHANGELOG.md` file based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/)
+    and add extra tests, if applicable, to `tests` folder. Also,
+    make sure to give yourself credit by adding your name at the end of the item(s)
+    that you add in the history like this `by [Your Name](https://github.com/your_handle)`.
+    Then, fetch the latest updates from the remote and resolve any merge conflicts:
 
     ```console
     git fetch upstream
@@ -146,41 +148,27 @@ Ready to contribute? Here's how to set up Seamless3DEP for local development.
 1. Then create a new environment for linting and another for testing:
 
     ```console
-    mamba create -n py11 python=3.11 nox tomli pre-commit codespell gdal
-    mamba activate py11
-    nox -s pre-commit
-    nox -s type-check
-    mamba create -n py38 python=3.8 nox tomli pre-commit codespell gdal
-    mamba activate py38
-    nox -s tests
+    pixi r lint
+    pixi r typecheck
+    pixi r -e test39 test
+    pixi r -e test313 test
     ```
 
-    Note that if Python 3.11 is already installed on your system, you can skip creating the `py11` environment and just use your system's Python 3.11 to run the linting and type-checking tests, like this:
+1. If you are making breaking changes make sure to reflect them in the
+    documentation, `README.md`, and tests if necessary.
 
-    ```console
-    mamba create -n py38 python=3.8 nox tomli pre-commit codespell gdal
-    mamba activate py38
-    nox
-    ```
-
-1. If you are making breaking changes make sure to reflect them in the documentation, `README.rst`, and tests if necessary.
-
-1. Commit your changes and push your branch to GitHub. Start the commit message with `ENH:`, `BUG:`, `DOC:` to indicate whether the commit is a new feature, documentation related, or a bug fix. For example:
+1. Commit your changes and push your branch to GitHub following
+    [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+    specification. For example:
 
     ```console
     git add .
-    git commit -m "ENH: A detailed description of your changes."
+    git commit -m "feat: a detailed description of your changes."
     git push origin name-of-your-branch
     ```
 
 1. Submit a pull request through the GitHub website.
 
-Note that to run a subset of tests you can use:
-
-```console
-nox -s tests -- -n=1 -k "test_name1 or test_name2"
-```
-
 ### Improving The Documentation
 
 Seamless3DEP could always use more documentation, whether as part of the

pyproject.toml

@@ -37,21 +37,35 @@ dynamic = [
 dependencies = [
   "rasterio",
 ]
-
+optional-dependencies.dev = [
+  "geopandas>=1",
+  "ipykernel",
+  "ipywidgets",
+  "pytest",
+  "pywbt>=0.2.8",
+  "rasterio>=1.4.3",
+  "rioxarray",
+]
 optional-dependencies.docs = [
   "black",
-  "mdx-truly-sane-lists",
   "mkdocs",
   "mkdocs-jupyter",
   "mkdocs-material",
   "mkdocstrings-python",
 ]
+optional-dependencies.lint = [
+  "codespell",
+  "pre-commit",
+]
 optional-dependencies.test = [
   "coverage[toml]",
   "pytest",
   "pytest-cov",
   "pytest-sugar",
 ]
+optional-dependencies.typecheck = [
+  "pyright",
+]
 urls.Changelog = "https://seamless-3dep.readthedocs.io/latest/CHANGELOG"
 urls.CI = "https://github.com/hyriver/seamless-3dep/actions"
 urls.Homepage = "https://seamless-3dep.readthedocs.io"
@@ -69,7 +83,7 @@ packages = [
 target-version = "py39"
 line-length = 100
 
-exclude = [ "__pycache__", "benchmarks" ]
+exclude = [ ".pixi", "__pycache__" ]
 
 lint.select = [
   # flake8-bugbear
@@ -185,7 +199,16 @@ skip = "__pycache__,_build,.mypy_cache,.git,./htmlcov,.pixi,pixi.lock,**.ipynb"
 ignore-words-list = "gage,gages"
 
 [tool.pytest.ini_options]
-addopts = "-v --cov-branch --cov-report=xml --durations=5"
+addopts = [
+  "--import-mode=importlib",
+  "-v",
+  "--cov",
+  "--cov-append",
+  "--cov-branch",
+  "--cov-report=xml",
+  "--junitxml=junit.xml",
+  "--durations=5",
+]
 doctest_optionflags = 'NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL NUMBER'
 testpaths = [
   "tests",
@@ -231,3 +254,47 @@ reportUntypedFunctionDecorator = false
 reportAttributeAccessIssue = false
 reportInvalidTypeForm = false
 typeCheckingMode = "strict"
+
+[tool.pixi.feature.docs.tasks]
+build-docs = "mkdocs build --strict"
+docs = "mkdocs serve"
+
+[tool.pixi.project]
+channels = [ "conda-forge" ]
+platforms = [ "linux-64", "osx-64", "osx-arm64", "win-64" ]
+
+[tool.pixi.pypi-dependencies]
+seamless_3dep = { path = ".", editable = true }
+
+[tool.pixi.feature.dev.dependencies]
+gdal = "*"
+
+[tool.pixi.feature.test.dependencies]
+gdal = "*"
+
+[tool.pixi.feature.py39.dependencies]
+python = "~=3.9.0"
+
+[tool.pixi.feature.py313.dependencies]
+python = "~=3.13.0"
+
+[tool.pixi.environments]
+dev = { features = [ "dev", "py313" ] }
+test39 = { features = [ "test", "py39" ] }
+test313 = { features = [ "test", "py313" ] }
+typecheck = { features = [ "typecheck", "py313" ] }
+lint = { features = [ "lint", "py313" ], no-default-feature = true }
+docs = { features = [ "docs", "dev", "py313" ] }
+
+[tool.pixi.feature.test.tasks]
+test = "pytest"
+report = { cmd = [ "coverage", "report" ], depends-on = [ "test" ] }
+html = { cmd = [ "coverage", "html" ], depends-on = [ "report" ] }
+
+[tool.pixi.feature.lint.tasks]
+lint = "pre-commit run --all-files"
+pcupdate = "pre-commit autoupdate"
+spell = "codespell -w"
+
+[tool.pixi.feature.typecheck.tasks]
+typecheck = "pyright"