Merge pull request #1207 from AMICI-dev/release_0.11.6

Release 0.11.6

## Python
* Bugfix for piecewise functions (#1199)
* Refactor swigging - generate one single wrapper (#1213)

## C++
* Fix warnings: account for zero indexing in nan/inf error (#1112)

## Doc
* Update Windows build instructions (#1200, #1202)
* Update README: Projects using AMICI (#1209)
* Add CODE_OF_CONDUCT.md (#1210)
* Update documentation for Python interface (#1208)

## CI
* Create sdist on GHA using swig4.0.1 (#1204)  (Fixing broken pypi package)
* Fix links after repository move
* Speed-up swig build: disable all languages except python (#1211)
* Fix doc generation on readthedocs (#1196)

.github/workflows/deploy_branch.yml

@@ -1,25 +1,7 @@
 name: Deploy Branch
-on: [push]
+on: [push, pull_request]
+
 jobs:
-  dockerhub:
-    # https://github.com/marketplace/actions/publish-docker
-    name: Deploy Dockerhub
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@master
-    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
-    - name: Publish to Registry
-      uses: elgohr/[email protected]
-      with:
-        name: dweindl/amici
-        username: ${{ secrets.DOCKER_USERNAME }}
-        password: ${{ secrets.DOCKER_PASSWORD }}
-        workdir: docker/
-        dockerfile: Dockerfile
-        tag_names: true
-
   sdist:
     name: Deploy Python Source Distribution
 
@@ -30,10 +12,12 @@ jobs:
       with:
         fetch-depth: 20
 
-    - name: apt
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+    - run: echo "::set-env name=SWIG::${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig"
+
+    - name: Build swig4
       run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig
+        sudo scripts/downloadAndBuildSwig.sh
 
     - name: Create AMICI sdist
       run: |

.github/workflows/deploy_protected.yml

@@ -0,0 +1,29 @@
+name: Deploy Protected
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  dockerhub:
+    # https://github.com/marketplace/actions/publish-docker
+    name: Deploy Dockerhub
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
+    - name: Publish to Registry
+      uses: elgohr/[email protected]
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: docker/
+        dockerfile: Dockerfile
+        tag_names: true

.github/workflows/deploy_release.yml

@@ -32,7 +32,7 @@ jobs:
     - name: Run doxygen
       run: |
         scripts/run-doxygen.sh
-        
+
     - name: Deploy 🚀
       uses: JamesIves/[email protected]
       with:
@@ -50,11 +50,13 @@ jobs:
       with:
         fetch-depth: 20
 
-    - name: apt
+    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+    - run: echo "::set-env name=SWIG::${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig"
+
+    - name: Build swig4
       run: |
-        sudo apt-get update \
-          && sudo apt-get install -y swig
-          
+        sudo scripts/downloadAndBuildSwig.sh
+
     - name: sdist
       run: |
         scripts/buildSdist.sh
@@ -65,4 +67,4 @@ jobs:
         user: __token__
         password: ${{ secrets.pypi_password }}
         packages_dir: python/sdist/dist
-        
+

.github/workflows/test_doc.yml

@@ -19,8 +19,6 @@ jobs:
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
-    - run: echo "::set-env name=AMICI_DIR::$(pwd)"
-
     - name: apt
       run: |
         sudo apt-get update \
@@ -47,6 +45,15 @@ jobs:
       - uses: actions/checkout@master
       - run: git fetch --prune --unshallow
 
+      - run: echo "::set-env name=AMICI_DIR::$(pwd)"
+      - run: echo "::set-env name=SWIG::${AMICI_DIR}/ThirdParty/swig-4.0.1/install/bin/swig"
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          # Semantic version range syntax or exact version of a Python version
+          python-version: '3.8'
+
       # install amici dependencies
       - name: apt
         run: |
@@ -55,13 +62,15 @@ jobs:
               g++ \
               libatlas-base-dev \
               libboost-serialization-dev \
-              libhdf5-serial-dev \
               python3-venv \
-              swig \
-      
-      - name: Install python package
+
+      - name: Build swig
+        run: |
+          sudo scripts/downloadAndBuildSwig.sh
+              
+      - name: pip
         run: |
-          scripts/installAmiciSource.sh
+          pip3 install setuptools
       
       - name: sphinx
         run: |

.github/workflows/test_install.yml

@@ -1,5 +1,5 @@
 name: Installation
-on: [push]
+on: [push, pull_request]
 
 jobs:
   archive:

.github/workflows/test_python_cplusplus.yml

@@ -1,5 +1,5 @@
 name: C++/Python Tests
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:

.github/workflows/test_python_ver_matrix.yml

@@ -26,6 +26,11 @@ jobs:
     - run: echo "::set-env name=AMICI_DIR::$(pwd)"
     - run: echo "::set-env name=BNGPATH::${AMICI_DIR}/ThirdParty/BioNetGen-2.3.2"
 
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@v1
       with:
         fetch-depth: 20

.gitignore

@@ -8,6 +8,7 @@ tests/cpputest/build/*
 tests/cpputest/build_xcode/*
 tests/cpputest/Testing/*
 
+doc-venv/*
 doc/*
 fonts/*
 images/*

.readthedocs.yml

@@ -18,10 +18,10 @@ sphinx:
 # Optionally build your docs in additional formats such as PDF and ePub
 formats:
   - pdf
-  
+
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: documentation/rtd_requirements.txt
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

INSTALL.md

@@ -138,7 +138,7 @@ on. This can be done by inserting the following code before calling
 (For further discussion see https://github.com/AMICI-dev/AMICI/issues/357)
 
 
-### Windows
+### Windows using GCC (mingw)
 
 To install AMICI on Windows using python, you can proceed as follows:
 
@@ -155,11 +155,11 @@ Some general remarks:
 Then, follow these steps:
 
 * A python environment for Windows is required. We recommend
-  [Anaconda](https://www.anaconda.com/distribution/) with python >=3.6.
-* Install [mingw64](https://sourceforge.net/projects/mingw-w64/files/latest/download)
+  [Anaconda](https://www.anaconda.com/distribution/) with python >=3.7.
+* Install [MinGW-W64](https://sourceforge.net/projects/mingw-w64/files/)
   (32bit will succeed to compile, but fail during linking).
-  During installation, select Version=8.1.0, Architecture=x64_64.
-  Add the following directory to `PATH`:
+  MinGW-W64 GCC-8.1.0 for `x86_64-posix-sjlj` ([direct link](https://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/mingw-builds/8.1.0/threads-posix/sjlj/x86_64-8.1.0-release-posix-sjlj-rt_v6-rev0.7z/download) has been shown to work on Windows 7 and 10 test systems.
+* Add the following directory to `PATH`:
     + `C:\mingw-w64\x86_64-8.1.0-posix-sjlj-rt_v6-rev0\mingw64\bin`
 * Make sure that this is the compiler that is found by the system
   (e.g. `where gcc` in a `cmd` should point to this installation).
@@ -202,6 +202,81 @@ Possible sources of errors:
   and [compileBLAS.cmd](https://github.com/AMICI-dev/AMICI/blob/master/scripts/compileBLAS.cmd)
   may serve as guidance on how to install openBLAS using msvc.
 
+### Windows using MSVC (Visual Studio)
+
+#### Visual Studio
+We assume that Visual Studio (not to be confused with Visual Studio Code) is already installed. Using Visual Studio Installer, the following components need to be included:
+
+* Microsoft Visual C++ (MSVC). This is part of multiple packages, including Desktop Development with C++.
+* Windows Universal C Runtime. This is an individual component and installs some DLLs that we need.
+
+#### openBLAS
+To install open BLAS, download the following scripts from AMICI:
+
+https://github.com/AMICI-dev/AMICI/blob/master/scripts/installOpenBLAS.ps1
+https://github.com/AMICI-dev/AMICI/blob/master/scripts/compileBLAS.cmd
+
+The first script needs to be called in Powershell, and it needs to call `compileBLAS.cmd`, so you will need to modify line 11:
+
+    C:\Users\travis\build\AMICI\scripts\compileBLAS.cmd
+
+so that it matches your directory structure.
+This will download openBLAS and compile it, creating
+
+    C:\BLAS\lib\openblas.lib
+    C:\BLAS\bin\openblas.dll
+
+You will also need to define two environment variables:
+
+    BLAS_LIBS="/LIBPATH:C:\BLAS\lib openblas.lib"
+    BLAS_CFLAGS="/IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10"
+
+One way to do that is to run a PowerShell script with the following commands:
+
+    [System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "/LIBPATH:C:\BLAS\lib openblas.lib", [System.EnvironmentVariableTarget]::User)
+    [System.Environment]::SetEnvironmentVariable("BLAS_LIBS", "/LIBPATH:C:\BLAS\lib openblas.lib", [System.EnvironmentVariableTarget]::Process)
+    [System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10", [System.EnvironmentVariableTarget]::User)
+    [System.Environment]::SetEnvironmentVariable("BLAS_CFLAGS", "-IC:\BLAS\OpenBLAS-v0.3.10\OpenBLAS-0.3.10", [System.EnvironmentVariableTarget]::Process)
+
+The call ending in `Process` sets the environment variable in the current process, and it is no longer in effect in the next process. The call ending in `User` is permanent, and takes effect the next time the user logs on.
+
+#### PATH
+Now we need to make sure that all required DLLs are within the scope of the PATH variable. In particular, the following directories need to be included in PATH:
+
+    C:\BLAS\bin
+    C:\Program Files (x86)\Windows Kits\10\Redist\ucrt\DLLs\x64
+
+The first one is needed for `openblas.dll` and the second is needed for the Windows Universal C Runtime.
+If any DLLs are missing in the PATH variable, Python will return the following error:
+
+    ImportError: DLL load failed: The specified module could not be found.
+
+This can be tested using the "where" command. For example
+
+    where openblas.dll
+
+should return
+
+    C:\BLAS\bin\openblas.dll
+
+Almost all of the DLLs are standard Windows DLLs and should be included in either Windows or Visual Studio. But, in case it is necessary to test this, here is a list of some DLLs required by AMICI (when compiled with MSVC):
+
+* `openblas.dll`
+* `python37.dll`
+* `MSVCP140.dll`
+* `KERNEL32.dll`
+* `VCRUNTIME140_1.dll`
+* `VCRUNTIME140.dll`
+* `api-ms-win-crt-convert-l1-1-0.dll`
+* `api-ms-win-crt-heap-l1-1-0.dll`
+* `api-ms-win-crt-stdio-l1-1-0.dll`
+* `api-ms-win-crt-string-l1-1-0.dll`
+* `api-ms-win-crt-runtime-l1-1-0.dll`
+* `api-ms-win-crt-time-l1-1-0.dll`
+* `api-ms-win-crt-math-l1-1-0.dll`
+
+`MSVCP140.dll`, `VCRUNTIME140.dll`, and `VCRUNTIME140_1.dll` are needed by MSVC (see Visual Studio above). `KERNEL32.dll` is part of Windows and in `C:\Windows\System32`. The `api-ms-win-crt-XXX-l1-1-0.dll` are needed by `openblas.dll` and are part of the Windows Universal C Runtime (see Visual Studio above).
+
 ### Custom installation
 
 AMICI Python package installation can be customized using a number of