Prep for v1 release

[sray014]

This PR makes several improvements to hecstac, specifically the RAS module by:

• Fixing 2d geometry handling so that it properly reads mesh areas from geometry hdf files if they exist within the file.
• Handle the coordinate reference systems correctly including situations where one is provided or when it can be extracted from the geom hdf file.
• Adding needed handling to check if a geom hdf has 2d geometry.
• Adding handling for retrieving the mesh areas for different crs situations.
• Updating thumbnail creation to work with new crs handling.
• Cleaning code that is not needed/unused.
• Fixing item asset href's.

[thwllms]

rashdf needs to be added to pyproject.toml

Edit: it seems like boto3 is an undeclared dependency as well? Wasn't expecting to need that for generating a RAS Item locally.

Also boto3-stubs[s3] and contextily.

[thwllms]

I tried generating a RAS Item with the Muncie model from the RAS 6.6 example projects and ran into an issue with a missing CRS... maybe this is okay if we consider the Muncie model to be an outlier for our immediate purposes?

>>> RASModelItem("/mnt/c/temp/Example_Projects_6_6/2D Unsteady Flow Hydraulics/Muncie/Muncie.prj", "asdf")
WARNING:root:Unable to parse project version
WARNING:root:Could not extract crs from /mnt/c/temp/Example_Projects_6_6/2D Unsteady Flow Hydraulics/Muncie/Muncie.g01.hdf
WARNING:root:No reference lines found.
WARNING:root:No mesh areas found for /mnt/c/temp/Example_Projects_6_6/2D Unsteady Flow Hydraulics/Muncie/Muncie.g01.hdf
WARNING:root:Could not extract crs from /mnt/c/temp/Example_Projects_6_6/2D Unsteady Flow Hydraulics/Muncie/Muncie.g02.hdf
WARNING:root:No reference lines found.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/thomaswilliams/dev/hecstac/hecstac/ras/item.py", line 83, in __init__
    self.add_ras_asset(fpath)
  File "/home/thomaswilliams/dev/hecstac/hecstac/ras/item.py", line 202, in add_ras_asset
    if asset.check_2d:
       ^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/ras/assets.py", line 382, in check_2d
    if self.hdf_object.mesh_areas(self.crs):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/ras/parser.py", line 1166, in mesh_areas
    raise CRSError("Mesh areas have no CRS and have none to be set to")
pyproj.exceptions.CRSError: Mesh areas have no CRS and have none to be set to

Edit: per discussion on 30 Jan call, CRS needs to be provided for Muncie.

[thwllms]

@sray014 I downloaded a Duwamish HMS model from USACE Model Library and tried to create an Item; got this... any ideas?

>>> HMSModelItem("/mnt/c/temp/duwamish/Duwamish_SST.hms", "asdf")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/item.py", line 48, in __init__
    self.pf = ProjectFile(self.hms_project_file, assert_uniform_version=False)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 115, in __init__
    self.scan_for_terrain_run_grid_gage_pdata()
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 139, in scan_for_terrain_run_grid_gage_pdata
    self.terrain = TerrainFile(path)
                   ^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 725, in __init__
    super().__init__(path, client=client, bucket=bucket)
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 56, in __init__
    self.read_content()
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 62, in read_content
    self.content = f.read()
                   ^^^^^^^^
  File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb2 in position 242: invalid start byte

Edit: it seems like the problem is that the HMS Terrain file encoding is latin1 (according to Vim, anyway)? 😵 I've literally never seen that before. No clue if that's an HMS thing, a Model Library thing, or what. This works:

>>> with open("/mnt/c/temp/duwamish/Duwamish_SST.terrain", "r", encoding="latin1") as f:
...     f.read()
...
'Terrain Data Manager: Duwamish SST\n     Version: 4.12\n     Filepath Separator: \\\nEnd:\n\nTerrain Data: Duwamish_10M\n     Description: \n     Terrain Directory: terrain\\Duwamish_10M\n     Vertical Units: Feet\n     Stream Threshold: 1.5 mi²\n     Last Modified Date: 7 November 2023\n     Last Modified Time: 02:17:44\nEnd:\n'

Edit (again): it seems like cp1252 might be the correct encoding after doing some research. I made a small tweak to try to get around this...

diff --git a/hecstac/hms/parser.py b/hecstac/hms/parser.py
index 2762be3..e7bb31e 100644
--- a/hecstac/hms/parser.py
+++ b/hecstac/hms/parser.py
@@ -58,8 +58,12 @@ class BaseTextFile(ABC):

     def read_content(self):
         if os.path.exists(self.path):
-            with open(self.path) as f:
-                self.content = f.read()
+            try:
+                with open(self.path) as f:
+                    self.content = f.read()
+            except UnicodeDecodeError as e:
+                with open(self.path, encoding="cp1252") as f:
+                    self.content = f.read()
         else:
             try:
                 response = self.client.get_object(Bucket=self.bucket, Key=self.path)

...but ran into a different error?

>>> HMSModelItem("/mnt/c/temp/duwamish/Duwamish_SST.hms", "asdf")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/item.py", line 53, in __init__
    self._geometry,
    ^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/item.py", line 106, in _geometry
    geometries = [b.basin_geom.simplify(0.001) for b in self.pf.basins]
                  ^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 490, in basin_geom
    return utils.remove_holes(self.feature_2_gdf("Subbasin").make_valid().to_crs(4326).union_all())
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 497, in feature_2_gdf
    for e in self.elements.get_element_type(element_type):
             ^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 367, in elements
    sqlite = SqliteDB(
             ^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/hecstac/hms/parser.py", line 864, in __init__
    self.subbasin_feats = gpd.read_file(self.path, layer="subbasin2d", engine=GPD_WRITE_ENGINE)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/geopandas/io/file.py", line 306, in _read_file
    return _read_file_fiona(
           ^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/geopandas/io/file.py", line 418, in _read_file_fiona
    df = GeoDataFrame.from_features(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/geopandas/geodataframe.py", line 737, in from_features
    "geometry": shape(feature["geometry"]) if feature["geometry"] else None
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/shapely/geometry/geo.py", line 107, in shape
    return MultiPolygon([[c[0], c[1:]] for c in ob["coordinates"]])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/shapely/geometry/multipolygon.py", line 89, in __new__
    return shapely.multipolygons(subs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/shapely/decorators.py", line 77, in wrapped
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/thomaswilliams/dev/hecstac/venv-hecstac/lib/python3.12/site-packages/shapely/creation.py", line 429, in multipolygons
    return lib.create_collection(geometries, typ, out=out, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ufunc 'create_collection' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

[thwllms]

@sray014 I think I've thrown a lot at you so I'll pause and let you respond to the comments so far. I could very easily be doing something weird on my end. Let me know.

[sray014]

@thwllms The HMS Item creation is more @mdeshotel area of expertise. Might be better to make an issue on that with the HMS item and focus on ras items for this PR. What do you think @slawler ?

[sclaw]

I added a review in #11. Let me know if you have any questions.