Merge pull request #601 from DHI/pathlib

pathlib instead of os.path

docs/conf.py

@@ -4,16 +4,6 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
 
 # -- Project information -----------------------------------------------------
 

mikeio/__init__.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 from platform import architecture
 
 # PEP0440 compatible formatted version, see:
@@ -117,7 +117,7 @@ def read(filename, *, items=None, time=None, keepdims=False, **kwargs) -> Datase
     >>> ds = mikeio.read("HD2D.dfsu", error_bad_data=False, fill_bad_data_value=0.0) # replace corrupt data with 0.0
     """
 
-    ext = os.path.splitext(filename)[1].lower()
+    ext = Path(filename).suffix.lower()
 
     if "dfs" not in ext:
         raise ValueError("mikeio.read() is only supported for Dfs files")
@@ -156,7 +156,7 @@ def open(filename: str, **kwargs):
 
     >>> dfs = mikeio.open("pt_spectra.dfs2", type="spectral")
     """
-    file_format = os.path.splitext(filename)[1].lower()[1:]
+    ext = Path(filename).suffix.lower()[1:]
 
     READERS = {
         "dfs0": Dfs0,
@@ -167,13 +167,13 @@ def open(filename: str, **kwargs):
         "mesh": Mesh,
     }
 
-    if file_format not in READERS:
+    if ext not in READERS:
         valid_formats = ", ".join(READERS.keys())
         raise Exception(
-            f"{file_format} is not a supported format for mikeio.open. Valid formats are {valid_formats}"
+            f"{ext} is not a supported format for mikeio.open. Valid formats are {valid_formats}"
         )
 
-    reader_klass = READERS[file_format]
+    reader_klass = READERS[ext]
 
     return reader_klass(filename, **kwargs)
 

mikeio/_track.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-import os
+from pathlib import Path
 from datetime import datetime
 from typing import Callable, Sequence, Tuple
 
@@ -36,20 +36,22 @@ def _extract_track(
 
     if isinstance(track, str):
         filename = track
-        if os.path.exists(filename):
-            ext = os.path.splitext(filename)[1].lower()
-            if ext == ".dfs0":
-                df = Dfs0(filename).to_dataframe()
-            elif ext == ".csv":
-                df = pd.read_csv(filename, index_col=0, parse_dates=True)
-                df.index = pd.DatetimeIndex(df.index)
-            else:
-                raise ValueError(f"{ext} files not supported (dfs0, csv)")
-
-            times = df.index
-            coords = df.iloc[:, 0:2].to_numpy(copy=True)
-        else:
+        path = Path(filename)
+        if not path.exists():
             raise ValueError(f"{filename} does not exist")
+
+        ext = path.suffix.lower()
+        if ext == ".dfs0":
+            df = Dfs0(filename).to_dataframe()
+        elif ext == ".csv":
+            df = pd.read_csv(filename, index_col=0, parse_dates=True)
+            df.index = pd.DatetimeIndex(df.index)
+        else:
+            raise ValueError(f"{ext} files not supported (dfs0, csv)")
+
+        times = df.index
+        coords = df.iloc[:, 0:2].to_numpy(copy=True)
+
     elif isinstance(track, Dataset):
         times = track.time
         coords = np.zeros(shape=(len(times), 2))

mikeio/dataset/_dataarray.py

@@ -291,7 +291,8 @@ def _is_compatible(self, other, raise_error=False):
             problems.append("Number of timesteps must be the same")
         if self.start_time != other.start_time:
             problems.append("start_time must be the same")
-        if type(self.geometry) != type(other.geometry):
+        #if type(self.geometry) != type(other.geometry):
+        if not isinstance(self.geometry, other.geometry.__class__):
             problems.append("The type of geometry must be the same")
         if hasattr(self.geometry, "__eq__"):
             if not (self.geometry == self.geometry):

mikeio/dataset/_dataset.py

@@ -1,5 +1,5 @@
 from __future__ import annotations
-import os
+from pathlib import Path
 import warnings
 from copy import deepcopy
 from datetime import datetime
@@ -1838,7 +1838,8 @@ def to_dfs(self, filename, **kwargs):
 
     @staticmethod
     def _validate_extension(filename, valid_extension):
-        ext = os.path.splitext(filename)[1].lower()
+        path = Path(filename)
+        ext = path.suffix.lower()
         if ext != valid_extension:
             raise ValueError(f"File extension must be {valid_extension}")
 

mikeio/dfs/_dfs.py

@@ -254,7 +254,7 @@ class _Dfs123:
 
     # TODO add all common arguments
     def __init__(self, filename=None):
-        self._filename = str(filename)
+        self._filename = str(filename) if filename else None
         self._projstr = None
         self._start_time = None
         self._end_time = None

mikeio/dfs/_dfs0.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 import warnings
 from datetime import datetime, timedelta
 
@@ -104,12 +104,13 @@ def __init__(self, filename=None):
         self._filename = str(filename)
 
         if filename:
-            self._read_header()
+            self._read_header(Path(filename))
 
     def __repr__(self):
         out = ["<mikeio.Dfs0>"]
 
-        if os.path.isfile(self._filename):
+        # TODO does this make sense:
+        if self._filename:
             out.append(f"timeaxis: {repr(self._timeaxistype)}")
 
         if self._n_items is not None:
@@ -122,11 +123,11 @@ def __repr__(self):
 
         return str.join("\n", out)
 
-    def _read_header(self):
-        if not os.path.exists(self._filename):
-            raise FileNotFoundError(self._filename)
+    def _read_header(self, path: Path):
+        if not path.exists():
+            raise FileNotFoundError(path)
 
-        dfs = DfsFileFactory.DfsGenericOpen(self._filename)
+        dfs = DfsFileFactory.DfsGenericOpen(str(path))
         self._source = dfs
         self._deletevalue = dfs.FileInfo.DeleteValueDouble  # NOTE: changed in cutil
 
@@ -164,10 +165,10 @@ def read(self, items=None, time=None, keepdims=False) -> Dataset:
         -------
         Dataset
             A Dataset with data dimensions [t]
-        """
-
-        if not os.path.exists(self._filename):
-            raise FileNotFoundError(f"File {self._filename} not found.")
+        """        
+        path = Path(self._filename)
+        if not path.exists():
+            raise FileNotFoundError(f"File {path} not found")
 
         # read data from file
         fdata, ftime, fitems = self.__read(self._filename)

mikeio/dfs/_dfs1.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 from mikecore.DfsBuilder import DfsBuilder  # type: ignore
 from mikecore.DfsFileFactory import DfsFileFactory  # type: ignore
@@ -20,7 +20,7 @@ def __init__(self, filename=None):
         self._x0 = 0
 
         if filename:
-            self._read_dfs1_header()
+            self._read_dfs1_header(path=Path(filename))
             origin = self._longitude, self._latitude
             self.geometry = Grid1D(
                 x0=self._x0,
@@ -34,7 +34,8 @@ def __init__(self, filename=None):
     def __repr__(self):
         out = ["<mikeio.Dfs1>"]
 
-        if os.path.isfile(self._filename):
+        # TODO does this make sense
+        if self._filename:
             out.append(f"dx: {self.dx:.5f}")
 
             if self._n_items is not None:
@@ -44,20 +45,20 @@ def __repr__(self):
                         out.append(f"  {i}:  {item}")
                 else:
                     out.append(f"number of items: {self._n_items}")
-            if os.path.isfile(self._filename):
-                if self._n_timesteps == 1:
-                    out.append("time: time-invariant file (1 step)")
-                else:
-                    out.append(f"time: {self._n_timesteps} steps")
-                    out.append(f"start time: {self._start_time}")
+
+            if self._n_timesteps == 1:
+                out.append("time: time-invariant file (1 step)")
+            else:
+                out.append(f"time: {self._n_timesteps} steps")
+                out.append(f"start time: {self._start_time}")
 
         return str.join("\n", out)
 
-    def _read_dfs1_header(self):
-        if not os.path.isfile(self._filename):
-            raise FileNotFoundError(self._filename)
+    def _read_dfs1_header(self, path: Path):
+        if not path.exists():
+            raise FileNotFoundError(path)
 
-        self._dfs = DfsFileFactory.Dfs1FileOpen(self._filename)
+        self._dfs = DfsFileFactory.Dfs1FileOpen(str(path))
         self._x0 = self._dfs.SpatialAxis.X0
         self._dx = self._dfs.SpatialAxis.Dx
         self._nx = self._dfs.SpatialAxis.XCount

mikeio/dfs/_dfs2.py

@@ -1,4 +1,3 @@
-import os
 from typing import List, Tuple
 
 from copy import deepcopy
@@ -120,7 +119,7 @@ def __init__(self, filename=None, type: str = "horizontal"):
 
         if filename:
             is_spectral = type.lower() in ["spectral", "spectra", "spectrum"]
-            self._read_dfs2_header(read_x0y0=is_spectral)
+            self._read_dfs2_header(filename=filename, read_x0y0=is_spectral)
             self._validate_no_orientation_in_geo()
             origin, orientation = self._origin_and_orientation_in_CRS()
 
@@ -140,7 +139,7 @@ def __init__(self, filename=None, type: str = "horizontal"):
     def __repr__(self):
         out = ["<mikeio.Dfs2>"]
 
-        if os.path.isfile(self._filename):
+        if self._filename:
             out.append(f"dx: {self.dx:.5f}")
             out.append(f"dy: {self.dy:.5f}")
 
@@ -160,11 +159,8 @@ def __repr__(self):
 
         return str.join("\n", out)
 
-    def _read_dfs2_header(self, read_x0y0: bool = False):
-        if not os.path.isfile(self._filename):
-            raise Exception(f"file {self._filename} does not exist!")
-
-        self._dfs = DfsFileFactory.Dfs2FileOpen(self._filename)
+    def _read_dfs2_header(self, filename, read_x0y0: bool = False):
+        self._dfs = DfsFileFactory.Dfs2FileOpen(str(filename))
         self._source = self._dfs
         if read_x0y0:
             self._x0 = self._dfs.SpatialAxis.X0

mikeio/dfs/_dfs3.py

@@ -1,5 +1,3 @@
-import os
-
 from typing import Tuple
 
 import numpy as np
@@ -142,7 +140,8 @@ def __init__(self, filename=None):
     def __repr__(self):
         out = ["<mikeio.Dfs3>"]
 
-        if os.path.isfile(self._filename):
+
+        if self._filename:
             out.append(f"geometry: {self.geometry}")
 
             if self._n_items is not None:
@@ -162,9 +161,6 @@ def __repr__(self):
         return str.join("\n", out)
 
     def _read_dfs3_header(self, read_x0y0z0: bool = False):
-        if not os.path.isfile(self._filename):
-            raise Exception(f"file {self._filename} does not exist!")
-
         self._dfs = DfsFileFactory.Dfs3FileOpen(self._filename)
 
         self._source = self._dfs

mikeio/dfsu/_dfsu.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 import os
+from pathlib import Path
 import warnings
 from datetime import datetime, timedelta
 from functools import wraps
@@ -175,10 +176,11 @@ def _read_header(self, input):
             return
 
         filename = input
-        if not os.path.isfile(filename):
-            raise Exception(f"file {filename} does not exist!")
+        path = Path(input)
+        if not path.exists():
+            raise FileNotFoundError(f"file {path} does not exist!")
 
-        ext = os.path.splitext(filename)[1].lower()
+        ext = path.suffix.lower()
 
         if ext == ".mesh":
             self._read_mesh_header(filename)

mikeio/dfsu/_factory.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 
 from mikecore.DfsuFile import DfsuFile, DfsuFileType  # type: ignore
 
@@ -25,7 +25,7 @@ def __new__(self, filename, *args, **kwargs):
 
     @staticmethod
     def _get_DfsuFileType_n_Obj(filename: str):
-        ext = os.path.splitext(filename)[-1].lower()
+        ext = Path(filename).suffix.lower()
         if "dfs" in ext:
             dfs = DfsuFile.Open(filename)
             type = DfsuFileType(dfs.DfsuFileType)