Add support for pathlib.Path (#93)

Add support for pathlib.Path for reading PEtab tables and other files

Closes #82

Co-authored-by: Dilan Pathirana <[email protected]>

Author: dweindl

petab/conditions.py

@@ -1,19 +1,20 @@
 """Functions operating on the PEtab condition table"""
 
-from typing import Iterable, Optional, List, Union
+from pathlib import Path
+from typing import Iterable, List, Optional, Union
 
 import numpy as np
 import pandas as pd
 
-from . import lint, core
+from . import core, lint
 from .C import *
 
 __all__ = ['get_condition_df', 'write_condition_df', 'create_condition_df',
            'get_parametric_overrides']
 
 
 def get_condition_df(
-        condition_file: Union[str, pd.DataFrame, None]
+        condition_file: Union[str, pd.DataFrame, Path, None]
 ) -> pd.DataFrame:
     """Read the provided condition file into a ``pandas.Dataframe``
 
@@ -25,7 +26,7 @@ def get_condition_df(
     if condition_file is None:
         return condition_file
 
-    if isinstance(condition_file, str):
+    if isinstance(condition_file, (str, Path)):
         condition_file = pd.read_csv(condition_file, sep='\t',
                                      float_precision='round_trip')
 
@@ -44,7 +45,7 @@ def get_condition_df(
     return condition_file
 
 
-def write_condition_df(df: pd.DataFrame, filename: str) -> None:
+def write_condition_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
     """Write PEtab condition table
 
     Arguments:

petab/core.py

@@ -1,5 +1,5 @@
 """PEtab core functions (or functions that don't fit anywhere else)"""
-
+from pathlib import Path
 import logging
 import os
 import re
@@ -43,7 +43,7 @@ def write_simulation_df(df: pd.DataFrame, filename: str) -> None:
     df.to_csv(filename, sep='\t', index=False)
 
 
-def get_visualization_df(visualization_file: str) -> pd.DataFrame:
+def get_visualization_df(visualization_file: Union[str, Path]) -> pd.DataFrame:
     """Read PEtab visualization table
 
     Arguments:
@@ -62,7 +62,9 @@ def get_visualization_df(visualization_file: str) -> pd.DataFrame:
     return vis_spec
 
 
-def write_visualization_df(df: pd.DataFrame, filename: str) -> None:
+def write_visualization_df(
+        df: pd.DataFrame, filename: Union[str, Path]
+) -> None:
     """Write PEtab visualization table
 
     Arguments:
@@ -241,8 +243,8 @@ def is_empty(val) -> bool:
 
 
 def create_combine_archive(
-        yaml_file: str,
-        filename: str,
+        yaml_file: Union[str, Path],
+        filename: Union[str, Path],
         family_name: Optional[str] = None,
         given_name: Optional[str] = None,
         email: Optional[str] = None,
@@ -260,7 +262,7 @@ def create_combine_archive(
         organization: Organization of archive creator
     """
 
-    path_prefix = os.path.dirname(yaml_file)
+    path_prefix = os.path.dirname(str(yaml_file))
     yaml_config = yaml.load_yaml(yaml_file)
 
     # function-level import, because module-level import interfered with
@@ -285,7 +287,7 @@ def _add_file_metadata(location: str, description: str = ""):
 
     # Add PEtab files and metadata
     archive.addFile(
-        yaml_file,
+        str(yaml_file),
         os.path.basename(yaml_file),
         libcombine.KnownFormats.lookupFormat("yaml"),
         True
@@ -353,7 +355,7 @@ def _add_file_metadata(location: str, description: str = ""):
     description.addCreator(creator)
 
     archive.addMetadata(".", description)
-    archive.writeToFile(filename)
+    archive.writeToFile(str(filename))
 
 
 def unique_preserve_order(seq: Sequence) -> List:

petab/measurements.py

@@ -1,16 +1,16 @@
 """Functions operating on the PEtab measurement table"""
 # noqa: F405
 
-
 import itertools
 import numbers
-from typing import List, Union, Dict
+from pathlib import Path
+from typing import Dict, List, Union
 from warnings import warn
 
 import numpy as np
 import pandas as pd
 
-from . import (lint, core, observables)
+from . import (core, lint, observables)
 from .C import *  # noqa: F403
 
 __all__ = ['assert_overrides_match_parameter_count',
@@ -26,7 +26,7 @@
 
 
 def get_measurement_df(
-        measurement_file: Union[None, str, pd.DataFrame]
+        measurement_file: Union[None, str, Path, pd.DataFrame]
 ) -> pd.DataFrame:
     """
     Read the provided measurement file into a ``pandas.Dataframe``.
@@ -40,7 +40,7 @@ def get_measurement_df(
     if measurement_file is None:
         return measurement_file
 
-    if isinstance(measurement_file, str):
+    if isinstance(measurement_file, (str, Path)):
         measurement_file = pd.read_csv(measurement_file, sep='\t',
                                        float_precision='round_trip')
 
@@ -50,7 +50,7 @@ def get_measurement_df(
     return measurement_file
 
 
-def write_measurement_df(df: pd.DataFrame, filename: str) -> None:
+def write_measurement_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
     """Write PEtab measurement table
 
     Arguments:

petab/observables.py

@@ -1,14 +1,15 @@
 """Functions for working with the PEtab observables table"""
 
+import re
 from collections import OrderedDict
-from typing import Union, List
+from pathlib import Path
+from typing import List, Union
 
 import libsbml
 import pandas as pd
-import re
 import sympy as sp
 
-from . import lint, core
+from . import core, lint
 from .C import *  # noqa: F403
 
 __all__ = ['create_observable_df',
@@ -20,7 +21,7 @@
 
 
 def get_observable_df(
-        observable_file: Union[str, pd.DataFrame, None]
+        observable_file: Union[str, pd.DataFrame, Path, None]
 ) -> pd.DataFrame:
     """
     Read the provided observable file into a ``pandas.Dataframe``.
@@ -34,7 +35,7 @@ def get_observable_df(
     if observable_file is None:
         return observable_file
 
-    if isinstance(observable_file, str):
+    if isinstance(observable_file, (str, Path)):
         observable_file = pd.read_csv(observable_file, sep='\t',
                                       float_precision='round_trip')
 
@@ -53,7 +54,7 @@ def get_observable_df(
     return observable_file
 
 
-def write_observable_df(df: pd.DataFrame, filename: str) -> None:
+def write_observable_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
     """Write PEtab observable table
 
     Arguments:

petab/parameters.py

@@ -1,14 +1,15 @@
 """Functions operating on the PEtab parameter table"""
 
 import numbers
-import pandas as pd
-import numpy as np
 from collections import OrderedDict
-from typing import Iterable, Set, List, Tuple, Dict, Union
+from pathlib import Path
+from typing import Dict, Iterable, List, Set, Tuple, Union
 
 import libsbml
+import numpy as np
+import pandas as pd
 
-from . import lint, core, measurements, conditions, observables
+from . import conditions, core, lint, measurements, observables
 from .C import *  # noqa: F403
 
 __all__ = ['create_parameter_df',
@@ -27,7 +28,7 @@
 
 
 def get_parameter_df(
-        parameter_file: Union[str, List[str], pd.DataFrame, None]
+        parameter_file: Union[str, Path, List[str], pd.DataFrame, None]
 ) -> pd.DataFrame:
     """
     Read the provided parameter file into a ``pandas.Dataframe``.
@@ -46,7 +47,7 @@ def get_parameter_df(
     if isinstance(parameter_file, pd.DataFrame):
         parameter_df = parameter_file
 
-    if isinstance(parameter_file, str):
+    if isinstance(parameter_file, (str, Path)):
         parameter_df = pd.read_csv(parameter_file, sep='\t',
                                    float_precision='round_trip')
 
@@ -82,7 +83,7 @@ def get_parameter_df(
     return parameter_df
 
 
-def write_parameter_df(df: pd.DataFrame, filename: str) -> None:
+def write_parameter_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
     """Write PEtab parameter table
 
     Arguments:

petab/problem.py

@@ -1,8 +1,7 @@
 """PEtab Problem class"""
 
 import os
-# Renamed to `Path_` to avoid unknown error during Sphinx doc build
-from pathlib import Path as Path_
+from pathlib import Path
 import tempfile
 from typing import Dict, Iterable, List, Optional, Union
 from warnings import warn
@@ -237,7 +236,7 @@ def from_folder(folder: str, model_name: str = None) -> 'Problem':
         )
 
     @staticmethod
-    def from_combine(filename: str) -> 'Problem':
+    def from_combine(filename: Union[Path, str]) -> 'Problem':
         """Read PEtab COMBINE archive (http://co.mbine.org/documents/archive).
 
         See also :py:func:`petab.create_combine_archive`.
@@ -258,7 +257,7 @@ def from_combine(filename: str) -> 'Problem':
                 "(python-libcombine) must be installed.")
 
         archive = libcombine.CombineArchive()
-        if archive.initializeFromArchive(filename) is None:
+        if archive.initializeFromArchive(str(filename)) is None:
             print(f"Invalid Combine Archive: {filename}")
             return None
 
@@ -273,7 +272,7 @@ def from_combine(filename: str) -> 'Problem':
 
     def to_files_generic(
         self,
-        prefix_path: Union[str, Path_],
+        prefix_path: Union[str, Path],
     ) -> None:
         """Save a PEtab problem to generic file names.
 
@@ -292,7 +291,7 @@ def to_files_generic(
         Returns:
             The path to the PEtab problem YAML file.
         """
-        prefix_path = Path_(prefix_path)
+        prefix_path = Path(prefix_path)
 
         # Generate generic filenames for data tables in the PEtab problem that
         # contain data.
@@ -326,7 +325,7 @@ def to_files(self,
                  visualization_file: Optional[str] = None,
                  observable_file: Optional[str] = None,
                  yaml_file: Optional[str] = None,
-                 prefix_path: Optional[Union[str, Path_]] = None,
+                 prefix_path: Optional[Union[str, Path]] = None,
                  relative_paths: bool = True,) -> None:
         """
         Write PEtab tables to files for this problem
@@ -359,9 +358,9 @@ def to_files(self,
                 If a destination was provided for a non-existing entity.
         """
         if prefix_path is not None:
-            prefix_path = Path_(prefix_path)
+            prefix_path = Path(prefix_path)
 
-            def add_prefix(path0: Union[None, str, Path_]) -> str:
+            def add_prefix(path0: Union[None, str, Path]) -> str:
                 if path0 is None:
                     return path0
                 return str(prefix_path / path0)

petab/sbml.py

@@ -1,10 +1,12 @@
 """Functions for interacting with SBML models"""
-from warnings import warn
 import logging
-from pandas.io.common import get_handle, is_url, is_file_like
 import re
-from typing import Dict, Any, List, Union, Tuple
+from pathlib import Path
+from typing import Any, Dict, List, Tuple, Union
+from warnings import warn
+
 import libsbml
+from pandas.io.common import get_handle, is_file_like, is_url
 
 logger = logging.getLogger(__name__)
 __all__ = ['add_global_parameter',
@@ -413,15 +415,18 @@ def get_model_parameters(sbml_model: libsbml.Model, with_values=False
             if sbml_model.getAssignmentRuleByVariable(p.getId()) is None}
 
 
-def write_sbml(sbml_doc: libsbml.SBMLDocument, filename: str) -> None:
+def write_sbml(
+        sbml_doc: libsbml.SBMLDocument,
+        filename: Union[Path, str]
+) -> None:
     """Write PEtab visualization table
 
     Arguments:
         sbml_doc: SBML document containing the SBML model
         filename: Destination file name
     """
     sbml_writer = libsbml.SBMLWriter()
-    ret = sbml_writer.writeSBMLToFile(sbml_doc, filename)
+    ret = sbml_writer.writeSBMLToFile(sbml_doc, str(filename))
     if not ret:
         raise RuntimeError(f"libSBML reported error {ret} when trying to "
                            f"create SBML file {filename}.")