Merge pull request #97 from cropsinsilico/language/julia

Language/julia

Author: langmm

.github/workflows/test-install.yml

@@ -5,6 +5,7 @@ env:
   BUILDDOCS: 0
   INSTALLC: 1
   INSTALLFORTRAN: 1
+  INSTALLJULIA: 1
   INSTALLLPY: 0
   INSTALLMATLAB: 0
   INSTALLMPI: 1
@@ -21,7 +22,15 @@ env:
   YGG_GHA_JOB_ID_SUFFIX: null
 jobs:
   build_sdist:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     name: Build source distribution
+    needs:
+    - test_pip
+    - test_conda
+    - test_rmq_pip
+    - test_rmq_conda
+    - test_stripped
+    - docs
     runs-on: ubuntu-latest
     steps:
     - name: Checkout sources
@@ -54,7 +63,15 @@ jobs:
         name: sdist
         path: ./dist/*
   build_wheels:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     name: Build wheels on ${{ matrix.os }}
+    needs:
+    - test_pip
+    - test_conda
+    - test_rmq_pip
+    - test_rmq_conda
+    - test_stripped
+    - docs
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout sources
@@ -76,16 +93,9 @@ jobs:
 
         '
     - env:
-        CIBW_ARCHS_LINUX: auto aarch64 ppc64le
-        CIBW_ARCHS_MACOS: x86_64 arm64
+        CIBW_ARCHS_LINUX: ${{ matrix.linux_arch }}
+        CIBW_ARCHS_MACOS: ${{ matrix.mac_arch }}
         CIBW_ARCHS_WINDOWS: ${{ matrix.windows_arch }}
-        CIBW_BEFORE_ALL_LINUX: yum install -y blas-devel lapack-devel
-        CIBW_ENVIRONMENT: PIP_ONLY_BINARY=numpy
-        CIBW_SKIP: cp2* cp33* cp34* cp35* cp36* pp* cp310-manylinux_i686 cp311-manylinux_i686
-          *-musllinux_*
-        CIBW_TEST_COMMAND: ygginfo && pytest -m subset_rapidjson --import-mode=importlib
-          {project}/tests
-        CIBW_TEST_REQUIRES: pytest flaky
       name: Build wheels
       uses: pypa/cibuildwheel@v2.12.1
     - name: Upload artifacts
@@ -98,6 +108,14 @@ jobs:
         include:
         - os: windows-2019
           windows_arch: x86
+        - linux_arch: aarch64
+          os: ubuntu-20.04
+        - linux_arch: ppc64le
+          os: ubuntu-20.04
+        linux_arch:
+        - auto
+        mac_arch:
+        - x86_64 arm64
         os:
         - ubuntu-20.04
         - macOS-11
@@ -290,6 +308,9 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
+      name: (PIP) Set up Julia
+      uses: julia-actions/setup-julia@v1
     - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows'
       name: Set up Matlab
       uses: matlab-actions/setup-matlab@v1
@@ -324,7 +345,7 @@ jobs:
       name: (MACOS,PIP) Set C compiler to llvm clang
       run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
-      name: (WINDOWS,CONDA) Set up miniconda base environment
+      name: (CONDA) Set up miniconda base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -381,8 +402,8 @@ jobs:
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') &&
         runner.os == 'macOS'
       name: (MACOS,CONDA) Set allow_multiple_omp config
-      run: 'install_name_tool -change "@rpath/libc++abi.1.dylib" "/usr/lib/libc++abi.1.dylib"
-        $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
+      run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib"
+        "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
 
         yggconfig --allow-multiple-omp
 
@@ -618,6 +639,9 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
+      name: (PIP) Set up Julia
+      uses: julia-actions/setup-julia@v1
     - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows'
       name: Set up Matlab
       uses: matlab-actions/setup-matlab@v1
@@ -652,7 +676,7 @@ jobs:
       name: (MACOS,PIP) Set C compiler to llvm clang
       run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
-      name: (WINDOWS,CONDA) Set up miniconda base environment
+      name: (CONDA) Set up miniconda base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -709,8 +733,8 @@ jobs:
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') &&
         runner.os == 'macOS'
       name: (MACOS,CONDA) Set allow_multiple_omp config
-      run: 'install_name_tool -change "@rpath/libc++abi.1.dylib" "/usr/lib/libc++abi.1.dylib"
-        $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
+      run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib"
+        "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
 
         yggconfig --allow-multiple-omp
 
@@ -938,6 +962,9 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
+      name: (PIP) Set up Julia
+      uses: julia-actions/setup-julia@v1
     - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows'
       name: Set up Matlab
       uses: matlab-actions/setup-matlab@v1
@@ -972,7 +999,7 @@ jobs:
       name: (MACOS,PIP) Set C compiler to llvm clang
       run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
-      name: (WINDOWS,CONDA) Set up miniconda base environment
+      name: (CONDA) Set up miniconda base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -1029,8 +1056,8 @@ jobs:
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') &&
         runner.os == 'macOS'
       name: (MACOS,CONDA) Set allow_multiple_omp config
-      run: 'install_name_tool -change "@rpath/libc++abi.1.dylib" "/usr/lib/libc++abi.1.dylib"
-        $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
+      run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib"
+        "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
 
         yggconfig --allow-multiple-omp
 
@@ -1241,6 +1268,9 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
+      name: (PIP) Set up Julia
+      uses: julia-actions/setup-julia@v1
     - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows'
       name: Set up Matlab
       uses: matlab-actions/setup-matlab@v1
@@ -1275,7 +1305,7 @@ jobs:
       name: (MACOS,PIP) Set C compiler to llvm clang
       run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
-      name: (WINDOWS,CONDA) Set up miniconda base environment
+      name: (CONDA) Set up miniconda base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -1332,8 +1362,8 @@ jobs:
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') &&
         runner.os == 'macOS'
       name: (MACOS,CONDA) Set allow_multiple_omp config
-      run: 'install_name_tool -change "@rpath/libc++abi.1.dylib" "/usr/lib/libc++abi.1.dylib"
-        $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
+      run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib"
+        "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
 
         yggconfig --allow-multiple-omp
 
@@ -1543,6 +1573,9 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - if: matrix.install-method == 'pip' && env.INSTALLJULIA == 1
+      name: (PIP) Set up Julia
+      uses: julia-actions/setup-julia@v1
     - if: env.INSTALLMATLAB == 1 && runner.os != 'Windows'
       name: Set up Matlab
       uses: matlab-actions/setup-matlab@v1
@@ -1577,7 +1610,7 @@ jobs:
       name: (MACOS,PIP) Set C compiler to llvm clang
       run: yggconfig --c-compiler=/usr/local/opt/llvm/bin/clang --c++-compiler=/usr/local/opt/llvm/bin/clang++
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba')
-      name: (WINDOWS,CONDA) Set up miniconda base environment
+      name: (CONDA) Set up miniconda base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
@@ -1634,8 +1667,8 @@ jobs:
     - if: (matrix.install-method == 'conda' || matrix.install-method == 'mamba') &&
         runner.os == 'macOS'
       name: (MACOS,CONDA) Set allow_multiple_omp config
-      run: 'install_name_tool -change "@rpath/libc++abi.1.dylib" "/usr/lib/libc++abi.1.dylib"
-        $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
+      run: '[[ -d $CONDA_PREFIX/lib/clang/9.0.1 ]] && install_name_tool -change "@rpath/libc++abi.1.dylib"
+        "/usr/lib/libc++abi.1.dylib" $CONDA_PREFIX/lib/clang/9.0.1/lib/darwin/libclang_rt.asan_osx_dynamic.dylib
 
         yggconfig --allow-multiple-omp
 

HISTORY.rst

@@ -2,9 +2,11 @@
 History
 =======
 
-1.9.0 (2023-04-11) Migrate to using extended version of rapidjson/python-rapidjson for serialization
+1.9.0 (2023-04-14) Migrate to using extended version of rapidjson/python-rapidjson for serialization and add support for models written in Julia
 ------------------
 
+* Added Julia interface with units implemented via Unitful
+* Added Julia versions of examples
 * Dropped support for Python 3.5
 * Changed rapidjson submodule to extended version
 * Vendor python-rapidjson extension

MANIFEST.in

@@ -19,6 +19,7 @@ recursive-include yggdrasil *.txt
 recursive-include yggdrasil *.json
 recursive-include yggdrasil *.f90
 recursive-include yggdrasil *.xml
+recursive-include yggdrasil *.jl
 recursive-include yggdrasil/examples *.py
 recursive-include yggdrasil/examples *.rst
 recursive-include yggdrasil/demos *.py
@@ -34,6 +35,8 @@ include yggdrasil/languages/LPy/lpy_model.py
 include yggdrasil/languages/R/DESCRIPTION
 include yggdrasil/languages/R/NAMESPACE
 include yggdrasil/languages/R/R/*.R
+include yggdrasil/languages/Julia/Yggdrasil/*.toml
+include yggdrasil/languages/Julia/Yggdrasil/src/*.jl
 include yggdrasil/languages/fortran/*.f90
 include yggdrasil/languages/fortran/*.c
 include yggdrasil/languages/fortran/*.h

docs/source/examples/make_example_rst.py

@@ -12,6 +12,7 @@
               'r': 'R',
               'R': 'R',
               'c': 'C',
+              'julia': 'Julia',
               'cpp': 'C++',
               'all': 'Mixed',
               'all_nomatlab': 'Mixed w/o Matlab',
@@ -90,15 +91,15 @@ def get_default_lang(k):
 
 def write_src_ref(fd, k):
     default = get_default_lang(k)
-    assert(default)
+    assert default
     write_src(fd, k, default, upone=True)
     fd.write('\n')
     write_ref_link(fd, k)
 
 
 def write_yml_ref(fd, k):
     default = get_default_lang(k)
-    assert(default)
+    assert default
     write_yml(fd, k, default, upone=True)
     fd.write('\n')
     write_ref_link(fd, k)

docs/source/install.rst

@@ -404,3 +404,12 @@ If you would like to use OpenSimRoot, you will need to install GNU make. If you
 * ``brew install make`` on Mac
 * ``apt-get install make`` on Linux
 * ``choco install make`` on Windows
+
+Additional Steps for Julia Models
+---------------------------------
+
+If you do not use conda/mamba to install ``julia``, or you are installing |yggdrasil| on a Windows machine or an M1/M2 Mac (there are not currently ``julia`` conda packages for these systems as of 2023/04/07, but this may change), you will need to install it yourself. Julia downloads can be found `here <https://julialang.org/downloads/>`_.
+
+Once julia is installed, you can complete the installation of the |yggdrasil| Julia interface via::
+
+  $ ygginstall julia

pyproject.toml

@@ -7,6 +7,25 @@ requires = [
 ]
 build-backend = "setuptools.build_meta"
 
+[tool.cibuildwheel]
+skip = "pp* cp2* cp33* cp34* cp35* cp36* *musllinux* cp310-manylinux_ppc64le cp311-manylinux_ppc64le"
+test-skip = "cp310-win32 cp310-manylinux_i686 cp311-win32 cp311-manylinux_i686 *ppc64le"
+test-requires = ["pytest", "flaky"]
+test-command = "ygginfo && pytest -m subset_rapidjson --import-mode=importlib {project}/tests"
+before-test = "pip install --only-binary=numpy,scipy numpy scipy"
+
+# [tool.cibuildwheel.linux]
+# before-all = "yum install -y openblas-devel"
+
+# [[tool.cibuildwheel.overrides]]
+# select = "cp3{7,8,9,10,11}-manylinux_i686"
+# before-all = ""
+
+# [[tool.cibuildwheel.overrides]]
+# select = "cp3{7,8,9,10,11}-manylinux_ppc64le"
+# before-test = "pip install --only-binary=numpy numpy"
+# before-all = "yum install -y openblas-devel"
+
 [tool.black]
 line-length = 88
 target-version = ['py27', 'py36', 'py37', 'py38']

recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "yggdrasil" %}
-{% set version = "1.9.0" %}
+{% set version = "1.9.1" %}
 {% set PY_VER_MAJOR = PY_VER.split('.')[0] %}
 {% set PY_VER_MINOR = PY_VER.split('.')[1] %}
 
@@ -73,6 +73,7 @@ requirements:
     - scipy
     - six
     - sysv_ipc  # [not win]
+    - toml
     - unyt
 
 test:
@@ -149,6 +150,18 @@ outputs:
         - czmq
         - lz4
         - zeromq
+  - name: yggdrasil.julia
+    build:
+      string: py{{ PY_VER_MAJOR }}{{ PY_VER_MINOR }}h{{ PKG_HASH }}_{{ PKG_BUILDNUM }}
+      run_exports:
+        - {{ pin_subpackage('yggdrasil.julia') }}
+    requirements:
+      host:
+        - juliaup
+        - python
+      run:
+        - {{ pin_subpackage('yggdrasil', exact=True) }}
+        - juliaup
   - name: yggdrasil.mpi
     build:
       string: py{{ PY_VER_MAJOR }}{{ PY_VER_MINOR }}h{{ PKG_HASH }}_{{ PKG_BUILDNUM }}

requirements.txt

@@ -13,4 +13,5 @@ requests
 scipy
 six
 sysv_ipc; platform_system != 'Windows'
+toml
 unyt

requirements_condaonly.txt

@@ -0,0 +1,17 @@
+cmake; platform_system != 'Windows'  # [conda,c]
+czmq             # [conda,zmq,c]
+julia>=1.1.1     # [conda,julia]
+matplotlib       # [conda]
+r-rcpp<=1.0.3; platform_system == 'Darwin'  # [conda,R]
+r-base           # [conda,R]
+r-bit64          # [conda,R]
+r-r6             # [conda,R]
+r-reticulate     # [conda,R]
+r-zeallot        # [conda,R]
+r-units          # [conda,R]
+zeromq           # [conda,zmq,c]
+# c-compiler; platform_system == 'Windows'    # [conda,c]
+# cxx-compiler; platform_system == 'Windows'  # [conda,c]
+m2w64-gcc-fortran; platform_system == 'Windows'       # [conda,fortran]
+m2w64-toolchain_win-64; platform_system == 'Windows'  # [conda,fortran]
+fortran-compiler; platform_system != 'Windows'  # [conda,fortran]

tests/conftest.py

@@ -638,7 +638,8 @@ def scripts():
         ('r', 'r_model.R'),
         ('fortran', ['hellofunc.f90', 'fortran_model.f90']),
         ('sbml', 'sbml_model.xml'),
-        ('osr', 'osr_model.xml')]
+        ('osr', 'osr_model.xml'),
+        ('julia', 'julia_model.jl')]
     scripts = {}
     for k, v in script_list:
         if isinstance(v, list):