From 9241c4623e136d450b121751cf491b181d98836b Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Thu, 16 May 2024 15:11:01 -0400 Subject: [PATCH 1/5] add an initial sambah_readme.md to the docs --- docs/sambah_readme.md | 25 +++++++++++++++++++++++++ mkdocs.yml | 2 ++ 2 files changed, 27 insertions(+) create mode 100644 docs/sambah_readme.md diff --git a/docs/sambah_readme.md b/docs/sambah_readme.md new file mode 100644 index 0000000..2733b58 --- /dev/null +++ b/docs/sambah_readme.md @@ -0,0 +1,25 @@ +# 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**: 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**: Concatenates netCDF data along an existing dimension ([source](https://github.com/nasa/stitchee)) +5. **PODAAC CONCISE**: Concatenates netCDF data along a newly created dimension ([source](https://github.com/podaac/concise)) + +## Known Limitations + +- + +## 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: +- Harmony API - Service Capabilities: diff --git a/mkdocs.yml b/mkdocs.yml index 8e65e07..4af2998 100644 --- a/mkdocs.yml +++ b/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" From c2ff92ed3bdecd63a0c3e8010ac7cbee247ddb1d Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Thu, 16 May 2024 15:21:36 -0400 Subject: [PATCH 2/5] bump versions on docs/ branches, but don't run integration test --- .github/workflows/build-pipeline.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 8db776f..32218e0 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.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 From 70fc6fd59b1c96db2c42dd7cfd232a78acbd9957 Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Fri, 17 May 2024 12:14:40 -0400 Subject: [PATCH 3/5] Update "known limitations" in sambah_readme.md --- docs/sambah_readme.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/sambah_readme.md b/docs/sambah_readme.md index 2733b58..29da7d8 100644 --- a/docs/sambah_readme.md +++ b/docs/sambah_readme.md @@ -11,7 +11,9 @@ executes several services: ## 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 modifying the filename and adding a history attribute. ## Missions supported From f834ec39db166d056513c4b0c3a2123596cd92c9 Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Fri, 17 May 2024 13:32:23 -0400 Subject: [PATCH 4/5] Update sambah_readme.md --- docs/sambah_readme.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/sambah_readme.md b/docs/sambah_readme.md index 29da7d8..267983b 100644 --- a/docs/sambah_readme.md +++ b/docs/sambah_readme.md @@ -5,15 +5,15 @@ 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**: 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**: Concatenates netCDF data along an existing dimension ([source](https://github.com/nasa/stitchee)) -5. **PODAAC CONCISE**: Concatenates netCDF data along a newly created dimension ([source](https://github.com/podaac/concise)) +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 modifying the filename and adding a history attribute. +- 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 From 02dde061e212f5176999be85c671c9e3311ea5d5 Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Fri, 17 May 2024 13:35:21 -0400 Subject: [PATCH 5/5] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 826a866..976e0da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ 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