Merge branch 'develop' into feature/issue-169-large-file-orders

.github/workflows/build-pipeline.yml

@@ -5,7 +5,7 @@ name: Build
 on:
   # Triggers the workflow on push events
   push:
-    branches: [ develop, release/**, main, feature/**, issue/**, issues/** ]
+    branches: [ develop, release/**, main, feature/**, issue/**, issues/** , docs/**]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -51,7 +51,8 @@ jobs:
         if: |
           ${{ startsWith(github.ref, 'refs/heads/issue') }}      ||
           ${{ startsWith(github.ref, 'refs/heads/dependabot/') }} ||
-          ${{ startsWith(github.ref, 'refs/heads/feature/') }}
+          ${{ startsWith(github.ref, 'refs/heads/feature/') }} ||
+          ${{ startsWith(github.ref, 'refs/heads/docs/') }}
         run: |
           new_ver="${{ steps.get-version.outputs.current_version }}+$(git rev-parse --short ${GITHUB_SHA})"
           poetry version $new_ver

CHANGELOG.md

@@ -11,10 +11,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [Issue #185](https://github.com/nasa/stitchee/issues/185): Added arguments for temporary file copies and overwriting output file in main stitchee function
 - [Issue #181](https://github.com/nasa/stitchee/issues/181): Add a group delimiter argument
 - [Issue #134](https://github.com/nasa/stitchee/issues/134): Add an integration test that runs stitchee on files first subsetted by the operational Harmony subsetter
+- [Issue #194](https://github.com/nasa/stitchee/issues/194): Add page about the SAMBAH service chain to the Readthedocs documentation
 ### Changed
 ### Deprecated
 ### Removed
 ### Fixed
+- [Issue #204](https://github.com/nasa/stitchee/issues/204): Fix integration test failure
 
 ## [1.2.1]
 

docs/sambah_readme.md

@@ -0,0 +1,27 @@
+# SAMBAH
+
+The Subsetter And Multi-dimensional Batched Aggregation in Harmony (SAMBAH) chain
+executes several services:
+
+1. **CMR Query**: Retrieves information from the Common Metadata Repository (CMR) ([source](https://github.com/nasa/harmony/tree/main/services/query-cmr))
+2. **PODAAC L2-Subsetter** (optional): Performs subsetting on level-2 data granules ([source](https://github.com/podaac/l2ss-py))
+3. **Batchee** (optional): Groups together filenames so that further operations (such as concatenation) can be performed separately on each group of files ([source](https://github.com/nasa/batchee))
+4. **Stitchee** (optional): Concatenates netCDF data along an existing dimension ([source](https://github.com/nasa/stitchee))
+5. **PODAAC CONCISE** (optional): Concatenates netCDF data along a newly created dimension ([source](https://github.com/podaac/concise))
+
+## Known Limitations
+
+- Panoply is unable to plot results when coordinate arrays contain null values on the edges.
+- Polygons and other Shapefile formats are not supported for subsetting. Support for this is in development.
+- A request for a single granule proceeds through the entire chain. Thus, the following modifications are made even though the data are not concatenated: (i) the filename is changed to the granule's collection ID + "_merged" and (ii) a history attribute is added.
+
+## Missions supported
+
+The SAMBAH service chain is currently configured to work only with data collections
+from the Tropospheric Emissions: Monitoring of Pollution (TEMPO) mission.
+
+## References
+
+- Service (UMM-S) record ID in CMR: [S2940253910-LARC_CLOUD](https://cmr.earthdata.nasa.gov/search/services.umm_json?concept_id=S2940253910-LARC_CLOUD)
+- Service versions in Harmony Production: <https://harmony.earthdata.nasa.gov/versions>
+- Harmony API - Service Capabilities: <https://harmony.earthdata.nasa.gov/docs#service-capabilities>

mkdocs.yml

@@ -22,6 +22,8 @@ theme:
 nav:
   - OVERVIEW:
       - "Readme": "index.md"
+  - SAMBAH Service Chain:
+      - "Description and known limitations": "sambah_readme.md"
   - EXAMPLES:
       - "Usage of STITCHEE via Harmony": "tutorial_examples.ipynb"
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "stitchee"
-version = "1.3.0a6"
+version = "1.3.0a12"
 description = "NetCDF4 Along-existing-dimension Concatenation Service"
 authors = ["Daniel Kaufman <daniel.kaufman@nasa.gov>"]
 readme = "README.md"

tests/integration/test_concat_with_subsetting_first.py

@@ -17,6 +17,7 @@ def test_concat_with_subsetting_first(temp_output_dir):
             "stop": dt.datetime(2024, 5, 13, 20, 0, 0),
         },
         spatial=BBox(-130, 30, -115, 35),
+        concatenate=False,
     )
     if not request.is_valid():
         raise RuntimeError
@@ -29,6 +30,7 @@ def test_concat_with_subsetting_first(temp_output_dir):
     # Download the result files.
     futures = harmony_client.download_all(job_id, directory=str(temp_output_dir))
     file_names = [f.result() for f in futures]
+    print(f"File names: {file_names}")
 
     # Try concatenating the resulting files
     output_path = stitchee(