Factor out CMIP recipe stages (#27)

* Factor out CMIP recipe stages

Moving more of the CMIP6 feedstock specific transforms into this repo

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update cmip_transforms.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add CI and add dependencies

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/ci.yaml

@@ -0,0 +1,47 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "*"
+  schedule:
+    - cron: "0 13 * * 1"
+
+jobs:
+  build:
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: 🫙 Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # checkout tags (which is not done by default)
+      - name: 🔁 Setup Python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - name: 🎯 Check cache hit
+        run: echo '${{ steps.setup-python.outputs.cache-hit }}'
+      - name: 🌈 Install leap-data-management-utils package
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e  ".[test]"
+      - name: 🔎 Check current version
+        run: python -c "import leap_data_management_utils; print(leap_data_management_utils.__version__)"
+      - name: 🏄‍♂️ Run Tests
+        shell: bash -l {0}
+        run: |
+          py.test leap_data_management_utils/tests -v

leap_data_management_utils/cmip_transforms.py

@@ -8,7 +8,9 @@
 import apache_beam as beam
 import zarr
 from google.cloud import bigquery
+from pangeo_forge_recipes.transforms import Indexed, T
 
+from leap_data_management_utils.cmip_testing import test_all
 from leap_data_management_utils.data_management_transforms import BQInterface
 
 
@@ -192,3 +194,63 @@ def _log_to_bigquery(self, store: zarr.storage.FSStore) -> zarr.storage.FSStore:
 
     def expand(self, pcoll: beam.PCollection) -> beam.PCollection:
         return pcoll | beam.Map(self._log_to_bigquery)
+
+
+@dataclass
+class Preprocessor(beam.PTransform):
+    """
+    Preprocessor for xarray datasets.
+    Set all data_variables except for `variable_id` attrs to coord
+    Add additional information
+
+    """
+
+    @staticmethod
+    def _keep_only_variable_id(item: Indexed[T]) -> Indexed[T]:
+        """
+        Many netcdfs contain variables other than the one specified in the `variable_id` facet.
+        Set them all to coords
+        """
+        index, ds = item
+        print(f'Preprocessing before {ds =}')
+        new_coords_vars = [var for var in ds.data_vars if var != ds.attrs['variable_id']]
+        ds = ds.set_coords(new_coords_vars)
+        print(f'Preprocessing after {ds =}')
+        return index, ds
+
+    @staticmethod
+    def _sanitize_attrs(item: Indexed[T]) -> Indexed[T]:
+        """Removes non-ascii characters from attributes see https://github.com/pangeo-forge/pangeo-forge-recipes/issues/586"""
+        index, ds = item
+        for att, att_value in ds.attrs.items():
+            if isinstance(att_value, str):
+                new_value = att_value.encode('utf-8', 'ignore').decode()
+                if new_value != att_value:
+                    print(
+                        f'Sanitized datasets attributes field {att}: \n {att_value} \n ----> \n {new_value}'
+                    )
+                    ds.attrs[att] = new_value
+        return index, ds
+
+    def expand(self, pcoll: beam.PCollection) -> beam.PCollection:
+        return (
+            pcoll
+            | 'Fix coordinates' >> beam.Map(self._keep_only_variable_id)
+            | 'Sanitize Attrs' >> beam.Map(self._sanitize_attrs)
+        )
+
+
+@dataclass
+class TestDataset(beam.PTransform):
+    """
+    Test stage for data written to zarr store
+    """
+
+    iid: str
+
+    def _test(self, store: zarr.storage.FSStore) -> zarr.storage.FSStore:
+        test_all(store, self.iid)
+        return store
+
+    def expand(self, pcoll: beam.PCollection) -> beam.PCollection:
+        return pcoll | 'Testing - Running all tests' >> beam.Map(self._test)

pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
     "google-cloud-bigquery",
     "pandas",
     "pangeo-forge-esgf",
+    "pangeo-forge-recipes",
     "pydantic-core",
     "pydantic>=2",
     "pyyaml",
@@ -40,7 +41,12 @@ dependencies = [
 
 [project.optional-dependencies]
 test = [
-    "pre-commit",
+    "pytest"
+]
+
+dev = [
+    "leap-data-leap_data_management_utils[test]",
+    "pre-commit"
 ]