Merge pull request #114 from ASFHyP3/develop

Release v1.4.1

.github/workflows/changelog-check.yml

@@ -13,4 +13,4 @@ on:
 
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.13.2
+    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@v0.13.2
+    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-check.yml

@@ -12,4 +12,4 @@ on:
 
 jobs:
   call-labeled-pr-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.13.2
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.14.0

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

@@ -9,7 +9,7 @@ on:
 
 jobs:
   call-release-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.13.2
+    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.14.0
     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/reusable-release.yml@v0.13.2
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.14.0
     with:
       release_prefix: burst2safe
     secrets:

.github/workflows/static-analysis.yml

@@ -5,17 +5,12 @@ on: [pull_request]
 jobs:
   call-secrets-analysis-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected]
-
-  check-with-black:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: psf/black@stable
-        with:
-          options: "--check --diff --color"
-          src: "."
+    uses: ASFHyP3/actions/.github/workflows/[email protected]
 
   call-ruff-workflow:
     # Docs: https://github.com/ASFHyP3/actions
-    uses: ASFHyP3/actions/.github/workflows/[email protected]
+    uses: ASFHyP3/actions/.github/workflows/[email protected]
+
+  call-mypy-workflow:
+    # Docs: https://github.com/ASFHyP3/actions
+    uses: ASFHyP3/actions/.github/workflows/[email protected]

.github/workflows/tag-version.yml

@@ -9,6 +9,6 @@ jobs:
   call-bump-version-workflow:
     # For first-time setup, create a v0.0.0 tag as shown here:
     # https://github.com/ASFHyP3/actions#reusable-bump-versionyml
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.13.2
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.14.0
     secrets:
       USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}

CHANGELOG.md

@@ -6,6 +6,17 @@ 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).
 
+## [1.4.1]
+
+### Added
+* The [`static-analysis`](.github/workflows/static-analysis.yml) workflow now includes `mypy` for type checking.
+
+### Removed
+* Removed `black` from the [`static-analysis`](.github/workflows/static-analysis.yml) workflow.
+
+### Fixed
+* Add missing [`src/burst2safe/__init__.py`](./src/burst2safe/__init__.py) file.
+
 ## [1.4.0]
 
 ### Added

environment.yml

@@ -18,3 +18,4 @@ dependencies:
   - pytest-cov
   - pytest-dependency
   - ruff
+  - mypy

pyproject.toml

@@ -29,6 +29,7 @@ classifiers=[
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -64,11 +65,6 @@ addopts = '-ra -q -m "not integration and not golden"'
 markers = ["integration", "golden"]
 testpaths = ["tests"]
 
-[tool.black]
-line-length = 120
-skip-string-normalization = true
-include = '\.pyx?$'
-
 [tool.ruff]
 line-length = 120
 # The directories to consider when resolving first- vs. third-party imports.
@@ -95,3 +91,11 @@ convention = "google"
 [tool.ruff.lint.isort]
 case-sensitive = true
 lines-after-imports = 2
+
+[tool.mypy]
+python_version = "3.9"
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_unreachable = true
+strict_equality = true
+check_untyped_defs = true

src/burst2safe/auth.py

@@ -2,7 +2,7 @@
 import os
 from pathlib import Path
 from platform import system
-from typing import Tuple
+from typing import Tuple, Union
 
 
 EARTHDATA_HOST = 'urs.earthdata.nasa.gov'
@@ -20,7 +20,7 @@ def get_netrc() -> Path:
     return netrc_file
 
 
-def find_creds_in_env(username_name, password_name) -> Tuple[str, str]:
+def find_creds_in_env(username_name, password_name) -> Union[Tuple[str, str], Tuple[None, None]]:
     """Find credentials for a service in the environment.
 
     Args:
@@ -38,7 +38,7 @@ def find_creds_in_env(username_name, password_name) -> Tuple[str, str]:
     return None, None
 
 
-def find_creds_in_netrc(service) -> Tuple[str, str]:
+def find_creds_in_netrc(service) -> Union[Tuple[str, str], Tuple[None, None]]:
     """Find credentials for a service in the netrc file.
 
     Args:
@@ -53,6 +53,7 @@ def find_creds_in_netrc(service) -> Tuple[str, str]:
         if service in netrc_credentials.hosts:
             username = netrc_credentials.hosts[service][0]
             password = netrc_credentials.hosts[service][2]
+            assert password is not None
             return username, password
 
     return None, None

src/burst2safe/base.py

@@ -1,9 +1,8 @@
 import hashlib
-from collections.abc import Iterable
 from copy import deepcopy
 from datetime import datetime, timedelta
 from pathlib import Path
-from typing import List, Optional
+from typing import List, Optional, Union, cast
 
 import lxml.etree as ET
 
@@ -24,9 +23,9 @@ def __init__(
             start_line: The starting line number of the first element.
             slc_lengths: The total line lengths of the SLCs corresponding to each element.
         """
-        self.inputs = inputs
-        self.start_line = start_line
-        self.slc_lengths = slc_lengths
+        self.inputs: list[ET.Element] = inputs
+        self.start_line: Optional[int] = start_line
+        self.slc_lengths: Optional[list[int]] = slc_lengths
 
         self.name = self.inputs[0].tag
         elements = flatten([element.findall('*') for element in self.inputs])
@@ -75,6 +74,7 @@ def get_unique_elements(self) -> List[ET.Element]:
         last_time = datetime.fromisoformat(list_of_element_lists[0][-1].find(self.time_field).text)
         uniques = [deepcopy(element) for element in list_of_element_lists[0]]
         if self.has_line:
+            assert self.slc_lengths is not None
             previous_line_count = self.slc_lengths[0]
 
         for i, element_list in enumerate(list_of_element_lists[1:]):
@@ -84,7 +84,9 @@ def get_unique_elements(self) -> List[ET.Element]:
 
             if self.has_line:
                 new_lines = [int(elem.find('line').text) + previous_line_count for elem in to_keep]
-                [set_text(elem.find('line'), line) for elem, line in zip(to_keep, new_lines)]
+                for elem, line in zip(to_keep, new_lines):
+                    set_text(elem.find('line'), line)
+                assert self.slc_lengths is not None
                 previous_line_count += self.slc_lengths[i]
 
             last_time = max([times[index] for index in keep_index])
@@ -116,10 +118,11 @@ def update_line_numbers(self, elements: List[ET.Element]) -> None:
         """
         for element in elements:
             standard_line = int(element.find('line').text)
+            assert self.start_line is not None
             element.find('line').text = str(standard_line - self.start_line)
 
     def filter_by_time(
-        self, elements: List[ET.Element], anx_bounds: tuple[float, float], buffer: timedelta
+        self, elements: List[ET.Element], anx_bounds: tuple[datetime, datetime], buffer: timedelta
     ) -> List[ET.Element]:
         """Filter elements by time.
 
@@ -143,8 +146,8 @@ def filter_by_time(
 
     def create_filtered_list(
         self,
-        anx_bounds: Optional[tuple[float, float]],
-        buffer: Optional[timedelta] = timedelta(seconds=3),
+        anx_bounds: tuple[datetime, datetime],
+        buffer: timedelta = timedelta(seconds=3),
         line_bounds: Optional[tuple[float, float]] = None,
     ) -> ET.Element:
         """Filter elements by time/line. Adjust line number if present.
@@ -210,7 +213,7 @@ def create_metadata_object(simple_name: str) -> ET.Element:
 
 
 def create_data_object(
-    simple_name: str, relative_path: Path, rep_id: str, mime_type: str, size_bytes: int, md5: str
+    simple_name: str, relative_path: Union[Path, str], rep_id: str, mime_type: str, size_bytes: int, md5: str
 ) -> ET.Element:
     """Create a data object element for a manifest.safe file.
 
@@ -241,7 +244,7 @@ def create_data_object(
 
 
 class Annotation:
-    def __init__(self, burst_infos: Iterable[BurstInfo], metadata_type: str, ipf_version: str, image_number: int):
+    def __init__(self, burst_infos: list[BurstInfo], metadata_type: str, ipf_version: str, image_number: int):
         """Initialize the Annotation object.
 
         Args:
@@ -256,11 +259,12 @@ def __init__(self, burst_infos: Iterable[BurstInfo], metadata_type: str, ipf_ver
         self.major_version, self.minor_version = [int(v) for v in ipf_version.split('.')]
         self.metadata_paths = drop_duplicates([x.metadata_path for x in burst_infos])
         self.swath, self.pol = burst_infos[0].swath, burst_infos[0].polarization
+        assert burst_infos[0].length is not None
         self.start_line = burst_infos[0].burst_index * burst_infos[0].length
         self.total_lines = len(burst_infos) * burst_infos[0].length
         self.stop_line = self.start_line + self.total_lines
-        self.min_anx = min([x.start_utc for x in burst_infos])
-        self.max_anx = max([x.stop_utc for x in burst_infos])
+        self.min_anx = min(cast(datetime, x.start_utc) for x in burst_infos)
+        self.max_anx = max(cast(datetime, x.stop_utc) for x in burst_infos)
 
         self.inputs = [
             get_subxml_from_metadata(path, metadata_type, self.swath, self.pol) for path in self.metadata_paths
@@ -276,11 +280,11 @@ def __init__(self, burst_infos: Iterable[BurstInfo], metadata_type: str, ipf_ver
 
         # annotation components to be extended by subclasses
         self.ads_header = None
-        self.xml = None
+        self.xml: Optional[ET.Element] = None
 
         # these attributes are updated when the annotation is written to a file
-        self.size_bytes = None
-        self.md5 = None
+        self.size_bytes: Optional[int] = None
+        self.md5: Optional[str] = None
 
     def create_ads_header(self):
         """Create the ADS header for the annotation."""
@@ -301,7 +305,7 @@ def merge_lists(self, list_name: str, line_bounds: Optional[tuple[int, int]] = N
         """
         list_elements = [input_xml.find(list_name) for input_xml in self.inputs]
         list_of_list_elements = ListOfListElements(list_elements, self.start_line, self.slc_lengths)
-        merged_list = list_of_list_elements.create_filtered_list([self.min_anx, self.max_anx], line_bounds=line_bounds)
+        merged_list = list_of_list_elements.create_filtered_list((self.min_anx, self.max_anx), line_bounds=line_bounds)
         return merged_list
 
     def write(self, out_path: Path, update_info=True) -> None:
@@ -311,6 +315,7 @@ def write(self, out_path: Path, update_info=True) -> None:
             out_path: The path to write the annotation to.
             update_info: Whether to update the size and md5 attributes of the annotation.
         """
+        assert self.xml is not None
         self.xml.write(out_path, pretty_print=True, xml_declaration=True, encoding='utf-8')
 
         if update_info:
@@ -345,6 +350,11 @@ def create_manifest_components(self):
 
         content_unit = create_content_unit(simple_name, unit_type, rep_id)
         metadata_object = create_metadata_object(simple_name)
+        assert self.size_bytes is not None
+        assert self.md5 is not None
         data_object = create_data_object(simple_name, rel_path, rep_id, mime_type, self.size_bytes, self.md5)
 
         return content_unit, metadata_object, data_object
+
+    def assemble(self):
+        raise NotImplementedError()

src/burst2safe/burst2safe.py

@@ -23,8 +23,8 @@ def burst2safe(
     granules: Optional[Iterable[str]] = None,
     orbit: Optional[int] = None,
     extent: Optional[Polygon] = None,
-    polarizations: Optional[Iterable[str]] = None,
-    swaths: Optional[Iterable[str]] = None,
+    polarizations: Optional[list[str]] = None,
+    swaths: Optional[list[str]] = None,
     mode: str = 'IW',
     min_bursts: int = 1,
     all_anns: bool = False,

src/burst2safe/burst2stack.py

@@ -3,7 +3,7 @@
 from argparse import ArgumentParser
 from datetime import datetime
 from pathlib import Path
-from typing import Iterable, List, Optional
+from typing import List, Optional
 
 from shapely.geometry import Polygon
 
@@ -25,8 +25,8 @@ def burst2stack(
     start_date: Optional[datetime] = None,
     end_date: Optional[datetime] = None,
     extent: Optional[Polygon] = None,
-    polarizations: Optional[Iterable[str]] = None,
-    swaths: Optional[Iterable[str]] = None,
+    polarizations: Optional[list[str]] = None,
+    swaths: Optional[list[str]] = None,
     mode: str = 'IW',
     min_bursts: int = 1,
     all_anns: bool = False,

src/burst2safe/calibration.py

@@ -1,4 +1,3 @@
-from collections.abc import Iterable
 from copy import deepcopy
 
 import lxml.etree as ET
@@ -10,7 +9,7 @@
 class Calibration(Annotation):
     """Class representing a calibration XML."""
 
-    def __init__(self, burst_infos: Iterable[BurstInfo], ipf_version: str, image_number: int):
+    def __init__(self, burst_infos: list[BurstInfo], ipf_version: str, image_number: int):
         """Create a calibration object.
 
         Args:

src/burst2safe/download.py

@@ -25,6 +25,7 @@ def get_url_dict(burst_infos: Iterable[BurstInfo], force: bool = False) -> dict:
     """
     url_dict = {}
     for burst_info in burst_infos:
+        assert burst_info.data_path is not None
         if force or not burst_info.data_path.exists():
             url_dict[burst_info.data_path] = burst_info.data_url
         if force or not burst_info.metadata_path.exists():
@@ -60,11 +61,12 @@ async def download_burst_url_async(session: aiohttp.ClientSession, url: str, fil
         file_path: The path to save the downloaded data to
     """
     response = await get_async(session, url)
-
+    assert response.content_disposition is not None
     if file_path.suffix in ['.tif', '.tiff']:
         returned_filename = response.content_disposition.filename
     elif file_path.suffix == '.xml':
         url_parts = str(response.url).split('/')
+        assert response.content_disposition.filename is not None
         ext = response.content_disposition.filename.split('.')[-1]
         returned_filename = f'{url_parts[3]}_{url_parts[5]}.{ext}'
     else:
@@ -116,4 +118,4 @@ def download_bursts(burst_infos: Iterable[BurstInfo]) -> None:
     full_dict = get_url_dict(burst_infos, force=True)
     missing_data = [x for x in full_dict.keys() if not x.exists]
     if missing_data:
-        raise ValueError(f'Error downloading, missing files: {", ".join(missing_data.name)}')
+        raise ValueError(f'Error downloading, missing files: {", ".join([x.name for x in missing_data])}')