Release 0.11.22

Merge pull request #1601 from AMICI-dev/release/0.12.0

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 ## v0.X Series
 
+### v0.11.22 (2021-12-02)
+
+* **Require sympy>=1.9,pysb>=1.13.1** by @FFroehlich, @dweindl
+  in https://github.com/AMICI-dev/AMICI/pull/1599
+* Fixed sympy deprecation warning by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1600
+* Updated Windows installation instructions for Python>=3.8 by @dweindl
+  in https://github.com/AMICI-dev/AMICI/pull/1597
+* Fixed plot labels by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1598
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.11.21...v0.11.22
+
 ### v0.11.21 (2021-11-21)
 
 Fixes:

documentation/python_installation.rst

@@ -266,6 +266,18 @@ by MSVC (see Visual Studio above). ``KERNEL32.dll`` is part of Windows and in
 ``C:\Windows\System32``. The ``api-ms-win-crt-XXX-l1-1-0.dll`` are needed by
 ``openblas.dll`` and are part of the Windows Universal C Runtime.
 
+.. note::
+
+    Since Python 3.8, the library directory needs to be set as follows:
+
+    .. code-block:: python
+
+        import os
+        # directory containing `openblas.dll`
+        os.add_dll_directory("C:\\BLAS\\bin")
+        import amici
+
+    Adding it to ``PATH`` will not work.
 
 Further topics
 ++++++++++++++

include/amici/solver.h

@@ -51,6 +51,9 @@ class Solver {
     /** Type of what is passed to Sundials solvers as user_data */
     using user_data_type = std::pair<Model *, Solver const*>;
 
+    /**
+     * @brief Default constructor
+     */
     Solver() = default;
 
     /**

include/amici/symbolic_functions.h

@@ -5,7 +5,7 @@ namespace amici {
 
 double log(double x);
 double dirac(double x);
-double heaviside(double x);
+double heaviside(double x, double x0);
 
 double min(double a, double b, double c);
 double Dmin(int id, double a, double b, double c);

python/amici/ode_export.py

@@ -845,11 +845,9 @@ def smart_is_zero_matrix(x: Union[sp.MutableDenseMatrix,
     """
 
     if isinstance(x, sp.MutableDenseMatrix):
-        nonzero = any(xx.is_zero is not True for xx in x._mat)
-    else:
-        nonzero = x.nnz() > 0
+        return all(xx.is_zero is True for xx in x.flat())
 
-    return not nonzero
+    return x.nnz() == 0
 
 
 class ODEModel:
@@ -1626,7 +1624,7 @@ def parse_events(self) -> None:
             expr.set_val(self._process_heavisides(expr.get_val(), roots))
 
         # remove all possible Heavisides from roots, which may arise from
-        # the substitution of `'w'` in `_collect_heaviside_roots`
+        # the substitution of `'w'` in `_get_unique_root`
         for root in roots:
             root.set_val(self._process_heavisides(root.get_val(), roots))
 
@@ -2354,6 +2352,14 @@ def _get_unique_root(
             unique identifier for root, or `None` if the root is not
             time-dependent
         """
+        # substitute 'w' expressions into root expressions now, to avoid
+        # rewriting '{model_name}_root.cpp' and '{model_name}_stau.cpp' headers
+        # to include 'w.h'
+        w_sorted = toposort_symbols(dict(zip(
+            [expr.get_id() for expr in self._expressions],
+            [expr.get_val() for expr in self._expressions],
+        )))
+        root_found = root_found.subs(w_sorted)
 
         if not self._expr_is_time_dependent(root_found):
             return None
@@ -2395,18 +2401,6 @@ def _collect_heaviside_roots(
             elif arg.has(sp.Heaviside):
                 root_funs.extend(self._collect_heaviside_roots(arg.args))
 
-        # substitute 'w' expressions into root expressions now, to avoid
-        # rewriting '{model_name}_root.cpp' and '{model_name}_stau.cpp' headers
-        # to include 'w.h'
-        w_sorted = toposort_symbols(dict(zip(
-            [expr.get_id()  for expr in self._expressions],
-            [expr.get_val() for expr in self._expressions],
-        )))
-        root_funs = [
-            r.subs(w_sorted)
-            for r in root_funs
-        ]
-
         return root_funs
 
     def _process_heavisides(

python/amici/plotting.py

@@ -9,6 +9,7 @@
 from matplotlib.axes import Axes
 from typing import Optional, Iterable
 
+
 def plotStateTrajectories(
         rdata: ReturnDataView,
         state_indices: Optional[Iterable[int]] = None,
@@ -27,7 +28,7 @@ def plotStateTrajectories(
 
     :param ax:
         matplotlib Axes instance to plot into
-    
+
     :param model:
         amici model instance
     """
@@ -37,18 +38,18 @@ def plotStateTrajectories(
         state_indices = range(rdata['x'].shape[1])
     for ix in state_indices:
         if model is None:
-            label = f'x_{ix}'
-        elif model.getStateNames()[ix] != '':
+            label = f'$x_{{{ix}}}$'
+        elif model.getStateNames()[ix]:
             label = model.getStateNames()[ix]
         else:
             label = model.getStateIds()[ix]
-        ax.plot(rdata['t'], rdata['x'][:, ix], label = label)
-        ax.set_xlabel('$t$ (s)')
-        ax.set_ylabel('$x_i(t)$ (mmol/ml)')
+        ax.plot(rdata['t'], rdata['x'][:, ix], label=label)
+        ax.set_xlabel('$t$')
+        ax.set_ylabel('$x(t)$')
         ax.legend()
         ax.set_title('State trajectories')
-    
-    
+
+
 def plotObservableTrajectories(
         rdata: ReturnDataView,
         observable_indices: Optional[Iterable[int]] = None,
@@ -77,13 +78,13 @@ def plotObservableTrajectories(
         observable_indices = range(rdata['y'].shape[1])
     for iy in observable_indices:
         if model is None:
-            label = f'y_{iy}'
-        elif model.getObservableNames()[iy] != '':
+            label = f'$y_{{{iy}}}$'
+        elif model.getObservableNames()[iy]:
             label = model.getObservableNames()[iy]
         else:
             label = model.getObservableIds()[iy]
-        ax.plot(rdata['t'], rdata['y'][:, iy], label = label)
-        ax.set_xlabel('$t$ (s)')
-        ax.set_ylabel('$y_i(t)$ (AU)')
+        ax.plot(rdata['t'], rdata['y'][:, iy], label=label)
+        ax.set_xlabel('$t$')
+        ax.set_ylabel('$y(t)$')
         ax.legend()
-        ax.set_title('Observables')
+        ax.set_title('Observable trajectories')