fix: relax dependencies

Dockerfile

@@ -1,24 +1,14 @@
-FROM osgeo/gdal:ubuntu-small-3.0.3
+FROM python:3.12-slim
 
 RUN : \
     && apt-get update \
     && apt-get install -y --no-install-recommends \
-    build-essential \
-    libjpeg-dev \
-    libxml2-dev \
-    libxslt1-dev \
-    zlib1g-dev \
-    python3.6 \
-    python3-dev \
-    python3-pip \
-    python3-venv \
+        libexpat1 \
     && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && pip3 install --no-cache-dir --upgrade pip setuptools \
-    && pip3 install --no-cache-dir rasterio==1.1.3 tox tox-venv --no-binary rasterio \
-    && :
-
+    && rm -rf /var/lib/apt/lists/*
 WORKDIR /hls_vi
+
 COPY ./ ./
+RUN pip install '.[test]' && pip install tox
 
 ENTRYPOINT [ "tox" ]

hls_vi/generate_indices.py

@@ -188,15 +188,15 @@ def read_band(tif_path: Path) -> np.ma.masked_array:
     #   atmospheric compensation where it's possible to have values >100% reflectance
     #   due to unmet assumptions about topography.
     # See, https://github.com/NASA-IMPACT/hls-vi/issues/44#issuecomment-2520592212
-    return np.ma.masked_less_equal(data, 0)
+    return np.ma.masked_less_equal(data, 0)  # type: ignore[no-any-return, no-untyped-call]
 
 
 def apply_fmask(data: np.ndarray, fmask: np.ndarray) -> np.ma.masked_array:
     # Per Table 9 in https://lpdaac.usgs.gov/documents/1698/HLS_User_Guide_V2.pdf
     # we wish to mask data where the Fmask has any one of the following bits set:
     # cloud shadow (bit 3), adjacent to cloud/shadow (bit 2), cloud (bit 1).
     cloud_like = int("00001110", 2)
-    return np.ma.masked_array(data, fmask & cloud_like != 0)
+    return np.ma.masked_array(data, fmask & cloud_like != 0)  # type: ignore[no-untyped-call]
 
 
 def apply_union_of_masks(bands: List[np.ma.masked_array]) -> List[np.ma.masked_array]:
@@ -214,7 +214,7 @@ def apply_union_of_masks(bands: List[np.ma.masked_array]) -> List[np.ma.masked_a
     # so bitwise "or" will  mask if "any" band has a masked value for that pixel
     mask = np.ma.nomask
     for band in bands:
-        mask = np.ma.mask_or(mask, band.mask)
+        mask = np.ma.mask_or(mask, band.mask)  # type: ignore[no-untyped-call]
 
     for band in bands:
         band.mask = mask
@@ -296,7 +296,7 @@ def write_granule_index(
 
 def evi(data: BandData) -> np.ma.masked_array:
     b, r, nir = data[Band.B], data[Band.R], data[Band.NIR]
-    return 2.5 * (nir - r) / (nir + 6 * r - 7.5 * b + 1)
+    return 2.5 * (nir - r) / (nir + 6 * r - 7.5 * b + 1)  # type: ignore[no-any-return]
 
 
 def msavi(data: BandData) -> np.ma.masked_array:
@@ -307,45 +307,45 @@ def msavi(data: BandData) -> np.ma.masked_array:
         sqrt_term >= 0,
         (2 * nir + 1 - np.sqrt(sqrt_term)) / 2,
         np.nan,
-    )
+    )  # type: ignore[no-untyped-call]
     result.fill_value = r.fill_value
 
     return result
 
 
 def nbr(data: BandData) -> np.ma.masked_array:
     nir, swir2 = data[Band.NIR], data[Band.SWIR2]
-    return (nir - swir2) / (nir + swir2)
+    return (nir - swir2) / (nir + swir2)  # type: ignore[no-any-return]
 
 
 def nbr2(data: BandData) -> np.ma.masked_array:
     swir1, swir2 = data[Band.SWIR1], data[Band.SWIR2]
-    return (swir1 - swir2) / (swir1 + swir2)
+    return (swir1 - swir2) / (swir1 + swir2)  # type: ignore[no-any-return]
 
 
 def ndmi(data: BandData) -> np.ma.masked_array:
     nir, swir1 = data[Band.NIR], data[Band.SWIR1]
-    return (nir - swir1) / (nir + swir1)
+    return (nir - swir1) / (nir + swir1)  # type: ignore[no-any-return]
 
 
 def ndvi(data: BandData) -> np.ma.masked_array:
     r, nir = data[Band.R], data[Band.NIR]
-    return (nir - r) / (nir + r)
+    return (nir - r) / (nir + r)  # type: ignore[no-any-return]
 
 
 def ndwi(data: BandData) -> np.ma.masked_array:
     g, nir = data[Band.G], data[Band.NIR]
-    return (g - nir) / (g + nir)
+    return (g - nir) / (g + nir)  # type: ignore[no-any-return]
 
 
 def savi(data: BandData) -> np.ma.masked_array:
     r, nir = data[Band.R], data[Band.NIR]
-    return 1.5 * (nir - r) / (nir + r + 0.5)
+    return 1.5 * (nir - r) / (nir + r + 0.5)  # type: ignore[no-any-return]
 
 
 def tvi(data: BandData) -> np.ma.masked_array:
     g, r, nir = data[Band.G], data[Band.R], data[Band.NIR]
-    return (120 * (nir - g) - 200 * (r - g)) / 2  # pyright: ignore[reportReturnType]
+    return (120 * (nir - g) - 200 * (r - g)) / 2  # type: ignore[no-any-return]
 
 
 class Index(Enum):
@@ -390,7 +390,7 @@ def __call__(self, data: BandData) -> np.ma.masked_array:
         # We need to round to whole numbers (i.e., 0 decimal places, which is
         # the default for np.round) because we convert to integer values, but
         # numpy's conversion to integer types performs truncation, not rounding.
-        return np.ma.round(scaled_index).astype(np.int16)
+        return np.ma.round(scaled_index).astype(np.int16)  # type: ignore[no-untyped-call, no-any-return]
 
 
 def parse_args() -> Tuple[Path, Path, str]:

hls_vi/generate_stac_items.py

@@ -11,8 +11,11 @@
 from pystac.extensions.projection import ProjectionExtension
 from pystac.extensions.scientific import ScientificExtension
 from pystac.extensions.view import ViewExtension
+from pystac.version import STACVersion
 from shapely.geometry import shape
 
+STACVersion.set_stac_version("1.0.0")
+
 # HLS_VI band information
 hls_vi_band_info = {
     "NDVI": {
@@ -101,8 +104,8 @@ def get_geometry(granule: untangle.Element) -> MultiPolygon:
             ring.append(geojson_point)
 
         closing_point = [
-            float(poly.Boundary.Point[0].PointLongitude.cdata),
-            float(poly.Boundary.Point[0].PointLatitude.cdata),
+            float(poly.Boundary.Point[0].PointLongitude.cdata),  # type: ignore[union-attr, index]
+            float(poly.Boundary.Point[0].PointLatitude.cdata),  # type: ignore[union-attr, index]
         ]
         ring.append(closing_point)
         ringtuple = (ring,)
@@ -174,13 +177,13 @@ def add_assets(
         url = f"https://{endpoint}/lp-prod-protected/HLSL30_VI.{version}/{item_id}/"
         public_url = f"https://{endpoint}/lp-prod-public/HLSL30_VI.{version}/{item_id}/"
 
-    for band_id, band_info in band_info.items():
+    for band_id, band_info_ in band_info.items():
         band_url = f"{url}{item_id}.{band_id}.tif"
         asset = pystac.Asset(
             href=band_url, media_type=pystac.MediaType.COG, roles=["data"]
         )
-        bands = [band_info["band"]]
-        EOExtension.ext(asset).bands = bands
+        bands = [band_info_["band"]]
+        EOExtension.ext(asset).bands = bands  # type: ignore
         item.add_asset(band_id, asset)
 
     thumbnail_url = f"{public_url}{item_id}.jpg"
@@ -283,7 +286,7 @@ def cmr_to_item(hls_vi_metadata: str, endpoint: str, version: str) -> Mapping[st
     process_view_geometry(item, granule)
     process_scientific(item, granule)
 
-    return item.to_dict()  # type: ignore
+    return item.to_dict()
 
 
 def create_item(

setup.py

@@ -2,24 +2,24 @@
 
 setup(
     name="hls_vi",
-    version="1.19",
+    version="1.20",
     packages=["hls_vi"],
     include_package_data=True,
     install_requires=[
-        "dataclasses;python_version<'3.7'",
         "geojson",
         "importlib_resources",
         "lxml>=3.6.0,<6",
-        "numpy>=1.19,<2",
-        "pystac[validation]==1.0.0rc2",
+        "numpy",
+        # we can't use pystac>=1.12.0 because they did a major/breaking bump to
+        # the projection extension (v1.x to v2) that renamed proj:epsg -> proj:code.
+        "pystac[validation]>=1.0.0rc2,<1.12.0",
         "rasterio",
         "shapely",
-        "typing-extensions",
         "untangle",
     ],
     extras_require={
         "test": [
-            "black[jupyter]==22.8.0",  # Last version to support Python 3.6 runtime
+            "black[jupyter]",
             "flake8",
             "mypy",
             "pytest",

tests/fixtures/HLS-VI_stac_item.json

@@ -101,8 +101,8 @@
   },
   "bbox": [-149.114568, 63.924491, -146.793616, 64.923996],
   "stac_extensions": [
-    "https://stac-extensions.github.io/eo/v1.0.0/schema.json",
-    "https://stac-extensions.github.io/projection/v1.0.0/schema.json",
+    "https://stac-extensions.github.io/eo/v1.1.0/schema.json",
+    "https://stac-extensions.github.io/projection/v1.1.0/schema.json",
     "https://stac-extensions.github.io/view/v1.0.0/schema.json",
     "https://stac-extensions.github.io/scientific/v1.0.0/schema.json"
   ]

tox.ini

@@ -4,19 +4,23 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py36
+envlist = py312
 
 [flake8]
 ignore = D203, W503
 exclude = .git,__pycache__,docs/source/conf.py,old,build,dist,site-packages,venv,bin
 max-complexity = 12
-max-line-length = 90
+max-line-length = 120
 
 [testenv]
 envdir = venv
 sitepackages = True
 extras =
   test
+allowlist_externals =
+  flake8
+  mypy
+  pytest
 commands =
   flake8
   mypy