Merge pull request #640 from ICB-DCM/develop

0.10.1 Release
AMICI-dev · Mar 4, 2019 · fb033df · fb033df
2 parents fda9636 + f9f4c76
commit fb033df
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diff --git a/.gitignore b/.gitignore
@@ -142,6 +142,8 @@ python/sdist/amici/amici_wrap_without_hdf5.cxx
 python/sdist/build/*
 python/sdist/amici/git_version.txt
 
+python/sdist/dist
+
 AMICI_guide.pdf
 
 ThirdParty/bionetgen.tar.gz

diff --git a/README.md b/README.md
@@ -18,6 +18,6 @@ Online documentation is available as [github-pages](http://icb-dcm.github.io/AMI
 ## Current build status
 
 [![PyPI version](https://badge.fury.io/py/amici.svg)](https://badge.fury.io/py/amici)
-[![Build Status](https://travis-ci.org/ICB-DCM/AMICI.svg?branch=master)](https://travis-ci.org/ICB-DCM/AMICI)
+[![Build Status](https://travis-ci.com/ICB-DCM/AMICI.svg?branch=master)](https://travis-ci.com/ICB-DCM/AMICI)
 [![CodeCov](https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/AMICI)
 [![Codacy](https://api.codacy.com/project/badge/Grade/945235766e344a7fa36278feab915ff6)](https://www.codacy.com/app/FFroehlich/AMICI?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ICB-DCM/AMICI&amp;utm_campaign=Badge_Grade)
diff --git a/include/amici/model.h b/include/amici/model.h
@@ -950,6 +950,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has parameter names set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether parameter names were set
      */
     virtual bool hasParameterNames() const;
@@ -962,6 +963,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has state names set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether state names were set
      */
     virtual bool hasStateNames() const;
@@ -974,6 +976,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has fixed parameter names set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether fixed parameter names were set
      */
     virtual bool hasFixedParameterNames() const;
@@ -986,6 +989,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has observable names set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether observabke names were set
      */
     virtual bool hasObservableNames() const;
@@ -998,6 +1002,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has parameter ids set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether parameter ids were set
      */
     virtual bool hasParameterIds() const;
@@ -1057,7 +1062,8 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has state ids set.
-     * @return
+     * Also returns true if the number of corresponding variables is just zero.
+     * @return boolean indicating whether state ids were set
      */
     virtual bool hasStateIds() const;
 
@@ -1069,6 +1075,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has fixed parameter ids set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether fixed parameter ids were set
      */
     virtual bool hasFixedParameterIds() const;
@@ -1081,6 +1088,7 @@ class Model : public AbstractModel {
 
     /**
      * @brief Reports whether the model has observable ids set.
+     * Also returns true if the number of corresponding variables is just zero.
      * @return boolean indicating whether observale ids were set
      */
     virtual bool hasObservableIds() const;

diff --git a/python/amici/pandas.py b/python/amici/pandas.py
@@ -367,28 +367,31 @@ def _get_names_or_ids(model, variable, by_id):
     # check whether variable type permitted
     variable_options = ['Parameter', 'FixedParameter', 'Observable', 'State']
     if variable not in variable_options:
-        raise ValueError('variable must be in ' + str(variable_options))
+        raise ValueError('Variable must be in ' + str(variable_options))
 
-    # functions to extract attributes
-    namegetter = getattr(model, 'get' + variable + 'Names')
-    idgetter = getattr(model, 'get' + variable + 'Ids')
+    # extract attributes
+    names = list(getattr(model, f'get{variable}Names')())
+    ids = list(getattr(model, f'get{variable}Ids')())
+
+    # find out if model has names and ids
+    has_names = getattr(model, f'has{variable}Names')()
+    has_ids = getattr(model, f'has{variable}Ids')()
 
     # extract labels
-    if not by_id and len(set(namegetter())) == len(namegetter()) \
-            and getattr(model, f"has{variable}Names")():
+    if not by_id and has_names and len(set(names)) == len(names):
         # use variable names
-        return list(namegetter())
-    elif getattr(model, f"has{variable}Ids")():
+        return names
+    elif has_ids:
         # use variable ids
-        return list(idgetter())
+        return ids
     else:
         # unable to create unique labels
         if by_id:
-            raise RuntimeError(f"Model {variable} ids are not set.")
+            msg = f"Model {variable} ids are not set."
         else:
-            raise RuntimeError(
-                f"Model {variable} names are not unique and "
-                f"{variable} ids are not set.")
+            msg = f"Model {variable} names are not unique and " \
+                  f"{variable} ids are not set."
+        raise ValueError(msg)
 
 
 def _get_specialized_fixed_parameters(

diff --git a/python/amici/sbml_import.py b/python/amici/sbml_import.py
@@ -40,7 +40,7 @@ class SbmlImporter:
 
         symbols: dict carrying symbolic definitions @type dict
 
-        SBMLreader: the libSBML sbml reader [!not storing this will result
+        sbml_reader: the libSBML sbml reader [!not storing this will result
         in a segfault!]
 
         sbml_doc: document carrying the sbml definition [!not storing this
@@ -76,58 +76,61 @@ class SbmlImporter:
 
     """
 
-    def __init__(self, SBMLFile, show_sbml_warnings=False):
+    def __init__(
+            self,
+            sbml_source: str,
+            show_sbml_warnings: bool = False,
+            from_file: bool = True):
         """Create a new Model instance.
 
         Arguments:
 
-        SBMLFile: Path to SBML file where the model is specified @type string
+            sbml_source:  Either a path to SBML file where the model is specified.
+            Or a model string as created by  sbml.sbmlWriter().writeSBMLToString().
+            @type string
 
-        show_sbml_warnings: indicates whether libSBML warnings should be
-        displayed @type bool
+            show_sbml_warnings: Indicates whether libSBML warnings should be
+            displayed (default = True). @type bool
+
+            from_file: Whether `sbml_source` is a file name (True, default), or an
+            sbml string (False). @type bool
 
         Returns:
-        SbmlImporter instance with attached SBML document
+
+            SbmlImporter instance with attached SBML document
 
         Raises:
 
         """
+        self.sbml_reader = sbml.SBMLReader()
+
+        if from_file:
+            sbml_doc = self.sbml_reader.readSBMLFromFile(sbml_source)
+        else:
+            sbml_doc = self.sbml_reader.readSBMLFromString(sbml_source)
+        self.sbml_doc = sbml_doc
 
         self.show_sbml_warnings = show_sbml_warnings
 
-        self.loadSBMLFile(SBMLFile)
+        # process document
+        self.process_document()
+
+        self.sbml = self.sbml_doc.getModel()
 
-        """Long and short names for model components"""
+        # Long and short names for model components
         self.symbols = dict()
         self.reset_symbols()
 
-    def reset_symbols(self):
-        """Reset the symbols attribute to default values
-
-        Arguments:
-
-        Returns:
-
-        Raises:
-
-        """
-        self.symbols = default_symbols
-
-    def loadSBMLFile(self, SBMLFile):
-        """Parse the provided SBML file.
+    def process_document(self):
+        """Validate and simplify document.
 
         Arguments:
-            SBMLFile: path to SBML file @type str
 
         Returns:
 
         Raises:
 
         """
-
-        self.SBMLreader = sbml.SBMLReader()
-        self.sbml_doc = self.SBMLreader.readSBML(SBMLFile)
-
         # Ensure we got a valid SBML model, otherwise further processing
         # might lead to undefined results
         self.sbml_doc.validateSBML()
@@ -149,7 +152,17 @@ def loadSBMLFile(self, SBMLFile):
         # check the error log just once after all conversion/validation calls.
         checkLibSBMLErrors(self.sbml_doc, self.show_sbml_warnings)
 
-        self.sbml = self.sbml_doc.getModel()
+    def reset_symbols(self):
+        """Reset the symbols attribute to default values
+
+        Arguments:
+
+        Returns:
+
+        Raises:
+
+        """
+        self.symbols = default_symbols
 
     def sbml2amici(self,
                    modelName,

diff --git a/src/model.cpp b/src/model.cpp
@@ -489,19 +489,19 @@ int Model::setParametersByNameRegex(std::string const& par_name_regex, realtype
     return n_found;
 }
 
-bool Model::hasStateIds() const { return nx_rdata && !getStateIds().empty(); }
+bool Model::hasStateIds() const { return nx_rdata == 0 || !getStateIds().empty(); }
 
 std::vector<std::string> Model::getStateIds() const {
     return std::vector<std::string>();
 }
 
-bool Model::hasFixedParameterIds() const { return nk() && !getFixedParameterIds().empty(); }
+bool Model::hasFixedParameterIds() const { return nk() == 0 || !getFixedParameterIds().empty(); }
 
 std::vector<std::string> Model::getFixedParameterIds() const {
     return std::vector<std::string>();
 }
 
-bool Model::hasObservableIds() const { return ny && !getObservableIds().empty(); }
+bool Model::hasObservableIds() const { return ny == 0 || !getObservableIds().empty(); }
 
 std::vector<std::string> Model::getObservableIds() const {
     return std::vector<std::string>();
@@ -794,23 +794,23 @@ int Model::plist(int pos) const{
     return plist_.at(pos);
 }
 
-bool Model::hasParameterNames() const { return np() && !getParameterNames().empty(); }
+bool Model::hasParameterNames() const { return np() == 0 || !getParameterNames().empty(); }
 
 std::vector<std::string> Model::getParameterNames() const { return std::vector<std::string>(); }
 
-bool Model::hasStateNames() const { return nx_rdata && !getStateNames().empty(); }
+bool Model::hasStateNames() const { return nx_rdata == 0 || !getStateNames().empty(); }
 
 std::vector<std::string> Model::getStateNames() const { return std::vector<std::string>(); }
 
-bool Model::hasFixedParameterNames() const { return nk() && !getFixedParameterNames().empty(); }
+bool Model::hasFixedParameterNames() const { return nk() == 0 || !getFixedParameterNames().empty(); }
 
 std::vector<std::string> Model::getFixedParameterNames() const { return std::vector<std::string>(); }
 
-bool Model::hasObservableNames() const { return ny && !getObservableNames().empty(); }
+bool Model::hasObservableNames() const { return ny == 0 || !getObservableNames().empty(); }
 
 std::vector<std::string> Model::getObservableNames() const { return std::vector<std::string>(); }
 
-bool Model::hasParameterIds() const { return np() && !getParameterIds().empty(); }
+bool Model::hasParameterIds() const { return np() == 0 || !getParameterIds().empty(); }
 
 std::vector<std::string> Model::getParameterIds() const {
     return std::vector<std::string>();

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-0.10.0
+0.10.1