Merge branch 'develop' into merge_safe

.github/workflows/changelog.yml

@@ -14,6 +14,4 @@ on:
 jobs:
   call-changelog-check-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected]
-    secrets:
-      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    uses: ASFHyP3/actions/.github/workflows/[email protected]

.github/workflows/create-jira-issue.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-create-jira-issue-workflow:
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
       JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}

.github/workflows/labeled-pr.yml

@@ -13,4 +13,4 @@ on:
 jobs:
   call-labeled-pr-check-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2

.github/workflows/release-checklist-comment.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   call-release-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     permissions:
       pull-requests: write
     secrets:

.github/workflows/release.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   call-release-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     with:
       release_prefix: HyP3 ISCE2
     secrets:

.github/workflows/static-analysis.yml

@@ -5,10 +5,10 @@ on: push
 jobs:
   call-secrets-analysis-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
 
   call-flake8-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     with:
       local_package_names: hyp3_isce2

.github/workflows/tag-version.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   call-bump-version-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     with:
       user: tools-bot
       email: [email protected]

.github/workflows/test-and-build.yml

@@ -13,20 +13,22 @@ on:
 jobs:
   call-pytest-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     with:
       local_package_name: hyp3_isce2
       python_versions: >-
-        ["3.9", "3.10"]
+        ["3.10", "3.11"]
 
   call-version-info-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected]
+    uses: ASFHyP3/actions/.github/workflows/[email protected]
+    with:
+      python_version: "3.10"
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected].0
+    uses: ASFHyP3/actions/.github/workflows/[email protected].2
     with:
       version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
       release_branch: main

CHANGELOG.md

@@ -6,6 +6,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.2]
+### Fixed
+* Renamed `hyp3_isce2.logging` to `hyp3_isce2.logger` to avoid shadowing built-in.
+* Source of product start times in `merge_tops_bursts` to use the `asf_search` umm record.
+
+## [1.1.1]
+### Fixed
+* Upgraded to `dem_sticher>=2.5.6` to resolve geoid download errors. Fixes [#215](https://github.com/ASFHyP3/hyp3-isce2/issues/215)
+
+## [1.1.0]
+### Removed
+* Support for Python 3.8 and 3.9 has been dropped, 3.10 is now the minimum version.
 
 ## [1.0.1]
 ### Changed

README.md

@@ -98,6 +98,37 @@ docker run -it --rm \
 
 **NOTE** Each workflow can also be accessed via an alternative CLI with the format (`[WORKFLOW_NAME] [WORKFLOW_ARGS]`)
 
+#### Docker Outputs
+
+To retain hyp3_isce2 output files running via Docker there are two recommended approaches:
+
+1. Use a volume mount
+
+Add the `-w /tmp -v [localdir]:/tmp` flags after docker run. `-w` changes the working directory of the container to `/tmp` and `-v` will mount whichever local directory you choose so that such that hyp3_isce3 outputs are preserved locally.
+
+1. Copy outputs to remote object storage
+
+Append the `--bucket` and `--bucket-prefix` to [WORKFLOW_ARGS]. *Only the final output files and zipped archive of those files is uploaded.* This also requires that AWS credentials to write to the bucket are available to the running container. For example, to write outputs to a hypothetical bucket `s3://hypothetical-bucket/test-run/`:
+
+```
+docker run -it --rm \
+    -e AWS_ACCESS_KEY_ID=[YOUR_KEY] \
+    -e AWS_SECRET_ACCESS_KEY=[YOUR_SECRET] \ 
+    -e AWS_SESSION_TOKEN=[YOUR_TOKEN] \ 
+    -e EARTHDATA_USERNAME=[YOUR_USERNAME_HERE] \
+    -e EARTHDATA_PASSWORD=[YOUR_PASSWORD_HERE] \
+    -e ESA_USERNAME=[YOUR_USERNAME_HERE] \
+    -e ESA_PASSWORD=[YOUR_PASSWORD_HERE] \
+    ghcr.io/asfhyp3/hyp3-isce2:latest \
+      ++process [WORKFLOW_NAME] \
+      [WORKFLOW_ARGS] \
+      --bucket "hypothetical-bucket" \
+      --bucket-prefix "test-run"
+```
+
+Tip: you can use [`docker run --env-file`](https://docs.docker.com/reference/cli/docker/container/run/#env) to capture all the necessary environment variables in a single file.
+
+
 ## Developer Setup
 1. Ensure that conda is installed on your system (we recommend using [mambaforge](https://github.com/conda-forge/miniforge#mambaforge) to reduce setup times).
 2. Download a local version of the `hyp3-isce2` repository (`git clone https://github.com/ASFHyP3/hyp3-isce2.git`)

environment.yml

@@ -3,11 +3,11 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.9
+  - python>=3.10
   - numpy
   - pip
   - isce2>=2.6.3
-  - dem_stitcher>=2.4.0
+  - dem_stitcher>=2.5.6
   - rasterio
   - shapely
   - jinja2

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hyp3_isce2"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 authors = [
     {name="tools-bot", email="[email protected]"},
 ]
@@ -16,14 +16,12 @@ classifiers=[
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
 ]
 dependencies = [
   "numpy",
-  "dem_stitcher>=2.4.0",
+  "dem_stitcher>=2.5.6",
   "rasterio",
   "shapely",
   "jinja2",

src/hyp3_isce2/insar_stripmap.py

@@ -18,7 +18,7 @@
 
 from hyp3_isce2 import stripmapapp_alos as stripmapapp
 from hyp3_isce2.dem import download_dem_for_isce2
-from hyp3_isce2.logging import configure_root_logger
+from hyp3_isce2.logger import configure_root_logger
 
 log = logging.getLogger(__name__)
 

src/hyp3_isce2/insar_tops.py

@@ -13,7 +13,7 @@
 from hyp3_isce2 import slc
 from hyp3_isce2 import topsapp
 from hyp3_isce2.dem import download_dem_for_isce2
-from hyp3_isce2.logging import configure_root_logger
+from hyp3_isce2.logger import configure_root_logger
 from hyp3_isce2.s1_auxcal import download_aux_cal
 from hyp3_isce2.utils import get_esa_credentials
 

src/hyp3_isce2/insar_tops_burst.py

@@ -35,7 +35,7 @@
     validate_bursts,
 )
 from hyp3_isce2.dem import download_dem_for_isce2
-from hyp3_isce2.logging import configure_root_logger
+from hyp3_isce2.logger import configure_root_logger
 from hyp3_isce2.s1_auxcal import download_aux_cal
 from hyp3_isce2.utils import (
     ParameterFile,

src/hyp3_isce2/merge_tops_bursts.py

@@ -127,9 +127,9 @@ def get_burst_metadata(product_paths: Iterable[Path]) -> Iterable[BurstProduct]:
     burst_ids = [result.properties['burst']['relativeBurstID'] for result in results]
     burst_indexes = [result.properties['burst']['burstIndex'] for result in results]
     polarization = [result.properties['polarization'] for result in results]
-    start_utc = [
-        datetime.datetime.strptime(result.properties['startTime'], '%Y-%m-%dT%H:%M:%S.%fZ') for result in results
-    ]
+
+    start_utc_strs = [result.umm['TemporalExtent']['RangeDateTime']['BeginningDateTime'] for result in results]
+    start_utc = [datetime.datetime.strptime(utc, '%Y-%m-%dT%H:%M:%S.%fZ') for utc in start_utc_strs]
     relative_orbits = [result.properties['pathNumber'] for result in results]
     n_lines = [int(meta['Radarnlines']) for meta in metas]
     n_samples = [int(meta['Radarnsamples']) for meta in metas]

src/hyp3_isce2/water_mask.py

@@ -125,6 +125,7 @@ def create_water_mask(input_image: str, output_image: str, gdal_format='ISCE', t
         merged_warped_path,
         f'--outfile={output_image}',
         '--calc="numpy.abs((A.astype(numpy.int16) + 1) - 2)"',  # Change 1's to 0's and 0's to 1's.
-        f'--format={gdal_format}'
+        f'--format={gdal_format}',
+        '--overwrite',
     ]
     subprocess.run(flip_values_command, check=True)

tests/test_merge_tops_bursts.py

@@ -27,13 +27,15 @@ def mock_asf_search_results(
     path_number: int,
 ) -> asf_search.ASFSearchResults:
     product = asf_search.ASFProduct()
-    product.umm = {'InputGranules': [slc_name]}
+    product.umm = {
+        'InputGranules': [slc_name],
+        'TemporalExtent': {'RangeDateTime': {'BeginningDateTime': '2020-06-04T02:23:13.963847Z'}},
+    }
     product.properties.update(
         {
             'burst': {'subswath': subswath, 'burstIndex': burst_index, 'relativeBurstID': burst_id},
             'polarization': polarization,
             'url': f'https://foo.com/{slc_name}/baz.zip',
-            'startTime': '2020-06-04T02:23:13.963847Z',
             'pathNumber': path_number,
         }
     )