Merge pull request #602 from ASFHyP3/develop

Release v9.0.2

.github/workflows/changelog.yml

@@ -13,4 +13,4 @@ on:
 
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.14.0

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

@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-create-jira-issue-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.14.0
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
       JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}

.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@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.14.0

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

@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-release-checklist-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.14.0
     secrets:
       USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   call-release-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.14.0
     with:
       release_prefix: HyP3 GAMMA
     secrets:

.github/workflows/static-analysis.yml

@@ -3,10 +3,12 @@ name: Static analysis
 on: push
 
 jobs:
+  # Docs: https://github.com/ASFHyP3/actions
   call-secrets-analysis-workflow:
-    # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.14.0
 
   call-ruff-workflow:
-    # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-ruff.yml@v0.14.0
+
+  call-mypy-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-mypy.yml@v0.14.0

.github/workflows/tag-version.yml

@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-bump-version-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.14.0
     secrets:
       USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}

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

@@ -18,14 +18,14 @@ env:
 
 jobs:
   call-pytest-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.14.0
     with:
       local_package_name: hyp3_gamma
       python_versions: >-
         ["3.10"]
 
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.12.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.14.0
     with:
       python_version: '3.10'
 

CHANGELOG.md

@@ -6,6 +6,10 @@ 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).
 
+## [9.0.2]
+### Added
+- The [`static-analysis`](.github/workflows/static-analysis.yml) Github Actions workflow now includes `mypy` for type checking.
+
 ## [9.0.1]
 ### Changed
 - The [`static-analysis`](.github/workflows/static-analysis.yml) Github Actions workflow now uses `ruff` rather than `flake8` for linting.

hyp3_gamma/__main__.py

@@ -120,9 +120,9 @@ def rtc():
 
 
 def phase_filter_valid_range(x: str) -> float:
-    x = float(x)
-    if 0.0 <= x <= 1.0:
-        return x
+    n = float(x)
+    if 0.0 <= n <= 1.0:
+        return n
     raise ValueError(f'{x} not in range [0.0, 1.0]')
 
 

hyp3_gamma/dem.py

@@ -46,6 +46,7 @@ def intersects_dem(geometry: ogr.Geometry) -> bool:
     for feature in get_dem_features():
         if feature.GetGeometryRef().Intersects(geometry):
             return True
+    return False
 
 
 def get_dem_file_paths(geometry: ogr.Geometry) -> list[str]:

hyp3_gamma/insar/ifm_sentinel.py

@@ -41,7 +41,9 @@ def get_bursts(mydir, name):
         if name in myfile:
             root = etree.parse(myfile)
             for coord in root.iter('azimuthAnxTime'):
-                time.append(float(coord.text))
+                text = coord.text
+                assert text is not None
+                time.append(float(text))
             for count in root.iter('burstList'):
                 total_bursts = int(count.attrib['count'])
 
@@ -166,7 +168,6 @@ def get_orbit_parameters(reference_file):
             meta = root.find('metadataSection')
             xmldata = meta.find('*[@ID="measurementOrbitReference"]').metadataWrap.xmlData
             orbit = xmldata.find('safe:orbitReference', root.nsmap)
-
             orbitnumber = orbit.find('safe:orbitNumber', root.nsmap)
             relative_orbitnumber = orbit.find('safe:relativeOrbitNumber', root.nsmap)
             cyclenumber = orbit.find('safe:cycleNumber', root.nsmap)
@@ -316,6 +317,7 @@ def make_parameter_file(
             root = etree.parse(myfile)
             for coord in root.iter('productFirstLineUtcTime'):
                 utc = coord.text
+                assert utc is not None
                 log.info(f'Found utc time {utc}')
                 t = utc.split('T')
                 log.info(f'{t}')
@@ -462,7 +464,7 @@ def insar_sentinel_gamma(
     interf_pwr_s1_lt_tops_proc(reference, secondary, hgt, rlooks=rlooks, alooks=alooks, iterations=3, step=2)
 
     g = open('offsetfit3.log')
-    offset = 1.0
+    offset = '1.0'
     for line in g:
         if 'final azimuth offset poly. coeff.:' in line:
             offset = line.split(':')[1]

hyp3_gamma/insar/unwrapping_geocoding.py

@@ -62,8 +62,8 @@ def coords_from_sarpix_coord(in_mli_par: str, ref_azlin: int, ref_rpix: int, hei
 
     selected_coords = [line for line in coord_log_lines if 'selected' in line]
     log.info(f'Selected sarpix coordinates: {selected_coords[0]}')
-    coord_lst = selected_coords[0].split()[:-1]
-    coord_lst = [float(s) for s in coord_lst]
+    coord_lst_str = selected_coords[0].split()[:-1]
+    coord_lst = [float(s) for s in coord_lst_str]
     return coord_lst
 
 
@@ -72,7 +72,7 @@ def get_coords(
     ref_azlin: int = 0,
     ref_rpix: int = 0,
     height: float = 0.0,
-    in_dem_par: str = None,
+    in_dem_par: str | None = None,
 ) -> dict:
     """Args:
         in_mli_par: GAMMA MLI par file
@@ -108,7 +108,7 @@ def read_bmp(file):
     return data
 
 
-def get_reference_pixel(coherence: np.array, window_size=(5, 5), coherence_threshold=0.3) -> tuple[int, int]:
+def get_reference_pixel(coherence: np.ndarray, window_size=(5, 5), coherence_threshold=0.3) -> tuple[int, int]:
     """Args:
         coherence: array of coherence values
         window_size: window size over which to sum coherence values for each pixel
@@ -118,8 +118,8 @@ def get_reference_pixel(coherence: np.array, window_size=(5, 5), coherence_thres
         array indices of the reference pixel
     """
 
-    def sum_valid_coherence_values(array: np.array) -> float:
-        if (array < coherence_threshold).any() or (array == 1.0).any():
+    def sum_valid_coherence_values(array: np.ndarray) -> float:
+        if (array < coherence_threshold).any() or (array == np.float64(1.0)).any():
             return 0.0
         return array.sum()
 
@@ -131,7 +131,7 @@ def sum_valid_coherence_values(array: np.array) -> float:
         cval=0.0,
     )
     x, y = np.unravel_index(np.argmax(pixel_weights), pixel_weights.shape)
-    return x, y
+    return int(x), int(y)
 
 
 def geocode_back(inname, outname, width, lt, demw, demn, type_):
@@ -208,6 +208,7 @@ def combine_water_mask(cc_mask_file, water_mask_sar_file):
     water_mask_sar_data = read_bmp(water_mask_sar_file)
     in_data[water_mask_sar_data == 0] = 0
     out_im = Image.fromarray(in_data)
+    assert in_palette is not None
     out_im.putpalette(in_palette)
     out_file = os.path.join(os.path.dirname(cc_mask_file), 'combined_mask.bmp')
     out_im.save(out_file)
@@ -326,12 +327,12 @@ def unwrapping_geocoding(
     )
 
     execute(
-        f'dispmap {ifgname}.adf.unw DEM/HGT_SAR_{rlooks}_{alooks} {mmli}.par' f' - {ifgname}.vert.disp 1',
+        f'dispmap {ifgname}.adf.unw DEM/HGT_SAR_{rlooks}_{alooks} {mmli}.par - {ifgname}.vert.disp 1',
         uselogging=True,
     )
 
     execute(
-        f'dispmap {ifgname}.adf.unw DEM/HGT_SAR_{rlooks}_{alooks} {mmli}.par' f' - {ifgname}.los.disp 0',
+        f'dispmap {ifgname}.adf.unw DEM/HGT_SAR_{rlooks}_{alooks} {mmli}.par - {ifgname}.los.disp 0',
         uselogging=True,
     )
 
@@ -489,8 +490,7 @@ def main():
         '-t',
         '--tri',
         default=0,
-        help='Triangulation method for mcf unwrapper: '
-        '0) filled traingular mesh (default); 1) Delaunay triangulation',
+        help='Triangulation method for mcf unwrapper: 0) filled traingular mesh (default); 1) Delaunay triangulation',
     )
     parser.add_argument('--alpha', default=0.6, type=float, help='adf filter alpha value (def=0.6)')
     args = parser.parse_args()

hyp3_gamma/metadata/create.py

@@ -45,7 +45,7 @@ def create_metadata_file_set_insar(
     processor_version: str,
     ref_point_coords: dict,
     phase_filter_parameter: float,
-) -> list[Path]:
+) -> list[Path | None]:
     payload = insar.marshal_metadata(
         product_dir=product_dir,
         reference_granule_name=reference_granule_name,

hyp3_gamma/metadata/insar.py

@@ -15,7 +15,7 @@ def __init__(self, payload: dict):
         self.product_dir = payload['product_dir']
         self.product_name = payload['product_dir'].name
 
-    def create_metadata_file_set(self) -> list[Path]:
+    def create_metadata_file_set(self) -> list[Path | None]:
         files = []
         generators = [
             self.create_readme,
@@ -44,32 +44,34 @@ def create_metadata_file_set(self) -> list[Path]:
     def create_readme(self) -> Path:
         reference_file = self.product_dir / f'{self.product_name}_amp.tif'
 
-        return self.create_metadata_file(
+        metadata_file = self.create_metadata_file(
             self.payload,
             'insar/readme.md.txt.j2',
             reference_file,
             out_ext='README.md.txt',
             strip_ext=True,
             name_only=True,
         )
+        assert metadata_file is not None
+        return metadata_file
 
-    def create_amp_xml(self) -> Path:
+    def create_amp_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_amp.tif'
         return self.create_metadata_file(self.payload, 'insar/amp_tif.xml.j2', reference_file)
 
-    def create_coherence_xml(self) -> Path:
+    def create_coherence_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_corr.tif'
         return self.create_metadata_file(self.payload, 'insar/corr_tif.xml.j2', reference_file)
 
-    def create_dem_tif_xml(self) -> Path:
+    def create_dem_tif_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_dem.tif'
         return self.create_metadata_file(self.payload, 'insar/dem.xml.j2', reference_file)
 
-    def create_los_displacement_xml(self) -> Path:
+    def create_los_displacement_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_los_disp.tif'
         return self.create_metadata_file(self.payload, 'insar/los_disp_tif.xml.j2', reference_file)
 
-    def create_look_vector_xmls(self) -> list[Path]:
+    def create_look_vector_xmls(self) -> list[Path | None]:
         reference_file_phi = self.product_dir / f'{self.product_name}_lv_phi.tif'
         reference_file_theta = self.product_dir / f'{self.product_name}_lv_theta.tif'
         output_files = [
@@ -78,7 +80,7 @@ def create_look_vector_xmls(self) -> list[Path]:
         ]
         return output_files
 
-    def create_browse_xmls(self) -> list[Path]:
+    def create_browse_xmls(self) -> list[Path | None]:
         reference_file_col = self.product_dir / f'{self.product_name}_color_phase.png'
         reference_file_unw = self.product_dir / f'{self.product_name}_unw_phase.png'
         output_files = [
@@ -87,27 +89,27 @@ def create_browse_xmls(self) -> list[Path]:
         ]
         return output_files
 
-    def create_unwrapped_phase_xml(self) -> Path:
+    def create_unwrapped_phase_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_unw_phase.tif'
         return self.create_metadata_file(self.payload, 'insar/unw_phase_tif.xml.j2', reference_file)
 
-    def create_vertical_displacement_xml(self) -> Path:
+    def create_vertical_displacement_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_vert_disp.tif'
         return self.create_metadata_file(self.payload, 'insar/vert_disp_tif.xml.j2', reference_file)
 
-    def create_wrapped_phase_xml(self) -> Path:
+    def create_wrapped_phase_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_wrapped_phase.tif'
         return self.create_metadata_file(self.payload, 'insar/wrapped_phase_tif.xml.j2', reference_file)
 
-    def create_inc_map_xml(self) -> Path:
+    def create_inc_map_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_inc_map.tif'
         return self.create_metadata_file(self.payload, 'insar/inc_map_tif.xml.j2', reference_file)
 
-    def create_inc_map_ell_xml(self) -> Path:
+    def create_inc_map_ell_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_inc_map_ell.tif'
         return self.create_metadata_file(self.payload, 'insar/inc_map_ell_tif.xml.j2', reference_file)
 
-    def create_water_mask_xml(self) -> Path:
+    def create_water_mask_xml(self) -> Path | None:
         reference_file = self.product_dir / f'{self.product_name}_water_mask.tif'
         return self.create_metadata_file(self.payload, 'insar/water_mask_tif.xml.j2', reference_file)