Feature 377 (#388)

* feature(ExpData) make ts mandatory, remove nt variable, change setter function to vector

* feature(ExpData) add more finegrained getter and setter routines for my, sigmay, mz, sigmaz

* feature(ExpData) rename my,mz,sigmay,sigmaz

* fix(core) fix downstream code after edata changes, streamline model::fdsigmaydp and model::fdsigmazdp

* fix(core) fix bad merge

* feature(core) better code style

* fix(core) add missing constructor to fix missing symbol in swig interface

* fix(doc) update documentation

* feature(test) add ExpData dimension checking routines and add unittests

* fix(CI) fix python coverage report by running in build venv

* fix(CI) ignore amici_without_hdf5.py in python report, remove -c flag from codecov uploads to not remove previous reports

* test(CI) whats wrong with the python upload?

* fix(CI) remove file display

* fix(doc) fix documentation

.travis.yml

@@ -30,8 +30,9 @@ matrix:
       env: ENABLE_GCOV_COVERAGE=TRUE
       after_success: 
         - ./scripts/run-codecov.sh
-        - bash <(curl -s https://codecov.io/bash) -f coverage_py.xml -X fix -cF python
-        - bash <(curl -s https://codecov.io/bash) -f coverage.info -X fix -cF cpp
+        - bash <(curl -s https://codecov.io/bash) -f coverage.info -X fix -F cpp
+        - bash <(curl -s https://codecov.io/bash) -f coverage_py.xml -X fix -F python
+
     - os: osx
       osx_image: xcode9.3
       compiler: clang
@@ -59,7 +60,7 @@ install:
     - pyenv versions
     - 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/3.7/bin:/Library/TeX/texbin:$PATH; fi
-    - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy coverage scipy
+    - pip3 install --user --upgrade pip setuptools wheel pkgconfig doxypypy scipy
     - ./scripts/buildSuiteSparse.sh
     - ./scripts/buildSundials.sh
     - ./scripts/buildCpputest.sh

CMakeLists.txt

@@ -8,7 +8,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(ENABLE_SWIG OFF)
+set(ENABLE_SWIG ON)
 
 # Compiler flags
 include(CheckCXXCompilerFlag)