#247 merge master

.gitignore

@@ -5,11 +5,13 @@
 /local/
 *.DS_Store
 *.mat
+*.csv
 
-# don't ignore important .txt files
+# don't ignore important .txt and .csv files
 !requirements*
 !LICENSE.txt
 !CMakeLists.txt
+!input/**/*.csv
 
 # running files
 *.pyc
@@ -70,6 +72,12 @@ pyvenv.cfg
 # sundials
 sundials
 sundials4
+sundials-*
+SuiteSparse-*
+build_sundials
+
+# downloads
+*.gz
 
 # third party
 third-party

.travis.yml

@@ -62,6 +62,7 @@ matrix:
           env:
             - PYTHON=3.7.4
             - PYBAMM_UNIT=true
+            - PYBAMM_KLU=true
           if: type != cron
         - python: "3.7"
           addons:
@@ -177,6 +178,8 @@ before_install: |
     brew update;
     # Per the `pyenv homebrew recommendations <https://github.com/yyuu/pyenv/wiki#suggested-build-environment>`_.
     brew install graphviz openssl readline;
+    # Other brew packages
+    brew install gcc cmake openblas suitesparse;
     # See https://docs.travis-ci.com/user/osx-ci-environment/#A-note-on-upgrading-packages.
     brew outdated pyenv || brew upgrade pyenv
     # virtualenv doesn't work without pyenv knowledge. venv in Python 3.3
@@ -200,12 +203,28 @@ before_install: |
 #       without the packages from -dev and -doc!
 install:
   - pip install --upgrade pip
+  # In order to download SUNDIALS and SuiteSparse
+  - pip install wget
   - pip install .
   - if [[ $PYBAMM_DOCS == true ]]; then pip install -e .[docs]; fi;
   - if [[ $PYBAMM_STYLE == true || $PYBAMM_EXAMPLES ]]; then pip install -e .[dev]; fi;
   - if [[ $PYBAMM_COVER == true ]]; then pip install coverage codecov; fi;
-  - if [[ $PYBAMM_SCIKITS_ODES == true ]]; then source scripts/install_scikits_odes.sh; fi;
-  - if [[ $PYBAMM_KLU == true ]]; then source scripts/install_sundials_4.1.0.sh; fi;
+  - |
+    if [[ $PYBAMM_SCIKITS_ODES == true ]]; then
+      python setup.py install_odes -f;
+      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
+    fi;
+  - |
+    if [[ $PYBAMM_KLU == true ]]; then
+      mkdir -p third-party;
+      cd third-party;
+      rm -rf pybind11;
+      git clone https://github.com/pybind/pybind11.git;
+      cd ../;
+      python setup.py install_klu -f;
+      export LD_LIBRARY_PATH=sundials/lib:$LD_LIBRARY_PATH
+      export LD_LIBRARY_PATH=SuiteSparse-5.6.0/lib:$LD_LIBRARY_PATH
+    fi;
 
 before_script:
 - python --version

CHANGELOG.md

@@ -3,9 +3,16 @@
 ## Features
 
 -   Added capacitance effects to lithium-ion models ()
+-   Added NCA parameter set ([#824](https://github.com/pybamm-team/PyBaMM/pull/824))
+-   Added functionality to `Solution` that automatically gets `t_eval` from the data when simulating drive cycles and performs checks to ensure the output has the required resolution to accurately capture the input current ([#819](https://github.com/pybamm-team/PyBaMM/pull/819))
+-   Added options to export a solution to matlab or csv ([#811](https://github.com/pybamm-team/PyBaMM/pull/811))
+-   Allow porosity to vary in space ([#809](https://github.com/pybamm-team/PyBaMM/pull/809))
+-   Added functionality to solve DAE models with non-smooth current inputs ([#808](https://github.com/pybamm-team/PyBaMM/pull/808))
+-   Added functionality to simulate experiments and testing protocols ([#807](https://github.com/pybamm-team/PyBaMM/pull/807))
 -   Added fuzzy string matching for parameters and variables ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
 -   Changed ParameterValues to raise an error when a parameter that wasn't previously defined is updated ([#796](https://github.com/pybamm-team/PyBaMM/pull/796))
 -   Added some basic models (BasicSPM and BasicDFN) in order to clearly demonstrate the PyBaMM model structure for battery models ([#795](https://github.com/pybamm-team/PyBaMM/pull/795))
+-   Allow initial conditions in the particle to depend on x ([#786](https://github.com/pybamm-team/PyBaMM/pull/786))
 -   Added the harmonic mean to the Finite Volume method, which is now used when computing fluxes ([#783](https://github.com/pybamm-team/PyBaMM/pull/783))
 -   Refactored `Solution` to make it a dictionary that contains all of the solution variables. This automatically creates `ProcessedVariable` objects when required, so that the solution can be obtained much more easily. ([#781](https://github.com/pybamm-team/PyBaMM/pull/781))
 -   Added notebook to explain broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
@@ -47,6 +54,8 @@
 
 ## Bug fixes
 
+-   Fixed a bug where the first line of the data wasn't loaded when parameters are loaded from data ([#819](https://github.com/pybamm-team/PyBaMM/pull/819))
+-   Made `graphviz` an optional dependency ([#810](https://github.com/pybamm-team/PyBaMM/pull/810))
 -   Fixed examples to run with basic pip installation ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
 -   Added events for CasADi solver when stepping ([#800](https://github.com/pybamm-team/PyBaMM/pull/800))
 -   Improved implementation of broadcasts ([#776](https://github.com/pybamm-team/PyBaMM/pull/776))
@@ -60,10 +69,13 @@
 -   Added missing temperature dependence in electrolyte and interface submodels ([#698](https://github.com/pybamm-team/PyBaMM/pull/698))
 -   Fixed differentiation of functions that have more than one argument ([#687](https://github.com/pybamm-team/PyBaMM/pull/687))
 -   Added warning if `ProcessedVariable` is called outside its interpolation range ([#681](https://github.com/pybamm-team/PyBaMM/pull/681))
+-   Updated installation instructions for Mac OS ([#680](https://github.com/pybamm-team/PyBaMM/pull/680))
 -   Improved the way `ProcessedVariable` objects are created in higher dimensions ([#581](https://github.com/pybamm-team/PyBaMM/pull/581))
 
 ## Breaking changes
 
+-   Model events are now represented as a list of `pybamm.Event` ([#759](https://github.com/pybamm-team/PyBaMM/issues/759)
+-   Removed `ParameterValues.update_model`, whose functionality is now replaced by `InputParameter` ([#801](https://github.com/pybamm-team/PyBaMM/pull/801))
 -   Removed `Outer` and `Kron` nodes as no longer used ([#777](https://github.com/pybamm-team/PyBaMM/pull/777))
 -   Moved `results` to separate repositories ([#761](https://github.com/pybamm-team/PyBaMM/pull/761))
 -   The parameters "Bruggeman coefficient" must now be specified separately as "Bruggeman coefficient (electrolyte)" and "Bruggeman coefficient (electrode)"

CMakeLists.txt

@@ -8,17 +8,18 @@ add_subdirectory(third-party/pybind11)
 pybind11_add_module(idaklu pybamm/solvers/c_solvers/idaklu.cpp)
 
 # Sundials
-set(SUNDIALS_INCLUDE "sundials4/include")
+set(SUNDIALS_INCLUDE "sundials/include")
 TARGET_INCLUDE_DIRECTORIES(idaklu PRIVATE ${SUNDIALS_INCLUDE})
 
-find_library(SUNMATSPARSE sundials_sunmatrixsparse PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(IDA sundials_ida PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(NVECTOR sundials_nvecserial PATHS "sundials4/lib" NO_DEFAULT_PATH)
-find_library(SUNKLU sundials_sunlinsolklu PATHS "sundials4/lib" NO_DEFAULT_PATH)
+find_library(SUNMATSPARSE sundials_sunmatrixsparse PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(IDA sundials_ida PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(NVECTOR sundials_nvecserial PATHS "sundials/lib" NO_DEFAULT_PATH)
+find_library(SUNKLU sundials_sunlinsolklu PATHS "sundials/lib" NO_DEFAULT_PATH)
 TARGET_LINK_LIBRARIES(idaklu PRIVATE ${SUNMATSPARSE} ${IDA} ${NVECTOR} ${SUNKLU})
 
 # link suitesparse
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR})
+set(SuiteSparse_ROOT SuiteSparse-5.6.0)
 find_package(SuiteSparse OPTIONAL_COMPONENTS KLU AMD COLAMD BTF)
 include_directories(${SuiteSparse_INCLUDE_DIRS})
 target_link_libraries(idaklu PRIVATE ${SuiteSparse_LIBRARIES})