Convert to sundials version 3.1.1 (#80)

* Move from recursive setup.py to standard python setup.py

* Add multi-precision logic to cython (no setup.py support yet)

* Add setup.py support for multi-precision

* Add CI support for multi-precision

* Add short explanation of how to use multi-precision code

* start of conversion to sundials 3.1.0
TODO:
 1/ update interface further
 2/ SUNDIALS_INDEX_TYPE should be settable

* move target to 3.1.1 sundials instead of 3.1.0

* Make sundials index type user settable

* New sundials will be a minor version bump. Put in doc how to see version

* cvode conversion to sundials 3.1.1

* nvector_serial conversion to sundials 3.1.1

* sundials dir conversion to sundials 3.1.1

* Add files to hold cython of new directories in 3.x sundials

* new linsol and matrix headers for 3.1.1

* bugfixes: compilation of common_defs.pyx now working

* add new error flag

* start with convertion of cvode to new methods

* finalize cvode API conversion to 3.1.1
Remaining issue: dense jac conversion to SUNMatrix, How ??

* Convert IDA to new API

* ENH: Allow usage of different index sizes

* ENH: Add SUNMatrix dense support

* ENH: Add SUNMatrix band support

* ENH: Don't include sundials_lapack header, not needed

* TST,CI: Drop python 3.3 and add python 3.7

* ENH: Skip lapack when building if sundials lacks lapack support

* Avoid error in test output when an integrator fails to
load on clean up of test (when del is called). Error in test
is sufficient.

* bugfix: fix unwanted lines in previous change

* Update examples to API changes

* Use uniform signature of (residual, cj) for jacobian

.travis.yml

@@ -31,53 +31,76 @@ matrix:
     # needed to work around https://github.com/travis-ci/travis-ci/issues/4794
     - python: 2.7
       env:
-      - TOXENV=py27 SUNDIALS_VERSION='2.7.0'
-    - python: 3.3
-      env:
-      - TOXENV=py33 SUNDIALS_VERSION='2.7.0'
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1'
     - python: 3.4
       env:
-      - TOXENV=py34 SUNDIALS_VERSION='2.7.0'
+      - TOXENV=py34 SUNDIALS_VERSION='3.1.1'
     - python: 3.5
       env:
-      - TOXENV=py35 SUNDIALS_VERSION='2.7.0'
+      - TOXENV=py35 SUNDIALS_VERSION='3.1.1'
     - python: 3.6
       env:
-      - TOXENV=py36 SUNDIALS_VERSION='2.7.0'
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1'
+    # commented as 3.7 not yet on travis
+    #- python: 3.7
+    #  env:
+    #  - TOXENV=py37 SUNDIALS_VERSION='3.1.1'
     - python: 3.5
       env:
-      - TOXENV=doctr SUNDIALS_VERSION='2.7.0'
+      - TOXENV=doctr SUNDIALS_VERSION='3.1.1'
     - python: 3.5
       env:
-      - TOXENV=docs SUNDIALS_VERSION='2.7.0'
+      - TOXENV=docs SUNDIALS_VERSION='3.1.1'
     - python: 3.5
       env:
-      - TOXENV=check-manifest SUNDIALS_VERSION='2.7.0'
+      - TOXENV=check-manifest SUNDIALS_VERSION='3.1.1'
     - python: 3.5
       env:
-      - TOXENV=checkreadme SUNDIALS_VERSION='2.7.0'
+      - TOXENV=checkreadme SUNDIALS_VERSION='3.1.1'
+
+    # Additional precisions
+    - python: 2.7
+      env:
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
+    - python: 3.6
+      env:
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
+    - python: 2.7
+      env:
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='extended'
+    - python: 3.6
+      env:
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='extended'
+
+  allow_failures:
+    - python: 2.7
+      env:
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
+    - python: 3.6
+      env:
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
 
     # Additional precisions
     - python: 2.7
       env:
-      - TOXENV=py27 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='single'
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
     - python: 3.6
       env:
-      - TOXENV=py36 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='single'
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
     - python: 2.7
       env:
-      - TOXENV=py27 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='extended'
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='extended'
     - python: 3.6
       env:
-      - TOXENV=py36 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='extended'
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='extended'
 
   allow_failures:
     - python: 2.7
       env:
-      - TOXENV=py27 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='single'
+      - TOXENV=py27 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
     - python: 3.6
       env:
-      - TOXENV=py36 SUNDIALS_VERSION='2.7.0' SUNDIALS_PRECISION='single'
+      - TOXENV=py36 SUNDIALS_VERSION='3.1.1' SUNDIALS_PRECISION='single'
 
 install:
   - source ci_support/ensure_sundials_installed.sh

ci_support/ensure_sundials_installed.sh

@@ -1,9 +1,10 @@
 #!/bin/sh
 
-SUNDIALS_DEFAULT_VERSION='2.7.0'
+SUNDIALS_DEFAULT_VERSION='3.1.1'
 SUNDIALS_DEFAULT_PRECISION='double'
+SUNDIALS_DEFAULT_INDEX_TYPE='int32_t'
 
-export SUNDIALS_DIR=$HOME/sundials/"${SUNDIALS_VERSION:-$SUNDIALS_DEFAULT_VERSION}"/"${SUNDIALS_PRECISION:-$SUNDIALS_DEFAULT_PRECISION}"
+export SUNDIALS_DIR=$HOME/sundials/"${SUNDIALS_VERSION:-$SUNDIALS_DEFAULT_VERSION}"/"${SUNDIALS_PRECISION:-$SUNDIALS_DEFAULT_PRECISION}"/"${SUNDIALS_INDEX_TYPE:-$SUNDIALS_DEFAULT_INDEX_TYPE}"
 SUNDIALS_LIBDIR=$SUNDIALS_DIR/lib
 SUNDIALS_INCLUDEDIR=$SUNDIALS_DIR/include
 

ci_support/install_sundials.sh

@@ -1,10 +1,11 @@
 #!/bin/sh
 set -ex
 
-SUNDIALS=sundials-"${SUNDIALS_VERSION:-2.7.0}"
+SUNDIALS=sundials-"${SUNDIALS_VERSION:-3.1.1}"
 SUNDIALS_FILE=$SUNDIALS.tar.gz
 SUNDIALS_URL=http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download/$SUNDIALS_FILE
 PRECISION="${SUNDIALS_PRECISION:-double}"
+INDEX_TYPE="${SUNDIALS_INDEX_TYPE:-int32_t}"
 
 wget "$SUNDIALS_URL"
 
@@ -16,5 +17,5 @@ mkdir sundials_build
 # ARKODE and examples are disabled as they does not support multiple precisions
 # (should be fixed in the 3.0 release)
 cd sundials_build &&
-    cmake -DCMAKE_INSTALL_PREFIX=$SUNDIALS_DIR -DLAPACK_ENABLE=ON -DSUNDIALS_PRECISION="$PRECISION" -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DEXAMPLES_INSTALL:BOOL=OFF ../$SUNDIALS &&
+    cmake -DCMAKE_INSTALL_PREFIX=$SUNDIALS_DIR -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE="$INDEX_TYPE" -DSUNDIALS_PRECISION="$PRECISION" -DBUILD_ARKODE:BOOL=OFF -DEXAMPLES_ENABLE:BOOL=OFF -DEXAMPLES_INSTALL:BOOL=OFF ../$SUNDIALS &&
     make && make install

common.py

@@ -21,8 +21,8 @@
 BUILD_REQUIRES = ['numpy', 'cython'] # This is need for older pip
 
 MAJOR = 2
-MINOR = 3
-MICRO = 3
+MINOR = 4
+MICRO = 0
 DEV = True
 
 CLASSIFIERS = [
@@ -35,10 +35,10 @@
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.2',
-        'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
 ]
 
 def build_verstring():

docs/examples/doublependulum.py

@@ -168,7 +168,7 @@ def ddaspk_res(self, tres, yy, yp, res):
 
     def ddaspk_jac(self, tres, yy, yp, cj, jac):
         """the jacobian function as required by ddaspk"""
-        self.jac.evaluate(tres, yy, yp, cj, jac)
+        self.jac.evaluate(tres, yy, yp, None, cj, jac)
 
 #classes for the equations, as needed for the chosen solution method
 class resindex2(ida.IDA_RhsFunction):
@@ -242,7 +242,7 @@ def set_dblpend(self, dblpend):
             the data """
         self.dblpend = dblpend
 
-    def evaluate(self, tres, yy, yp, cj, jac):
+    def evaluate(self, tres, yy, yp, residual, cj, jac):
 
         m1 = self.dblpend.m1
         m2 = self.dblpend.m2

docs/examples/ode/simpleoscillator_jac.py

@@ -1,12 +1,12 @@
-# Authors: B. Malengier 
+# Authors: B. Malengier
 """
-This example shows the most simple way of using a solver. 
+This example shows the most simple way of using a solver.
 We solve free vibration of a simple oscillator::
         m \ddot{u} + k u = 0, u(0) = u_0, \dot{u}(0) = \dot{u}_0
 using the CVODE solver, which means we use a rhs function of \dot{u}.
 Solution::
         u(t) = u_0*cos(sqrt(k/m)*t)+\dot{u}_0*sin(sqrt(k/m)*t)/sqrt(k/m)
-    
+
 """
 from __future__ import print_function
 from numpy import asarray, cos, sin, sqrt
@@ -22,11 +22,11 @@ def rhseqn(t, x, xdot):
     """ we create rhs equations for the problem"""
     xdot[0] = x[1]
     xdot[1] = - k/m * x[0]
-    
-def jaceqn(t, x, jac):
+
+def jaceqn(t, x, fx, jac):
     jac[0,1] = 1
     jac[1,0] = -k/m
-    
+
 #instantiate the solver
 from scikits.odes import ode
 solver = ode('cvode', rhseqn, jacfn=jaceqn)

docs/examples/ode/simpleoscillator_prec.py

@@ -7,11 +7,11 @@
 using the CVODE solver. The rhs function is given by \dot{u}. The
 preconditioning is implemented in prec_solvefn which solves the
 system P = I - gamma * J, where J is the Jacobian of the rhs.
-The jac_times_vecfn calculates the Jacobian times vector product 
-using the analytic Jacobian. 
+The jac_times_vecfn calculates the Jacobian times vector product
+using the analytic Jacobian.
 Solution::
         u(t) = u_0*cos(sqrt(k/m)*t)+\dot{u}_0*sin(sqrt(k/m)*t)/sqrt(k/m)
-    
+
 """
 from __future__ import print_function
 from numpy import asarray, cos, sin, sqrt
@@ -32,17 +32,17 @@ def prec_solvefn(t, y, r, z, gamma, delta, lr):
 def jac_times_vecfn(v, Jv, t, y, user_data):
     """ Calculate Jacobian times vector product Jv = J*v"""
     Jv[0] = v[1]
-    Jv[1] = -k/m * v[0] 
+    Jv[1] = -k/m * v[0]
 
 #define function for the right-hand-side equations which has specific signature
 def rhseqn(t, x, xdot):
     """ we create rhs equations for the problem"""
     xdot[0] = x[1]
     xdot[1] = - k/m * x[0]
-    
+
 #instantiate the solver using a left-preconditioned BiCGStab as linear solver
 from scikits.odes import ode
-solver = ode('cvode', rhseqn, linsolver='spbcg', precond_type='left', prec_solvefn=prec_solvefn, jac_times_vecfn=jac_times_vecfn)
+solver = ode('cvode', rhseqn, linsolver='spbcgs', precond_type='left', prec_solvefn=prec_solvefn, jac_times_vecfn=jac_times_vecfn)
 #obtain solution at a required time
 result = solver.solve([0., 1., 2.], initx)
 

docs/installation.rst

@@ -10,17 +10,17 @@ Before building ``odes``, you need to have installed:
       distributions, ``python-devel`` on Fedora)
     * C compiler
     * Fortran compiler (e.g. gfortran)
-    * `Sundials 2.7.0 <https://computation.llnl.gov/casc/sundials/download/download.html>`_ 
+    * `Sundials 3.1.1 <https://computation.llnl.gov/casc/sundials/download/download.html>`_ 
 
 In addition, if building from a git checkout, you'll also need Cython.
 
 It is required that Sundials is built with the BLAS/LAPACK interface enabled, so check
 the Fortran Settings section. A typical install if sundials download package is
-extracted into directory sundials-2.7.0 is on a \*nix system::
+extracted into directory sundials-3.1.1 is on a \*nix system::
 
-    mkdir build-sundials-2.7.0
-    cd build-sundials-2.7.0/
-    cmake -DLAPACK_ENABLE=ON -DCMAKE_INSTALL_PREFIX=<install_path> ../sundials-2.7.0/
+    mkdir build-sundials-3.1.1
+    cd build-sundials-3.1.1/
+    cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_TYPE=int32_t -DCMAKE_INSTALL_PREFIX=<install_path> ../sundials-3.1.1/
     make install
 
 .. warning::
@@ -43,6 +43,15 @@ which will download the latest version from PyPI. This will handle the installat
 
 If you have installed SUNDIALS in a non-standard path (e.g. ``/usr/`` or ``/usr/local/``), you can set ``$SUNDIALS_INST`` in your environment to the installation prefix of SUNDIALS (i.e. value of ``<install_path>`` mentioned above).
 
+
+Testing your version of ``odes``
+................................
+To test the version in python, use in the python shell::
+
+    >>> import pkg_resources
+    >>> pkg_resources.get_distribution("scikits.odes").version
+
+    
 Running the Tests
 .................
 You need nose to run the tests. To install nose, run::
@@ -52,6 +61,10 @@ You need nose to run the tests. To install nose, run::
 To run the tests, in the python shell::
 
     >>> import scikits.odes as od; od.test()
+    
+Note that the sundials library must be in your ``LD_LIBRARY_PATH``. So, make sure the directory ``$SUNDIALS_INST/lib`` is included. You can do this for example as follows (assuming sundials was installed in ``/usr/local``::
+
+    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 Installation of ODES from git checkout
 ---------------------------------------------

scikits/odes/dae.py

@@ -442,7 +442,8 @@ def __del__(self):
         """
         Clean up what is needed
         """
-        del self._integrator
+        if hasattr(self, '_integrator'):
+            del self._integrator
 
 #------------------------------------------------------------------------------
 # DAE integrators