From b4ffd241a40cfccaf630a5100f6f38dc1c368c3c Mon Sep 17 00:00:00 2001
From: Tyler Sutterley <tsutterl@uw.edu>
Date: Fri, 9 Jan 2026 10:52:37 -0800
Subject: [PATCH] add pixi build for easy install

---
 .gitattributes                         |    2 +
 .github/workflows/python-publish.yml   |    4 +-
 .github/workflows/python-request.yml   |   36 +-
 .gitignore                             |    1 +
 pixi.lock                              | 8110 ++++++++++++++++++++++++
 pointCollection/scripts/fix_indices.py |    2 +-
 pyproject.toml                         |   48 +
 7 files changed, 8178 insertions(+), 25 deletions(-)
 create mode 100644 .gitattributes
 create mode 100644 pixi.lock

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..887a2c1
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index aaa92f8..f7ea262 100755
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -21,12 +21,12 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build setuptools wheel twine
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*
 
diff --git a/.github/workflows/python-request.yml b/.github/workflows/python-request.yml
index 574cf78..7f3b53a 100755
--- a/.github/workflows/python-request.yml
+++ b/.github/workflows/python-request.yml
@@ -13,39 +13,31 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.11]
     env:
       OS: ${{ matrix.os }}
-      PYTHON: ${{ matrix.python-version }}
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up mamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        micromamba-version: 'latest'
-        environment-file: environment.yml
-        init-shell: bash
-        environment-name: pointCollection
-        cache-environment: true
-        post-cleanup: 'all'
-        create-args: >-
-          python=${{ matrix.python-version }}
-          flake8
-          pytest
-          pytest-cov
-          cython
+    - name: Set up pixi environment
+      uses: prefix-dev/setup-pixi@v0.9.1
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        pixi run lint
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        pixi run lint "--exit-zero --max-complexity=10 --max-line-length=127"
+    - name: Install pointCollection
+      run: |
+        # install the package in editable mode
+        pip install --no-deps --editable .
     - name: Test with pytest
       run: |
-        pip install --no-deps .
-        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        pytest --verbose --capture=no 
+        pixi run coverage
+    - name: Archive code coverage results
+      uses: actions/upload-artifact@v4
+      with:
+        name: code-coverage-report-${{ matrix.os }}
+        path: coverage.xml
diff --git a/.gitignore b/.gitignore
index 029ae89..07dcdae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -17,6 +17,7 @@ eggs/
 lib/
 lib64/
 parts/
+.pixi/
 sdist/
 var/
 wheels/
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 0000000..b5c6c74
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,8110 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.12.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py314h5bd0f2a_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.0.5-pyh29332c3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyhcf101f3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
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+      - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.1.4-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.5-py314hc02f841_0.conda
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diff --git a/pointCollection/scripts/fix_indices.py b/pointCollection/scripts/fix_indices.py
index 46005d9..6c6708e 100755
--- a/pointCollection/scripts/fix_indices.py
+++ b/pointCollection/scripts/fix_indices.py
@@ -5,7 +5,7 @@
 import glob
 import re
 
-main():
+def main():
 
     file_re=re.compile('file_\d+')
 
diff --git a/pyproject.toml b/pyproject.toml
index dc260c7..eb4c3eb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -81,3 +81,51 @@ python_files = [
 testpaths = [
     "test"
 ]
+
+[tool.pixi.workspace]
+name = "pointCollection"
+authors = ["pointCollection contributors"]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64", "win-64"]
+
+[tool.pixi.pypi-dependencies]
+pointCollection = { path = ".", editable = true }
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+dev = { features = ["dev"], solve-group = "default" }
+
+[tool.pixi.tasks.jupyter]
+cmd = "jupyter-notebook"
+cwd = "notebooks"
+description = "Start Jupyter Notebooks in the notebooks directory"
+
+[tool.pixi.tasks.export-env]
+args = [ { "arg" = "flags", "default" = "" } ]
+cmd = "pixi workspace export conda-environment {{ flags }} > environment.yml"
+description = "Export workspace to a conda environment file" 
+
+[tool.pixi.feature.dev.tasks.coverage]
+cmd = "pytest --cov=pointCollection --junitxml=pytest.xml --cov-report=xml test"
+description = "Run the pytest suite and create coverage reports"
+
+[tool.pixi.feature.dev.tasks.lint]
+args = [ { "arg" = "flags", "default" = "--select=E9,F63,F7,F82 --show-source" }, { "arg" = "directory", "default" = "." } ]
+cmd = "flake8 {{ directory }} --count {{ flags }} --statistics --extend-exclude 'build/,*.ipynb_checkpoints/,.pixi/'"
+description = "Run flake8 to check for compilation errors"
+
+[tool.pixi.dependencies]
+gdal = "*"
+h5py = "*"
+matplotlib-base = "*"
+netCDF4 = "*"
+notebook = "*"
+numpy = "*"
+pyproj = "*"
+scipy = ">=1.10.1"
+shapely = "*"
+
+[tool.pixi.feature.dev.dependencies]
+flake8 = "*"
+pytest = ">=4.6"
+pytest-cov = "*"