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Merge pull request #468 from PEtab-dev/release_0.1.9
Release 0.1.9 Library: * Allow URL as filenames for YAML files and SBML models (Closes #187) (#459) * Allow model time in observable formulas (#445) * Make float parsing from CSV round-trip (#444) * Validator: Error message for missing IDs, with line numbers. (#467) * Validator: Detect duplicated observable IDs (#446) * Some documentation and CI fixes / updates * Visualization: Add option to save visualization specification (#457) * Visualization: Column XValue not mandatory anymore (#429) * Visualization: Add sorting of indices of dataframes for the correct sorting of x-values (#430) * Visualization: Default value for the column x_label in vis_spec (#431)
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‎.github/ISSUE_TEMPLATE/petab-specification-changes.md‎

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---
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name: PEtab specification changes
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about: Suggest a change to the PEtab specification (beyond fixes / clarifications)
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title: ''
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labels: file format
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assignees: ''
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---
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**Which problem would you like to address? Please describe.**
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A clear and concise description of which use case you want to address and, if applicable, why the current specifications do not fulfill your requirements.
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**Describe the solution you would like**
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A clear and concise description of the changes you want to propose. Please describe any additional fields / files you would want to add, including allowed inputs and implications.
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**Describe alternatives you have considered**
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A clear and concise description of any alternative solutions or features you have considered.
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**Additional context**
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Add any other context about the request here.

‎CHANGELOG.md‎

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## 0.1 series
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### 0.1.9
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Library:
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* Allow URL as filenames for YAML files and SBML models (Closes #187) (#459)
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* Allow model time in observable formulas (#445)
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* Make float parsing from CSV round-trip (#444)
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* Validator: Error message for missing IDs, with line numbers. (#467)
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* Validator: Detect duplicated observable IDs (#446)
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* Some documentation and CI fixes / updates
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* Visualization: Add option to save visualization specification (#457)
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* Visualization: Column XValue not mandatory anymore (#429)
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* Visualization: Add sorting of indices of dataframes for the correct sorting
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of x-values (#430)
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* Visualization: Default value for the column x_label in vis_spec (#431)
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### 0.1.8
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‎doc/compile_doc.sh‎

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#!/bin/sh
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# Build a pdflatex document from the documentation
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# format A3
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pandoc documentation_data_format.rst \
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-o documentation_data_format.pdf \
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-V geometry:margin=1.5in -V geometry:a3paper -V fontsize=10pt \
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--toc \
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--pdf-engine pdflatex
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# format A2 landscape
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# pandoc documentation_data_format.rst \
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# -o documentation_data_format.pdf \
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# -V geometry:margin=.5in -V geometry:a4paper -V geometry:landscape -V fontsize=10pt \
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# --toc \
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# --pdf-engine pdflatex

‎doc/conf.py‎

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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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exclude_patterns = ['build/doctrees', 'build/html']
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master_doc = 'index'
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‎doc/documentation_data_format.rst‎

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@@ -3,7 +3,6 @@ PEtab data format specification
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Format version: 1
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-----------------
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This document explains the PEtab data format.
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+--------------+------------------+------------------------------------+-----+---------------------------------------+
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| conditionId2 | ... | ... | ... | ... |
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+--------------+------------------+------------------------------------+-----+---------------------------------------+
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|... | ... | ... | ... |... |
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| ... | ... | ... | ... | .. |
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+--------------+------------------+------------------------------------+-----+---------------------------------------+
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Row- and column-ordering are arbitrary, although specifying ``conditionId``
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+-------------+-----------------+-------------------------+-------------+------------+--------------+----------+-----+
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| parameterId | [parameterName] | parameterScale | lowerBound | upperBound | nominalValue | estimate | ... |
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+=============+=================+=========================+=============+============+==============+==========+=====+
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|STRING | [STRING] | log10\|lin\|log | NUMERIC | NUMERIC | NUMERIC | 0\|1 | ... |
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| STRING | [STRING] | log10\|lin\|log | NUMERIC | NUMERIC | NUMERIC | 0\|1 | ... |
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+-------------+-----------------+-------------------------+-------------+------------+--------------+----------+-----+
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| ... | ... | ... | ... | ... | ... | ... | ... |
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| ... | ... | ... | ... | ... | ... | ... | ... |
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+-------------+-----------------+-------------------------+-------------+------------+--------------+----------+-----+
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*(wrapped for readability)*

‎petab/core.py‎

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@@ -206,7 +206,7 @@ def flatten_timepoint_specific_output_overrides(
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) == 0).any():
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tmp = tmp_ + counter * "_" + str(i_noise + i_sc + 1)
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counter += 1
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if not tmp_.empty and not tmp_.empty:
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if not tmp_.empty:
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replacements[tmp.values[0]] = tmp_.values[0]
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df.loc[idxs == 0, OBSERVABLE_ID] = tmp
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# Append the result in a new df

‎petab/lint.py‎

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Returns:
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``True`` if valid, ``False`` otherwise
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"""
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if pd.isna(x):
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return False
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return re.match(r'^[a-zA-Z_]\w*$', x) is not None
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Raises:
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ValueError - in case of invalid IDs
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"""
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invalids = []
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for _id in ids:
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if not is_valid_identifier(_id):
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invalids.append(_id)
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invalids = [(index, _id)
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for index, _id in enumerate(ids)
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if not is_valid_identifier(_id)]
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if invalids:
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raise ValueError(f"Invalid {kind} ID(s): {invalids}")
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# The first row is the header row, and Python lists are zero-indexed,
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# hence need to add 2 for the correct line number.
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offset = 2
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error_output = '\n'.join([
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f'Line {index+offset}: ' +
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('Missing ID' if pd.isna(_id) else _id)
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for index, _id in invalids])
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raise ValueError(f"Invalid {kind} ID(s):\n{error_output}")

‎petab/problem.py‎

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# load SBML model from pickled string
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sbml_string = state.pop('sbml_string', None)
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if sbml_string:
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self.sbml_reader = libsbml.SBMLReader()
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self.sbml_document = \
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self.sbml_reader.readSBMLFromString(sbml_string)
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self.sbml_model = self.sbml_document.getModel()
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self.sbml_reader, self.sbml_document, self.sbml_model = \
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sbml.load_sbml_from_string(sbml_string)
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self.__dict__.update(state)
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parameter_df = parameters.get_parameter_df(parameter_file)
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if sbml_file:
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sbml_reader = libsbml.SBMLReader()
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sbml_document = sbml_reader.readSBML(sbml_file)
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sbml_model = sbml_document.getModel()
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sbml_reader, sbml_document, sbml_model = \
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sbml.get_sbml_model(sbml_file)
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if visualization_files:
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# If there are multiple tables, we will merge them

‎petab/sbml.py‎

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from warnings import warn
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import logging
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import re
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from typing import Dict, Any, List, Union
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from typing import Dict, Any, List, Union, Tuple
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import libsbml
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logger = logging.getLogger(__name__)
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if not ret:
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raise RuntimeError(f"libSBML reported error {ret} when trying to "
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f"create SBML file {filename}.")
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def get_sbml_model(
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filepath_or_buffer
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) -> Tuple[libsbml.SBMLReader, libsbml.SBMLDocument, libsbml.Model]:
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"""Get an SBML model from file or URL or file handle
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:param filepath_or_buffer:
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File or URL or file handle to read the model from
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:return: The SBML document, model and reader
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"""
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from pandas.io.common import get_filepath_or_buffer, is_url, is_file_like
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if is_file_like(filepath_or_buffer) or is_url(filepath_or_buffer):
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buffer = get_filepath_or_buffer(filepath_or_buffer, mode='r')[0]
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if is_url(filepath_or_buffer):
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buffer = ''.join(line.decode('utf-8') for line in buffer)
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else:
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buffer = ''.join(line for line in buffer)
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# URL or already opened file, we will load the model from a string
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return load_sbml_from_string(buffer)
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return load_sbml_from_file(filepath_or_buffer)
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def load_sbml_from_string(
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sbml_string: str
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) -> Tuple[libsbml.SBMLReader, libsbml.SBMLDocument, libsbml.Model]:
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"""Load SBML model from string
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:param sbml_string: Model as XML string
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:return: The SBML document, model and reader
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"""
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sbml_reader = libsbml.SBMLReader()
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sbml_document = \
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sbml_reader.readSBMLFromString(sbml_string)
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sbml_model = sbml_document.getModel()
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return sbml_reader, sbml_document, sbml_model
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def load_sbml_from_file(
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sbml_file: str
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) -> Tuple[libsbml.SBMLReader, libsbml.SBMLDocument, libsbml.Model]:
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"""Load SBML model from file
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:param sbml_file: Filename of the SBML file
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:return: The SBML document, model and reader
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"""
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sbml_reader = libsbml.SBMLReader()
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sbml_document = sbml_reader.readSBML(sbml_file)
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sbml_model = sbml_document.getModel()
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return sbml_reader, sbml_document, sbml_model

‎petab/version.py‎

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"""PEtab library version"""
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__version__ = '0.1.8'
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__version__ = '0.1.9'

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