Fix escape sequence (#108)

* Fix escape sequence

* Fix remaining invalid escape sequence

* Tweaks to extend_by_integration

* try using newer CI image

* Add boost to path

* msbj and stab_lim_det

* max_num_steps_between_jac

* CI: fix boost include path

* handle array

* bump pycvodes req. version & CI: suppress notebook output

.ci/test_py2.sh

@@ -12,4 +12,4 @@ done
 python2 -m pip install --user virtualenv
 python2 -m virtualenv /tmp/test_py2
 sed -i -E -e "/python_requires/d" setup.py
-bash -c "source /tmp/test_py2/bin/activate; pip install pytest '.[all]' && pytest -rs --pyargs ${PKG_NAME}"
+bash -c "source /tmp/test_py2/bin/activate; pip install 'numpy<1.17' pytest '.[all]' && pytest -rs --pyargs ${PKG_NAME}"

.drone.yml

@@ -20,11 +20,11 @@ pipeline:
 
   test-sund-3.2.1-klu:
     group: testing
-    image: bjodah/bjodahimg18:v1.5
+    image: bjodah/bjodahimg18:v3.0
     environment:
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_71_0/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
     commands:
@@ -39,11 +39,11 @@ pipeline:
 
   test-sund-4.1.0-nolapack-noklu-extended:
     group: testing
-    image: bjodah/bjodahimg18:v1.5
+    image: bjodah/bjodahimg18:v3.0
     environment:
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_71_0/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
     commands:
@@ -59,11 +59,11 @@ pipeline:
       - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
 
   test-py2:
-    image: bjodah/bjodahimg18:v1.5
+    image: bjodah/bjodahimg18:v3.0
     environment:
       - OMP_NUM_THREADS=1
       - ANYODE_NUM_THREADS=2
-      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost_1_71_0/include
       - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
       - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
     commands:
@@ -72,7 +72,7 @@ pipeline:
 
   test-conda-recipe:
     group: testing
-    image: bjodah/bjodahimg18dev:v1.5
+    image: bjodah/bjodahimg18dev:v3.0
     commands:
       - export CONDA_PKGS_DIRS=$(pwd)/ci_cache/conda_packages
       - PATH=/opt/miniconda3/bin:$PATH conda update conda-build

pyodesys/convergence.py

@@ -37,7 +37,7 @@ def integrate_tolerance_series(odesys, atols, rtols, x, y0, params=(),
         Passed on to ``odesys.integrate``.
     fit : callable
     val : callable
-    \*\*kwargs:
+    \\*\\*kwargs:
         Passed on to ``odesys.integrate``.
 
     Returns

pyodesys/core.py

@@ -310,7 +310,7 @@ def adaptive(self, y0, x0, xend, params=(), **kwargs):
             Final value of the independent variable.
         params : array_like
             See :meth:`integrate`.
-        \*\*kwargs :
+        \\*\\*kwargs :
             See :meth:`integrate`.
 
         Returns
@@ -332,7 +332,7 @@ def predefined(self, y0, xout, params=(), **kwargs):
         xout : array_like
         params : array_like
             See :meth:`integrate`.
-        \*\*kwargs:
+        \\*\\*kwargs:
             See :meth:`integrate`
 
         Returns
@@ -461,11 +461,11 @@ def _integrate_scipy(self, intern_xout, intern_y0, intern_p,
 
         Parameters
         ----------
-        \*args :
+        \\*args :
             See :meth:`integrate`.
         name : str (default: 'lsoda'/'dopri5' when jacobian is available/not)
             What integrator wrapped in scipy.integrate.ode to use.
-        \*\*kwargs :
+        \\*\\*kwargs :
             Keyword arguments passed onto `set_integrator(...) <
         http://docs.scipy.org/doc/scipy/reference/generated/
         scipy.integrate.ode.set_integrator.html#scipy.integrate.ode.set_integrator>`_
@@ -671,11 +671,11 @@ def _integrate_gsl(self, *args, **kwargs):
 
         Parameters
         ----------
-        \*args :
+        \\*args :
             see :meth:`integrate`
         method : str (default: 'bsimp')
             what stepper to use, see :py:attr:`gslodeiv2.steppers`
-        \*\*kwargs :
+        \\*\\*kwargs :
             keyword arguments passed onto
             :py:func:`gslodeiv2.integrate_adaptive`/:py:func:`gslodeiv2.integrate_predefined`
 
@@ -834,7 +834,7 @@ def integrate_auto_switch(odes, kw, x, y0, params=(), **kwargs):
     x : array_like
     y0 : array_like
     params : array_like
-    \*\*kwargs:
+    \\*\\*kwargs:
         See :meth:`ODESys.integrate`
 
     Notes

pyodesys/native/sources/_cvode_wrapper.pyx

@@ -93,7 +93,8 @@ def integrate_adaptive(floating [:, ::1] y0,
                        realtype get_dx_max_factor=0.0, bool error_outside_bounds=False,
                        realtype max_invariant_violation=0.0, special_settings=None,
                        bool autonomous_exprs=False, int nprealloc=500, bool ew_ele=False,
-                       vector[realtype] constraints=[]):
+                       vector[realtype] constraints=[], long int max_num_steps_between_jac=0,
+                       bool stab_lim_det=False):
     cdef:
         realtype ** xyout = <realtype **>malloc(y0.shape[0]*sizeof(realtype *))
         realtype [:,::1] xyout_view
@@ -192,7 +193,7 @@ def integrate_adaptive(floating [:, ::1] y0,
             &_dx0[0], &_dx_min[0], &_dx_max[0], with_jacobian, iter_type_from_name(_iter_t),
             linear_solver_from_name(linear_solver.lower().encode('UTF-8')),
             maxl, eps_lin, nderiv, return_on_root, autorestart, return_on_error, with_jtimes,
-            tidx, ew_ele_arr if ew_ele else NULL, constraints
+            tidx, ew_ele_arr if ew_ele else NULL, constraints, max_num_steps_between_jac, stab_lim_det
         )
         xout, yout = [], []
         for idx in range(y0.shape[0]):
@@ -250,7 +251,8 @@ def integrate_predefined(floating [:, ::1] y0,
                          bool record_order=False, bool record_fpe=False,
                          realtype get_dx_max_factor=0.0, bool error_outside_bounds=False,
                          realtype max_invariant_violation=0.0, special_settings=None,
-                         bool autonomous_exprs=False, ew_ele=False, vector[realtype] constraints=[]):
+                         bool autonomous_exprs=False, ew_ele=False, vector[realtype] constraints=[],
+                         long int max_num_steps_between_jac=0, bool stab_lim_det=False):
     cdef:
         vector[CvodesOdeSys *] systems
         list nfos = []
@@ -339,7 +341,8 @@ def integrate_predefined(floating [:, ::1] y0,
         <realtype *> xout_arr.data, <realtype *> yout_arr.data, mxsteps, &_dx0[0], &_dx_min[0],
         &_dx_max[0], with_jacobian, iter_type_from_name(_iter_t),
         linear_solver_from_name(linear_solver.lower().encode('UTF-8')),
-        maxl, eps_lin, nderiv, autorestart, return_on_error, with_jtimes, ew_ele_arr if ew_ele else NULL, constraints)
+        maxl, eps_lin, nderiv, autorestart, return_on_error, with_jtimes,
+        ew_ele_arr if ew_ele else NULL, constraints, max_num_steps_between_jac, stab_lim_det)
 
     for idx in range(y0.shape[0]):
         nreached = result[idx].first

pyodesys/plotting.py

@@ -215,7 +215,7 @@ def plot_phase_plane(x, y, indices=None, plot=None, names=None, ax=None, **kwarg
         Uses ``matplotlib.pyplot.plot`` if ``None``
     names: iterable of strings
         Labels for x and y axis.
-    \*\*kwargs:
+    \\*\\*kwargs:
         Keyword arguemtns passed to ``plot()``.
 
     """

pyodesys/results.py

@@ -213,7 +213,7 @@ def plot(self, info_vlines_kw=None, between=None, deriv=False, title_info=0, **k
         deriv : bool
             Plot derivatives (internal variables).
         names : iterable of str
-        \*\*kwargs:
+        \\*\\*kwargs:
             See :func:`pyodesys.plotting.plot_result`
         """
         if between is not None:
@@ -255,7 +255,7 @@ def plot_phase_plane(self, indices=None, **kwargs):
         ----------
         indices : iterable of int
         names : iterable of str
-        \*\*kwargs:
+        \\*\\*kwargs:
             See :func:`pyodesys.plotting.plot_phase_plane`
 
         """
@@ -285,7 +285,7 @@ def extend_by_integration(self, xend, params=None, odesys=None, autonomous=None,
                 else self.odesys.numpy.linspace(x0, xend, npoints+1)
             ), self.yout[..., -1, :], params or self.params, **kwargs
         )
-        self.xout = self.odesys.numpy.concatenate((self.xout, res.xout[1:] + (x0 if autonomous else 0)))
+        self.xout = self.odesys.numpy.concatenate((self.xout, res.xout[1:] + (x0 if autonomous else 0*x0)))
         self.yout = self.odesys.numpy.concatenate((self.yout, res.yout[..., 1:, :]))
         new_info = {k: v for k, v in self.info.items() if not (
             k.startswith('internal') and odesys is not self.odesys)}
@@ -298,7 +298,9 @@ def extend_by_integration(self, xend, params=None, odesys=None, autonomous=None,
             elif k == 'success':
                 new_info[k] = new_info[k] and v
             elif k.endswith('_xvals'):
-                new_info[k] = self.odesys.numpy.concatenate((new_info[k], v + (x0 if autonomous else 0)))
+                if len(v) == 0:
+                    continue
+                new_info[k] = self.odesys.numpy.concatenate((new_info[k], v + (x0 if autonomous else 0*x0)))
             elif k.endswith('_indices'):
                 new_info[k].extend([itm + nx0 - 1 for itm in v])
             elif isinstance(v, str):

pyodesys/symbolic.py

@@ -181,7 +181,7 @@ class SymbolicSys(ODESys):
         When ``True``, jacobian will be derived and stored (if ``jac = True``)
         in compressed sparse column (CSC) format and the jacobian callback
         will return an instance of ``scipy.sparse.csc_matrix``.
-    \*\*kwargs:
+    \\*\\*kwargs:
         See :py:class:`ODESys`
 
     Attributes
@@ -405,7 +405,7 @@ def from_callback(cls, rhs, ny=None, nparams=None, first_step_factory=None,
             its return value from dict to array.
         par_by_name : bool
             Make ``p`` passed to ``rhs`` a dict (keys from :attr:`param_names`).
-        \*\*kwargs :
+        \\*\\*kwargs :
             Keyword arguments passed onto :class:`SymbolicSys`.
 
         Examples
@@ -818,7 +818,7 @@ class TransformedSys(SymbolicSys):
     check_transforms : bool
         Passed as keyword argument ``check`` to :func:`.util.transform_exprs_dep` and
         :func:`.util.transform_exprs_indep`.
-    \*\*kwargs :
+    \\*\\*kwargs :
         Keyword arguments passed onto :class:`SymbolicSys`.
 
     """
@@ -904,7 +904,7 @@ def from_callback(cls, cb, ny=None, nparams=None, dep_transf_cbs=None,
         roots_cb : callable
             Callback with signature ``roots(x, y[:], p[:], backend=math) -> r[:]``.
             Callback should return untransformed roots.
-        \*\*kwargs :
+        \\*\\*kwargs :
             Keyword arguments passed onto :class:`TransformedSys`.
 
         """
@@ -972,7 +972,7 @@ def symmetricsys(dep_tr=None, indep_tr=None, SuperClass=TransformedSys, **kwargs
         Forward and backward transformation to be applied to the
         independent variable.
     SuperClass : class
-    \*\*kwargs :
+    \\*\\*kwargs :
         Default keyword arguments for the TransformedSys subclass.
 
     Returns
@@ -1042,7 +1042,7 @@ class ScaledSys(TransformedSys):
         scaling of the independent variable (default: 1)
     params :
         see :class:`SymbolicSys`
-    \*\*kwargs :
+    \\*\\*kwargs :
         Keyword arguments passed onto :class:`TransformedSys`.
 
     Examples
@@ -1102,7 +1102,7 @@ def from_callback(cls, cb, ny=None, nparams=None, dep_scaling=1, indep_scaling=1
             scaling of the dependent variables (default: 1)
         indep_scaling: number (>0)
             scaling of the independent variable (default: 1)
-        \*\*kwargs :
+        \\*\\*kwargs :
             Keyword arguments passed onto :class:`ScaledSys`.
 
         Examples
@@ -1143,7 +1143,7 @@ class PartiallySolvedSystem(SymbolicSys):
         the signature: ``my_factory(x0, y0, p0, backend) -> dict``, where the returned
         dictionary maps dependent variabels (from ``original_system.dep``)
         to new expressions in remaining variables and initial conditions.
-    \*\*kwargs : dict
+    \\*\\*kwargs : dict
         Keyword arguments passed onto :class:`SymbolicSys`.
 
     Attributes
@@ -1285,7 +1285,7 @@ def from_linear_invariants(cls, ori_sys, preferred=None, **kwargs):
         preferred : iterable of preferred dependent variables
             Due to numerical rounding it is preferable to choose the variables
             which are expected to be of the largest magnitude during integration.
-        \*\*kwargs :
+        \\*\\*kwargs :
             Keyword arguments passed on to constructor.
         """
         _be = ori_sys.be

scripts/render_notebooks.sh

@@ -1,4 +1,20 @@
 #!/bin/bash -e
+QUIET_EXIT_CODE=0
+function quiet_unless_fail {
+    # suppresses function output unless exit status is != 0
+    OUTPUT_FILE=$(tempfile)
+    #/bin/rm --force /tmp/suppress.out 2>/dev/null
+    EXECMD=${1+"$@"}
+    $EXECMD > ${OUTPUT_FILE} 2>&1
+    QUIET_EXIT_CODE=$?
+    if [ ${QUIET_EXIT_CODE} -ne 0 ]; then
+	cat ${OUTPUT_FILE}
+	echo "The following command exited with exit status ${QUIET_EXIT_CODE}: ${EXECMD}"
+    fi
+    /bin/rm ${OUTPUT_FILE}
+}
+
+
 cd examples/
 
 PREC=`python3 -c "from pycvodes._config import env; print(env.get('SUNDIALS_PRECISION', 'double'))"`
@@ -10,6 +26,10 @@ for ipynb in *.ipynb; do
     if [[ $PREC != "double" && $ipynb == "_robertson.ipynb" ]]; then
         continue
     fi
-    jupyter nbconvert --debug --to=html --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=900 $ipynb
+    quiet_unless_fail jupyter nbconvert --debug --to=html --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=900 "${ipynb}" \
+        | grep -v -e "^\[NbConvertApp\] content: {'data':.*'image/png'"
+    if [ ${QUIET_EXIT_CODE} -ne 0 ]; then
+        exit ${QUIET_EXIT_CODE}
+    fi
 done
 ../scripts/render_index.sh *.html

setup.py

@@ -78,7 +78,7 @@ def _path_under_setup(*args):
 _author, _author_email = open(_path_under_setup('AUTHORS'), 'rt').readline().split('<')
 
 extras_req = {
-    'integrators': ['pyodeint>=0.10.1', 'pycvodes>=0.11.12', 'pygslodeiv2>=0.9.1'],
+    'integrators': ['pyodeint>=0.10.1', 'pycvodes>=0.11.15', 'pygslodeiv2>=0.9.1'],
     'native': ['pycompilation>=0.4.3', 'pycodeexport>=0.1.2', 'appdirs'],
     'docs': ['Sphinx', 'sphinx_rtd_theme', 'numpydoc'],
     'testing': ['pytest', 'pytest-cov', 'pytest-flakes', 'pytest-pep8', 'rstcheck']