Merge pull request #140 from podaac/release/2.3.0

Release/2.3.0

Author: jamesfwood

.github/workflows/build-pipeline.yml

@@ -4,7 +4,7 @@ name: Build
 on:
   # Triggers the workflow on push events
   push:
-    branches: [ develop, release/**, main, feature/** ]
+    branches: [ develop, release/**, main, feature/**, issue/**, issues/**, dependabot/** ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -36,7 +36,10 @@ jobs:
           echo "pyproject_name=$(poetry version | awk '{print $1}')" >> $GITHUB_ENV
       - name: Bump pre-alpha version
         # If triggered by push to a feature branch
-        if: ${{ startsWith(github.ref, 'refs/heads/feature/') }}
+        if: |
+          ${{ startsWith(github.ref, 'refs/heads/issue') }}      ||
+          ${{ startsWith(github.ref, 'refs/heads/dependabot/') }} ||
+          ${{ startsWith(github.ref, 'refs/heads/feature/') }}
         run: |
           new_ver="${{ steps.get-version.outputs.current_version }}+$(git rev-parse --short ${GITHUB_SHA})"
           poetry version $new_ver
@@ -97,6 +100,17 @@ jobs:
             -Dsonar.projectName=l2ss-py
             -Dsonar.projectVersion=${{ env.software_version }}
             -Dsonar.python.version=3.7,3.8,3.9
+      - name: Run Snyk as a blocking step
+        uses: snyk/actions/python-3.8@master
+        env:
+            SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
+        with:
+          command: test
+          args: >
+              --org=${{ secrets.SNYK_ORG_ID }}
+              --project-name=${{ github.repository }}
+              --severity-threshold=high
+              --fail-on=all
       - name: Run Snyk on Python
         uses: snyk/actions/python-3.8@master
         env:
@@ -160,6 +174,7 @@ jobs:
           name: python-artifact
           path: dist/*
       - name: Publish to test.pypi.org
+        id: pypi-test-publish
         if: |
           github.ref == 'refs/heads/develop' ||
           startsWith(github.ref, 'refs/heads/release')
@@ -170,34 +185,43 @@ jobs:
           poetry publish -r testpypi
       - name: Publish to pypi.org
         if: ${{ github.ref == 'refs/heads/main' }}
+        id: pypi-publish
         env:
           POETRY_PYPI_TOKEN_PYPI: ${{secrets.POETRY_PYPI_TOKEN_PYPI}}
         run: |
           poetry publish
       - name: Log in to the Container registry
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
+        if: |
+          steps.pypi-test-publish.conclusion == 'success' ||
+          steps.pypi-publish.conclusion == 'success'
         uses: docker/login-action@v1
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: Extract metadata (tags, labels) for Docker
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
+        if: |
+          steps.pypi-test-publish.conclusion == 'success' ||
+          steps.pypi-publish.conclusion == 'success'
         id: meta
-        uses: docker/metadata-action@v3
+        uses: docker/metadata-action@v4
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
             type=semver,pattern={{version}},value=${{ env.software_version }}
             type=raw,value=${{ env.venue }}
       - name: Wait for package
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
+        if: |
+          steps.pypi-test-publish.conclusion == 'success' ||
+          steps.pypi-publish.conclusion == 'success'
         run: |
           pip install tenacity
           ${GITHUB_WORKSPACE}/.github/workflows/wait-for-pypi.py ${{env.pyproject_name}}[harmony]==${{ env.software_version }}
       - name: Build and push Docker image
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
-        uses: docker/build-push-action@v2
+        if: |
+          steps.pypi-test-publish.conclusion == 'success' ||
+          steps.pypi-publish.conclusion == 'success'
+        uses: docker/build-push-action@v3
         with:
           context: .
           file: docker/Dockerfile
@@ -208,21 +232,16 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
       - name: Run Snyk on Docker Image
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
+        if: |
+          steps.pypi-test-publish.conclusion == 'success' ||
+          steps.pypi-publish.conclusion == 'success'
         # Snyk can be used to break the build when it detects vulnerabilities.
         # In this case we want to upload the issues to GitHub Code Scanning
         continue-on-error: true
         uses: snyk/actions/docker@master
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         with:
-          image: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.software_version }}
+          image: ${{ steps.meta.outputs.tags[0] }}
           args: >
             --severity-threshold=high
-            --file=./docker/Dockerfile
-            --sarif-file-output=docker.sarif
-      - name: Upload result to GitHub Code Scanning
-        if: ${{ !startsWith(github.ref, 'refs/heads/feature') }}
-        uses: github/codeql-action/upload-sarif@v2
-        with:
-          sarif_file: ./

CHANGELOG.md

@@ -12,6 +12,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 ### Security
 
+
+## [2.3.0]
+### Added
+- [issue/126](https://github.com/podaac/l2ss-py/issues/126): Added flexibility to variable subsetting
+for variables to not have leading slash in the front
+- [issue/136](https://github.com/podaac/l2ss-py/issues/136): Added type annotations throughout the package code
+### Changed
+### Deprecated 
+### Removed
+### Fixed
+- PODAAC-5065: integration with SMAP_RSS_L2_SSS_V5, fix way xarray open granules that have `seconds since 2000-1-1 0:0:0 0` as a time unit.
+- [issue/127](https://github.com/podaac/l2ss-py/issues/127): Fixed bug when subsetting variables in grouped datasets. Variable names passed to `subset` will now have `/` replaced by `GROUP_DELIM` so they can be located in flattened datasets 
+### Security
+
 ## [2.2.0]
 ### Added
 ### Changed
@@ -40,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [issue/105](https://github.com/podaac/l2ss-py/issues/105): Added function to convert np object to python native objects.
 ### Security
 
+
 ## [2.0.0]
 ### Added
 - [issue/98](https://github.com/podaac/l2ss-py/issues/98): Added logic to handle time decoding for he5 tai93 files. Changed the min and max inputs to tai93 format and compared to the time format in the file
@@ -51,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Breaking Change** [issue/99](https://github.com/podaac/l2ss-py/issues/99): Removed support for python 3.7
 ### Fixed
 - [issue/95](https://github.com/podaac/l2ss-py/issues/95): Fix non variable subsets for OMI since variables are not in the same group as the lat lon variables 
+
 ### Security
 
 

cmr/ops_associations.txt

@@ -53,3 +53,5 @@ C2254232941-POCLOUD
 C2251464384-POCLOUD
 C2247621105-POCLOUD
 C2152045877-POCLOUD
+C1940471193-POCLOUD
+C2205121315-POCLOUD

podaac/subsetter/dimension_cleanup.py

@@ -11,11 +11,14 @@
 ======================
 Functions which improve upon existing netCDF4 library existing functions
 """
-
 import collections
+from typing import List, Tuple
+
+import netCDF4 as nc
+import xarray as xr
 
 
-def remove_duplicate_dims(nc_dataset):
+def remove_duplicate_dims(nc_dataset: nc.Dataset) -> Tuple[nc.Dataset, List[str]]:
     """
     xarray cannot read netCDF4 datasets with duplicate dimensions.
     Function goes through a dataset to catch any variables with duplicate dimensions.
@@ -67,7 +70,7 @@ def remove_duplicate_dims(nc_dataset):
     return nc_dataset, dup_new_varnames
 
 
-def rename_dup_vars(dataset, rename_vars):
+def rename_dup_vars(dataset: xr.Dataset, rename_vars: List[str]) -> xr.Dataset:
     """
     NetCDF4 rename function raises and HDF error for variable in S5P files with duplicate dimensions
     This method will use xarray to rename the variables