slider bug fix

.github/workflows/build_wheels_and_publish.yml

@@ -0,0 +1,70 @@
+name: Build and deployment
+
+on:
+  push:
+    branches: master
+
+jobs:
+  build-wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest]
+        python-version: [3.6, 3.7]
+        include:
+          - os: ubuntu-latest
+            python-version: 3.8
+          - os: windows-latest
+            python-version: 3.6
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+       python-version: ${{ matrix.python-version }}
+
+    - name: Build manylinux Python wheels
+      if: matrix.os == 'ubuntu-latest'
+      uses: './build_manylinux_wheels'
+
+    - name: Install standard python dependencies
+      if: matrix.os != 'ubuntu-latest'
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+
+    - name: Install build-time deps for MacOS
+      if: matrix.os == 'macos-latest'
+      run: |
+        brew update
+        brew install graphviz
+        brew install sundials
+        git clone https://github.com/pybind/pybind11.git
+
+    - name: Build wheels for MacOS and Windows
+      if: matrix.os != 'ubuntu-latest'
+      run: |
+        python -m pip wheel . -w dist/ --no-deps
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v1
+      with:
+        name: dist
+        path: dist
+
+
+  publish-pyi:
+    name: Upload wheels to PyPI 
+    needs: build-wheels
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v1
+        with:
+          name: dist
+
+      - name: Publish wheels
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TESTPYPI_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/

.github/workflows/test_on_push.yml

@@ -93,14 +93,22 @@ jobs:
         export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
         pip install -e .[docs]
         python run-tests.py --doctest
-    
+
     - name: Install dev dependencies and run example tests
       if: matrix.os != 'windows-latest'
       run: |
         export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
         pip install -e .[dev]
         python run-tests.py --examples
-
-    - name: Instal and run coverage
-      if: success() && (matrix.os == 'unbuntu-latest' && matrix.python-version == 3.7)
+
+    - name: Install and run coverage
+      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7)
+      run: |
+        pip install coverage
+        export LD_LIBRARY_PATH=$HOME/.local/lib:scikits.odes/sundials5/lib:$LD_LIBRARY_PATH
+        coverage run run-tests.py --nosub
+        coverage xml
+
+    - name: Upload coverage report
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
       uses: codecov/codecov-action@v1

.gitignore

@@ -80,6 +80,7 @@ sundials4
 sundials-*
 SuiteSparse-*
 build_sundials
+KLU_module_deps
 
 # downloads
 *.gz
@@ -96,6 +97,9 @@ cmake_install.cmake
 
 
 third-party/pybind11
+pybind11/
+
+setup.log
+
+
 
-# Build dependencies/
-KLU_module_deps

CHANGELOG.md

@@ -31,6 +31,7 @@ New SEI models, simplification of submodel structure, as well as optimisations a
 
 ## Bug fixes
 
+-   Fix a bug where slider plots do not update properly in notebooks ([#1041](https://github.com/pybamm-team/PyBaMM/pull/1041))
 -   Fix storing and plotting external variables in the solution ([#1026](https://github.com/pybamm-team/PyBaMM/pull/1026))
 -   Fix running a simulation with a model that is already discretized ([#1025](https://github.com/pybamm-team/PyBaMM/pull/1025))
 -   Fix CI not triggering for PR. ([#1013](https://github.com/pybamm-team/PyBaMM/pull/1013))

build_manylinux_wheels/Dockerfile

@@ -0,0 +1,17 @@
+FROM quay.io/pypa/manylinux2010_x86_64:2020-05-29-c06f15c
+
+ENV PLAT manylinux2010_x86_64
+
+RUN yum -y remove cmake
+RUN yum -y install wget openblas-devel
+RUN /opt/python/cp37-cp37m/bin/pip install --upgrade pip cmake
+RUN ln -s /opt/python/cp37-cp37m/bin/cmake /usr/bin/cmake
+
+COPY install_sundials.sh /install_sundials.sh
+RUN chmod +x /install_sundials.sh
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+
+RUN ./install_sundials.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

build_manylinux_wheels/action.yml

@@ -0,0 +1,17 @@
+# action.yml
+# Based on  RalfG/python-wheels-manylinux-build/action.yml by Ralf Gabriels
+
+name: 'Python wheels manylinux build'
+author: 'Thibault Lestang'
+description: 'Build manylinux wheels for PyBaMM'
+inputs:
+  python-versions:
+    description: 'Python versions to target, space-separated'
+    required: true
+    default: 'cp36-cp36m cp37-cp37m'
+
+runs:
+  using: 'docker'
+  image: 'Dockerfile'
+  args:
+    - ${{ inputs.python-versions }}

build_manylinux_wheels/entrypoint.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+set -e -x
+
+# CLI arguments
+PY_VERSIONS=$1
+
+git clone https://github.com/pybind/pybind11.git /github/workspace/pybind11
+# Compile wheels
+arrPY_VERSIONS=(${PY_VERSIONS// / })
+for PY_VER in "${arrPY_VERSIONS[@]}"; do
+    # Update pip
+    /opt/python/"${PY_VER}"/bin/pip install --upgrade --no-cache-dir pip
+
+    # Build wheels
+    /opt/python/"${PY_VER}"/bin/pip wheel /github/workspace/ -w /github/workspace/wheelhouse/ --no-deps || { echo "Building wheels failed."; exit 1; }
+done
+ls -l /github/workspace/wheelhouse/
+
+# Bundle external shared libraries into the wheels
+for whl in /github/workspace/wheelhouse/*-linux*.whl; do
+    auditwheel repair "$whl" --plat "${PLAT}" -w /github/workspace/dist/ || { echo "Repairing wheels failed."; auditwheel show "$whl"; exit 1; }
+done
+
+echo "Succesfully built wheels:"
+ls -l /github/workspace/dist/

build_manylinux_wheels/install_sundials.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+mkdir /deps
+wget https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v5.7.2.tar.gz .
+wget https://computing.llnl.gov/projects/sundials/download/sundials-5.3.0.tar.gz .
+tar -xf v5.7.2.tar.gz --directory /deps
+tar -xf sundials-5.3.0.tar.gz --directory /deps
+rm v5.7.2.tar.gz
+rm sundials-5.3.0.tar.gz
+
+SUITESPARSE_DIR=/deps/SuiteSparse-5.7.2
+SUNDIALS_DIR=/deps/sundials-5.3.0
+
+for dir in SuiteSparse_config AMD COLAMD BTF KLU
+do
+    cd $SUITESPARSE_DIR/$dir;
+    make library
+    make install INSTALL=/usr
+    cd ../
+done
+
+KLU_INCLUDE_DIR=/usr/include
+KLU_LIBRARY_DIR=/usr/lib
+mkdir -p /deps/build_sundials
+cd /deps/build_sundials
+cmake -DLAPACK_ENABLE=ON\
+      -DSUNDIALS_INDEX_SIZE=32\
+      -DEXAMPLES_ENABLE:BOOL=OFF\
+      -DKLU_ENABLE=ON\
+      -DKLU_INCLUDE_DIR=$KLU_INCLUDE_DIR\
+      -DKLU_LIBRARY_DIR=$KLU_LIBRARY_DIR\
+      -DCMAKE_INSTALL_PREFIX=/usr\
+      $SUNDIALS_DIR
+make install
+

docs/index.rst

@@ -22,10 +22,20 @@ PyBaMM is available on GNU/Linux, MacOS and Windows.
 Using pip
 ----------
 
+GNU/Linux and Windows
+~~~~~~~~~~~~~~~~~~~~~~
+
 .. code:: bash
 
    pip install pybamm
 
+macOS
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: bash
+
+   brew install sundials && pip install pybamm
+
 Using conda
 -------------
 PyBaMM is available as a conda package through the conda-forge channel.

docs/install/GNU-linux.rst

@@ -1,10 +1,11 @@
-GNU-Linux & MacOS
-======================
+===================
+ GNU-Linux & MacOS
+===================
 
 .. contents::
 
 Prerequisites
----------------
+=============
 
 To use and/or contribute to PyBaMM, you must have Python 3.6 or 3.7
 installed (note that 3.8 is not yet supported).
@@ -37,10 +38,12 @@ then follow instructions in link on adding brew to path, and run
    brew install python3
 
 Install PyBaMM
------------------
+==============
+
+.. _user-install-label:
 
 User install
-~~~~~~~~~~~~
+------------
 
 We recommend to install PyBaMM within a virtual environment, in order
 not to alter any distribution python files. To create a virtual
@@ -64,10 +67,20 @@ the environment and go back to your original system, just type:
 
    deactivate
 
-PyBaMM can be installed via pip:
+PyBaMM can be installed via pip. On macOS, it is necessary to install the `SUNDIALS <https://computing.llnl.gov/projects/sundials/>`__
+library beforehand.
+
+GNU/Linux and Windows
+~~~~~~~~~~~~~~~~~~~~~
+.. code:: bash
+
+   pip install pybamm
 
+macOS
+~~~~~
 .. code:: bash
 
+   brew install sundials
    pip install pybamm
 
 PyBaMM’s dependencies (such as ``numpy``, ``scipy``, etc) will be
@@ -79,38 +92,35 @@ For an introduction to virtual environments, see
 .. _scikits.odes-label:
 
 Optional - scikits.odes solver
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+------------------------------
 
 Users can install `scikits.odes <https://github.com/bmcage/odes>`__ in
 order to use the wrapped SUNDIALS ODE and DAE
 `solvers <https://pybamm.readthedocs.io/en/latest/source/solvers/scikits_solvers.html>`__.
+Currently, only GNU/Linux and macOS are supported.
 
-**A pre-requisite** is the installation of a BLAS library (such as
-`openblas <https://www.openblas.net/>`__). On Ubuntu/debian
-
-::
+GNU/Linux
+~~~~~~~~~
 
-   sudo apt install libopenblas-dev
-
-and on Mac OS
+.. code:: bash
 
-::
+	  apt install libopenblas-dev
+	  pybamm_install_odes --install-sundials
 
-   brew install openblas
+The ``pybamm_install_odes`` command is installed with PyBaMM. It automatically downloads and installs the SUNDIALS library on your
+system (under ``~/.local``), before installing ``sckits.odes`` (by running ``pip install scikits.odes``).
 
-After installing PyBaMM, the following command can be used to
-automatically install ``scikits.odes`` and its dependencies
+macOS
+~~~~~
 
-::
-
-   $ pybamm_install_odes --install-sundials
+.. code:: bash
 
-The ``--install-sundials`` option is used to activate automatic
-downloads and installation of the sundials library, which is required by
-``scikits.odes``.
+	  pip install scikits.odes
+   
+Assuming that the SUNDIALS were installed as described :ref:`above<user-install-label>`.
 
 Developer install
-~~~~~~~~~~~~~~~~~~
+-----------------
 
 If you wish to contribute to PyBaMM, you should get the latest version
 from the GitHub repository. To do so, you must have Git and graphviz
@@ -159,7 +169,7 @@ Before you start contributing to PyBaMM, please read the `contributing
 guidelines <CONTRIBUTING.md>`__.
 
 Uninstall PyBaMM
---------------------
+================
 
 PyBaMM can be uninstalled by running
 
@@ -170,7 +180,7 @@ PyBaMM can be uninstalled by running
 in your virtual environment.
 
 Troubleshooting
--------------------
+===============
 
 **Problem:** I’ve made edits to source files in PyBaMM, but these are
 not being used when I run my Python script.

pybamm/plotting/quick_plot.py

@@ -465,14 +465,14 @@ def plot(self, t):
         Parameters
         ----------
         t : float
-            Dimensional time (in hours) at which to plot.
+            Dimensional time (in 'time_units') at which to plot.
         """
 
         import matplotlib.pyplot as plt
         import matplotlib.gridspec as gridspec
         from matplotlib import cm, colors
 
-        t_in_seconds = t / self.time_scaling_factor
+        t_in_seconds = t * self.time_scaling_factor
         self.fig = plt.figure(figsize=self.figsize)
 
         self.gridspec = gridspec.GridSpec(self.n_rows, self.n_cols)
@@ -526,8 +526,8 @@ def plot(self, t):
                 ax.set_ylim(y_min, y_max)
                 (self.time_lines[key],) = ax.plot(
                     [
-                        t_in_seconds * self.time_scaling_factor,
-                        t_in_seconds * self.time_scaling_factor,
+                        t_in_seconds / self.time_scaling_factor,
+                        t_in_seconds / self.time_scaling_factor,
                     ],
                     [y_min, y_max],
                     "k--",