Merge pull request #494 from PEtab-dev/develop

Release 0.1.13

Author: yannikschaelte

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## 0.1 series
 
+### 0.1.13
+
+* Fix for pandas 1.2.0 -- use `get_handle` instead of `get_filepath_or_buffer`
+* Fix erroneous `petab_test_suite` symlink (all #493)
+
 ### 0.1.12
 
 * Documentation update:

petab/sbml.py

@@ -1,6 +1,7 @@
 """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
 import libsbml
@@ -416,19 +417,10 @@ def get_sbml_model(
         File or URL or file handle to read the model from
     :return: The SBML document, model and reader
     """
-
-    from pandas.io.common import get_filepath_or_buffer, is_url, is_file_like
-
     if is_file_like(filepath_or_buffer) or is_url(filepath_or_buffer):
-        buffer = get_filepath_or_buffer(filepath_or_buffer, mode='r')[0]
-        if is_url(filepath_or_buffer):
-            buffer = ''.join(line.decode('utf-8') for line in buffer)
-        else:
-            buffer = ''.join(line for line in buffer)
-
+        handle = get_handle(filepath_or_buffer, mode='r').handle
         # URL or already opened file, we will load the model from a string
-
-        return load_sbml_from_string(buffer)
+        return load_sbml_from_string(''.join(handle))
 
     return load_sbml_from_file(filepath_or_buffer)
 

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = '0.1.12'
+__version__ = '0.1.13'

petab/yaml.py

@@ -6,7 +6,7 @@
 import jsonschema
 import numpy as np
 import yaml
-from pandas.io.common import get_filepath_or_buffer
+from pandas.io.common import get_handle
 
 from .C import *  # noqa: F403
 
@@ -123,13 +123,8 @@ def load_yaml(yaml_config: Union[Dict, str]) -> Dict:
     if isinstance(yaml_config, dict):
         return yaml_config
 
-    filepath_or_buffer = get_filepath_or_buffer(yaml_config, mode='r')[0]
-    if isinstance(filepath_or_buffer, str):
-        # a filename
-        with open(filepath_or_buffer, 'r') as f:
-            return yaml.safe_load(f)
-    # a stream
-    return yaml.safe_load(filepath_or_buffer)
+    handle = get_handle(yaml_config, mode='r').handle
+    return yaml.safe_load(handle)
 
 
 def is_composite_problem(yaml_config: Union[Dict, str]) -> bool:

setup.py

@@ -53,7 +53,7 @@ def absolute_links(txt):
       url='https://github.com/PEtab-dev/PEtab',
       packages=find_packages(exclude=['doc*', 'test*']),
       install_requires=['numpy>=1.15.1',
-                        'pandas>=1.0.1',
+                        'pandas>=1.2.0',
                         'matplotlib>=2.2.3',
                         'python-libsbml>=5.17.0',
                         'sympy',

tests/test_petab.py

@@ -545,7 +545,7 @@ def test_load_remote():
     """Test loading remote files"""
 
     yaml_url = "https://raw.githubusercontent.com/PEtab-dev/petab_test_suite" \
-               "/master/cases/0001/_0001.yaml"
+               "/master/petabtests/cases/0001/_0001.yaml"
     petab_problem = petab.Problem.from_yaml(yaml_url)
 
     assert petab_problem.sbml_model is not None