reslove conflicts in bctides

CITATION.cff

@@ -0,0 +1,14 @@
+cff-version: 1.2.0
+message: "If you used this software as part of your work, please use the following citation format."
+authors:
+  - family-names: Calzada
+    given-names: Jaime R
+    orcid: https://orcid.org/0000-0002-3172-1906
+  - family-names: Cui
+    given-names: Linlin
+  - family-names: Zhang
+    given-names: Joseph
+title: "PySCHISM"
+version: v0.1.5
+doi: 10.5281/zenodo.7623122
+date-released: 2023-02-08

README.md

@@ -1,5 +1,6 @@
 # PySCHISM
 [![codecov](https://codecov.io/gh/schism-dev/pyschism/branch/main/graph/badge.svg?token=VE9PHEACBZ)](https://codecov.io/gh/schism-dev/pyschism)
+[![DOI](https://zenodo.org/badge/233075737.svg)](https://zenodo.org/badge/latestdoi/233075737)
 
 ## A Python interface for SCHISM model runs.
 
@@ -58,11 +59,22 @@ hgrid = Hgrid.open('hgrid.gr3')
 hgrid.write("/path/to/output/file.2dm", fmt='2dm')
 ```
 ---
+## References
+
+If you used this software as part of your work, please use the following citation format.
+
+Jaime R Calzada, Linlin Cui, & Joseph Zhang. (2023). schism-dev/pyschism: v0.1.5 (v0.1.5). Zenodo. https://doi.org/10.5281/zenodo.7623122
+
+---
+
+
+
 Questions, comments and suggestions are welcome. Please follow the instructions on the `CONTRIBUTING.md` file for contributions. For bug reports and feature requests, please open an issue using the issue tracker.
-Author contact: [email protected]
+Main author name: Jaime R Calzada
+Author contact: [email protected]
 
 
 ---
     “Marconi is a good fellow. Let him continue. He is using seventeen of my patents.”
     Nikola Tesla
----
+---

pyschism/driver.py

@@ -364,6 +364,7 @@ def __init__(
                 self.config.forcings.nws.windrot = gridgr3.Windrot.default(
                     self.config.hgrid
                 )
+                self.param.opt.model_type_pahm = self.config.forcings.nws.model.value
 
             self.param.opt.wtiminc = self.param.core.dt
             self.param.opt.nws = self.config.forcings.nws.dtype.value

pyschism/forcing/bctides/bctides.py

@@ -1,9 +1,10 @@
 from datetime import datetime, timedelta
-from functools import cached_property
+from functools import cached_property, lru_cache
 import pathlib
 from typing import Dict, Union
 import logging
 
+from ordered_set import OrderedSet
 import numpy as np
 
 from pyschism import dates
@@ -310,7 +311,7 @@ def __init__(self, gdf):
             )
 
     def get_active_forcing_constituents(self):
-        active_constituents = set()
+        active_constituents = OrderedSet()
         for row in self.gdf.itertuples():
             if row.iettype is not None:
                 if row.iettype.iettype in [3, 5]:
@@ -328,7 +329,7 @@ def get_active_forcing_constituents(self):
         return list(active_constituents)
 
     def get_active_potential_constituents(self):
-        active_constituents = set()
+        active_constituents = OrderedSet()
         for row in self.gdf.itertuples():
             if row.iettype is not None:
                 if row.iettype.iettype in [3, 5]:
@@ -345,16 +346,14 @@ def get_active_potential_constituents(self):
 
         return list(active_constituents)
 
-    @cached_property
-    def constituents(self):
-        return sorted(
-            list(
-                set(
-                    [
-                        *self.get_active_potential_constituents(),
-                        *self.get_active_forcing_constituents(),
-                    ]
-                )
+    @lru_cache
+    def get_active_constituents(self):
+        return list(
+            OrderedSet(
+                [
+                    *self.get_active_potential_constituents(),
+                    *self.get_active_forcing_constituents(),
+                ]
             )
         )
 

pyschism/forcing/nws/best_track.py

@@ -2,26 +2,31 @@
 import io
 import logging
 import os
-from os import PathLike
 import pathlib
+from enum import IntEnum
+from os import PathLike
 from typing import Union
 
-from matplotlib import pyplot
-from matplotlib.axis import Axis
 from matplotlib.transforms import Bbox
 import numpy as numpy
 from pandas import DataFrame
 from pyproj import CRS, Transformer
 from shapely import ops
 from shapely.geometry import Point, Polygon
 from stormevents.nhc import VortexTrack
-from stormevents.nhc.atcf import ATCF_Mode
 import utm
 
 from pyschism.enums import NWSType
 from pyschism.forcing.nws.base import NWS
-from pyschism.forcing.nws.nws2.sflux import SfluxDataset
-from pyschism.mesh import gridgr3
+
+
+class HurricaneModel(IntEnum):
+    SYMMETRIC = 1
+    GAHM = 10
+
+    @classmethod
+    def _missing_(cls, value):
+        raise ValueError(f"Invalid hurricane model specified: {value}, choose from: {cls.__members__}")
 
 
 class BestTrackForcing(VortexTrack, NWS):
@@ -31,9 +36,10 @@ def __init__(
         storm: Union[str, PathLike, DataFrame, io.BytesIO],
         start_date: datetime = None,
         end_date: datetime = None,
-        mode: ATCF_Mode = None,
+        hurricane_model: Union[str, HurricaneModel] = 'gahm'
     ):
 
+        self.model = hurricane_model
 
         VortexTrack.__init__(
             self,
@@ -44,12 +50,10 @@ def __init__(
             advisories=['BEST'],
         )
 
-
     def __str__(self):
         """Returns string used in param.nml"""
         return f"{self.dtype.value}"
 
-
     @classmethod
     def from_nhc_bdeck(
         cls,
@@ -99,6 +103,26 @@ def dtype(self) -> NWSType:
         """Returns the datatype of the object"""
         return NWSType(-1)
 
+    @property
+    def model(self) -> HurricaneModel:
+        """Return hurricane model used for this best track forcing"""
+        return self._model
+
+    @model.setter
+    def model(self, value: Union[str, HurricaneModel]):
+        """Set hurricane model used for this best track forcing"""
+        if isinstance(value, str):
+            if value.upper() not in HurricaneModel.__members__:
+                raise ValueError(f"Invalid hurricane model specified: {value}, choose from: {HurricaneModel.__members__}")
+            value = HurricaneModel[value.upper()]
+        elif isinstance(value, int):
+            value = HurricaneModel(value)
+        elif isinstance(value, HurricaneModel):
+            pass
+        else:
+            raise ValueError(f"Invalid hurricane model specified: {value}")
+        self._model = value
+
     def clip_to_bbox(self, bbox, bbox_crs):
         msg = f'bbox must be a {Bbox} instance.'
         assert isinstance(bbox, Bbox), msg

pyschism/forcing/source_sink/nwm.py

@@ -338,7 +338,7 @@ def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
                             if not is_within_directory(path, member_path):
                                 raise Exception("Attempted Path Traversal in Tar File")
 
-                        tar.extractall(path, members, numeric_owner) 
+                        tar.extractall(path, members, numeric_owner=numeric_owner)
 
 
                     safe_extract(src, DATADIR)

setup.cfg

@@ -11,5 +11,8 @@ url = https://github.com/schism-dev/pyschism.git
 exe = True
 tests = tests/
 
+[flake8]
+max-line-length = 130
+
 [mypy]
 plugins = sqlmypy

setup.py

@@ -102,33 +102,33 @@ def run(self):
         "build_schism": BuildSchism
     },
     install_requires=[
-        'pygeos',
+        'boto3',
+        'cdsapi',
+        'cf-python',
+        'cfgrib',
+        'f90nml',
+        'fsspec',
         'geopandas',
-        'netcdf-flattener>=1.2.0',
+        'metpy',
         'netCDF4',
-        'f90nml',
+        'netcdf-flattener>=1.2.0',
+        'numba',
+        'ordered-set',
         'psutil',
-        'scipy',
-        'wget',
-        'cf-python',
-        'metpy',
-        'sqlalchemy',
+        'pygeos',
         'pyugrid',
-        'boto3',
         'rtree',
-        'numba',
+        'scipy',
+        'seawater',
+        'sqlalchemy',
+        'stormevents',
         'tqdm',
         'tqdm-logging-wrapper',
-        'xmltodict',
-        'cdsapi',
-        'seawater',
+        'utm',
+        'wget',
         'xarray',
-        'cfgrib',
+        'xmltodict',
         'zarr',
-        'fsspec',
-        'stormevents',
-        'utm',
-        # 'dask_geopandas @ git+git://github.com/geopandas/dask-geopandas.git@master',
     ],
     entry_points={'console_scripts': ['pyschism = pyschism.__main__:main']},
     tests_require=['nose'],