Merge pull request #477 from dbekaert/dev

Release v0.4.1

.github/workflows/build.yml

@@ -12,14 +12,13 @@ on:
 
 jobs:
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.7.0
     with:
-      conda_env_name: RAiDER
       python_version: '3.10'
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
-    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.7.0
     with:
       version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
       release_branch: main

.github/workflows/changelog.yml

@@ -13,6 +13,6 @@ on:
 
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.7.0
     secrets:
       USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/deploy-docs.yml

@@ -14,12 +14,10 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/provision-with-micromamba@v14
         with:
-          mamba-version: "*"
-          python-version: '3.10'
-          activate-environment: RAiDER
-          environment-file: environment.yml
+          extra-specs: |
+            python=3.10
 
       - name: install RAiDER
         shell: bash -l {0}

.github/workflows/labeled-pr.yml

@@ -12,4 +12,4 @@ on:
 
 jobs:
   call-labeled-pr-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.7.0

.github/workflows/release.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   call-release-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.7.0
     with:
       release_prefix: RAiDER
       develop_branch: dev

.github/workflows/tag.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   call-bump-version-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.6.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.7.0
     with:
       user: dbekaert
       email: bekaertdavid@gmail.com

CHANGELOG.md

@@ -6,6 +6,21 @@ 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).
 
+
+## [0.4.1]
+
+### New/Updated Features
++ Reorder target points for intersection
++ Use exact coordinates of DEM to interpolate heights to target lat/lons
++ Support DEM interpolation to station file
++ Implement end-to-end test for intersection of cube with lat/lon files
++ Implement end-to-end test for calculation at stations delay
++ Update AOI to store the output directory so DEM is written to right place
++ `calcDelaysGUNW` will optionally download a GUNW product from AWS S3, process it, and upload a new version of the GUNW product in-place with the tropospheric correction layers added so that RAiDER can be used in ARIA GUNW production via HyP3. **Importantly**, tropospheric correction of GUNW products is still being activitely developed; this workflow, as well as the correction itself, is subject to change.
+
+### Fixed
++ Package data is more explicitly handled so that it is included in the conda-forge build; see [#467](https://github.com/dbekaert/RAiDER/pull/467)
+
 ## [0.4.0]
 
 Adding of new GUNW support to RAiDER. This is an interface delivery allowing for subsequent integration into HYP3 (input/output parsing is not expected to change; computed data is not yet verified). 

Dockerfile

@@ -44,5 +44,5 @@ RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.profile && \
 
 RUN python -m pip install --no-cache-dir /RAiDER/
 
-ENTRYPOINT ["/usr/bin/bash"]
-CMD ["-l"]
+ENTRYPOINT ["/RAiDER/tools/RAiDER/etc/entrypoint.sh"]
+CMD ["--help"]

README.md

@@ -59,7 +59,7 @@ or the current development version:
 docker pull ghcr.io/dbekaert/raider:test
 ```
 
-To run the container and jump into a bash shell inside:
+To run `raider.py` inside the container:
 ```
 docker run -it --rm ghcr.io/dbekaert/raider:latest
 ```
@@ -68,6 +68,11 @@ To mount your current directory inside the container so that files will be writt
 docker run -it -v ${PWD}:/home/raider/work --rm ghcr.io/dbekaert/raider:latest
 cd work
 ```
+To jump into a `bash` shell inside the container:
+```
+docker run -it --rm --entrypoint /bin/bash ghcr.io/dbekaert/raider:latest -l
+```
+
 For more docker run options, see: <https://docs.docker.com/engine/reference/run/>.
 
 
@@ -98,7 +103,7 @@ For development, we recommend installing directly from source.
 ```
 git clone https://github.com/dbekaert/RAiDER.git
 cd RAiDER
-conda create -f environment.yml
+conda env create -f environment.yml
 conda activate RAiDER
 python -m pip install -e .
 ```

docs/WeatherModels.md

@@ -18,7 +18,7 @@ ERA-5/ERA-I products require access to the ESA Copernicus servers. GMAO and MERR
 ------
 
 ## 2. NOAA weather models (HRRR)
-High-resolution rapid refresh (HRRR) weather model data products are generated by __[NOAA](https://rapidrefresh.noaa.gov/hrrr/)__ for the coninental US (CONUS) but not archived beyond three days. However, a public __[archive](home.chpc.utah.edu/~u0553130/Brian_Blaylock/hrrr_FAQ.html)__ is available at the University of Utah. This archive does not require a license agreement. This model has the highest spatial resolution available in RAiDER, with a horizontal grid spacing of about 3 km, and is provided in a Lambert conformal conic projection. 
+High-resolution rapid refresh (HRRR) weather model data products are generated by __[NOAA](https://rapidrefresh.noaa.gov/hrrr/)__ for the coninental US (CONUS) but not archived beyond three days. However, a public __[archive](https://home.chpc.utah.edu/~u0553130/Brian_Blaylock/hrrr_FAQ.html)__ is available at the University of Utah. This archive does not require a license agreement. This model has the highest spatial resolution available in RAiDER, with a horizontal grid spacing of about 3 km, and is provided in a Lambert conformal conic projection. 
 
 ------
 

environment.yml

@@ -11,6 +11,7 @@ dependencies:
  - python>=3.8
  - pip
  # For running
+ - boto3
  - cdsapi
  - cfgrib
  - cmake

pyproject.toml

@@ -50,11 +50,15 @@ repository = "https://github.com/dbekaert/RAiDER"
 "generateGACOSVRT.py"   = "RAiDER.models.generateGACOSVRT:main"
 
 [tool.setuptools]
+include-package-data = true
 zip-safe = false
 
 [tool.setuptools.packages.find]
 where = ["tools"]
 
+[tool.setuptools.package-data]
+"*" = ["*.yml", "*.yaml"]
+
 [tool.isort]
 known_first_party = "RAiDER"
 multi_line_output = 5

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    long: mark a test as a long

test/__init__.py

@@ -20,3 +20,4 @@ def pushd(dir):
 TEST_DIR = test_dir.absolute()
 DATA_DIR = os.path.join(TEST_DIR, "data")
 GEOM_DIR = os.path.join(TEST_DIR, 'test_geom')
+WM = 'GMAO'

test/_entrypoints.py

@@ -1,4 +1,5 @@
 
+
 def test_raider__main__2(script_runner):
     ret = script_runner.run('generateGACOSVRT.py')
     assert ret.success

test/test_GUNW.py

@@ -1,29 +1,30 @@
+import glob
 import os
 import shutil
-import numpy as np
-import pytest
-import shutil
 import subprocess
-import xarray as xr
+
+import numpy as np
 import rasterio as rio
+import xarray as xr
 
 from test import TEST_DIR
 
+WM = 'GMAO'
 
 def test_GUNW():
     ## eventually to be implemented
     # home = os.path.expanduser('~')
     # netrc = os.path.join(home, '.netrc')
-# 
+#
     # ## make netrc
     # if not os.path.exists(netrc):
         # name, passw = os.getenv('URSname'), os.getenv('URSpass')
         # cmd = f'echo "machine urs.earthdata.nasa.gov login {name} password {passw}" > ~/.netrc'
         # subprocess.run(cmd.split())
-# 
+#
         # cmd = f'chmod 600 {netrc}'
         # subprocess.run(cmd.split())
-# 
+#
     SCENARIO_DIR = os.path.join(TEST_DIR, "GUNW")
     os.makedirs(SCENARIO_DIR, exist_ok=True)
     GUNW = 'S1-GUNW-D-R-071-tops-20200130_20200124-135156-34956N_32979N-PP-913f-v2_0_4.nc'
@@ -36,7 +37,7 @@ def test_GUNW():
     # proc = subprocess.run(cmd.split(), stdout=subprocess.PIPE, universal_newlines=True)
     # assert np.isclose(proc.returncode, 0)
 
-    cmd  = f'raider.py ++process calcDelaysGUNW {updated_GUNW} -m GMAO -o {SCENARIO_DIR}'
+    cmd  = f'raider.py ++process calcDelaysGUNW -f {updated_GUNW} -m {WM} -o {SCENARIO_DIR}'
     proc = subprocess.run(cmd.split(), stdout=subprocess.PIPE, universal_newlines=True)
     assert np.isclose(proc.returncode, 0)
 
@@ -45,7 +46,9 @@ def test_GUNW():
     transform = (0.1, 0.0, -119.35, 0, -0.1, 35.05)
     group = 'science/grids/corrections/external/troposphere'
     for v in 'troposphereWet troposphereHydrostatic'.split():
+        ds = rio.open(f'netcdf:{updated_GUNW}:{group}/{v}')
         with rio.open(f'netcdf:{updated_GUNW}:{group}/{v}') as ds:
+            ds.crs.to_epsg()
             assert np.isclose(ds.crs.to_epsg(), epsg), 'CRS incorrect'
             assert ds.transform.almost_equals(transform), 'Affine Transform incorrect'
 
@@ -56,9 +59,10 @@ def test_GUNW():
 
         crs = rio.crs.CRS.from_wkt(ds['crs'].crs_wkt)
         assert np.isclose(crs.to_epsg(), epsg), 'CRS incorrect'
-        
+
 
     # Clean up files
     shutil.rmtree(SCENARIO_DIR)
     os.remove('GUNW_20200130-20200124.yaml')
-    return 
+    [os.remove(f) for f in glob.glob(f'{WM}*')]
+    return