Miscellaneous fixes, python packaging and python API improvements (#327)

* fix(swig) Make enums and constants available in python

* fix(python) edata is regular pointer, not unique_ptr here

* refactor(cmake)

* fix(python) Fix linking order. Fix C++ standard.

* feature(python) Add verbosity switch for model compilation

* feature(python) Add verbosity switch for sbml2amici

* fix(python) Make swig aware of enums in time to generate appropriate mappers

* doc(python) Extend python API steadystate example. Change to notebook.

* fix(python) Check edata type. Here it can be regular or unique pointer

* fix(python) Check edata type. Here it can be regular or unique pointer

* doc(python) Cleanup notebook

* doc(python) Add finite differences sensitivity check to example

* feature(python) Allow blas selection for amici base package installation via environment variables #320

* doc(python) Add model info to example

* Fix(python) Fix negative log likelihood

* Feature(python) Expose std::vector<amici::AMICI_parameter_scaling> as ParameterScalingVector

* doc(core) Fix dimension order

* ci(python) Run gradient check for example models (don't fail test yet)

* ci(travis) Install scipy

* build(cmake) CMake cleanup

* ci(travis) Test creating and installing sdist on ci server

* fix(python) Increase chances of finding swig on OSX #320

* ci(python) Don't use pyenv pip which is broken by recent update

  File '/opt/pyenv/versions/3.6/bin/pip3', line 7, in <module>
    from pip import main
ImportError: cannot import name 'main'

* fix(python) Catch hdf5.cpp not found problem #320

* doc(doxygen) Ignore autogenerated file

* fix(python) Set sensitivity flag for dydp (thx FFroehlich)

* feature(python) Exception on package setup failure

* fix(python) Fix sx summation. Fixes sx gradient check (thx FFroehlich)

* fix(python) fix sy computation in python generated models

* Fix typo, rewrap models, remove notebook test code

Author: dweindl

.travis.yml

@@ -58,13 +58,17 @@ install:
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv versions; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pyenv shell 2.7 3.6; fi
     - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Users/travis/Library/Python/3.6/bin:$PATH; fi
-    - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy coverage
+    - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy coverage scipy
     - ./scripts/buildSuiteSparse.sh
     - ./scripts/buildSundials.sh
     - ./scripts/buildCpputest.sh
     - ./scripts/buildAmici.sh
 
 script:  
+    - cd $BASE_DIR/python/sdist
+    - python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
+    - python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
+    - cd $BASE_DIR
     - ./scripts/run-cpputest.sh
     - ./scripts/run-cppcheck.sh
     - cd $BASE_DIR/build && make python-tests && cd $BASE_DIR

include/amici/rdata.h

@@ -83,7 +83,7 @@ class ReturnData {
     /** state (dimension: nt x nx, row-major) */
     std::vector<realtype> x;
 
-    /** parameter derivative of state (dimension: nt x nx x nplist,
+    /** parameter derivative of state (dimension: nt x nplist x nx,
      * row-major) */
     std::vector<realtype> sx;
 
@@ -93,12 +93,12 @@ class ReturnData {
     /** observable standard deviation (dimension: nt x ny, row-major) */
     std::vector<realtype> sigmay;
 
-    /** parameter derivative of observable (dimension: nt x ny x nplist,
+    /** parameter derivative of observable (dimension: nt x nplist x ny,
      * row-major) */
     std::vector<realtype> sy;
 
     /** parameter derivative of observable standard deviation (dimension: nt x
-     * ny x nplist, row-major) */
+     * nplist x ny, row-major) */
     std::vector<realtype> ssigmay;
 
     /** observable (dimension: nt x ny, row-major) */

matlab/mtoc/config/Doxyfile.template

@@ -697,6 +697,7 @@ EXCLUDE_PATTERNS       = "_SourceDir_/models/*" \
                          "_SourceDir_/matlab/auxiliary/*" \
                          "_SourceDir_/matlab/SBMLImporter/*" \
                          "_SourceDir_/python/test/*" \
+                         "_SourceDir_/python/sdist/*" \
                          "_SourceDir_/build/*" \ 
                          "_SourceDir_/build_xcode/*" \
                          "_SourceDir_/swig/*"

models/model_dirac/model_dirac.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_dirac_h
 #define _amici_model_dirac_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -62,7 +62,7 @@ class Model_model_dirac : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_dirac(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_dirac(J, t, x, p, k, h, w, dwdx);

models/model_events/model_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_events_h
 #define _amici_model_events_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -76,7 +76,7 @@ class Model_model_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_events(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_events(J, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint/model_jakstat_adjoint.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_h
 #define _amici_model_jakstat_adjoint_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_jakstat_adjoint(J, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_o2_h
 #define _amici_model_jakstat_adjoint_o2_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint_o2(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_jakstat_adjoint_o2(J, t, x, p, k, h, w, dwdx);

models/model_nested_events/model_nested_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_nested_events_h
 #define _amici_model_nested_events_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -65,7 +65,7 @@ class Model_model_nested_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_nested_events(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_nested_events(J, t, x, p, k, h, w, dwdx);

models/model_neuron/model_neuron.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_h
 #define _amici_model_neuron_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -79,7 +79,7 @@ class Model_model_neuron : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_neuron(J, t, x, p, k, h, w, dwdx);

models/model_neuron_o2/model_neuron_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_o2_h
 #define _amici_model_neuron_o2_h
-/* Generated by amiwrap (R2017b) 2632f34b3b684c381e19069e73b4b1277492fcf1 */
+/* Generated by amiwrap (R2017b) 53e279f979516a66d9b07a42c171c4fa35b6f26d */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -81,7 +81,7 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron_o2(*this); };
 
-    const  char* getAmiciVersion() const { return "2632f34b3b684c381e19069e73b4b1277492fcf1"; };
+    const  char* getAmiciVersion() const { return "53e279f979516a66d9b07a42c171c4fa35b6f26d"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_neuron_o2(J, t, x, p, k, h, w, dwdx);