Release 0.1.22

Merge pull request #94 from PEtab-dev/release/0.1.22

Author: dweindl

.github/workflows/ci_tests.yml

@@ -1,14 +1,18 @@
 name: CI
 
-# trigger
-on: [push, workflow_dispatch]
+on:
+  push:
+  workflow_dispatch:
+  schedule:
+    - cron:  '48 4 * * *'
 
 jobs:
   build:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python-version: [3.7, 3.8, 3.9, "3.10"]
+    runs-on: ${{ matrix.platform }}
 
     steps:
     - name: Check out repository
@@ -33,13 +37,18 @@ jobs:
         pip install -r .ci_pip_reqs.txt
         pip install -e .[reports,combine]
 
+    - name: Run flake8
+      run: |
+        python -m flake8 --exclude=build,doc,example,tmp --extend-ignore=F403,F405
+      if: matrix.platform == 'ubuntu-latest'
+
     - name: Run tests
       run: |
         pytest --cov --cov-report=xml tests
-        python -m flake8 --exclude=build,doc,example,tmp --extend-ignore=F403,F405
 
     - name: Coverage
       uses: codecov/codecov-action@v1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
+      if: matrix.platform == 'ubuntu-latest'

CHANGELOG.md

@@ -2,6 +2,31 @@
 
 ## 0.1 series
 
+### 0.1.22
+
+* Allow zero bounds for log parameters by @FFroehlich in
+  https://github.com/PEtab-dev/libpetab-python/pull/83
+* Adapt to Matplotlib 3.5 by @dweindl in
+  https://github.com/PEtab-dev/libpetab-python/pull/86
+* Allow specifying file format for visualization by @dweindl in
+  https://github.com/PEtab-dev/libpetab-python/pull/85
+* Visualization: Don't mess with rcParams by @dweindl in
+  https://github.com/PEtab-dev/libpetab-python/pull/90
+* Linter: Check condition IDs are unique by @dweindl in
+  https://github.com/PEtab-dev/libpetab-python/pull/92
+* Add support for `pathlib` for reading PEtab tables by @dweindl, @dilpath
+  in https://github.com/PEtab-dev/libpetab-python/pull/93,
+  https://github.com/PEtab-dev/libpetab-python/pull/91
+* Run tests also on Python 3.10 by @dweindl in
+  https://github.com/PEtab-dev/libpetab-python/pull/88
+* Fix remote file retrieval on Windows @dweindl, @dilpath
+  in https://github.com/PEtab-dev/libpetab-python/pull/91
+* Fix test suite for Windows @dweindl, @dilpath
+  in https://github.com/PEtab-dev/libpetab-python/pull/91
+
+**Full Changelog**:
+https://github.com/PEtab-dev/libpetab-python/compare/v0.1.21...v0.1.22
+
 ### 0.1.21
 
 * PEtab spec compliance: measurements must now be not null, and numeric (#76)

README.md

@@ -1,5 +1,4 @@
 [![CI](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml/badge.svg?branch=master)](https://github.com/PEtab-dev/libpetab-python/actions/workflows/ci_tests.yml)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/fd7dd5cee68e449983be5c43f230c7f3)](https://www.codacy.com/gh/PEtab-dev/libpetab-python)
 [![codecov](https://codecov.io/gh/PEtab-dev/libpetab-python/branch/master/graph/badge.svg)](https://codecov.io/gh/PEtab-dev/libpetab-python)
 [![PyPI version](https://badge.fury.io/py/petab.svg)](https://badge.fury.io/py/petab)
 

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:
@@ -177,7 +179,8 @@ def flatten_timepoint_specific_output_overrides(
 
 
 def concat_tables(
-        tables: Union[str, pd.DataFrame, Iterable[Union[pd.DataFrame, str]]],
+        tables: Union[str, Path, pd.DataFrame,
+                      Iterable[Union[pd.DataFrame, str, Path]]],
         file_parser: Optional[Callable] = None
 ) -> pd.DataFrame:
     """Concatenate DataFrames provided as DataFrames or filenames, and a parser
@@ -196,14 +199,14 @@ def concat_tables(
     if isinstance(tables, pd.DataFrame):
         return tables
 
-    if isinstance(tables, str):
+    if isinstance(tables, (str, Path)):
         return file_parser(tables)
 
     df = pd.DataFrame()
 
     for tmp_df in tables:
         # load from file, if necessary
-        if isinstance(tmp_df, str):
+        if isinstance(tmp_df, (str, Path)):
             tmp_df = file_parser(tmp_df)
 
         df = df.append(tmp_df, sort=False,
@@ -241,14 +244,14 @@ 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,
         organization: Optional[str] = None,
 ) -> None:
-    """Create COMBINE archive (http://co.mbine.org/documents/archive) based
+    """Create COMBINE archive (https://co.mbine.org/documents/archive) based
     on PEtab YAML file.
 
     Arguments:
@@ -260,7 +263,7 @@ 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 +288,7 @@ 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 +356,7 @@ 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/lint.py

@@ -108,6 +108,10 @@ def check_condition_df(
 
     check_ids(df.index.values, kind='condition')
 
+    if not df.index.is_unique:
+        raise AssertionError("Non-unique condition IDs: "
+                             f"{df.index.values[df.index.duplicated()]}")
+
     for column_name in req_cols:
         if not np.issubdtype(df[column_name].dtype, np.number):
             assert_no_leading_trailing_whitespace(
@@ -466,7 +470,7 @@ def check_parameter_bounds(parameter_df: pd.DataFrame) -> None:
                 raise AssertionError(
                     f"{LOWER_BOUND} greater than {UPPER_BOUND} for "
                     f"{PARAMETER_ID} {row.name}.")
-            if (row[LOWER_BOUND] <= 0.0 or row[UPPER_BOUND] < 0.0) \
+            if (row[LOWER_BOUND] < 0.0 or row[UPPER_BOUND] < 0.0) \
                     and row[PARAMETER_SCALE] in [LOG, LOG10]:
                 raise AssertionError(
                     f"Bounds for {row[PARAMETER_SCALE]} scaled parameter "

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: