Support pathlib.Path for result/history files

ICB-DCM · Dec 14, 2023 · e905eb2 · e905eb2
1 parent 00d281d
commit e905eb2
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Showing 5 changed files with 36 additions and 27 deletions.
diff --git a/pypesto/history/hdf5.py b/pypesto/history/hdf5.py
@@ -151,15 +151,17 @@ def finalize(self, message: str = None, exitflag: str = None) -> None:
 
     @staticmethod
     def load(
-        id: str, file: str, options: Union[HistoryOptions, dict] = None
+        id: str,
+        file: Union[str, Path],
+        options: Union[HistoryOptions, dict] = None,
     ) -> 'Hdf5History':
         """Load the History object from memory."""
         history = Hdf5History(id=id, file=file, options=options)
         if options is None:
             history.recover_options(file)
         return history
 
-    def recover_options(self, file: str):
+    def recover_options(self, file: Union[str, Path]):
         """Recover options when loading the hdf5 history from memory.
 
         Done by testing which entries were recorded.

diff --git a/pypesto/history/options.py b/pypesto/history/options.py
@@ -49,7 +49,7 @@ def __init__(
         trace_record_res: bool = True,
         trace_record_sres: bool = True,
         trace_save_iter: int = 10,
-        storage_file: Union[str, None] = None,
+        storage_file: Union[str, Path, None] = None,
     ):
         super().__init__()
 

diff --git a/pypesto/store/auto.py b/pypesto/store/auto.py
@@ -4,6 +4,7 @@
 import datetime
 import logging
 import os
+from pathlib import Path
 from typing import Callable, Union
 
 import h5py
@@ -15,7 +16,7 @@
 
 
 def autosave(
-    filename: Union[str, Callable, None],
+    filename: Union[Path, str, Callable, None],
     result: Result,
     store_type: str,
     overwrite: bool = False,
@@ -43,6 +44,9 @@ def autosave(
     if filename is None:
         return
 
+    if isinstance(filename, Path):
+        filename = str(filename)
+
     if filename == "Auto":
         filename = default_filename
     elif isinstance(filename, str):

diff --git a/pypesto/store/read_from_hdf5.py b/pypesto/store/read_from_hdf5.py
@@ -2,6 +2,8 @@
 
 import ast
 import logging
+from pathlib import Path
+from typing import Union
 
 import h5py
 import numpy as np
@@ -48,7 +50,7 @@ def read_hdf5_profile(
 
 def read_hdf5_optimization(
     f: h5py.File,
-    file_name: str,
+    file_name: Union[Path, str],
     opt_id: str,
 ) -> 'OptimizerResult':
     """Read HDF5 results per start.
@@ -91,12 +93,12 @@ class ProblemHDF5Reader:
         HDF5 problem file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """Initialize reader.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 problem file name
         """
         self.storage_filename = storage_filename
@@ -153,13 +155,13 @@ class OptimizationResultHDF5Reader:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize reader.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 result file name
         """
         self.storage_filename = storage_filename
@@ -187,12 +189,12 @@ class SamplingResultHDF5Reader:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """Initialize reader.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 result file name
         """
         self.storage_filename = storage_filename
@@ -226,7 +228,7 @@ class ProfileResultHDF5Reader:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize reader.
 
@@ -261,7 +263,7 @@ def read(self) -> Result:
 
 
 def read_result(
-    filename: str,
+    filename: Union[Path, str],
     problem: bool = True,
     optimize: bool = False,
     profile: bool = False,
@@ -339,7 +341,7 @@ def read_result(
     return result
 
 
-def load_objective_config(filename: str):
+def load_objective_config(filename: Union[str, Path]):
     """Load the objective information stored in f.
 
     Parameters

diff --git a/pypesto/store/save_to_hdf5.py b/pypesto/store/save_to_hdf5.py
@@ -3,6 +3,7 @@
 import logging
 import os
 from numbers import Integral
+from pathlib import Path
 from typing import Union
 
 import h5py
@@ -52,16 +53,16 @@ class ProblemHDF5Writer:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize writer.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 problem file name
         """
-        self.storage_filename = storage_filename
+        self.storage_filename = str(storage_filename)
 
     def write(self, problem, overwrite: bool = False):
         """Write HDF5 problem file from pyPESTO problem object."""
@@ -105,16 +106,16 @@ class OptimizationResultHDF5Writer:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize Writer.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 result file name
         """
-        self.storage_filename = storage_filename
+        self.storage_filename = str(storage_filename)
 
     def write(self, result: Result, overwrite=False):
         """Write HDF5 result file from pyPESTO result object."""
@@ -154,16 +155,16 @@ class SamplingResultHDF5Writer:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize Writer.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 result file name
         """
-        self.storage_filename = storage_filename
+        self.storage_filename = str(storage_filename)
 
     def write(self, result: Result, overwrite: bool = False):
         """Write HDF5 sampling file from pyPESTO result object."""
@@ -207,16 +208,16 @@ class ProfileResultHDF5Writer:
         HDF5 result file name
     """
 
-    def __init__(self, storage_filename: str):
+    def __init__(self, storage_filename: Union[str, Path]):
         """
         Initialize Writer.
 
         Parameters
         ----------
-        storage_filename: str
+        storage_filename:
             HDF5 result file name
         """
-        self.storage_filename = storage_filename
+        self.storage_filename = str(storage_filename)
 
     def write(self, result: Result, overwrite: bool = False):
         """Write HDF5 result file from pyPESTO result object."""
@@ -266,7 +267,7 @@ def _write_profiler_result(
 
 def write_result(
     result: Result,
-    filename: str,
+    filename: Union[str, Path],
     overwrite: bool = False,
     problem: bool = True,
     optimize: bool = False,