diff --git a/.github/workflows/build_nix.yml b/.github/workflows/build_nix.yml index 4c0720832..a85df60e4 100644 --- a/.github/workflows/build_nix.yml +++ b/.github/workflows/build_nix.yml @@ -8,9 +8,9 @@ on: branches: [ master ] env: - TICK_DEBUG: 0 - TICK_WERROR: 0 + MKN_COMPILE_THREADS: 2 MKN_GCC_PREFERRED: 1 + PYTHON_EMBED_LIB: 1 jobs: build: @@ -21,10 +21,10 @@ jobs: fail-fast: false max-parallel: 4 matrix: - python-version: ['3.7', '3.9', '3.10', '3.11'] # '3.8' has "'tp_print' is deprecated [-Werror,-Wdeprecated-declarations]" + python-version: ['3.9', '3.10', '3.11'] # , '3.12' - not ready yet steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: true @@ -43,22 +43,22 @@ jobs: gcc -v swig -version - - name: pip + - name: pip # tensorflow not released for 3.12 as of 26-OCT-2023 run: | python3 -m pip install wheel pip --upgrade python3 -m pip install -r requirements.txt - python3 -m pip install tensorflow-cpu + [ "${{ matrix.python-version }}" != "3.12" ] && python3 -m pip install tensorflow-cpu - name: build run: | curl -Lo mkn https://github.com/mkn/mkn/releases/download/latest/mkn_nix chmod +x mkn - PATH=$PWD:$PATH KLOG=3 ./sh/mkn.sh + PATH=$PWD:$PATH KLOG=3 mkn -C lib clean build -g 0 -tOa "-fPIC -std=c++17" - name: cpptest run: | - PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh + PATH=$PWD:$PATH KLOG=3 mkn -C lib -p gtest build run test -dOta "-fPIC -std=c++17" - name: pytest run: | - python3 setup.py pytest + python3 -m unittest discover -v . "*_test.py" diff --git a/.github/workflows/build_osx.yml.off b/.github/workflows/build_osx.yml similarity index 73% rename from .github/workflows/build_osx.yml.off rename to .github/workflows/build_osx.yml index edb4f5343..e3c9da05a 100644 --- a/.github/workflows/build_osx.yml.off +++ b/.github/workflows/build_osx.yml @@ -8,8 +8,8 @@ on: branches: [ master ] env: - TICK_DEBUG: 0 - TICK_WERROR: 0 + MKN_COMPILE_THREADS: 2 + jobs: @@ -21,10 +21,10 @@ jobs: fail-fast: false max-parallel: 4 matrix: - python-version: ['3.7', '3.9', '3.10'] # '3.8' has "'tp_print' is deprecated [-Werror,-Wdeprecated-declarations]" + python-version: ['3.9', '3.10', '3.11', '3.12'] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: true @@ -48,16 +48,18 @@ jobs: python3 -m pip install wheel pip --upgrade python3 -m pip install -r requirements.txt + - name: build run: | curl -Lo mkn https://github.com/mkn/mkn/releases/download/latest/mkn_osx chmod +x mkn - PATH=$PWD:$PATH KLOG=3 ./sh/mkn.sh + PATH=$PWD:$PATH KLOG=3 mkn -C lib clean build -g 0 -tOa "-fPIC -std=c++17" - name: cpptest run: | - PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh + PATH=$PWD:$PATH KLOG=3 mkn -C lib -p gtest build run test -dOta "-fPIC -std=c++17" - name: pytest run: | python -m unittest discover -v . "*_test.py" +# echo "Tests not run until test failures assessed./" diff --git a/.github/workflows/build_win.yml b/.github/workflows/build_win.yml index 02f9e873d..cec446217 100644 --- a/.github/workflows/build_win.yml +++ b/.github/workflows/build_win.yml @@ -8,11 +8,10 @@ on: branches: [ master ] env: - TICK_DEBUG: 0 - TICK_WERROR: 0 MKN_CL_PREFERRED: 1 MKN_COMPILE_THREADS: 2 + jobs: build: name: Python ${{ matrix.python-version }} @@ -22,7 +21,7 @@ jobs: fail-fast: false max-parallel: 4 matrix: - python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] + python-version: ['3.9', '3.10', '3.11', '3.12'] steps: - uses: actions/checkout@v3 @@ -49,15 +48,16 @@ jobs: python3 -m pip install wheel pip --upgrade python3 -m pip install -r requirements.txt + - name: build run: | # MINGW link interferres with MSVC link.exe bash -c "rm /bin/link" bash -c "curl -Lo mkn.exe https://github.com/mkn/mkn/releases/download/latest/mkn.exe" - bash -c 'PATH=$PWD:$PATH KLOG=3 ./sh/mkn.sh' + bash -c 'PATH=$PWD:$PATH KLOG=3 mkn -C lib clean build -g 0 -tOa "-EHsc -std:c++17"' - name: cpptest run: | - bash -c 'PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh' + bash -c 'PATH=$PWD:$PATH KLOG=3 mkn -C lib -p gtest build run test -dOta "-EHsc -std:c++17"' - name: pytest run: | diff --git a/.github/workflows/merge_master.yaml b/.github/workflows/merge_master.yaml new file mode 100644 index 000000000..90ec5efc1 --- /dev/null +++ b/.github/workflows/merge_master.yaml @@ -0,0 +1,108 @@ +name: Master merge + +# on: +# push: +# branches: [ master ] +# workflow_dispatch: + +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + +env: + MKN_GCC_PREFERRED: 1 + MKN_COMPILE_THREADS: 2 + +jobs: + + build_linux: + runs-on: ubuntu-latest + container: quay.io/pypa/manylinux2014_x86_64 + + strategy: + fail-fast: false + max-parallel: 4 + matrix: + python-version: ['cp39-cp39', 'cp310-cp310', 'cp311-cp311', 'cp312-cp312'] + + steps: + - name: add Python dir to path + run: | + echo "/opt/python/${{ matrix.python-version }}/bin" >> $GITHUB_PATH + - uses: actions/checkout@v3 + with: + submodules: true + - name: Build for Python ${{ matrix.python-version }} + run: | + git config --global --add safe.directory '*' + python3 -V + python3 -m pip install -U pip + python3 -m pip install -U build twine wheel + python3 -m pip install -U -r requirements.txt + + curl -Lo mkn https://github.com/mkn/mkn/releases/download/latest/mkn_manylinux + chmod +x mkn + PATH=$PWD:$PATH KLOG=3 mkn -C lib clean build -g 0 -tOa "-fPIC -std=c++17" + python3 -m build + python3 -m twine check dist/* + rename 'linux_x86_64' 'manylinux_2_28_x86_64' dist/*.whl + + - name: Make wheels universal + run: for wheel in $(ls dist/*.whl); do auditwheel repair $wheel; done + - name: Save packages as artifacts + uses: actions/upload-artifact@v3 + with: + name: wheels + path: wheelhouse/*.whl + + + test_wheels: + needs: [build_linux] + strategy: + matrix: + os: [ubuntu-latest] # ,macos-11, windows-latest + python-version: ['3.9', '3.10', '3.11', '3.12'] + runs-on: ${{ matrix.os }} + steps: + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + architecture: x64 + - uses: actions/download-artifact@v3 + with: + name: wheels + path: dist + - name: install wheel (Unix) + if: runner.os != 'Windows' + run: | + pip install --find-links $GITHUB_WORKSPACE/dist tick + - name: install wheel (Windows) + if: runner.os == 'Windows' + run: | + pip install --find-links $env:GITHUB_WORKSPACE\dist tick + - uses: actions/checkout@v3 + - name: run tests + run: | + python3 -V + pip install -r requirements.txt + cd tick && python3 -m unittest discover -v . "*_test.py" + + upload_test_pypi: + needs: [test_wheels] + runs-on: ubuntu-latest + # upload to test PyPI on github pushes + # if: github.event_name == 'push' && github.repository_owner == 'Tick' + steps: + - uses: actions/download-artifact@v3 + with: + name: wheels + path: dist + - uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.TEST_PYPI_PASSWORD }} + repository-url: https://test.pypi.org/legacy/ + skip-existing: false diff --git a/.github/workflows/pythonpublish-linux.yml b/.github/workflows/pythonpublish-linux.yml index eb9505254..837e9d1c5 100644 --- a/.github/workflows/pythonpublish-linux.yml +++ b/.github/workflows/pythonpublish-linux.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest container: jeandet/manylinuxcpp2017 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: true diff --git a/.github/workflows/pythonpublish-osx.yml b/.github/workflows/pythonpublish-osx.yml index acaf7c9a5..afacf329d 100644 --- a/.github/workflows/pythonpublish-osx.yml +++ b/.github/workflows/pythonpublish-osx.yml @@ -14,14 +14,14 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: ['3.7', '3.8', '3.9', '3.10'] + python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] name: Python ${{ matrix.python-version }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: true - - uses: actions/setup-python@v1 + - uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} architecture: x64 diff --git a/.github/workflows/pythonpublish-win.yml b/.github/workflows/pythonpublish-win.yml index 6fb5af9d8..4f38233ab 100644 --- a/.github/workflows/pythonpublish-win.yml +++ b/.github/workflows/pythonpublish-win.yml @@ -17,11 +17,11 @@ jobs: python-version: ['3.7', '3.8', '3.9', '3.10'] name: Python ${{ matrix.python-version }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: true - - uses: actions/setup-python@v1 + - uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} architecture: x64 diff --git a/.gitignore b/.gitignore index 3c23e2486..45d52312d 100644 --- a/.gitignore +++ b/.gitignore @@ -58,3 +58,5 @@ tools/benchmark/data env*/ venv*/ tickf.yml +dist +tick.egg-info/ diff --git a/.travis.yml.off b/.travis.yml.off deleted file mode 100644 index 7e60a20ba..000000000 --- a/.travis.yml.off +++ /dev/null @@ -1,48 +0,0 @@ -language: generic - -branches: - only: - - master - -# Cache is irrelevant for linux/docker builds, but useful to speed up osx -cache: - directories: - - $HOME/.pyenv - - $HOME/googletest - -matrix: - include: - - os: linux - services: docker - env: - - DOCKER_IMAGE=xdatainitiative/tick_debian:0.5.1 - - PYVER=3.6.8 - - os: linux - services: docker - env: - - DOCKER_IMAGE=xdatainitiative/tick_debian:0.5.1 - - PYVER=3.7.3 - - os: osx - language: generic - sudo: required - env: - - PYVER=3.6.8 - osx_image: xcode10.2 - - os: osx - language: generic - sudo: required - env: - - PYVER=3.7.3 - osx_image: xcode10.2 - -install: - - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source tools/travis/osx_install.sh; fi - - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker pull $DOCKER_IMAGE; fi - -script: - - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source tools/travis/osx_run.sh; fi - - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker run -v `pwd`:/io -e PYVER=${PYVER} "$DOCKER_IMAGE" /io/tools/travis/docker_run.sh; fi - -notifications: - slack: - secure: 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 diff --git a/MANIFEST.in b/MANIFEST.in index 8249414e5..aaad6eca8 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,8 +1,3 @@ -# Setuptools is not aware of source headers, or non-module SWIG files, so we -# grab them here -global-include *.h -global-include *.i -global-include *.inl +recursive-include tick * +recursive-exclude lib * -# Getting the Cereal header-only library -recursive-include lib/third_party/cereal/include *.h *.hpp \ No newline at end of file diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index acd78fc4b..000000000 --- a/appveyor.yml +++ /dev/null @@ -1,47 +0,0 @@ - -version: 0.6.{build} - -branches: - only: - - master - -max_jobs: 1 - -image: -- Visual Studio 2019 - -init: - - git config --global core.autocrlf input - -clone_depth: 1 - -hosts: - queue-server: 127.0.0.1 - db.server.com: 127.0.0.2 - -platform: x64 - -configuration: Release - -cache: - - C:\ProgramData\chocolatey\bin -> appveyor.yml # swig.exe - - C:\ProgramData\chocolatey\lib -> appveyor.yml # supporting swig Lib files. - -install: - - git submodule update --init - - curl -o mkn.exe -L https://github.com/Dekken/maiken/raw/binaries/win10_x64/mkn.exe - - IF NOT EXIST C:\ProgramData\chocolatey\bin\swig.exe choco install tools\windows\swig.4.0.0.nupkg --yes --limit-output - -build_script: - - SET PATH=C:\Program Files\Git\usr\bin;%PATH% - - cp "C:\Program Files (x86)\Windows Kits\10\bin\10.0.18362.0\x64\rc.exe" %CD% - - cp %CD%\rc.exe %CD%\lib - - call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Auxiliary\Build\vcvars64.bat" - - cl # print compiler version - # doesnt exist for somereason? - #- mkdir -p "C:\Program Files (x86)\Windows Kits\10\include\10.0.16299.0\cppwinrt" - - bash -c "PATH=\"$PWD:/c/Python37-x64/:/c/Program Files/Git/usr/bin:$PATH\"; tools/appveyor/run.sh" - -artifacts: - - path: "dist\\*.whl" - name: Wheels diff --git a/lib/mkn.yaml b/lib/mkn.yaml index 253f0b2fc..c0636d6ce 100644 --- a/lib/mkn.yaml +++ b/lib/mkn.yaml @@ -2,34 +2,22 @@ name: tick -self: - serialization - preprocessing - array_test - hawkes/simulation - hawkes/inference - solver - robust - survival +self: tick.py property: - postfix: x86_64-linux-gnu - py_maj: 3 - py_min: 6m - py_ver: cpython- - lib_name: .${py_ver}${py_maj}${py_min}-${postfix} lib_path: ./../tick - cargs: -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION - -D_FILE_OFFSET_BITS=64 -DPYTHON_LINK -DNDEBUG - win_cargs: -GL -MD -EHsc -DBUILDING_DLL - nixish_cargs: -fwrapv -O2 -Wall + cargs: -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D_FILE_OFFSET_BITS=64 -DPYTHON_LINK + win_cargs: -GL -MD -EHsc -DBUILDING_DLL -std:c++17 + nixish_cargs: -fwrapv -fstack-protector-strong - -Wformat -Werror -Wdate-time - -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 - -ffast-math -Wno-uninitialized + -Wformat -Wdate-time + -D_FORTIFY_SOURCE=2 -fPIC -std=c++17 + -Wno-uninitialized nix_cargs: ${nixish_cargs} + # sprintf deprecated but used in swig and only OSX complains + # https://developer.apple.com/forums/thread/714675 -Wno-deprecated-declarations bsd_cargs: ${nixish_cargs} nixish_largs: -fstack-protector-strong -Wformat @@ -40,12 +28,13 @@ property: -Wl,-z,relro -Wl,-z,relro bsd_largs: ${nixish_largs} - nixish_test_cargs: -Wno-error=unused-local-typedefs -fPIC - -Wno-error=sign-compare -Wno-sign-compare profile: - name: arg arg: ${cargs} + inc: + ./include + ./third_party/cereal/include if_arg: win: ${win_cargs} nix: ${nix_cargs} @@ -53,167 +42,48 @@ profile: if_link: nix_lib: ${nix_largs} bsd_lib: ${bsd_largs} - win: -LTCG # -nodefaultlib:libucrt.lib ucrt.lib -MANIFEST:EMBED,ID=2 -MANIFESTUAC:NO - - - name: base - parent: arg - self: array - src: - ./cpp/base - ./swig/tick/base - install: ${lib_path}/base/build - out: _base${lib_name} - - - name: array - parent: arg - inc: - ./include - ./third_party/cereal/include - src: - ./cpp/array - ./swig/tick/array - install: ${lib_path}/array/build - out: _array${lib_name} - - - name: array_test - parent: arg - self: base - src: - ./cpp/array_test - ./swig/tick/array_test - install: ${lib_path}/array_test/build - out: _array_test${lib_name} + win: -LTCG + mod: | + lang.python3{compile{with: numpy}, link{delete: CoreFoundation }} - - name: base_model + - name: tick.py parent: arg - self: base - src: - ./cpp/base_model - ./swig/tick/base_model - install: ${lib_path}/base_model/build - out: _base_model${lib_name} - - - name: hawkes/model - parent: arg - self: base_model - src: - ./cpp/hawkes/model - ./swig/tick/hawkes/model - install: ${lib_path}/hawkes/model/build - out: _hawkes_model${lib_name} - - - name: hawkes/simulation - parent: arg - self: random - src: - ./cpp/hawkes/simulation - ./swig/tick/hawkes/simulation - install: ${lib_path}/hawkes/simulation/build - out: _hawkes_simulation${lib_name} - - - name: hawkes/inference - parent: arg - self: hawkes/model - src: - ./cpp/hawkes/inference - ./swig/tick/hawkes/inference - install: ${lib_path}/hawkes/inference/build - out: _hawkes_inference${lib_name} - - - name: linear_model - parent: arg - self: base_model - src: - ./cpp/linear_model - ./swig/tick/linear_model - install: ${lib_path}/linear_model/build - out: _linear_model${lib_name} - - - name: prox - parent: arg - self: base - src: - ./cpp/prox - ./swig/tick/prox - install: ${lib_path}/prox/build - out: _prox${lib_name} - - - name: preprocessing + src: cpp swig/tick + install: ${lib_path}/tick_cpp + out: _tick_cpp + mod: + - name: lang.swig + compile: + inc: include swig + src: swig/tick/module.i + outdir: ../tick/tick_cpp + objfile: tick_module_wrap.cpp + + - name: gtest_lib + src: cpp parent: arg - self: base - src: - ./cpp/preprocessing - ./swig/tick/preprocessing - install: ${lib_path}/preprocessing/build - out: _preprocessing${lib_name} - - name: random - parent: arg - self: base - src: - ./cpp/random - ./swig/tick/random - install: ${lib_path}/random/build - out: _crandom${lib_name} - - - name: robust - parent: arg - self: linear_model - src: - ./cpp/robust - ./swig/tick/robust - install: ${lib_path}/robust/build - out: _robust${lib_name} - - - name: solver - parent: arg - self: random linear_model prox robust - src: - ./cpp/solver - ./swig/tick/solver - install: ${lib_path}/solver/build - out: _solver${lib_name} - - - name: survival - parent: arg - self: base_model - src: - ./cpp/survival - ./swig/tick/survival - install: ${lib_path}/survival/build - out: _survival${lib_name} - - - name: serialization + - name: gtest + dep: google.test parent: arg - self: linear_model solver prox robust survival - install: ${lib_path}/serialization/build - out: _serialization${lib_name} - -### See file ./sh/gtest/sh - - name: exe - arg: ${cargs} - if_arg: - win: -Ox -GL -MD -EHsc -std:c++11 - nix: ${nix_cargs} - bsd: ${bsd_cargs} - if_link: - nix_lib: ${nix_largs} - bsd_lib: ${bsd_largs} - win: -nodefaultlib:libucrt.lib ucrt.lib -MANIFEST:EMBED,ID=2 -MANIFESTUAC:NO -LTCG - - - name: gtest_nodep - parent: exe - main: cpp-test/hawkes/model/hawkes_models_gtest.cpp + self: gtest_lib arg: -DADD_MAIN - mode: none - if_arg: - g++: ${nixish_test_cargs} - clang++: ${nixish_test_cargs} - win: -DGTEST_LINKED_AS_SHARED_LIBRARY - if_link: - g++: -Wl,-rpath=$PWD - dep: google.test#c++11 - - - name: gtest - parent: gtest_nodep - self: solver hawkes/model hawkes/simulation hawkes/inference robust survival + test: | + cpp-test/linear_model/models_gtest.cpp + cpp-test/solver/saga_gtest.cpp + cpp-test/solver/svrg_gtest.cpp + cpp-test/array/linear_system_gtest.cpp + cpp-test/array/atomic_array_gtest.cpp + cpp-test/array/varray_gtest.cpp + cpp-test/array/array_gtest.cpp + cpp-test/array/major_gtest.cpp + cpp-test/array/serializer_gtest.cpp + cpp-test/base/utils_gtest.cpp + cpp-test/base/time_func_gtest.cpp + cpp-test/hawkes/model/hawkes_models_gtest.cpp + cpp-test/hawkes/simulation/hawkes_kernel_time_func_gtest.cpp + cpp-test/hawkes/simulation/hawkes_kernel_exp_gtest.cpp + cpp-test/hawkes/simulation/hawkes_kernel_sumexp_gtest.cpp + cpp-test/hawkes/simulation/hawkes_kernel_0_gtest.cpp + cpp-test/hawkes/simulation/hawkes_kernel_power_law_gtest.cpp + cpp-test/hawkes/inference/hawkes_em_gtest.cpp diff --git a/lib/swig/tick/array/ssparsearray_typemap_out.i b/lib/swig/tick/array/ssparsearray_typemap_out.i index cc2dd150e..a37ce4205 100644 --- a/lib/swig/tick/array/ssparsearray_typemap_out.i +++ b/lib/swig/tick/array/ssparsearray_typemap_out.i @@ -117,13 +117,13 @@ DLL_PUBLIC PyObject *_XSparseArray2d2NumpyArray(XSPARSEARRAY2D_TYPE *sig) PyObject *scipy_sparse_csr, *csr_matrix, *instance, *scipy_sparse_csc, *csc_matrix; - scipy_sparse_csr = PyImport_ImportModule("scipy.sparse.csr"); + scipy_sparse_csr = PyImport_ImportModule("scipy.sparse"); if(!scipy_sparse_csr) throw std::runtime_error("scipy_sparse_csr failed"); csr_matrix = PyObject_GetAttrString(scipy_sparse_csr, "csr_matrix"); if(!csr_matrix) throw std::runtime_error("csr_matrix failed"); if(!PyCallable_Check(csr_matrix)) throw std::runtime_error("csr_matrix check failed"); - scipy_sparse_csc = PyImport_ImportModule("scipy.sparse.csc"); + scipy_sparse_csc = PyImport_ImportModule("scipy.sparse"); if(!scipy_sparse_csc) throw std::runtime_error("scipy_sparse_csc failed"); csc_matrix = PyObject_GetAttrString(scipy_sparse_csc, "csc_matrix"); if(!csc_matrix) throw std::runtime_error("csc_matrix failed"); @@ -203,8 +203,15 @@ DLL_PUBLIC PyObject *_XSparseArray2d2NumpyArray(XSPARSEARRAY2D_TYPE *sig) throw std::runtime_error("SparseArray2d Reference count unexpected in SWIG layer - recompile with -DDEBUG_SHAREDARRAY and check"); } + if (PyObject_SetAttrString(instance, "_indices", (PyObject *)indices)) + throw std::runtime_error("set indices failed"); + if (PyObject_SetAttrString(instance, "_row_indices", (PyObject *)row_indices)) + throw std::runtime_error("set row_indices failed"); + // is required for arrays to be de-allocated properly when owned by python if(((PyObject *)array)->ob_refcnt > 2) Py_DECREF(array); + if(((PyObject *)indices)->ob_refcnt > 1) Py_DECREF(indices); + if(((PyObject *)row_indices)->ob_refcnt > 1) Py_DECREF(row_indices); return (PyObject *) instance; } diff --git a/lib/swig/tick/array_test/array_test_module.i b/lib/swig/tick/array_test/array_test_module.i index 7037bd455..ea671fc35 100644 --- a/lib/swig/tick/array_test/array_test_module.i +++ b/lib/swig/tick/array_test/array_test_module.i @@ -2,6 +2,7 @@ %module array_test +%include tick/array/array_module.i %include tick/base/defs.i %{ diff --git a/lib/swig/tick/module.i b/lib/swig/tick/module.i new file mode 100644 index 000000000..12b69b1b7 --- /dev/null +++ b/lib/swig/tick/module.i @@ -0,0 +1,22 @@ + +%module tick_cpp + +%include tick/array/array_module.i +%include tick/array_test/array_test_module.i + +%include tick/base/base_module.i + +%include tick/random/crandom_module.i + +%include tick/base_model/base_model_module.i +%include tick/linear_model/linear_model_module.i + +%include tick/prox/prox_module.i + +%include tick/hawkes/model/hawkes_model_module.i +%include tick/hawkes/simulation/hawkes_simulation_module.i +%include tick/hawkes/inference/hawkes_inference_module.i +%include tick/preprocessing/preprocessing_module.i +%include tick/robust/robust_module.i +%include tick/solver/solver_module.i +%include tick/survival/survival_module.i diff --git a/lib/swig/tick/prox/prox_module.i b/lib/swig/tick/prox/prox_module.i index ec9d7444b..1efcfdd99 100644 --- a/lib/swig/tick/prox/prox_module.i +++ b/lib/swig/tick/prox/prox_module.i @@ -36,6 +36,10 @@ %shared_ptr(ProxL1Double); %shared_ptr(ProxL1Float); +%shared_ptr(TProxSortedL1); +%shared_ptr(TProxSortedL1); +%shared_ptr(ProxSortedL1); + %shared_ptr(ProxL1wDouble); %shared_ptr(ProxL1wFloat); @@ -104,6 +108,8 @@ %include prox_slope.i +%include prox_sorted_l1.i + %include prox_multi.i %include prox_equality.i diff --git a/lib/swig/tick/prox/prox_sorted_l1.i b/lib/swig/tick/prox/prox_sorted_l1.i new file mode 100644 index 000000000..cabca960c --- /dev/null +++ b/lib/swig/tick/prox/prox_sorted_l1.i @@ -0,0 +1,26 @@ +// License: BSD 3 clause + +%{ +#include "tick/prox/prox_slope.h" +%} + +template +class TProxSortedL1 : public TProx { + public: + TProxSortedL1(); + //TProxSortedL1(T lambda, T fdr, bool positive); + + //TProxSortedL1(T lambda, T fdr, unsigned long start, unsigned long end, bool positive); + + inline T get_weight_i(unsigned long i); + + bool compare(const TProxSortedL1 &that); +}; + +%template(ProxSortedL1Double) TProxSortedL1; +typedef TProxSortedL1 ProxSortedL1Double; +TICK_MAKE_TK_PICKLABLE(TProxSortedL1, ProxSortedL1Double, double, double); + +%template(ProxSortedL1Float) TProxSortedL1; +typedef TProxSortedL1 ProxSortedL1Float; +TICK_MAKE_TK_PICKLABLE(TProxSortedL1, ProxSortedL1Float, float, float); diff --git a/old_setup.py b/old_setup.py new file mode 100644 index 000000000..4e1ae3ea3 --- /dev/null +++ b/old_setup.py @@ -0,0 +1,955 @@ +#!/usr/bin/env python +# -*- coding: utf8 -*- + +# python setup.py build_ext --inplace + +""" +setup.py file +""" +import multiprocessing +import os +import pathlib +import platform +import re +import shutil +import subprocess +import sys +import sysconfig +import time +import unittest +import warnings + +from abc import ABC + +from setuptools import find_packages, setup, Command +from setuptools.command.install import install +from setuptools.extension import Extension + +# deprecated! +import distutils +from distutils.command.build import build +from distutils.command.clean import clean +from distutils import sysconfig as distconfig +# deprecated! + + + +from packaging import version + +force_blas = False +if "--force-blas" in sys.argv: + force_blas = True + sys.argv.remove("--force-blas") + +# Available debug flags +# +# DEBUG_C_ARRAY : count #allocations of C-arrays +# DEBUG_ARRAY : Track creation/destruction of Array objects +# DEBUG_SHAREDARRAY : Track creation/destruction of SharedArray objects +# DEBUG_VARRAY : Track VArray +# DEBUG_COSTLY_THROW : Enables some costly tests to throw error +# (such as Array[i] if i not in range) +# DEBUG_VERBOSE : Error messages from CPP extensions will include +# backtrace and error loc + +# debug_flags = ['DEBUG_C_ARRAY', 'DEBUG_ARRAY', 'DEBUG_COSTLY_THROW', +# 'DEBUG_SHAREDARRAY', 'DEBUG_VARRAY', 'DEBUG_VERBOSE'] + +TICK_DEBUG=1 +# allow disable debug +if os.environ.get('TICK_DEBUG') is not None: + TICK_DEBUG=os.environ['TICK_DEBUG'] + +TICK_WERROR=1 +# allow disable Werror +if os.environ.get('TICK_WERROR') is not None: + TICK_WERROR=os.environ['TICK_WERROR'] + +debug_flags = [] + +if TICK_DEBUG == 1 or TICK_DEBUG == "1": + debug_flags = ['DEBUG_COSTLY_THROW'] + +TICK_CMAKE_GENERATOR=None +if os.environ.get('TICK_CMAKE_GENERATOR') is not None: + TICK_CMAKE_GENERATOR=os.environ['TICK_CMAKE_GENERATOR'] + +# If true, add compilation flags to use fast (but maybe inaccurate) math +# See https://gcc.gnu.org/wiki/FloatingPointMath +use_fast_math = True + +version_info = sys.version_info + +python_min_ver = (3, 6, 0) +python_ver = (version_info.major, version_info.minor, version_info.micro) + +if python_ver < python_min_ver: + txt = 'Python version {0}.{1}.{2} ' \ + 'lower than the required version >= {3}.{4}.{5}.' + + warnings.warn(txt.format(*(python_ver + python_min_ver))) + +# The next block ensures that we build a link-time linkable dynamic library for +# OSX builds instead of a bundle. +# +# Snippet from http://stackoverflow.com/a/32765319/2299947 +if sys.platform == 'darwin': + vars = distconfig.get_config_vars() + vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib') + +# If we're installing via a wheel or not +is_building_tick = any(arg in ("build", + "build_ext", + "bdist", + "bdist_wheel", + "develop",) for arg in sys.argv) + +# Obtain the numpy include directory. +# This logic works across numpy versions. +numpy_available = False +numpy_include = "" +blas_info = {} +try: + import numpy as np + from numpy.distutils.system_info import get_info + + try: + numpy_include = np.get_include() + except AttributeError: + numpy_include = np.get_numpy_include() + + # Determine if we have an available BLAS implementation + if force_blas: # activated with build --force-blas + blas_info = get_info("blas_opt", 0) + elif platform.system() == 'Windows': + try: + with open(os.devnull, 'w') as devnull: + exitCode = subprocess.check_output( + "python tools/python/blas/check_cblas.py build_ext", + stderr=devnull, + shell=True) + blas_info = get_info("blas_opt", 0) + except subprocess.CalledProcessError as subError: + print("Error executing check_cblas.py - cblas not found") + else: + try: + with open(os.devnull, 'w') as devnull: + exitCode = subprocess.check_output( + "python tools/python/blas/check_mkl.py build_ext", + stderr=devnull, + shell=True) + blas_info = get_info("blas_opt", 0) + except subprocess.CalledProcessError as subError: + print("Error executing check_mkl.py - mkl not found") + + numpy_available = True +except ImportError as e: + if is_building_tick: + print(e) + warnings.warn("numpy is not installed:\n" + " - Include directory for numpy integration may not be " + "correct\n " + " - BLAS will not be used for this build\n") + +# sometimes disabling blas is desired +if os.environ.get('TICK_NO_OPTS') is not None: + if os.environ['TICK_NO_OPTS'] == '1': + blas_info = {} + +# By default, we assume that scipy uses 32 bit integers for indices in sparse +# arrays +sparse_indices_flag = "-DTICK_SPARSE_INDICES_INT32" +try: + from scipy.sparse import sputils + + sparsearray_type = sputils.get_index_dtype() + + if sparsearray_type == np.int64: + sparse_indices_flag = "-DTICK_SPARSE_INDICES_INT64" +except ImportError as e: + if is_building_tick and numpy_available: + print(e) + warnings.warn("scipy is not installed, unable to determine " + "sparse array integer type (assuming 32 bits)\n") + +if os.name == 'posix': + if platform.system() == 'Darwin': + os_version = platform.mac_ver()[0] + # keep only major + minor + os_version = '.'.join(os_version.split('.')[:2]) + + if version.parse(os_version) < version.parse('10.9'): + raise ValueError( + 'You need to have at least mac os 10.9 to build this package') + + # We set this variable manually because anaconda set it to a deprecated + # one + os.environ['MACOSX_DEPLOYMENT_TARGET'] = os_version + +# check for debug pyenv - PYVER must be exported as env var. Debug pyenv setup: +# PYENV=3.7.0 +# CFLAGS="-O0 -ggdb" CONFIGURE_OPTS="--enable-shared" pyenv install -kg $PYVER +# PYENV=${PYENV}-debug +# eval "$(pyenv init -)" +# pyenv global ${PYVER} +# pyenv local ${PYVER} + +PYVER = "" +PYVER_DBG = "" +if os.environ.get('PYVER') is not None: + PYVER = os.environ['PYVER'] + if PYVER.endswith("-debug"): + PYVER_DBG = "-pydebug" + +# Directory containing built .so files before they are moved either +# in source (with build flag --inplace) or to site-packages (by install) +# E.g. build/lib.macosx-10.11-x86_64-3.5 +build_dir = "build/lib.{}-{}"+PYVER_DBG +build_dir = build_dir.format(distutils.util.get_platform(), + ".".join(sys.version.split(".")[:2])) + +class SwigExtension(Extension): + """This only adds information about extension construction, useful for + library sharing + """ + + def __init__(self, *args, module_ref=None, ext_name=None, **kwargs): + super().__init__(*args, **kwargs) + self.module_ref = module_ref + self.ext_name = ext_name + +class SwigPath: + """Small class to handle module creation and check project structure + """ + + def __init__(self, module_path, extension_name): + module_path = os.path.normpath(module_path) + + + # Module C++ source directory (e.g. lib/cpp/tick/base) + self.src = os.path.join(module_path, 'src') + + # Module SWIG interface files directory (e.g. tick/array/swig) + self.swig = "lib/swig/" + module_path[5:] + + # Module build directory. Will contain generated .py files, and .so + # files if built with flag --inplace. + # + # E.g. tick/array/build + self.build = os.path.join(module_path, 'build') + + self.extension_name = extension_name + self.private_extension_name = '_' + extension_name + + # Transform folder path to module path + self.extension_path = self.build \ + .replace('.', '') \ + .replace('/', '.') \ + + '.' + self.private_extension_name + + # Filename of the produced .so file (e.g. _array.so) + self.lib_filename = '{}{}'.format(self.private_extension_name, + sysconfig.get_config_var('EXT_SUFFIX')) + +def create_extension(extension_name, module_dir, + cpp_files, h_files, swig_files, folders=[], + include_modules=None, extra_compile_args=None, + swig_opts=None): + ... + +def create_extension(extension_name, module_dir, + cpp_files, h_files, swig_files, folders=[], + include_modules=None, extra_compile_args=None, + swig_opts=None): + swig_path = SwigPath(module_dir, extension_name) + extension_path = swig_path.extension_path + + # Add directory to filenames + def add_dir_name(dir_name, filenames): + return list(os.path.join(dir_name, filename) for filename in filenames) + + swig_files = add_dir_name("lib/swig/tick/" + module_dir[7:], swig_files) + + for folder in folders: + for file in os.listdir(folder): + file_path = os.path.join(folder, file) + if os.path.isfile(file_path): + _, ext = os.path.splitext(file) + if ext == '.cpp': + cpp_files += [os.path.join(folder, file)] + elif ext == ".txt": + pass + elif ext == ".inl": + pass + else: + warnings.warn('Included file %s in folder %s has an ' + 'unknown extension "%s"' % (file, + folder, + ext)) + + min_swig_opts = ['-py3', + '-c++', + '-Ilib/swig', + '-Ilib/include', + '-outdir', swig_path.build, + ] + + if swig_opts is None: + swig_opts = min_swig_opts + else: + swig_opts.extend(min_swig_opts) + + # Here we set the minimum compile flags. + min_extra_compile_args = ["-D_FILE_OFFSET_BITS=64", + "-DPYTHON_LINK", + "-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION", + '-Ilib/include', + sparse_indices_flag, + '-std=c++11', + '-O2', # -O3 is sometimes dangerous and has caused segfaults on Travis + '-DNDEBUG', # some assertions fail without this (TODO tbh) + ] + if TICK_DEBUG == 0 or TICK_DEBUG == "0": + min_extra_compile_args.append("-g0") + + if use_fast_math: + min_extra_compile_args.append('-ffast-math') + + if extra_compile_args is None: + extra_compile_args = min_extra_compile_args + else: + extra_compile_args.extend(min_extra_compile_args) + + extra_compile_args.append("-Wall") + + if platform.system() == 'Windows': + extra_compile_args.append("-DBUILDING_DLL") + elif TICK_WERROR == 1 or TICK_WERROR == "1": + ## Added -Wall to get all warnings and -Werror to treat them as errors + extra_compile_args.append("-Werror") + + libraries = [] + library_dirs = [] + runtime_library_dirs = [] + extra_link_args = [] + define_macros = [] + extra_include_dirs = ["include", "swig"] + + # Deal with (optional) BLAS + extra_compile_args.extend(blas_info.get("extra_compile_args", [])) + extra_link_args.extend(blas_info.get("extra_link_args", [])) + libraries.extend(blas_info.get("libraries", [])) + library_dirs.extend(blas_info.get("library_dirs", [])) + define_macros.extend(blas_info.get("define_macros", [])) + + if 'define_macros' in blas_info and \ + any(key == 'HAVE_CBLAS' for key, _ in blas_info['define_macros']): + define_macros.append(('TICK_USE_CBLAS', None)) + if "libraries" in blas_info and "mkl_rt" in blas_info["libraries"]: + define_macros.append(('TICK_USE_MKL', None)) + extra_include_dirs.extend(blas_info["include_dirs"]) + if platform.system() != 'Windows': + for lib_dir in blas_info["library_dirs"]: + extra_link_args.append( + "-Wl,-rpath,"+ lib_dir + ) + # if not Linux assume MacOS + if platform.system() != 'Linux': + rel_path = os.path.relpath(lib_dir, swig_path.build) + if os.path.exists(rel_path): + extra_link_args.append("-Wl,-rpath,@loader_path/"+ rel_path) + + if include_modules is None: + include_modules = [] + + # Include all what need for module link + for mod in include_modules: + if mod.__class__ != SwigPath: + raise ValueError("Unhandled class for included module") + + for opts in [swig_opts, extra_compile_args]: + opts.extend(["-I" + mod.swig]) + + # Because setuptools produces shared object files with non-standard + # On windows we need to use ".lib" rather than ".pyd" + # when linking libs to other libs + if platform.system() == 'Windows': + lib = os.path.join(build_dir, mod.build, "_"+mod.extension_name) + lib += os.path.splitext(sysconfig.get_config_var("EXT_SUFFIX"))[0] + libraries.append(lib) + elif platform.system() == 'Linux': + lib_dir = os.path.abspath(os.path.join(build_dir, mod.build)) + extra_link_args.append("-L"+lib_dir) + extra_link_args.append("-Wl,-rpath,"+lib_dir) + extra_link_args.append("-l:"+mod.lib_filename) + else: + extra_link_args.append(os.path.abspath( + os.path.join(build_dir, mod.build, mod.lib_filename))) + + # Make sure that the runtime linker can find shared object + # dependencies by using the relative path to the dependency library. + rel_path = os.path.relpath(mod.build, swig_path.build) + if platform.system() == 'Linux': + # $ORIGIN refers to the location of the current shared object file + # at runtime + runtime_library_dirs.append("\$ORIGIN/%s" % rel_path) + elif platform.system() == 'Windows': + pass + else: # Assuming non-Windows builds for now + # For OSX builds we use @loader_path instead + extra_link_args.append( + "-Wl,-rpath,%s" % '@loader_path/%s' % rel_path + ) + + # Setting the SONAME/install_name for the built libraries. It ensures that + # the runtime linker will have a chance to find the libraries even after + # they're moved (during install, for example) + filename = swig_path.lib_filename + if platform.system() == 'Linux': + extra_link_args.append('-Wl,-soname,%s' % filename) + elif platform.system() == 'Windows': + pass + else: + # For OSX the install_name needs to be prefixed with @rpath + extra_link_args.append('-Wl,-install_name,@rpath/%s' % filename) + + for df in debug_flags: + full_flag = "-D" + df + + extra_compile_args.append(full_flag) + + if df == 'DEBUG_COSTLY_THROW': + swig_opts.append(full_flag) + + # Adding Cereal serialization library + extra_include_dirs.append("lib/third_party/cereal/include") + + # Adding numpy include directory + if numpy_include: + extra_include_dirs.append(numpy_include) + + # This is to override the use of IMPLIB in distutils + # which puts the lib/exp files in the wrong directory + # see: https://github.com/python/cpython/blob/08bb8a41cc976343795bd0e241cd7388e9f44ad5/Lib/distutils/_msvccompiler.py#L467 + if platform.system() == 'Windows': + implib = "/IMPLIB:" + os.path.abspath( + os.path.join(build_dir, swig_path.build, "_"+extension_name)) + implib += os.path.splitext(sysconfig.get_config_var("EXT_SUFFIX"))[0] + extra_link_args.append(implib + ".lib") + + core_module = SwigExtension(extension_path, module_ref=swig_path, + sources=swig_files + cpp_files, + extra_compile_args=extra_compile_args, + extra_link_args=extra_link_args, + define_macros=define_macros, + swig_opts=swig_opts, + libraries=libraries, + include_dirs=extra_include_dirs, + library_dirs=library_dirs, + runtime_library_dirs=runtime_library_dirs, + depends=h_files, + language="c++", + ext_name=extension_name) + + return core_module + + +############################## +# Create extensions +############################## + +array_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/array" + ], + "swig_files": ["array_module.i"], + "module_dir": "./tick/array/", + "extension_name": "array" +} + +array_extension = create_extension(**array_extension_info) + +base_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/base", + "lib/cpp/base/math" + ], + "swig_files": ["base_module.i"], + "module_dir": "./tick/base", + "extension_name": "base", + "include_modules": [array_extension.module_ref] +} + +base_extension = create_extension(**base_extension_info) + +base_array_modules = [array_extension.module_ref, base_extension.module_ref] + +array_test_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": ["lib/cpp/array_test"], + "swig_files": ["array_test_module.i"], + "module_dir": "./tick/array_test/", + "extension_name": "array_test", + "include_modules": base_array_modules, +} + +test_extension = create_extension(**array_test_extension_info) + +random_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": ["lib/cpp/random"], + "swig_files": ["crandom_module.i"], + "module_dir": "./tick/random/", + "extension_name": "crandom", + "include_modules": base_array_modules +} + +random_extension = create_extension(**random_extension_info) + +base_model_core_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/base_model" + ], + "swig_files": ["base_model_module.i"], + "module_dir": "./tick/base_model/", + "extension_name": "base_model", + "include_modules": base_array_modules +} +base_model_core = create_extension(**base_model_core_info) + +linear_model_core_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/linear_model" + ], + "swig_files": ["linear_model_module.i"], + "module_dir": "./tick/linear_model/", + "extension_name": "linear_model", + "include_modules": base_array_modules + + [ + base_model_core.module_ref, + ] +} +linear_model_core = create_extension(**linear_model_core_info) + +hawkes_simulation_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/hawkes/simulation", + "lib/cpp/hawkes/simulation/hawkes_baselines", + "lib/cpp/hawkes/simulation/hawkes_kernels" + ], + "swig_files": [ + "hawkes_simulation_module.i" + ], + "module_dir": "./tick/hawkes/simulation/", + "extension_name": "hawkes_simulation", + "include_modules": base_array_modules + [random_extension.module_ref] +} +hawkes_simulation_extension = \ + create_extension(**hawkes_simulation_extension_info) + +hawkes_model_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/hawkes/model", + "lib/cpp/hawkes/model/base", + "lib/cpp/hawkes/model/list_of_realizations", + ], + "swig_files": [ + "hawkes_model_module.i" + ], + "module_dir": "./tick/hawkes/model/", + "extension_name": "hawkes_model", + "include_modules": base_array_modules + [base_model_core.module_ref] +} +hawkes_model_extension = create_extension(**hawkes_model_extension_info) + +hawkes_inference_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/hawkes/inference", + ], + "swig_files": [ + "hawkes_inference_module.i" + ], + "module_dir": "./tick/hawkes/inference/", + "extension_name": "hawkes_inference", + "include_modules": base_array_modules + + [ + base_model_core.module_ref, + hawkes_model_extension.module_ref, + ] +} +hawkes_inference_extension = create_extension(**hawkes_inference_extension_info) + +prox_core_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/prox" + ], + "swig_files": ["prox_module.i"], + "module_dir": "./tick/prox/", + "extension_name": "prox", + "include_modules": base_array_modules +} +prox_core = create_extension(**prox_core_info) + +robust_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/robust" + ], + "swig_files": ["robust_module.i"], + "module_dir": "./tick/robust/", + "extension_name": "robust", + "include_modules": base_array_modules + [ + base_model_core.module_ref,linear_model_core.module_ref] +} +robust_extension = create_extension(**robust_extension_info) + +solver_core_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/solver" + ], + "swig_files": ["solver_module.i"], + "module_dir": "./tick/solver/", + "extension_name": "solver", + "include_modules": base_array_modules + [random_extension.module_ref, + base_model_core.module_ref, + linear_model_core.module_ref, + prox_core.module_ref, + robust_extension.module_ref] +} +solver_core = create_extension(**solver_core_info) + +preprocessing_core_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/preprocessing" + ], + "swig_files": ["preprocessing_module.i"], + "module_dir": "./tick/preprocessing/", + "extension_name": "preprocessing", + "include_modules": base_array_modules +} + +preprocessing_core = create_extension(**preprocessing_core_info) + +survival_extension_info = { + "cpp_files": [], + "h_files": [], + "folders": [ + "lib/cpp/survival" + ], + "swig_files": ["survival_module.i"], + "module_dir": "./tick/survival/", + "extension_name": "survival", + "include_modules": base_array_modules + [base_model_core.module_ref] +} +survival_extension = create_extension(**survival_extension_info) + +tick_modules = [ + array_extension, base_extension, test_extension, + random_extension, base_model_core, linear_model_core, + hawkes_simulation_extension, hawkes_model_extension, + hawkes_inference_extension, + prox_core, preprocessing_core, + robust_extension, survival_extension, solver_core +] + +# Abstract class for tick-specific commands that need access to common build +# directories +class TickCommand(Command, ABC): + tick_dir = os.path.abspath(os.path.join(os.curdir, 'tick')) + cpp_build_dir = os.path.abspath(os.path.join(build_dir, 'cpptest')) + + user_options = [] + + def initialize_options(self): + """Set default values for options.""" + pass + + def finalize_options(self): + """Post-process options.""" + pass + + +class TickBuild(build): + swig_min_ver = (4, 0, 0) + + @staticmethod + def extract_swig_version(swig_ver_str): + m = re.search('SWIG Version (\d+).(\d+).(\d+)', swig_ver_str) + + if not m: + txt = 'Could not extract SWIG version from string: {0}' + + warnings.warn(txt.format(swig_ver_str)) + + return 0, 0, 0 + + return tuple(int(x) for x in m.groups()[0:3]) + + def run(self): + swig_ver = self.extract_swig_version( + str(subprocess.check_output(['swig', '-version']))) + + if swig_ver < self.swig_min_ver: + txt = 'SWIG version {0}.{1}.{2} ' \ + 'lower than the required version >= {3}.{4}.{5}. ' \ + 'This will likely cause build errors!' + + warnings.warn(txt.format(*(swig_ver + self.swig_min_ver))) + + self.run_command('build_ext') + build.run(self) + + +class TickInstall(install): + def run(self): + self.run_command('build_ext') + install.run(self) + + +class BuildRunCPPTests(TickCommand): + description = 'build and run tick C++ tests' + + def run(self): + self.run_command('makecpptest') + self.run_command('runcpptest') + + +class RunCPPTests(TickCommand): + description = 'run tick C++ tests' + + def run(self): + make_cmd = ['make', 'check'] + subprocess.check_call(make_cmd, cwd=self.cpp_build_dir) + + +class BuildCPPTests(TickCommand): + build_jobs = 1 + description = 'build tick C++ tests' + user_options = [ + ('build-jobs=', 'j', + 'number of parallel build jobs (default is number of available CPU ' + 'cores reported by Python)'), + ] + + def initialize_options(self): + """Set default values for options.""" + self.build_jobs = multiprocessing.cpu_count() + + def run(self): + relpath = os.path.relpath(self.tick_dir, self.cpp_build_dir) + cmake_exe = os.environ.get('TICK_CMAKE', 'cmake') + + + cmake_cmd = [cmake_exe, + '-DTICK_REBUILD_LIBS=OFF', + '-DBENCHMARK=OFF', + relpath + '/../lib'] + + if TICK_CMAKE_GENERATOR is not None: + cmake_cmd.extend(['-G', '{}'.format(TICK_CMAKE_GENERATOR)]) + + # Feed the path to the built C++ extensions so CMake does not have to + # build them again + for mod in tick_modules: + full_path = os.path.abspath( + os.path.join(mod.module_ref.build, mod.module_ref.lib_filename)) + + cmake_cmd.append( + '-DTICK_LIB_{}={}'.format(mod.ext_name.upper(), full_path)) + + if 'define_macros' in blas_info and \ + any(key == 'HAVE_CBLAS' for key, _ in blas_info['define_macros']): + cmake_cmd.append('-DUSE_BLAS=ON') + + os.makedirs(os.path.join(self.cpp_build_dir, 'cpptest'), exist_ok=True) + subprocess.check_call(cmake_cmd, cwd=self.cpp_build_dir) + + make_cmd = ['make', 'VERBOSE=1', 'all', '-j{}'.format(self.build_jobs)] + subprocess.check_call(make_cmd, cwd=self.cpp_build_dir) + + +class RunCPPLint(TickCommand): + description = 'run cpplint on tick C++ source files' + + CPPLINT_DIRS = [ + 'lib/include', + 'lib/cpp', + ] + + def run(self): + try: + import cpplint as cl + + cl_state = cl._cpplint_state + error_count = 0 + + for dir in self.CPPLINT_DIRS: + print("Processing {}".format(dir)) + + cl_state.ResetErrorCounts() + filenames = list(pathlib.Path(dir).glob('**/*.h')) + \ + list(pathlib.Path(dir).glob('**/*.cpp')) + + for filename in filenames: + cl.ProcessFile(str(filename), cl_state.verbose_level) + cl_state.PrintErrorCounts() + + error_count += cl_state.error_count + print('') + + if error_count > 0: + raise RuntimeError("Codestyle check by cpplint failed") + + except ImportError: + warnings.warn("Stylecheck by cpplint failed because cpplint " + "is not installed as a Python module") + + +class RunPyLint(TickCommand): + # We need to define if and how we run pylint + + description = 'run tick PyLint codestyle check' + start_dir = '.' + + @staticmethod + def run(): + raise NotImplementedError('Running pylint from setup.py' + 'not supported yet') + +class RunPyTests(TickCommand): + description = 'run tick Python tests' + start_dir = '.' + + user_options = [ + ('start-dir=', 's', + 'directory to start looking for Python tests (e.g. tick/simulation)'), + ] + + def initialize_options(self): + """Set default values for options.""" + self.start_dir = '.' + + def run(self): + if platform.system() == 'Windows': + print("The pytest command has issues with threads on Windows") + print('Instead please run:') + print('python3 -m unittest discover -v . "*_test.py"') + exit(1) + loader = unittest.TestLoader() + alltests = loader.discover(self.start_dir, pattern="*_test.py") + result = unittest.TextTestRunner(verbosity=2).run(alltests) + sys.exit(not result.wasSuccessful()) + + +class RunTestSuites(TickCommand): + description = 'run tick Python and C++ tests' + + def run(self): + self.run_command('cpptest') + self.run_command('pytest') + + +class CleanTick(clean): + description = 'cleans all generated and built files' + + def run(self): + seconds_until_clean = 5 + + print("Cleaning source directories in %d seconds..." % + seconds_until_clean) + + time.sleep(seconds_until_clean) + + clean.run(self) + + shutil.rmtree(build_dir, ignore_errors=True) + + patterns = [ + '**/*.so', + '**/*_wrap.cpp', + '**/__pycache__/*.pyc', + '**/__pycache__', + ] + + for paths in (pathlib.Path(os.curdir).glob(p) for p in patterns): + for path in paths: + print("Deleting {}".format(path)) + + if path.is_dir(): + path.rmdir() + else: + path.unlink() + + +setup(name="tick", + version='0.7.0.1', + author="Emmanuel Bacry, " + "Stephane Gaiffas, " + "Martin Bompaire, " + "Søren V. Poulsen, " + "Maryan Morel, " + "Simon Bussy, " + "Philip Deegan", + author_email='martin.bompaire@polytechnique.edu, ' + 'philip.deegan@polytechnique.edu', + url="https://x-datainitiative.github.io/tick/", + description="Module for statistical learning, with a particular emphasis " + "on time-dependent modelling", + ext_modules=tick_modules, + install_requires=['numpy', + 'scipy', + 'numpydoc', + 'matplotlib', + 'sphinx', + 'pandas', + 'dill', + 'scikit-learn'], + packages=find_packages(), + cmdclass={'build': TickBuild, + 'install': TickInstall, + 'makecpptest': BuildCPPTests, + 'runcpptest': RunCPPTests, + 'cpptest': BuildRunCPPTests, + 'cpplint': RunCPPLint, + 'pytest': RunPyTests, + 'pylint': RunPyLint, + 'test': RunTestSuites, + 'clean': CleanTick}, + classifiers=['Development Status :: 3 - Alpha', + 'Intended Audience :: Science/Research', + 'Intended Audience :: Developers', + 'Programming Language :: C++', + 'Programming Language :: Python', + 'Topic :: Software Development', + 'Topic :: Scientific/Engineering', + 'Operating System :: POSIX', + 'Operating System :: Unix', + 'Operating System :: MacOS', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + 'Programming Language :: Python :: 3.8', + 'License :: OSI Approved :: BSD License'], + ) diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..6f1834ab9 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,33 @@ +[project] +name = "tick" +version = "0.7.0.2" + +dependencies = [ + 'numpy', + 'numpydoc', + 'scipy', + 'matplotlib', + 'scikit-learn', + 'dill', + 'pandas', + 'packaging', +] + +description = "Module for statistical learning, with a particular emphasis on time-dependent modelling" +readme = "README.md" +requires-python = ">=3.7" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", +] + +[project.urls] +"Homepage" = "https://x-datainitiative.github.io/tick/" +"Bug Tracker" = "https://github.com/X-DataInitiative/tick/issues" + +[build-system] +requires = [ + "setuptools>=42", "wheel", "packaging", +] + diff --git a/setup.py b/setup.py index 61a9393b4..2d05e7b09 100644 --- a/setup.py +++ b/setup.py @@ -1,950 +1,45 @@ -#!/usr/bin/env python -# -*- coding: utf8 -*- -# python setup.py build_ext --inplace - -""" -setup.py file -""" -import multiprocessing -import os -import pathlib -import platform -import re -import shutil -import subprocess -import sys -import sysconfig -import time -import unittest -import warnings - -from abc import ABC - -from setuptools import find_packages, setup, Command -from setuptools.command.install import install -from setuptools.extension import Extension - -# deprecated! -import distutils -from distutils.command.build import build -from distutils.command.clean import clean -from distutils import sysconfig as distconfig -# deprecated! - - - -from packaging import version - -force_blas = False -if "--force-blas" in sys.argv: - force_blas = True - sys.argv.remove("--force-blas") - -# Available debug flags -# -# DEBUG_C_ARRAY : count #allocations of C-arrays -# DEBUG_ARRAY : Track creation/destruction of Array objects -# DEBUG_SHAREDARRAY : Track creation/destruction of SharedArray objects -# DEBUG_VARRAY : Track VArray -# DEBUG_COSTLY_THROW : Enables some costly tests to throw error -# (such as Array[i] if i not in range) -# DEBUG_VERBOSE : Error messages from CPP extensions will include -# backtrace and error loc - -# debug_flags = ['DEBUG_C_ARRAY', 'DEBUG_ARRAY', 'DEBUG_COSTLY_THROW', -# 'DEBUG_SHAREDARRAY', 'DEBUG_VARRAY', 'DEBUG_VERBOSE'] - -TICK_DEBUG=1 -# allow disable debug -if os.environ.get('TICK_DEBUG') is not None: - TICK_DEBUG=os.environ['TICK_DEBUG'] - -TICK_WERROR=1 -# allow disable Werror -if os.environ.get('TICK_WERROR') is not None: - TICK_WERROR=os.environ['TICK_WERROR'] - -debug_flags = [] - -if TICK_DEBUG == 1 or TICK_DEBUG == "1": - debug_flags = ['DEBUG_COSTLY_THROW'] - -TICK_CMAKE_GENERATOR=None -if os.environ.get('TICK_CMAKE_GENERATOR') is not None: - TICK_CMAKE_GENERATOR=os.environ['TICK_CMAKE_GENERATOR'] - -# If true, add compilation flags to use fast (but maybe inaccurate) math -# See https://gcc.gnu.org/wiki/FloatingPointMath -use_fast_math = True - -version_info = sys.version_info - -python_min_ver = (3, 6, 0) -python_ver = (version_info.major, version_info.minor, version_info.micro) - -if python_ver < python_min_ver: - txt = 'Python version {0}.{1}.{2} ' \ - 'lower than the required version >= {3}.{4}.{5}.' - - warnings.warn(txt.format(*(python_ver + python_min_ver))) - -# The next block ensures that we build a link-time linkable dynamic library for -# OSX builds instead of a bundle. -# -# Snippet from http://stackoverflow.com/a/32765319/2299947 -if sys.platform == 'darwin': - vars = distconfig.get_config_vars() - vars['LDSHARED'] = vars['LDSHARED'].replace('-bundle', '-dynamiclib') - -# If we're installing via a wheel or not -is_building_tick = any(arg in ("build", - "build_ext", - "bdist", - "bdist_wheel", - "develop",) for arg in sys.argv) - -# Obtain the numpy include directory. -# This logic works across numpy versions. -numpy_available = False -numpy_include = "" -blas_info = {} -try: - import numpy as np - from numpy.distutils.system_info import get_info - - try: - numpy_include = np.get_include() - except AttributeError: - numpy_include = np.get_numpy_include() - - # Determine if we have an available BLAS implementation - if force_blas: # activated with build --force-blas - blas_info = get_info("blas_opt", 0) - elif platform.system() == 'Windows': - try: - with open(os.devnull, 'w') as devnull: - exitCode = subprocess.check_output( - "python tools/python/blas/check_cblas.py build_ext", - stderr=devnull, - shell=True) - blas_info = get_info("blas_opt", 0) - except subprocess.CalledProcessError as subError: - print("Error executing check_cblas.py - cblas not found") - else: - try: - with open(os.devnull, 'w') as devnull: - exitCode = subprocess.check_output( - "python tools/python/blas/check_mkl.py build_ext", - stderr=devnull, - shell=True) - blas_info = get_info("blas_opt", 0) - except subprocess.CalledProcessError as subError: - print("Error executing check_mkl.py - mkl not found") - - numpy_available = True -except ImportError as e: - if is_building_tick: - print(e) - warnings.warn("numpy is not installed:\n" - " - Include directory for numpy integration may not be " - "correct\n " - " - BLAS will not be used for this build\n") - -# sometimes disabling blas is desired -if os.environ.get('TICK_NO_OPTS') is not None: - if os.environ['TICK_NO_OPTS'] == '1': - blas_info = {} - -# By default, we assume that scipy uses 32 bit integers for indices in sparse -# arrays -sparse_indices_flag = "-DTICK_SPARSE_INDICES_INT32" -try: - from scipy.sparse import sputils - - sparsearray_type = sputils.get_index_dtype() - - if sparsearray_type == np.int64: - sparse_indices_flag = "-DTICK_SPARSE_INDICES_INT64" -except ImportError as e: - if is_building_tick and numpy_available: - print(e) - warnings.warn("scipy is not installed, unable to determine " - "sparse array integer type (assuming 32 bits)\n") - -if os.name == 'posix': - if platform.system() == 'Darwin': - os_version = platform.mac_ver()[0] - # keep only major + minor - os_version = '.'.join(os_version.split('.')[:2]) - - if version.parse(os_version) < version.parse('10.9'): - raise ValueError( - 'You need to have at least mac os 10.9 to build this package') - - # We set this variable manually because anaconda set it to a deprecated - # one - os.environ['MACOSX_DEPLOYMENT_TARGET'] = os_version - -# check for debug pyenv - PYVER must be exported as env var. Debug pyenv setup: -# PYENV=3.7.0 -# CFLAGS="-O0 -ggdb" CONFIGURE_OPTS="--enable-shared" pyenv install -kg $PYVER -# PYENV=${PYENV}-debug -# eval "$(pyenv init -)" -# pyenv global ${PYVER} -# pyenv local ${PYVER} - -PYVER = "" -PYVER_DBG = "" -if os.environ.get('PYVER') is not None: - PYVER = os.environ['PYVER'] - if PYVER.endswith("-debug"): - PYVER_DBG = "-pydebug" - -# Directory containing built .so files before they are moved either -# in source (with build flag --inplace) or to site-packages (by install) -# E.g. build/lib.macosx-10.11-x86_64-3.5 -build_dir = "build/lib.{}-{}"+PYVER_DBG -build_dir = build_dir.format(distutils.util.get_platform(), - ".".join(sys.version.split(".")[:2])) - -class SwigExtension(Extension): - """This only adds information about extension construction, useful for - library sharing - """ - - def __init__(self, *args, module_ref=None, ext_name=None, **kwargs): - super().__init__(*args, **kwargs) - self.module_ref = module_ref - self.ext_name = ext_name - -class SwigPath: - """Small class to handle module creation and check project structure - """ - - def __init__(self, module_path, extension_name): - module_path = os.path.normpath(module_path) - - - # Module C++ source directory (e.g. lib/cpp/tick/base) - self.src = os.path.join(module_path, 'src') - - # Module SWIG interface files directory (e.g. tick/array/swig) - self.swig = "lib/swig/" + module_path[5:] - - # Module build directory. Will contain generated .py files, and .so - # files if built with flag --inplace. - # - # E.g. tick/array/build - self.build = os.path.join(module_path, 'build') - - self.extension_name = extension_name - self.private_extension_name = '_' + extension_name - - # Transform folder path to module path - self.extension_path = self.build \ - .replace('.', '') \ - .replace('/', '.') \ - + '.' + self.private_extension_name - - # Filename of the produced .so file (e.g. _array.so) - self.lib_filename = '{}{}'.format(self.private_extension_name, - sysconfig.get_config_var('EXT_SUFFIX')) - - -def create_extension(extension_name, module_dir, - cpp_files, h_files, swig_files, folders=[], - include_modules=None, extra_compile_args=None, - swig_opts=None): - swig_path = SwigPath(module_dir, extension_name) - extension_path = swig_path.extension_path - - # Add directory to filenames - def add_dir_name(dir_name, filenames): - return list(os.path.join(dir_name, filename) for filename in filenames) - - swig_files = add_dir_name("lib/swig/tick/" + module_dir[7:], swig_files) - - for folder in folders: - for file in os.listdir(folder): - file_path = os.path.join(folder, file) - if os.path.isfile(file_path): - _, ext = os.path.splitext(file) - if ext == '.cpp': - cpp_files += [os.path.join(folder, file)] - elif ext == ".txt": - pass - elif ext == ".inl": - pass - else: - warnings.warn('Included file %s in folder %s has an ' - 'unknown extension "%s"' % (file, - folder, - ext)) - - min_swig_opts = ['-py3', - '-c++', - '-Ilib/swig', - '-Ilib/include', - '-outdir', swig_path.build, - ] - - if swig_opts is None: - swig_opts = min_swig_opts - else: - swig_opts.extend(min_swig_opts) - - # Here we set the minimum compile flags. - min_extra_compile_args = ["-D_FILE_OFFSET_BITS=64", - "-DPYTHON_LINK", - "-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION", - '-Ilib/include', - sparse_indices_flag, - '-std=c++11', - '-O2', # -O3 is sometimes dangerous and has caused segfaults on Travis - '-DNDEBUG', # some assertions fail without this (TODO tbh) - ] - if TICK_DEBUG == 0 or TICK_DEBUG == "0": - min_extra_compile_args.append("-g0") - - if use_fast_math: - min_extra_compile_args.append('-ffast-math') - - if extra_compile_args is None: - extra_compile_args = min_extra_compile_args - else: - extra_compile_args.extend(min_extra_compile_args) - - extra_compile_args.append("-Wall") - - if platform.system() == 'Windows': - extra_compile_args.append("-DBUILDING_DLL") - elif TICK_WERROR == 1 or TICK_WERROR == "1": - ## Added -Wall to get all warnings and -Werror to treat them as errors - extra_compile_args.append("-Werror") - - libraries = [] - library_dirs = [] - runtime_library_dirs = [] - extra_link_args = [] - define_macros = [] - extra_include_dirs = ["include", "swig"] - - # Deal with (optional) BLAS - extra_compile_args.extend(blas_info.get("extra_compile_args", [])) - extra_link_args.extend(blas_info.get("extra_link_args", [])) - libraries.extend(blas_info.get("libraries", [])) - library_dirs.extend(blas_info.get("library_dirs", [])) - define_macros.extend(blas_info.get("define_macros", [])) - - if 'define_macros' in blas_info and \ - any(key == 'HAVE_CBLAS' for key, _ in blas_info['define_macros']): - define_macros.append(('TICK_USE_CBLAS', None)) - if "libraries" in blas_info and "mkl_rt" in blas_info["libraries"]: - define_macros.append(('TICK_USE_MKL', None)) - extra_include_dirs.extend(blas_info["include_dirs"]) - if platform.system() != 'Windows': - for lib_dir in blas_info["library_dirs"]: - extra_link_args.append( - "-Wl,-rpath,"+ lib_dir - ) - # if not Linux assume MacOS - if platform.system() != 'Linux': - rel_path = os.path.relpath(lib_dir, swig_path.build) - if os.path.exists(rel_path): - extra_link_args.append("-Wl,-rpath,@loader_path/"+ rel_path) - - if include_modules is None: - include_modules = [] - - # Include all what need for module link - for mod in include_modules: - if mod.__class__ != SwigPath: - raise ValueError("Unhandled class for included module") - - for opts in [swig_opts, extra_compile_args]: - opts.extend(["-I" + mod.swig]) - - # Because setuptools produces shared object files with non-standard - # On windows we need to use ".lib" rather than ".pyd" - # when linking libs to other libs - if platform.system() == 'Windows': - lib = os.path.join(build_dir, mod.build, "_"+mod.extension_name) - lib += os.path.splitext(sysconfig.get_config_var("EXT_SUFFIX"))[0] - libraries.append(lib) - elif platform.system() == 'Linux': - lib_dir = os.path.abspath(os.path.join(build_dir, mod.build)) - extra_link_args.append("-L"+lib_dir) - extra_link_args.append("-Wl,-rpath,"+lib_dir) - extra_link_args.append("-l:"+mod.lib_filename) - else: - extra_link_args.append(os.path.abspath( - os.path.join(build_dir, mod.build, mod.lib_filename))) - - # Make sure that the runtime linker can find shared object - # dependencies by using the relative path to the dependency library. - rel_path = os.path.relpath(mod.build, swig_path.build) - if platform.system() == 'Linux': - # $ORIGIN refers to the location of the current shared object file - # at runtime - runtime_library_dirs.append("\$ORIGIN/%s" % rel_path) - elif platform.system() == 'Windows': - pass - else: # Assuming non-Windows builds for now - # For OSX builds we use @loader_path instead - extra_link_args.append( - "-Wl,-rpath,%s" % '@loader_path/%s' % rel_path - ) - - # Setting the SONAME/install_name for the built libraries. It ensures that - # the runtime linker will have a chance to find the libraries even after - # they're moved (during install, for example) - filename = swig_path.lib_filename - if platform.system() == 'Linux': - extra_link_args.append('-Wl,-soname,%s' % filename) - elif platform.system() == 'Windows': - pass - else: - # For OSX the install_name needs to be prefixed with @rpath - extra_link_args.append('-Wl,-install_name,@rpath/%s' % filename) - - for df in debug_flags: - full_flag = "-D" + df - - extra_compile_args.append(full_flag) - - if df == 'DEBUG_COSTLY_THROW': - swig_opts.append(full_flag) - - # Adding Cereal serialization library - extra_include_dirs.append("lib/third_party/cereal/include") - - # Adding numpy include directory - if numpy_include: - extra_include_dirs.append(numpy_include) - - # This is to override the use of IMPLIB in distutils - # which puts the lib/exp files in the wrong directory - # see: https://github.com/python/cpython/blob/08bb8a41cc976343795bd0e241cd7388e9f44ad5/Lib/distutils/_msvccompiler.py#L467 - if platform.system() == 'Windows': - implib = "/IMPLIB:" + os.path.abspath( - os.path.join(build_dir, swig_path.build, "_"+extension_name)) - implib += os.path.splitext(sysconfig.get_config_var("EXT_SUFFIX"))[0] - extra_link_args.append(implib + ".lib") - - core_module = SwigExtension(extension_path, module_ref=swig_path, - sources=swig_files + cpp_files, - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - define_macros=define_macros, - swig_opts=swig_opts, - libraries=libraries, - include_dirs=extra_include_dirs, - library_dirs=library_dirs, - runtime_library_dirs=runtime_library_dirs, - depends=h_files, - language="c++", - ext_name=extension_name) - - return core_module - - -############################## -# Create extensions -############################## - -array_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/array" - ], - "swig_files": ["array_module.i"], - "module_dir": "./tick/array/", - "extension_name": "array" -} - -array_extension = create_extension(**array_extension_info) - -base_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/base", - "lib/cpp/base/math" - ], - "swig_files": ["base_module.i"], - "module_dir": "./tick/base", - "extension_name": "base", - "include_modules": [array_extension.module_ref] -} - -base_extension = create_extension(**base_extension_info) - -base_array_modules = [array_extension.module_ref, base_extension.module_ref] - -array_test_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": ["lib/cpp/array_test"], - "swig_files": ["array_test_module.i"], - "module_dir": "./tick/array_test/", - "extension_name": "array_test", - "include_modules": base_array_modules, -} - -test_extension = create_extension(**array_test_extension_info) - -random_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": ["lib/cpp/random"], - "swig_files": ["crandom_module.i"], - "module_dir": "./tick/random/", - "extension_name": "crandom", - "include_modules": base_array_modules -} - -random_extension = create_extension(**random_extension_info) - -base_model_core_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/base_model" - ], - "swig_files": ["base_model_module.i"], - "module_dir": "./tick/base_model/", - "extension_name": "base_model", - "include_modules": base_array_modules -} -base_model_core = create_extension(**base_model_core_info) - -linear_model_core_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/linear_model" - ], - "swig_files": ["linear_model_module.i"], - "module_dir": "./tick/linear_model/", - "extension_name": "linear_model", - "include_modules": base_array_modules + - [ - base_model_core.module_ref, - ] -} -linear_model_core = create_extension(**linear_model_core_info) - -hawkes_simulation_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/hawkes/simulation", - "lib/cpp/hawkes/simulation/hawkes_baselines", - "lib/cpp/hawkes/simulation/hawkes_kernels" - ], - "swig_files": [ - "hawkes_simulation_module.i" - ], - "module_dir": "./tick/hawkes/simulation/", - "extension_name": "hawkes_simulation", - "include_modules": base_array_modules + [random_extension.module_ref] -} -hawkes_simulation_extension = \ - create_extension(**hawkes_simulation_extension_info) - -hawkes_model_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/hawkes/model", - "lib/cpp/hawkes/model/base", - "lib/cpp/hawkes/model/list_of_realizations", - ], - "swig_files": [ - "hawkes_model_module.i" - ], - "module_dir": "./tick/hawkes/model/", - "extension_name": "hawkes_model", - "include_modules": base_array_modules + [base_model_core.module_ref] -} -hawkes_model_extension = create_extension(**hawkes_model_extension_info) - -hawkes_inference_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/hawkes/inference", - ], - "swig_files": [ - "hawkes_inference_module.i" - ], - "module_dir": "./tick/hawkes/inference/", - "extension_name": "hawkes_inference", - "include_modules": base_array_modules + - [ - base_model_core.module_ref, - hawkes_model_extension.module_ref, - ] -} -hawkes_inference_extension = create_extension(**hawkes_inference_extension_info) - -prox_core_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/prox" - ], - "swig_files": ["prox_module.i"], - "module_dir": "./tick/prox/", - "extension_name": "prox", - "include_modules": base_array_modules -} -prox_core = create_extension(**prox_core_info) - -robust_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/robust" - ], - "swig_files": ["robust_module.i"], - "module_dir": "./tick/robust/", - "extension_name": "robust", - "include_modules": base_array_modules + [ - base_model_core.module_ref,linear_model_core.module_ref] -} -robust_extension = create_extension(**robust_extension_info) - -solver_core_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/solver" - ], - "swig_files": ["solver_module.i"], - "module_dir": "./tick/solver/", - "extension_name": "solver", - "include_modules": base_array_modules + [random_extension.module_ref, - base_model_core.module_ref, - linear_model_core.module_ref, - prox_core.module_ref, - robust_extension.module_ref] -} -solver_core = create_extension(**solver_core_info) - -preprocessing_core_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/preprocessing" - ], - "swig_files": ["preprocessing_module.i"], - "module_dir": "./tick/preprocessing/", - "extension_name": "preprocessing", - "include_modules": base_array_modules -} - -preprocessing_core = create_extension(**preprocessing_core_info) - -survival_extension_info = { - "cpp_files": [], - "h_files": [], - "folders": [ - "lib/cpp/survival" - ], - "swig_files": ["survival_module.i"], - "module_dir": "./tick/survival/", - "extension_name": "survival", - "include_modules": base_array_modules + [base_model_core.module_ref] -} -survival_extension = create_extension(**survival_extension_info) - -tick_modules = [ - array_extension, base_extension, test_extension, - random_extension, base_model_core, linear_model_core, - hawkes_simulation_extension, hawkes_model_extension, - hawkes_inference_extension, - prox_core, preprocessing_core, - robust_extension, survival_extension, solver_core -] - -# Abstract class for tick-specific commands that need access to common build -# directories -class TickCommand(Command, ABC): - tick_dir = os.path.abspath(os.path.join(os.curdir, 'tick')) - cpp_build_dir = os.path.abspath(os.path.join(build_dir, 'cpptest')) - - user_options = [] - - def initialize_options(self): - """Set default values for options.""" - pass - - def finalize_options(self): - """Post-process options.""" - pass - - -class TickBuild(build): - swig_min_ver = (4, 0, 0) - - @staticmethod - def extract_swig_version(swig_ver_str): - m = re.search('SWIG Version (\d+).(\d+).(\d+)', swig_ver_str) - - if not m: - txt = 'Could not extract SWIG version from string: {0}' - - warnings.warn(txt.format(swig_ver_str)) - - return 0, 0, 0 - - return tuple(int(x) for x in m.groups()[0:3]) - - def run(self): - swig_ver = self.extract_swig_version( - str(subprocess.check_output(['swig', '-version']))) - - if swig_ver < self.swig_min_ver: - txt = 'SWIG version {0}.{1}.{2} ' \ - 'lower than the required version >= {3}.{4}.{5}. ' \ - 'This will likely cause build errors!' - - warnings.warn(txt.format(*(swig_ver + self.swig_min_ver))) - - self.run_command('build_ext') - build.run(self) - - -class TickInstall(install): - def run(self): - self.run_command('build_ext') - install.run(self) - - -class BuildRunCPPTests(TickCommand): - description = 'build and run tick C++ tests' - - def run(self): - self.run_command('makecpptest') - self.run_command('runcpptest') - - -class RunCPPTests(TickCommand): - description = 'run tick C++ tests' - - def run(self): - make_cmd = ['make', 'check'] - subprocess.check_call(make_cmd, cwd=self.cpp_build_dir) - - -class BuildCPPTests(TickCommand): - build_jobs = 1 - description = 'build tick C++ tests' - user_options = [ - ('build-jobs=', 'j', - 'number of parallel build jobs (default is number of available CPU ' - 'cores reported by Python)'), - ] - - def initialize_options(self): - """Set default values for options.""" - self.build_jobs = multiprocessing.cpu_count() - - def run(self): - relpath = os.path.relpath(self.tick_dir, self.cpp_build_dir) - cmake_exe = os.environ.get('TICK_CMAKE', 'cmake') - - - cmake_cmd = [cmake_exe, - '-DTICK_REBUILD_LIBS=OFF', - '-DBENCHMARK=OFF', - relpath + '/../lib'] - - if TICK_CMAKE_GENERATOR is not None: - cmake_cmd.extend(['-G', '{}'.format(TICK_CMAKE_GENERATOR)]) - - # Feed the path to the built C++ extensions so CMake does not have to - # build them again - for mod in tick_modules: - full_path = os.path.abspath( - os.path.join(mod.module_ref.build, mod.module_ref.lib_filename)) - - cmake_cmd.append( - '-DTICK_LIB_{}={}'.format(mod.ext_name.upper(), full_path)) - - if 'define_macros' in blas_info and \ - any(key == 'HAVE_CBLAS' for key, _ in blas_info['define_macros']): - cmake_cmd.append('-DUSE_BLAS=ON') - - os.makedirs(os.path.join(self.cpp_build_dir, 'cpptest'), exist_ok=True) - subprocess.check_call(cmake_cmd, cwd=self.cpp_build_dir) - - make_cmd = ['make', 'VERBOSE=1', 'all', '-j{}'.format(self.build_jobs)] - subprocess.check_call(make_cmd, cwd=self.cpp_build_dir) - - -class RunCPPLint(TickCommand): - description = 'run cpplint on tick C++ source files' - - CPPLINT_DIRS = [ - 'lib/include', - 'lib/cpp', - ] - - def run(self): - try: - import cpplint as cl - - cl_state = cl._cpplint_state - error_count = 0 - - for dir in self.CPPLINT_DIRS: - print("Processing {}".format(dir)) - - cl_state.ResetErrorCounts() - filenames = list(pathlib.Path(dir).glob('**/*.h')) + \ - list(pathlib.Path(dir).glob('**/*.cpp')) - - for filename in filenames: - cl.ProcessFile(str(filename), cl_state.verbose_level) - cl_state.PrintErrorCounts() - - error_count += cl_state.error_count - print('') - - if error_count > 0: - raise RuntimeError("Codestyle check by cpplint failed") - - except ImportError: - warnings.warn("Stylecheck by cpplint failed because cpplint " - "is not installed as a Python module") - - -class RunPyLint(TickCommand): - # We need to define if and how we run pylint - - description = 'run tick PyLint codestyle check' - start_dir = '.' - - @staticmethod - def run(): - raise NotImplementedError('Running pylint from setup.py' - 'not supported yet') - -class RunPyTests(TickCommand): - description = 'run tick Python tests' - start_dir = '.' - - user_options = [ - ('start-dir=', 's', - 'directory to start looking for Python tests (e.g. tick/simulation)'), - ] - - def initialize_options(self): - """Set default values for options.""" - self.start_dir = '.' - - def run(self): - if platform.system() == 'Windows': - print("The pytest command has issues with threads on Windows") - print('Instead please run:') - print('python3 -m unittest discover -v . "*_test.py"') - exit(1) - loader = unittest.TestLoader() - alltests = loader.discover(self.start_dir, pattern="*_test.py") - result = unittest.TextTestRunner(verbosity=2).run(alltests) - sys.exit(not result.wasSuccessful()) - - -class RunTestSuites(TickCommand): - description = 'run tick Python and C++ tests' - - def run(self): - self.run_command('cpptest') - self.run_command('pytest') - - -class CleanTick(clean): - description = 'cleans all generated and built files' - - def run(self): - seconds_until_clean = 5 - - print("Cleaning source directories in %d seconds..." % - seconds_until_clean) - - time.sleep(seconds_until_clean) - - clean.run(self) - - shutil.rmtree(build_dir, ignore_errors=True) - - patterns = [ - '**/*.so', - '**/*_wrap.cpp', - '**/__pycache__/*.pyc', - '**/__pycache__', - ] - - for paths in (pathlib.Path(os.curdir).glob(p) for p in patterns): - for path in paths: - print("Deleting {}".format(path)) - - if path.is_dir(): - path.rmdir() - else: - path.unlink() - - -setup(name="tick", - version='0.7.0.1', - author="Emmanuel Bacry, " - "Stephane Gaiffas, " - "Martin Bompaire, " - "Søren V. Poulsen, " - "Maryan Morel, " - "Simon Bussy, " - "Philip Deegan", - author_email='martin.bompaire@polytechnique.edu, ' - 'philip.deegan@polytechnique.edu', - url="https://x-datainitiative.github.io/tick/", - description="Module for statistical learning, with a particular emphasis " - "on time-dependent modelling", - ext_modules=tick_modules, - install_requires=['numpy', - 'scipy', - 'numpydoc', - 'matplotlib', - 'sphinx', - 'pandas', - 'dill', - 'scikit-learn'], - packages=find_packages(), - cmdclass={'build': TickBuild, - 'install': TickInstall, - 'makecpptest': BuildCPPTests, - 'runcpptest': RunCPPTests, - 'cpptest': BuildRunCPPTests, - 'cpplint': RunCPPLint, - 'pytest': RunPyTests, - 'pylint': RunPyLint, - 'test': RunTestSuites, - 'clean': CleanTick}, - classifiers=['Development Status :: 3 - Alpha', - 'Intended Audience :: Science/Research', - 'Intended Audience :: Developers', - 'Programming Language :: C++', - 'Programming Language :: Python', - 'Topic :: Software Development', - 'Topic :: Scientific/Engineering', - 'Operating System :: POSIX', - 'Operating System :: Unix', - 'Operating System :: MacOS', - 'Programming Language :: Python :: 3.6', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'License :: OSI Approved :: BSD License'], - ) +from setuptools import find_packages, setup + +setup( + name="tick", + version='0.7.0.2', + author="Emmanuel Bacry, " + "Stephane Gaiffas, " + "Martin Bompaire, " + "Søren V. Poulsen, " + "Maryan Morel, " + "Simon Bussy, " + "Philip Deegan", + author_email='martin.bompaire@polytechnique.edu, ' + 'philip.deegan@polytechnique.edu', + url="https://x-datainitiative.github.io/tick/", + description="Module for statistical learning, with a particular emphasis " + "on time-dependent modelling", + # ext_modules=tick_modules, + install_requires=['numpy', + 'scipy', + 'numpydoc', + 'matplotlib', + 'sphinx', + 'pandas', + 'dill', + 'scikit-learn'], + # packages=find_packages(exclude=["lib", "dist"]), + cmdclass={}, + classifiers=['Development Status :: 3 - Alpha', + 'Intended Audience :: Science/Research', + 'Intended Audience :: Developers', + 'Programming Language :: C++', + 'Programming Language :: Python', + 'Topic :: Software Development', + 'Topic :: Scientific/Engineering', + 'Operating System :: POSIX', + 'Operating System :: Unix', + 'Operating System :: MacOS', + 'Programming Language :: Python :: 3.7', + 'Programming Language :: Python :: 3.8', + 'License :: OSI Approved :: BSD License'], + include_package_data=True, + packages=find_packages(exclude=["lib/","tests/"]), +) diff --git a/sh/configure_env.sh b/sh/configure_env.sh deleted file mode 100755 index 44e8a2f2a..000000000 --- a/sh/configure_env.sh +++ /dev/null @@ -1,337 +0,0 @@ - # -# Author: Philip Deegan -# Email : philip.deegan@polytechnique.edu -# Date : 21 - September - 2017 -# -# This script is to be included to setup variables to build tick -# It is done so to be cross platform and heterogeneous -# -# Variables -# $PY = "python" binary -# $PCONF = "python-config" binary -# $SWIG = "swig" binary -# $LDARGS=Linking arguments -# $LIB_POSTFIX= python library format -# $LIB_POSTEXT= system library file extention -# $PROFILES= array of mkn profiles to build -# -###################################################################### - -set -e - -echo "Entering configure_env.sh" - -[ ! -d "$ROOT/lib/third_party/cereal/include" ] && \ - git submodule update --init - -# Finding the system python binary -# To override, export PY variable with full path to python binary -[ -z "$PY" ] && which python3 &> /dev/null && PY="python3" -[ -z "$PY" ] && which python &> /dev/null && PY="python" -[ -z "$PY" ] && echo "python or python3 not on path, exiting with error" && exit 1 - -PYVER=$($PY -c "import sys; print(sys.version_info[0])") -if (( $PYVER < 3)); then - echo "Python version 3 is required, if installed export PY variable - e.g. export PY=/path/to/python3" - echo "ERROR: 1" - exit 1 -fi - -PYVER_MIN=$($PY -c "import sys; print(sys.version_info[1])") - -# We get the filename expected for C++ shared libraries -LIB_POSTFIX=$($PY -c "import distutils; from distutils import sysconfig; print(sysconfig.get_config_var('EXT_SUFFIX'))") -[ -z "$LIB_POSTFIX" ] && echo "LIB_POSTFIX undefined: ERROR" && exit 1 -unameOut="$(uname -s)" - -IS_WINDOWS=0 -if [[ "$unameOut" == "CYGWIN"* ]] || [[ "$unameOut" == "MINGW"* ]] || [[ "$unameOut" == "MSYS_NT"* ]]; then - IS_WINDOWS=1 -fi - -function relpath(){ - echo $($PY -c "import os.path; print(os.path.relpath('$1', '$2'))") -} -function linkread(){ -if (( $IS_WINDOWS )); then - echo $(readlink -f $1) -else - echo $($PY -c "import os; print(os.path.realpath(\"$1\"))") -fi -} - -################# -if (( $IS_WINDOWS )); then - function pathreal(){ - P=$1 - which cygpath.exe 2>&1 > /dev/null - CYGPATH=$? - (( $CYGPATH == 0 )) && P=$(cygpath -w $P) - echo "$P" | sed -e "s/\\\/\\\\\\\/g" - } -else - function pathreal(){ - echo $1 - } -fi -################# - -PY_LIBDIR=$(python3 -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))") - -# if windows - python-config does not exist -if (( $IS_WINDOWS )); then - echo "Windows detected" - - CL_PATH=0 - GCC_PATH=0 - which cl.exe &> /dev/null && CL_PATH=$(which cl.exe) - which gcc.exe &> /dev/null && GCC_PATH=$(which gcc.exe) - if [[ $CL_PATH == 0 ]] && [[ $GCC_PATH == 0 ]] ; then - echo "Neither cl.exe or gcc.exe on path: Error" - exit 1 - fi - - if [ -n "$CL_PATH" ]; then - # Msys and cygwin can have their own "link.exe" - # which interferes with MSVC link.exe - PATH="$(dirname $CL_PATH):$PATH" - fi - - PYDIR=$(dirname "$(which $PY)") - echo PYDIR $PYDIR - PYINC="$PYDIR/include" - [ ! -d "$PYINC" ] && \ - echo "$PYNUMINC does not exist - python in inconsistent state - reinstall" - - PYNUMINC="$PYDIR/Lib/site-packages/numpy/core/include" - [ ! -d "$PYNUMINC" ] && \ - echo "$PYNUMINC does not exist - install numpy" - - # Deducing include paths for python and numpy - [ -z "$PINC" ] && PINC="$PYINC" - [ -z "$PNIC" ] && PNIC="$PYNUMINC"; - - PINC_DRIVE=$(echo "$PINC" | cut -d'/' -f2) - PINC="${PINC_DRIVE}:/${PINC:3}" - PNIC="${PINC_DRIVE}:/${PNIC:3}" - - PY_INCS="${PINC};${PNIC}" - - B_PATH="$PYDIR/libs" - [ -z "$LIB_POSTEXT" ] && LIB_POSTEXT="lib" - -else - # Finding the installed version of "python-config" to later find - # include paths and linker flags - # To override export PCONF variable with full path to python-config binary - [ -z "$PCONF" ] && which python3-config &> /dev/null && PCONF="python3-config" - [ -z "$PCONF" ] && which python3.${PYVER_MIN}-config &> /dev/null && PCONF="python3.${PYVER_MIN}-config" - [ -z "$PCONF" ] && which python-config &> /dev/null && PCONF="python-config" \ - && echo "WARNING: python-config may be the incorrect version!" - [ -z "$PCONF" ] && echo "python-config or python3-config not found on PATH, exiting with error" && exit 1; - - # Deducing include paths for python and numpy - [ -z "$PINC" ] && for i in $($PCONF --includes | tr ' ' '\n' | sort -u); do PINC="${PINC}${i:2}:"; done - [ -z "$PNIC" ] && PNIC=$($PY -c "import numpy as np; print(np.get_include())"); - - PY_INCS="${PINC}:${PNIC}" - - LDARGS="$($PCONF --ldflags)" - (($PYVER >= 3)) && (($PYVER_MIN > 8)) && LDARGS="$($PCONF --ldflags --embed)" - B_PATH=".:${PY_LIBDIR}" - [ -z "$LIB_POSTEXT" ] && LIB_POSTEXT="${LIB_POSTFIX##*.}" -fi -LIB_POSTFIX="${LIB_POSTFIX%.*}" - -# Finding the installed version of "swig" to later find -# To override export SWIG variable with full path to swig binary -[ -z "$SWIG" ] && which swig &> /dev/null && SWIG="swig" -[ -z "$SWIG" ] && echo "swig not found on PATH, exiting with error" && exit 1; -[ -z "$SWIG_C_FLAGS" ] && SWIG_C_FLAGS="-DDEBUG_COSTLY_THROW" - -# Here: "sed" is used to remove unnecessary parts of the link flags -# given to us by python-config -LDARGS=$(echo "$LDARGS" | sed -e "s/ -lintl//g") -LDARGS=$(echo "$LDARGS" | sed -e "s/ -ldl//g") -LDARGS=$(echo "$LDARGS" | sed -e "s/ -framework//g") -LDARGS=$(echo "$LDARGS" | sed -e "s/ -Wl,-stack_size,1000000//g") -LDARGS=$(echo "$LDARGS" | sed -e "s/ CoreFoundation//g") - -[ ! -z "$LDFLAGS" ] && LDARGS="${LDARGS} ${LDFLAGS}" - -# IFS = Internal Field Separator - allows looping over lines with spaces -IFS=$'\n' - -ANACONDA=0 -LIBLDARGS="" -# Add library path if using anaconda python -PYVER=$($PY --version 2>&1 ) -if [[ "$PYVER" == *"Anaconda"* ]]; then - ANACONDA=1 - ANACONDA_LIB_PATH=$(linkread $(dirname $(which $PY))/../lib) - if [[ "$unameOut" == "Darwin"* ]]; then - ## Unknown reason why these are not required for Anaconda - - ## Not just that but neither is the -lpython - ## The line below is left intentionally commented as a reference of what should be linked - LDARGS="" #-L${ANACONDA_LIB_PATH} -Wl,-rpath,${ANACONDA_LIB_PATH} $LDARGS -lmkl_rt -lpthread" - LIBLDARGS="-dynamiclib -undefined dynamic_lookup -Wl,-headerpad_max_install_names" - fi -fi - -PROFILES=( - array - base - base_model - random - linear_model - prox - hawkes/simulation - hawkes/model - hawkes/inference - preprocessing - robust - survival - solver - array_test -) -function hash_index() { - case $1 in - 'array') echo 0;; - 'base') echo 1;; - 'base_model') echo 2;; - 'random') echo 3;; - 'linear_model') echo 4;; - 'prox') echo 5;; - 'hawkes/simulation') echo 6;; - 'hawkes/model') echo 7;; - 'hawkes/inference') echo 8;; - 'preprocessing') echo 9;; - 'robust') echo 10;; - 'survival') echo 11;; - 'solver') echo 12;; - 'array_test') echo 13;; - esac -} -LIBRARIES=( - "tick/array/build/_array$LIB_POSTFIX" - "tick/base/build/_base$LIB_POSTFIX" - "tick/base_model/build/_base_model$LIB_POSTFIX" - "tick/random/build/_crandom$LIB_POSTFIX" - "tick/linear_model/build/_linear_model$LIB_POSTFIX" - "tick/prox/build/_prox$LIB_POSTFIX" - "tick/hawkes/simulation/build/_hawkes_simulation$LIB_POSTFIX" - "tick/hawkes/model/build/_hawkes_model$LIB_POSTFIX" - "tick/hawkes/inference/build/_hawkes_inference$LIB_POSTFIX" - "tick/preprocessing/build/_preprocessing$LIB_POSTFIX" - "tick/robust/build/_robust$LIB_POSTFIX" - "tick/survival/build/_survival$LIB_POSTFIX" - "tick/solver/build/_solver$LIB_POSTFIX" - "tick/array_test/build/array_test${LIB_POSTFIX}" -) - -LIB_LD_PER_LIB=() -ITER=0 -for PROFILE in "${PROFILES[@]}"; do - LIBS= - TREE=($(mkn tree -p $PROFILE -C lib)) - TREE_LEN=${#TREE[@]} - for idx in $(seq $TREE_LEN -1 0); do - LINE="${TREE[idx]}" - set +e - echo "$LINE" | grep "+" | grep "tick" 2>&1 > /dev/null - WIN=$? - set -e - if [[ "$WIN" == "0" ]]; then - INDEX=$(echo "$LINE" | cut -d '[' -f2 | cut -d ']' -f1) - EX=$(hash_index $INDEX) - ADD_LIB=${LIBRARIES[$EX]} - if [ -n "$ADD_LIB" ]; then - if [ -n "$LIBS" ]; then - set +e - echo "$LIBS" | grep "$ADD_LIB" 2>&1 > /dev/null - WIN=$? - set -e - [[ "$WIN" == "0" ]] && continue - fi - - if [[ "$unameOut" == "Darwin"* ]]; then - LIBS="$LIBS $(linkread ${ADD_LIB}.${LIB_POSTEXT})" - REL=$(dirname ${LIBRARIES[$ITER]}) - RPATH=$(dirname $ADD_LIB) - if [ "$REL" != "$PATH" ]; then - LIBS="$LIBS -Wl,-rpath,@loader_path/$(relpath $RPATH $REL)" - fi - else - LIBS="$LIBS $(pathreal $(linkread ${ADD_LIB}.${LIB_POSTEXT}))" - fi - fi - fi - done - if [[ "$unameOut" == "Darwin"* ]]; then - FIL=$(basename ${LIBRARIES[$ITER]}) - CLANG_LARGS+=" -Wl,-install_name,@rpath/${FIL}.${LIB_POSTEXT}" - fi - LIB_LD_PER_LIB+=("$LIBS") - ITER=$(($ITER + 1)) -done - - -## -# The mkn -x option overrides the default settings file -# to allow to build with differernt compilers/configurations -MKN_X="${MKN_X_FILE}" -[ -n "${MKN_X_FILE}" ] && MKN_X_FILE=(-x $MKN_X) - -## -# We allow for compiler specific linking arguments -THIS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -pushd $THIS_DIR/.. 2>&1 > /dev/null -COMMAND=$(mkn compile -Rp array ${MKN_X_FILE[@]} -C lib | head -1 ) -if [[ "$COMMAND" == *"icpc "* ]]; then - LDARGS+="$(echo " -Wl,-rpath,${ROOT}")" -fi -popd 2>&1 > /dev/null -# -## - -## -# MKN_P_ARRAY exists to allow platfrom -# specific properties to be passed to mkn if required -MKN_P_ARRAY=(lib_name=$LIB_POSTFIX) -MKN_P="" -for PROP in "${MKN_P_ARRAY[@]}"; do - MKN_P+=${PROP}, -done -MKN_P_SIZE=${#MKN_P} -MKN_P_SIZE=$((MKN_P_SIZE - 1)) -X_MKN_P="${MKN_P:0:${MKN_P_SIZE}}" -MKN_P=($X_MKN_P) - -# The argument passed to "mkn -P" is "MKN_P" -# such that all entries in the MKN_P_ARRAY -# become CSV values in MKN_P -# Any commas (,) in array entries must -# be escaped with a single backslash (\) -## - -V_MKN_WITH="$MKN_WITH" -MKN_WITH_SIZE=${#V_MKN_WITH} -(( $MKN_WITH_SIZE > 0 )) && MKN_WITH=(-w $V_MKN_WITH) - -## -# if a file included from source ends with a non-zero exitting command -# the "set -e" can cause the script to exit - -MKN_O=${MKN_O:-9} -MKN_G=${MKN_G:-0} -MKN=${MKN:-mkn} - -export MKN_LIB_LINK_LIB=1 -export TICK_CONFIGURED=1 - -echo "Finished configure_env.sh for python (${PYVER}) with the following args" -echo "LDARGS = ${LDARGS}" -echo "" -## - - diff --git a/sh/full_clean.sh b/sh/full_clean.sh index f41b7da1d..09b5e88a5 100755 --- a/sh/full_clean.sh +++ b/sh/full_clean.sh @@ -5,6 +5,7 @@ CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" ## Using the python executable defined in env. variable TICK_PYTHON otherwise fall back to "python" PYTHON_EXEC=${TICK_PYTHON:=python3} +find lib/swig/ -name "*.cpp" | xargs rm rm -rf $CWD/../lib/bin ${PYTHON_EXEC} $CWD/../setup.py clean diff --git a/sh/gtest.sh b/sh/gtest.sh deleted file mode 100755 index 0033ce007..000000000 --- a/sh/gtest.sh +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env bash -# -# Author: Philip Deegan -# Email : philip.deegan@polytechnique.edu -# Date : 26 - September - 2017 -# -# This script builds and launches google test files for tick -# -# Requires the mkn build tool -# -# Input arguments are optional but if used are to be the -# test files to be compiled and run, otherwise all files -# with the syntax "*gtest.cpp" are used -# -# Tests are expected to finish with the following code -# -# #ifdef ADD_MAIN -# int main(int argc, char** argv) { -# ::testing::InitGoogleTest(&argc, argv); -# ::testing::FLAGS_gtest_death_test_style = "fast"; -# return RUN_ALL_TESTS(); -# } -# #endif // ADD_MAIN -# -# This is used to inject main functions for testing/execution -# -###################################################################### - -CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -FILES=() -array=( "$@" ) -arraylength=${#array[@]} -for (( i=1; i<${arraylength}+1; i++ )); -do - FILES+=("${array[$i-1]}") -done - -pushd $CWD/.. 2>&1 > /dev/null -ROOT=$PWD -popd 2>&1 > /dev/null - -source $ROOT/sh/configure_env.sh - -CARGS="" -if (( ! $IS_WINDOWS )); then - CARGS=" -fPIC -std=c++11 " -fi - -pushd $ROOT/lib 2>&1 > /dev/null - [ "$arraylength" == "0" ] && FILES=($(find cpp-test -name "*gtest.cpp")) - - [ ! -z "$CXXFLAGS" ] && CARGS="$CXXFLAGS $CARGS" - [ ! -z "$LDFLAGS" ] && LDARGS="${LDARGS} ${LDFLAGS}" - - mkn build -p gtest -tSa "$CARGS -DGTEST_CREATE_SHARED_LIBRARY" \ - -d google.test,+ ${MKN_X_FILE[@]} "${MKN_WITH[@]}" - - LIB="" - if [[ "$unameOut" == "Darwin"* ]]; then - for P in "${PROFILES[@]}"; do - LIB="${LIB} -Wl,-rpath,@loader_path/../../$(dirname ${LIBRARIES[$(hash_index $P)]})" - done - fi - - RUN="run" - [[ $DEBUG == 1 ]] && RUN="dbg" - set -x - for FILE in "${FILES[@]}"; do - - echo FILE $FILE - - mkn clean build -p gtest -a "${CARGS} -DGTEST_LINKED_AS_SHARED_LIBRARY" -g 9 -O 0 \ - -tl "${LDARGS} ${LIB}" -b "$PY_INCS" \ - -M "${FILE}" -P "${MKN_P}" "${MKN_WITH[@]}" \ - -B $B_PATH ${RUN} ${MKN_X_FILE[@]} - - done - -popd 2>&1 > /dev/null diff --git a/sh/gtest_static.sh b/sh/gtest_static.sh deleted file mode 100755 index 01d1782fe..000000000 --- a/sh/gtest_static.sh +++ /dev/null @@ -1,76 +0,0 @@ -#!/usr/bin/env bash -# -# Author: Philip Deegan -# Email : philip.deegan@polytechnique.edu -# Date : 26 - September - 2017 -# -# This script builds and launches google test files for tick -# -# Requires the mkn build tool -# -# Input arguments are optional but if used are to be the -# test files to be compiled and run, otherwise all files -# with the syntax "*gtest.cpp" are used -# -# Tests are expected to finish with the following code -# -# #ifdef ADD_MAIN -# int main(int argc, char** argv) { -# ::testing::InitGoogleTest(&argc, argv); -# ::testing::FLAGS_gtest_death_test_style = "fast"; -# return RUN_ALL_TESTS(); -# } -# #endif // ADD_MAIN -# -# This is used to inject main functions for testing/execution -# -###################################################################### - -CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -FILES=() -array=( "$@" ) -arraylength=${#array[@]} -for (( i=1; i<${arraylength}+1; i++ )); -do - FILES+=("${array[$i-1]}") -done - -cd $CWD/.. -ROOT=$PWD -source $ROOT/sh/configure_env.sh - -cd $ROOT/lib -[ "$arraylength" == "0" ] && FILES=($(find cpp-test -name "*gtest.cpp")) - -[ ! -z "$CXXFLAGS" ] && CARGS="$CXXFLAGS $CARGS" -[ ! -z "$LDFLAGS" ] && LDARGS="${LDARGS} ${LDFLAGS}" - -mkn clean build -p gtest -tKa "${CXXFLAGS} -DGTEST_CREATE_SHARED_LIBRARY" \ - -d google.test,+ ${MKN_X_FILE[@]} - -mkdir -p $ROOT/gtest - -for FILE in "${FILES[@]}"; do - - echo FILE $FILE - rm -rf bin/gtest* - - mkn compile -p gtest -a "${CARGS} -DGTEST_LINKED_AS_SHARED_LIBRARY" \ - -tb "$PY_INCS" \ - -M "${FILE}" -P "${MKN_P[@]}" \ - ${MKN_X_FILE[@]} -B "$B_PATH" ${MKN_WITH[@]} - - mv bin/gtest bin/gtest_nodep - - for P in "${PROFILES[@]}"; do - cp bin/$P/obj/* bin/gtest_nodep/obj - done - cp bin/gtest_nodep/tmp/* bin/gtest_nodep/obj - - mkn link -p gtest_nodep \ - -tl "${LDARGS}" \ - -M "${FILE}" -P "${MKN_P[@]}" \ - -KB $B_PATH ${MKN_X_FILE[@]} - mv bin/gtest_nodep/tick $ROOT/gtest/$(basename $FILE) -done diff --git a/sh/mkn.sh b/sh/mkn.sh deleted file mode 100755 index 1a4dbaca5..000000000 --- a/sh/mkn.sh +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env bash -# -# Author: Philip Deegan -# Email : philip.deegan@polytechnique.edu -# Date : 21 - September - 2017 -# -# This script compiles tick C++ libs in parallel -# with optimally detected number of threads -# -# Requires the mkn build tool -# -# Input arguments are optional but if used are to be the -# modules to be compile, otherwise all modules are -# compiled - use command "mkn profiles" to view available -# modules/profiles -# -# ccache is recommended -# -###################################################################### - -set -e - -CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -pushd $CWD/.. 2>&1 > /dev/null -ROOT=$PWD -popd 2>&1 > /dev/null - -source $CWD/configure_env.sh - -COMPILE=1 -LINK=1 -RELEASE=${RELEASE:-0} - -CLI_ARGS=( "$@" ) -CLI_ARGS_LEN=${#CLI_ARGS[@]} -if (( $CLI_ARGS_LEN > 0 )); then - NPROFILES=() - for (( i=1; i<${CLI_ARGS_LEN}+1; i++ )); do - C=${CLI_ARGS[$i-1]} - case $C in - -c=*|--compile=*) - COMPILE="${C#*=}" - shift # past argument=value - ;; - -l=*|--link=*) - LINK="${C#*=}" - shift # past argument=value - ;; - *) - NPROFILES+=("$C") - ;; - esac - done - NPROFILES_LEN=${#NPROFILES[@]} - (( $NPROFILES_LEN > 0 )) && PROFILES=("${NPROFILES[@]}") -fi - -TICK_INDICES=$($PY $ROOT/tools/python/numpy/check_sparse_indices.py) -MKN_C_FLAGS=" $TICK_INDICES" - -[ -n "$CXXFLAGS" ] && MKN_C_FLAGS+=" ${CXXFLAGS} " -[ "$DEBUG" == "1" ] && MKN_C_FLAGS+=" -DDEBUG_COSTLY_THROW" - -[ -n "$SWIG" ] && [ "$SWIG" != "0" ] && source $ROOT/sh/swig.sh - -cd $ROOT - -MKN_PROFILES=$(IFS=,; echo "${PROFILES[*]}") -(( $COMPILE == 1 )) && \ - MKN_BETA=1 $MKN compile -Dt ${MKN_COMPILE_THREADS} -a "${MKN_C_FLAGS[@]}" -b "$PY_INCS" \ - ${MKN_X_FILE[@]} -p ${MKN_PROFILES} -C lib "${MKN_WITH[@]}" -g $MKN_G -O $MKN_O - -if (( $IS_WINDOWS )); then - export MKN_LIB_EXT=".pyd" -else - (( $RELEASE )) && export MKN_LIB_PRE="" -fi - -(( $LINK == 1 )) && \ - for P in "${PROFILES[@]}"; do - EX=$(hash_index $P) - LIBLD=${LIB_LD_PER_LIB[$EX]} - - $MKN link -Sp $P -l "${LIBLDARGS} ${LDARGS} $LIBLD" \ - -P "${MKN_P}" -C lib "${MKN_WITH[@]}" \ - ${MKN_X_FILE[@]} -B "$B_PATH" -g $MKN_G -O $MKN_O - - if (( $RELEASE == 0 )); then - PUSHD=${LIBRARIES[$EX]} - pushd $ROOT/$(dirname ${PUSHD}) 2>&1 > /dev/null - if (( $IS_WINDOWS == 0 )); then - # regular lib* kept for gtest linking, no gtest during release - for f in $(find . -maxdepth 1 -type f ! -name "*.py" ! -name "__*" ); do - SUB=${f:2:3} - [ "$SUB" == "lib" ] && cp "$f" "${f:5}" - done - fi - popd 2>&1 > /dev/null - fi - done - -echo "Finished - Success" diff --git a/sh/swig.sh b/sh/swig.sh index f9c593a23..494ffb585 100755 --- a/sh/swig.sh +++ b/sh/swig.sh @@ -58,7 +58,7 @@ for P in "${PROFILES[@]}"; do [ -f "${SWIG_BASE}/$P/${B}_wrap.cpp" ] && \ rm "${SWIG_BASE}/$P/${B}_wrap.cpp" [ ! -f "${SWIG_BASE}/$P/${B}_wrap.cpp" ] && \ - $SWIG -python -py3 -c++ ${INCS[@]} \ + $SWIG -python -c++ ${INCS[@]} \ -outdir $DIR/build "$SWIG_C_FLAGS" \ -o ${SWIG_BASE}/$P/${B}_wrap.cpp $IF else @@ -70,7 +70,7 @@ for P in "${PROFILES[@]}"; do [ -f "${SWIG_BASE}/$P/${B}_wrap.cpp" ] && \ rm "${SWIG_BASE}/$P/${B}_wrap.cpp" [ ! -f "${SWIG_BASE}/$P/${B}_wrap.cpp" ] && \ - $SWIG -python -py3 -c++ ${INCS[@]} \ + $SWIG -python -c++ ${INCS[@]} \ -outdir $DIR/build "$SWIG_C_FLAGS" \ -o ${SWIG_BASE}/$P/${B}_wrap.cpp $IF done @@ -80,7 +80,7 @@ for P in "${PROFILES[@]}"; do [ -f "${SWIG_BASE}/$P/${P1}_wrap.cpp" ] && \ rm "${SWIG_BASE}/$P/${P1}_wrap.cpp" [ ! -f "${SWIG_BASE}/$P/${P}_wrap.cpp" ] && \ - $SWIG -python -py3 -c++ ${INCS[@]} \ + $SWIG -python -c++ ${INCS[@]} \ -outdir $DIR/build "$SWIG_C_FLAGS" -o ${SWIG_BASE}/$P/${P1}_wrap.cpp \ "${DIR}/swig/${P1}.i" fi diff --git a/tick/__init__.py b/tick/__init__.py index f76722cbd..e69de29bb 100644 --- a/tick/__init__.py +++ b/tick/__init__.py @@ -1,6 +0,0 @@ -# -*- coding: utf-8 -*- -"""tick module -""" -# License: BSD 3 clause - -import tick.base diff --git a/tick/array/__init__.py b/tick/array/__init__.py index aaf6997db..e69de29bb 100644 --- a/tick/array/__init__.py +++ b/tick/array/__init__.py @@ -1,3 +0,0 @@ -# License: BSD 3 clause - -from .build import array diff --git a/tick/array/build/__init__.py b/tick/array/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/array/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/array/serialize.py b/tick/array/serialize.py index 25358a958..489571661 100644 --- a/tick/array/serialize.py +++ b/tick/array/serialize.py @@ -5,7 +5,7 @@ import numpy as np import scipy -from tick.array.build.array import ( +from tick.tick_cpp import ( tick_float_array_to_file, tick_float_array2d_to_file, tick_float_sparse2d_to_file, @@ -64,7 +64,7 @@ def serialize_array(array, filepath): raise ValueError('Only 1d and 2d arrays can be serrialized') else: if len(array.shape) == 2: - if isinstance(array, scipy.sparse.csc.csc_matrix): + if isinstance(array, scipy.sparse.csc_matrix): serializer = tick_float_colmaj_sparse2d_to_file else: serializer = tick_float_sparse2d_to_file @@ -83,7 +83,7 @@ def serialize_array(array, filepath): raise ValueError('Only 1d and 2d arrays can be serrialized') else: if len(array.shape) == 2: - if isinstance(array, scipy.sparse.csc.csc_matrix): + if isinstance(array, scipy.sparse.csc_matrix): serializer = tick_double_colmaj_sparse2d_to_file else: serializer = tick_double_sparse2d_to_file diff --git a/tick/array_test/tests/array_memory_test.py b/tick/array_test/tests/array_memory_test.py index 4e72b83d8..43320afc2 100644 --- a/tick/array_test/tests/array_memory_test.py +++ b/tick/array_test/tests/array_memory_test.py @@ -8,9 +8,9 @@ import scipy from scipy.sparse import csr_matrix -from tick.array.build.array import tick_double_sparse2d_from_file -from tick.array.build.array import tick_double_sparse2d_to_file -from tick.array_test.build import array_test as test +from tick.tick_cpp import tick_double_sparse2d_from_file +from tick.tick_cpp import tick_double_sparse2d_to_file +from tick import tick_cpp as test class Test(unittest.TestCase): diff --git a/tick/array_test/tests/array_methods_test.py b/tick/array_test/tests/array_methods_test.py index 9ccf1170a..6c28500e5 100644 --- a/tick/array_test/tests/array_methods_test.py +++ b/tick/array_test/tests/array_methods_test.py @@ -5,7 +5,8 @@ import unittest import numpy as np from numpy.linalg import norm -from tick.array_test.build import array_test as test + +from tick import tick_cpp as test from scipy.sparse import csr_matrix import itertools diff --git a/tick/array_test/tests/array_performance_test.py b/tick/array_test/tests/array_performance_test.py index 2985ba707..420ee7949 100644 --- a/tick/array_test/tests/array_performance_test.py +++ b/tick/array_test/tests/array_performance_test.py @@ -5,7 +5,7 @@ import unittest import numpy as np -from tick.array_test.build.array_test import test_sum_double_pointer, \ +from tick.tick_cpp import test_sum_double_pointer, \ test_sum_ArrayDouble, test_sum_SArray_shared_ptr, test_sum_VArray_shared_ptr """ ref_size = 10000 diff --git a/tick/array_test/tests/array_typemap_test.py b/tick/array_test/tests/array_typemap_test.py index edbd08542..4077f2fc4 100644 --- a/tick/array_test/tests/array_typemap_test.py +++ b/tick/array_test/tests/array_typemap_test.py @@ -5,7 +5,7 @@ import unittest import numpy as np from scipy.sparse import csr_matrix -from tick.array_test.build import array_test as test +from tick import tick_cpp as test class Test(unittest.TestCase): diff --git a/tick/base/__init__.py b/tick/base/__init__.py index 85f530886..23003b6d0 100644 --- a/tick/base/__init__.py +++ b/tick/base/__init__.py @@ -20,11 +20,10 @@ def _set_mpl_backend(): _set_mpl_backend() -from tick.array import * -from .timefunc import TimeFunction from .base import Base -from ..random import * +from .timefunc import TimeFunction from .decorators import actual_kwargs from .threadpool import ThreadPool +from ..random import * __all__ = ["Base", "TimeFunction", "actual_kwargs"] diff --git a/tick/base/base.py b/tick/base/base.py index dc9d755fa..5892a23fe 100644 --- a/tick/base/base.py +++ b/tick/base/base.py @@ -1,6 +1,7 @@ # License: BSD 3 clause # import warnings + import os import inspect from datetime import datetime diff --git a/tick/base/build/__init__.py b/tick/base/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/base/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/base/tests/base_test.py b/tick/base/tests/base_test.py index 7338259ef..9cdac5615 100644 --- a/tick/base/tests/base_test.py +++ b/tick/base/tests/base_test.py @@ -5,7 +5,7 @@ import unittest from tick.base import Base -from tick.base.build.base import A0 as _A0 +from tick.tick_cpp import A0 as _A0 # Architecture of the classes # Base @@ -473,7 +473,7 @@ def frop(x): self.a0.readonly_prop = x msg = "can't set attribute" - if sys.version_info[1] == 11: + if sys.version_info[1] >= 11: msg = "property 'readonly_prop' of 'A0' object has no setter" self.assertRaisesRegex(AttributeError, msg, frop, 45) diff --git a/tick/base/tests/exceptions_test.py b/tick/base/tests/exceptions_test.py index 9a12fce86..e11af352e 100644 --- a/tick/base/tests/exceptions_test.py +++ b/tick/base/tests/exceptions_test.py @@ -5,7 +5,7 @@ import platform import unittest -from tick.base.build.base import throw_out_of_range, \ +from tick.tick_cpp import throw_out_of_range, \ throw_system_error, throw_invalid_argument, throw_domain_error, \ throw_runtime_error, throw_string diff --git a/tick/base/tests/standard_normal_distribution_test.py b/tick/base/tests/standard_normal_distribution_test.py index a792d6892..a0458f04a 100644 --- a/tick/base/tests/standard_normal_distribution_test.py +++ b/tick/base/tests/standard_normal_distribution_test.py @@ -3,7 +3,7 @@ # -*- coding: utf8 -*- import unittest -from tick.base.build.base import standard_normal_cdf, \ +from tick.tick_cpp import standard_normal_cdf, \ standard_normal_inv_cdf from scipy.stats import norm diff --git a/tick/base/timefunc.py b/tick/base/timefunc.py index eb97588d8..4d2e0fd3c 100644 --- a/tick/base/timefunc.py +++ b/tick/base/timefunc.py @@ -1,6 +1,6 @@ # License: BSD 3 clause -from tick.base.build.base import TimeFunction as _TimeFunction +from tick.tick_cpp import TimeFunction as _TimeFunction import numpy as np from tick.base.base import Base diff --git a/tick/base_model/build/__init__.py b/tick/base_model/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/base_model/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/hawkes/inference/build/__init__.py b/tick/hawkes/inference/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/hawkes/inference/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/hawkes/inference/hawkes_adm4.py b/tick/hawkes/inference/hawkes_adm4.py index a26e30ab7..0438e3880 100644 --- a/tick/hawkes/inference/hawkes_adm4.py +++ b/tick/hawkes/inference/hawkes_adm4.py @@ -4,7 +4,7 @@ from tick.hawkes import ModelHawkesExpKernLogLik, SimuHawkesExpKernels from tick.hawkes.inference.base import LearnerHawkesNoParam -from tick.hawkes.inference.build.hawkes_inference import (HawkesADM4 as +from tick.tick_cpp import (HawkesADM4 as _HawkesADM4) from tick.prox import ProxNuclear from tick.prox.prox_l1 import ProxL1 diff --git a/tick/hawkes/inference/hawkes_basis_kernels.py b/tick/hawkes/inference/hawkes_basis_kernels.py index 9b280594f..7870edc90 100644 --- a/tick/hawkes/inference/hawkes_basis_kernels.py +++ b/tick/hawkes/inference/hawkes_basis_kernels.py @@ -3,7 +3,7 @@ import numpy as np from tick.hawkes.inference.base import LearnerHawkesNoParam -from tick.hawkes.inference.build.hawkes_inference import (HawkesBasisKernels as +from tick.tick_cpp import (HawkesBasisKernels as _HawkesBasisKernels) from tick.solver.base.utils import relative_distance diff --git a/tick/hawkes/inference/hawkes_conditional_law.py b/tick/hawkes/inference/hawkes_conditional_law.py index 5c22bf2c2..a125a6d4c 100644 --- a/tick/hawkes/inference/hawkes_conditional_law.py +++ b/tick/hawkes/inference/hawkes_conditional_law.py @@ -9,7 +9,7 @@ from scipy.linalg import solve from tick.base import Base, ThreadPool -from tick.hawkes.inference.build.hawkes_inference import (PointProcessCondLaw) +from tick.tick_cpp import (PointProcessCondLaw) # noinspection PyPep8Naming diff --git a/tick/hawkes/inference/hawkes_cumulant_matching.py b/tick/hawkes/inference/hawkes_cumulant_matching.py index c1b1e3afe..7c1fc28c1 100644 --- a/tick/hawkes/inference/hawkes_cumulant_matching.py +++ b/tick/hawkes/inference/hawkes_cumulant_matching.py @@ -6,10 +6,10 @@ from tick.base import Base from tick.hawkes.inference.base import LearnerHawkesNoParam -from tick.hawkes.inference.build.hawkes_inference import (HawkesCumulant as +from tick.tick_cpp import (HawkesCumulant as _HawkesCumulant) -from tick.hawkes.inference.build.hawkes_inference import (HawkesTheoreticalCumulant as +from tick.tick_cpp import (HawkesTheoreticalCumulant as _HawkesTheoreticalCumulant) diff --git a/tick/hawkes/inference/hawkes_em.py b/tick/hawkes/inference/hawkes_em.py index b0cee8ecf..5e5c217fe 100644 --- a/tick/hawkes/inference/hawkes_em.py +++ b/tick/hawkes/inference/hawkes_em.py @@ -4,7 +4,7 @@ import numpy as np from tick.hawkes.inference.base import LearnerHawkesNoParam -from tick.hawkes.inference.build.hawkes_inference import (HawkesEM as +from tick.tick_cpp import (HawkesEM as _HawkesEM) from tick.solver.base.utils import relative_distance diff --git a/tick/hawkes/inference/hawkes_sumgaussians.py b/tick/hawkes/inference/hawkes_sumgaussians.py index 6748c456b..b534cc221 100644 --- a/tick/hawkes/inference/hawkes_sumgaussians.py +++ b/tick/hawkes/inference/hawkes_sumgaussians.py @@ -5,8 +5,7 @@ from scipy.stats import norm from tick.hawkes.inference.base import LearnerHawkesNoParam -from tick.hawkes.inference.build.hawkes_inference import (HawkesSumGaussians as - _HawkesSumGaussians) +from tick.tick_cpp import (HawkesSumGaussians as _HawkesSumGaussians) from tick.solver.base.utils import relative_distance diff --git a/tick/hawkes/model/__init__.py b/tick/hawkes/model/__init__.py index 4d6c26fb8..039d23190 100644 --- a/tick/hawkes/model/__init__.py +++ b/tick/hawkes/model/__init__.py @@ -1,7 +1,7 @@ # License: BSD 3 clause import tick.base -import tick.base_model.build.base_model + from .model_hawkes_expkern_leastsq import ModelHawkesExpKernLeastSq from .model_hawkes_expkern_loglik import ModelHawkesExpKernLogLik diff --git a/tick/hawkes/model/base/model_hawkes.py b/tick/hawkes/model/base/model_hawkes.py index 6d9e72e9c..e47dc4ef2 100644 --- a/tick/hawkes/model/base/model_hawkes.py +++ b/tick/hawkes/model/base/model_hawkes.py @@ -5,7 +5,7 @@ from tick.base_model import N_CALLS_LOSS, PASS_OVER_DATA from tick.base_model.model_first_order import ModelFirstOrder -from tick.hawkes.model.build.hawkes_model import ( +from tick.tick_cpp import ( ModelHawkesSumExpKernLeastSq, ModelHawkesExpKernLeastSq, ModelHawkesSumExpKernLogLik, diff --git a/tick/hawkes/model/build/__init__.py b/tick/hawkes/model/build/__init__.py deleted file mode 100644 index a2a66bd75..000000000 --- a/tick/hawkes/model/build/__init__.py +++ /dev/null @@ -1,21 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand -# As observed here "base_model" are required - -from tick.base.opsys import add_to_path_if_windows - - -def required(): - import os, sys - root = os.path.dirname( - os.path.realpath(os.path.join(__file__, "../../.."))) - - if "tick.base_model.build" not in sys.modules: - p = os.path.realpath(os.path.join(root, "base_model/build")) - os.environ["PATH"] = p + os.pathsep + os.environ["PATH"] - - -add_to_path_if_windows(__file__, [required]) diff --git a/tick/hawkes/model/model_hawkes_expkern_leastsq.py b/tick/hawkes/model/model_hawkes_expkern_leastsq.py index cf841c8dd..e5b150fb4 100644 --- a/tick/hawkes/model/model_hawkes_expkern_leastsq.py +++ b/tick/hawkes/model/model_hawkes_expkern_leastsq.py @@ -3,7 +3,7 @@ import numpy as np from tick.base_model import LOSS_AND_GRAD -from tick.hawkes.model.build.hawkes_model import (ModelHawkesExpKernLeastSq as +from tick.tick_cpp import (ModelHawkesExpKernLeastSq as _ModelHawkesExpKernLeastSq) from .base import ModelHawkes diff --git a/tick/hawkes/model/model_hawkes_expkern_loglik.py b/tick/hawkes/model/model_hawkes_expkern_loglik.py index 164ed11ef..264704710 100644 --- a/tick/hawkes/model/model_hawkes_expkern_loglik.py +++ b/tick/hawkes/model/model_hawkes_expkern_loglik.py @@ -4,8 +4,7 @@ from tick.base_model import ModelSecondOrder, ModelSelfConcordant, \ LOSS_AND_GRAD -from tick.hawkes.model.build.hawkes_model import (ModelHawkesExpKernLogLik as - _ModelHawkesExpKernLogLik) +from tick.tick_cpp import (ModelHawkesExpKernLogLik as _ModelHawkesExpKernLogLik) from .base import ModelHawkes diff --git a/tick/hawkes/model/model_hawkes_sumexpkern_leastsq.py b/tick/hawkes/model/model_hawkes_sumexpkern_leastsq.py index 84da3f5b0..b5dbacbde 100644 --- a/tick/hawkes/model/model_hawkes_sumexpkern_leastsq.py +++ b/tick/hawkes/model/model_hawkes_sumexpkern_leastsq.py @@ -6,7 +6,7 @@ import numpy as np from tick.base_model import LOSS_AND_GRAD -from tick.hawkes.model.build.hawkes_model import ( +from tick.tick_cpp import ( ModelHawkesSumExpKernLeastSq as _ModelHawkesSumExpKernLeastSq) from .base import ModelHawkes diff --git a/tick/hawkes/model/model_hawkes_sumexpkern_loglik.py b/tick/hawkes/model/model_hawkes_sumexpkern_loglik.py index dd84b2454..5ba689441 100644 --- a/tick/hawkes/model/model_hawkes_sumexpkern_loglik.py +++ b/tick/hawkes/model/model_hawkes_sumexpkern_loglik.py @@ -4,7 +4,7 @@ from tick.base_model import ModelSecondOrder, ModelSelfConcordant, \ LOSS_AND_GRAD -from tick.hawkes.model.build.hawkes_model import ( +from tick.tick_cpp import ( ModelHawkesSumExpKernLogLik as _ModelHawkesSumExpKernLogLik) from .base import ModelHawkes diff --git a/tick/hawkes/simulation/build/__init__.py b/tick/hawkes/simulation/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/hawkes/simulation/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel.py index 3fc474b21..9110c740b 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel.py @@ -1,7 +1,7 @@ # License: BSD 3 clause from tick.base import Base -from tick.hawkes.simulation.build.hawkes_simulation import (HawkesKernel as +from tick.tick_cpp import (HawkesKernel as _HawkesKernel) diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_0.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_0.py index ce2d66a53..7b36a3e86 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_0.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_0.py @@ -1,6 +1,6 @@ # License: BSD 3 clause -from tick.hawkes.simulation.build.hawkes_simulation import (HawkesKernel0 as +from tick.tick_cpp import (HawkesKernel0 as _HawkesKernel0) from .hawkes_kernel import HawkesKernel diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_exp.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_exp.py index 0d89a717c..9ab0b5aa0 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_exp.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_exp.py @@ -1,6 +1,6 @@ # License: BSD 3 clause -from tick.hawkes.simulation.build.hawkes_simulation import (HawkesKernelExp as +from tick.tick_cpp import (HawkesKernelExp as _HawkesKernelExp) from .hawkes_kernel import HawkesKernel diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_power_law.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_power_law.py index c618fb64f..da4904566 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_power_law.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_power_law.py @@ -1,6 +1,6 @@ # License: BSD 3 clause -from tick.hawkes.simulation.build.hawkes_simulation import ( +from tick.tick_cpp import ( HawkesKernelPowerLaw as _HawkesKernelPowerLaw) from .hawkes_kernel import HawkesKernel diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_sum_exp.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_sum_exp.py index 215b5f3ca..825736576 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_sum_exp.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_sum_exp.py @@ -2,7 +2,7 @@ import numpy as np -from tick.hawkes.simulation.build.hawkes_simulation import ( +from tick.tick_cpp import ( HawkesKernelSumExp as _HawkesKernelSumExp) from . import HawkesKernelExp from .hawkes_kernel import HawkesKernel diff --git a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_time_func.py b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_time_func.py index 1482c0f35..97a041afe 100644 --- a/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_time_func.py +++ b/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_time_func.py @@ -1,6 +1,6 @@ # License: BSD 3 clause -from tick.hawkes.simulation.build.hawkes_simulation import ( +from tick.tick_cpp import ( HawkesKernelTimeFunc as _HawkesKernelTimeFunc) from .hawkes_kernel import HawkesKernel diff --git a/tick/hawkes/simulation/simu_hawkes.py b/tick/hawkes/simulation/simu_hawkes.py index 5a50e4ba2..53e9e7829 100644 --- a/tick/hawkes/simulation/simu_hawkes.py +++ b/tick/hawkes/simulation/simu_hawkes.py @@ -8,7 +8,7 @@ from tick.base import TimeFunction from tick.hawkes.simulation.base import SimuPointProcess -from tick.hawkes.simulation.build.hawkes_simulation import Hawkes as _Hawkes +from tick.tick_cpp import Hawkes as _Hawkes from .hawkes_kernels import HawkesKernel0 diff --git a/tick/hawkes/simulation/simu_inhomogeneous_poisson.py b/tick/hawkes/simulation/simu_inhomogeneous_poisson.py index 1dc4be6f0..f84e05b2c 100644 --- a/tick/hawkes/simulation/simu_inhomogeneous_poisson.py +++ b/tick/hawkes/simulation/simu_inhomogeneous_poisson.py @@ -4,7 +4,7 @@ from tick.base import TimeFunction from tick.hawkes.simulation.base import SimuPointProcess -from tick.hawkes.simulation.build.hawkes_simulation import ( +from tick.tick_cpp import ( InhomogeneousPoisson as _InhomogeneousPoisson) diff --git a/tick/hawkes/simulation/simu_poisson_process.py b/tick/hawkes/simulation/simu_poisson_process.py index b65d0d2ed..ec4d58e4d 100644 --- a/tick/hawkes/simulation/simu_poisson_process.py +++ b/tick/hawkes/simulation/simu_poisson_process.py @@ -3,7 +3,7 @@ import numpy as np from tick.hawkes.simulation.base import SimuPointProcess -from tick.hawkes.simulation.build.hawkes_simulation import Poisson as _Poisson +from tick.tick_cpp import Poisson as _Poisson class SimuPoissonProcess(SimuPointProcess): diff --git a/tick/linear_model/__init__.py b/tick/linear_model/__init__.py index dedb5fa9b..3ea015f33 100644 --- a/tick/linear_model/__init__.py +++ b/tick/linear_model/__init__.py @@ -1,7 +1,6 @@ # License: BSD 3 clause import tick.base -import tick.base_model.build.base_model from .linear_regression import LinearRegression from .logistic_regression import LogisticRegression diff --git a/tick/linear_model/build/__init__.py b/tick/linear_model/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/linear_model/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/linear_model/model_hinge.py b/tick/linear_model/model_hinge.py index a3e528b26..2b9e1d9c2 100644 --- a/tick/linear_model/model_hinge.py +++ b/tick/linear_model/model_hinge.py @@ -2,8 +2,8 @@ import numpy as np from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder -from .build.linear_model import ModelHingeDouble as _ModelHingeDouble -from .build.linear_model import ModelHingeFloat as _ModelHingeFloat +from tick.tick_cpp import ModelHingeDouble as _ModelHingeDouble +from tick.tick_cpp import ModelHingeFloat as _ModelHingeFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/linear_model/model_linreg.py b/tick/linear_model/model_linreg.py index a38fdd033..4bb9876d6 100644 --- a/tick/linear_model/model_linreg.py +++ b/tick/linear_model/model_linreg.py @@ -6,8 +6,8 @@ from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelLipschitz -from .build.linear_model import ModelLinRegDouble as _ModelLinRegDouble -from .build.linear_model import ModelLinRegFloat as _ModelLinRegFloat +from tick.tick_cpp import ModelLinRegDouble as _ModelLinRegDouble +from tick.tick_cpp import ModelLinRegFloat as _ModelLinRegFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/linear_model/model_logreg.py b/tick/linear_model/model_logreg.py index 3faba1981..8f3523134 100644 --- a/tick/linear_model/model_logreg.py +++ b/tick/linear_model/model_logreg.py @@ -5,8 +5,8 @@ from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelLipschitz -from .build.linear_model import ModelLogRegDouble as _ModelLogRegDouble -from .build.linear_model import ModelLogRegFloat as _ModelLogRegFloat +from tick.tick_cpp import ModelLogRegDouble as _ModelLogRegDouble +from tick.tick_cpp import ModelLogRegFloat as _ModelLogRegFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/linear_model/model_poisreg.py b/tick/linear_model/model_poisreg.py index 166821547..2542abae2 100644 --- a/tick/linear_model/model_poisreg.py +++ b/tick/linear_model/model_poisreg.py @@ -5,10 +5,10 @@ from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelSecondOrder, ModelSelfConcordant -from .build.linear_model import ModelPoisRegDouble as _ModelPoisRegDouble -from .build.linear_model import ModelPoisRegFloat as _ModelPoisRegFloat -from .build.linear_model import LinkType_identity as identity -from .build.linear_model import LinkType_exponential as exponential +from tick.tick_cpp import ModelPoisRegDouble as _ModelPoisRegDouble +from tick.tick_cpp import ModelPoisRegFloat as _ModelPoisRegFloat +from tick.tick_cpp import LinkType_identity as identity +from tick.tick_cpp import LinkType_exponential as exponential __author__ = 'Stephane Gaiffas' diff --git a/tick/linear_model/model_quadratic_hinge.py b/tick/linear_model/model_quadratic_hinge.py index 8c23b3179..824b7f7b2 100644 --- a/tick/linear_model/model_quadratic_hinge.py +++ b/tick/linear_model/model_quadratic_hinge.py @@ -4,8 +4,8 @@ from numpy.linalg import svd from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelLipschitz -from .build.linear_model import ModelQuadraticHingeDouble as _ModelModelQuadraticHingeDouble -from .build.linear_model import ModelQuadraticHingeFloat as _ModelModelQuadraticHingeFloat +from tick.tick_cpp import ModelQuadraticHingeDouble as _ModelModelQuadraticHingeDouble +from tick.tick_cpp import ModelQuadraticHingeFloat as _ModelModelQuadraticHingeFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/linear_model/model_smoothed_hinge.py b/tick/linear_model/model_smoothed_hinge.py index 22904561e..e8284f20e 100644 --- a/tick/linear_model/model_smoothed_hinge.py +++ b/tick/linear_model/model_smoothed_hinge.py @@ -4,8 +4,8 @@ from numpy.linalg import svd from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelLipschitz -from .build.linear_model import ModelSmoothedHingeDouble as _ModelSmoothedHingeDouble -from .build.linear_model import ModelSmoothedHingeFloat as _ModelSmoothedHingeFloat +from tick.tick_cpp import ModelSmoothedHingeDouble as _ModelSmoothedHingeDouble +from tick.tick_cpp import ModelSmoothedHingeFloat as _ModelSmoothedHingeFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/preprocessing/build/__init__.py b/tick/preprocessing/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/preprocessing/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/preprocessing/longitudinal_features_lagger.py b/tick/preprocessing/longitudinal_features_lagger.py index 549ab7461..fd335131b 100644 --- a/tick/preprocessing/longitudinal_features_lagger.py +++ b/tick/preprocessing/longitudinal_features_lagger.py @@ -3,7 +3,7 @@ import numpy as np import scipy.sparse as sps from tick.preprocessing.base import LongitudinalPreprocessor -from .build.preprocessing import LongitudinalFeaturesLagger\ +from tick.tick_cpp import LongitudinalFeaturesLagger\ as _LongitudinalFeaturesLagger from .utils import check_longitudinal_features_consistency,\ check_censoring_consistency diff --git a/tick/preprocessing/longitudinal_features_product.py b/tick/preprocessing/longitudinal_features_product.py index ced0321f5..174b6abd3 100644 --- a/tick/preprocessing/longitudinal_features_product.py +++ b/tick/preprocessing/longitudinal_features_product.py @@ -7,7 +7,7 @@ from scipy.special import comb from joblib import Parallel, delayed from tick.preprocessing.base import LongitudinalPreprocessor -from .build.preprocessing import SparseLongitudinalFeaturesProduct +from tick.tick_cpp import SparseLongitudinalFeaturesProduct from .utils import check_longitudinal_features_consistency diff --git a/tick/prox/build/__init__.py b/tick/prox/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/prox/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/prox/prox_binarsity.py b/tick/prox/prox_binarsity.py index ad7abd90d..6fcfcff92 100644 --- a/tick/prox/prox_binarsity.py +++ b/tick/prox/prox_binarsity.py @@ -1,8 +1,8 @@ # License: BSD 3 clause from .base import ProxWithGroups -from .build.prox import ProxBinarsityDouble as _ProxBinarsityDouble -from .build.prox import ProxBinarsityFloat as _ProxBinarsityFloat +from tick.tick_cpp import ProxBinarsityDouble as _ProxBinarsityDouble +from tick.tick_cpp import ProxBinarsityFloat as _ProxBinarsityFloat import numpy as np diff --git a/tick/prox/prox_elasticnet.py b/tick/prox/prox_elasticnet.py index e0ded074d..fe9d3c59c 100644 --- a/tick/prox/prox_elasticnet.py +++ b/tick/prox/prox_elasticnet.py @@ -4,8 +4,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxElasticNetDouble as _ProxElasticNetDouble -from .build.prox import ProxElasticNetFloat as _ProxElasticNetFloat +from tick.tick_cpp import ProxElasticNetDouble as _ProxElasticNetDouble +from tick.tick_cpp import ProxElasticNetFloat as _ProxElasticNetFloat __author__ = 'Maryan Morel' diff --git a/tick/prox/prox_equality.py b/tick/prox/prox_equality.py index 52c281326..cee54cb4f 100644 --- a/tick/prox/prox_equality.py +++ b/tick/prox/prox_equality.py @@ -6,8 +6,8 @@ import sys from .base import Prox -from .build.prox import ProxEqualityDouble as _ProxEqualityDouble -from .build.prox import ProxEqualityFloat as _ProxEqualityFloat +from tick.tick_cpp import ProxEqualityDouble as _ProxEqualityDouble +from tick.tick_cpp import ProxEqualityFloat as _ProxEqualityFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_group_l1.py b/tick/prox/prox_group_l1.py index 0464cde2f..a89072364 100644 --- a/tick/prox/prox_group_l1.py +++ b/tick/prox/prox_group_l1.py @@ -1,8 +1,8 @@ # License: BSD 3 clause from .base import ProxWithGroups -from .build.prox import ProxGroupL1Double as _ProxGroupL1Double -from .build.prox import ProxGroupL1Float as _ProxGroupL1Float +from tick.tick_cpp import ProxGroupL1Double as _ProxGroupL1Double +from tick.tick_cpp import ProxGroupL1Float as _ProxGroupL1Float import numpy as np diff --git a/tick/prox/prox_l1.py b/tick/prox/prox_l1.py index f9b5052fc..b9ac7ea70 100644 --- a/tick/prox/prox_l1.py +++ b/tick/prox/prox_l1.py @@ -4,8 +4,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxL1Double as _ProxL1Double -from .build.prox import ProxL1Float as _ProxL1Float +from tick.tick_cpp import ProxL1Double as _ProxL1Double +from tick.tick_cpp import ProxL1Float as _ProxL1Float __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_l1w.py b/tick/prox/prox_l1w.py index 995da5306..acf2364eb 100644 --- a/tick/prox/prox_l1w.py +++ b/tick/prox/prox_l1w.py @@ -4,8 +4,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxL1wDouble as _ProxL1wDouble -from .build.prox import ProxL1wFloat as _ProxL1wFloat +from tick.tick_cpp import ProxL1wDouble as _ProxL1wDouble +from tick.tick_cpp import ProxL1wFloat as _ProxL1wFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_l2.py b/tick/prox/prox_l2.py index df397ce30..4462b6c46 100644 --- a/tick/prox/prox_l2.py +++ b/tick/prox/prox_l2.py @@ -2,8 +2,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxL2Double as _ProxL2Double -from .build.prox import ProxL2Float as _ProxL2Float +from tick.tick_cpp import ProxL2Double as _ProxL2Double +from tick.tick_cpp import ProxL2Float as _ProxL2Float __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_l2sq.py b/tick/prox/prox_l2sq.py index 002509557..c1eeeedcf 100644 --- a/tick/prox/prox_l2sq.py +++ b/tick/prox/prox_l2sq.py @@ -4,8 +4,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxL2SqDouble as _ProxL2sqDouble -from .build.prox import ProxL2SqFloat as _ProxL2sqFloat +from tick.tick_cpp import ProxL2SqDouble as _ProxL2sqDouble +from tick.tick_cpp import ProxL2SqFloat as _ProxL2sqFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_multi.py b/tick/prox/prox_multi.py index 28c30192b..6c3be9879 100644 --- a/tick/prox/prox_multi.py +++ b/tick/prox/prox_multi.py @@ -4,8 +4,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxMultiDouble as _ProxMultiDouble -from .build.prox import ProxMultiFloat as _ProxMultiFloat +from tick.tick_cpp import ProxMultiDouble as _ProxMultiDouble +from tick.tick_cpp import ProxMultiFloat as _ProxMultiFloat from tick.prox import ProxZero __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_oscar.py b/tick/prox/prox_oscar.py index 4a9e83829..919d94db3 100644 --- a/tick/prox/prox_oscar.py +++ b/tick/prox/prox_oscar.py @@ -5,9 +5,9 @@ from tick.prox.base import Prox import numpy as np -from .build.prox import ProxSortedL1Double as _ProxSortedL1Double -from .build.prox import ProxSortedL1Float as _ProxSortedL1Float -from .build.prox import WeightsType_bh, WeightsType_oscar +from tick.tick_cpp import ProxSortedL1Double as _ProxSortedL1Double +from tick.tick_cpp import ProxSortedL1Float as _ProxSortedL1Float +from tick.tick_cpp import WeightsType_bh, WeightsType_oscar # TODO: put also the OSCAR weights # TODO: we should be able to put any weights we want... diff --git a/tick/prox/prox_positive.py b/tick/prox/prox_positive.py index 732a495d3..d711fee69 100644 --- a/tick/prox/prox_positive.py +++ b/tick/prox/prox_positive.py @@ -5,8 +5,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxPositiveDouble as _ProxPositiveDouble -from .build.prox import ProxPositiveFloat as _ProxPositiveFloat +from tick.tick_cpp import ProxPositiveDouble as _ProxPositiveDouble +from tick.tick_cpp import ProxPositiveFloat as _ProxPositiveFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_slope.py b/tick/prox/prox_slope.py index 28ad3a789..5d2bc3f85 100644 --- a/tick/prox/prox_slope.py +++ b/tick/prox/prox_slope.py @@ -3,8 +3,8 @@ from tick.prox.base import Prox import numpy as np -from .build.prox import ProxSlopeDouble as _ProxSlopeDouble -from .build.prox import ProxSlopeFloat as _ProxSlopeFloat +from tick.tick_cpp import ProxSlopeDouble as _ProxSlopeDouble +from tick.tick_cpp import ProxSlopeFloat as _ProxSlopeFloat dtype_map = { np.dtype("float64"): _ProxSlopeDouble, diff --git a/tick/prox/prox_tv.py b/tick/prox/prox_tv.py index 25bf39dd8..5f2f2891f 100644 --- a/tick/prox/prox_tv.py +++ b/tick/prox/prox_tv.py @@ -5,8 +5,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxTVDouble as _ProxTVDouble -from .build.prox import ProxTVFloat as _ProxTVFloat +from tick.tick_cpp import ProxTVDouble as _ProxTVDouble +from tick.tick_cpp import ProxTVFloat as _ProxTVFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/prox/prox_zero.py b/tick/prox/prox_zero.py index 4abf722e7..c46774c04 100644 --- a/tick/prox/prox_zero.py +++ b/tick/prox/prox_zero.py @@ -5,8 +5,8 @@ import numpy as np from .base import Prox -from .build.prox import ProxZeroDouble as _ProxZeroDouble -from .build.prox import ProxZeroFloat as _ProxZeroFloat +from tick.tick_cpp import ProxZeroDouble as _ProxZeroDouble +from tick.tick_cpp import ProxZeroFloat as _ProxZeroFloat __author__ = 'Stephane Gaiffas' diff --git a/tick/random/__init__.py b/tick/random/__init__.py index 72efa4308..8c50e721f 100644 --- a/tick/random/__init__.py +++ b/tick/random/__init__.py @@ -1,4 +1,4 @@ # License: BSD 3 clause -import tick.array -from .build.crandom import * +from tick.tick_cpp import (test_uniform, test_gaussian, test_poisson, + test_exponential, test_uniform_int, test_discrete, test_uniform_threaded) diff --git a/tick/random/build/__init__.py b/tick/random/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/random/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/random/tests/qqplots.py b/tick/random/tests/qqplots.py index 842308741..1b4541069 100644 --- a/tick/random/tests/qqplots.py +++ b/tick/random/tests/qqplots.py @@ -1,11 +1,17 @@ import numpy as np from scipy import stats -import statsmodels.api as sm from matplotlib import pyplot as plt from tick.random import test_uniform, test_gaussian, test_poisson, \ test_exponential, test_uniform_int, test_discrete, test_uniform_threaded +import sys +try: + import statsmodels.api as sm +except ImportError: + print("statsmodels module not found, skipping") + + class QQplot: def __init__(self, test_seed: int = 12099, @@ -60,6 +66,10 @@ def exponential(self): def main(): + try: + import statsmodels.api as sm + except ImportError: + return qqplot = QQplot() qqplot.poisson() qqplot.uniform() diff --git a/tick/robust/__init__.py b/tick/robust/__init__.py index f6797618f..dc0e82a7c 100644 --- a/tick/robust/__init__.py +++ b/tick/robust/__init__.py @@ -1,8 +1,6 @@ # License: BSD 3 clause import tick.base -import tick.base_model.build.base_model -import tick.linear_model.build.linear_model from .robust_linear_regression import RobustLinearRegression diff --git a/tick/robust/build/__init__.py b/tick/robust/build/__init__.py deleted file mode 100644 index cd1b0219e..000000000 --- a/tick/robust/build/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand - -from tick.base.opsys import add_to_path_if_windows - -add_to_path_if_windows(__file__) diff --git a/tick/robust/model_absolute_regression.py b/tick/robust/model_absolute_regression.py index aa6c4e029..9bba60c0a 100644 --- a/tick/robust/model_absolute_regression.py +++ b/tick/robust/model_absolute_regression.py @@ -2,7 +2,7 @@ import numpy as np from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder -from .build.robust import ModelAbsoluteRegressionDouble as _ModelAbsoluteRegression +from tick.tick_cpp import ModelAbsoluteRegressionDouble as _ModelAbsoluteRegression __author__ = 'Stephane Gaiffas' diff --git a/tick/robust/model_epsilon_insensitive.py b/tick/robust/model_epsilon_insensitive.py index 75d789062..0215d4e57 100644 --- a/tick/robust/model_epsilon_insensitive.py +++ b/tick/robust/model_epsilon_insensitive.py @@ -2,7 +2,7 @@ import numpy as np from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder -from .build.robust import ModelEpsilonInsensitiveDouble as _ModelEpsilonInsensitive +from tick.tick_cpp import ModelEpsilonInsensitiveDouble as _ModelEpsilonInsensitive __author__ = 'Stephane Gaiffas' diff --git a/tick/robust/model_huber.py b/tick/robust/model_huber.py index 7ed6f4284..3c193802c 100644 --- a/tick/robust/model_huber.py +++ b/tick/robust/model_huber.py @@ -3,7 +3,7 @@ import numpy as np from numpy.linalg import svd from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, ModelLipschitz -from .build.robust import ModelHuberDouble as _ModelHuber +from tick.tick_cpp import ModelHuberDouble as _ModelHuber __author__ = 'Stephane Gaiffas' diff --git a/tick/robust/model_linreg_with_intercepts.py b/tick/robust/model_linreg_with_intercepts.py index e4ce89662..37fa18d2d 100644 --- a/tick/robust/model_linreg_with_intercepts.py +++ b/tick/robust/model_linreg_with_intercepts.py @@ -5,7 +5,7 @@ from tick.base_model import ModelFirstOrder, ModelLipschitz from .base import ModelGeneralizedLinearWithIntercepts -from .build.robust import \ +from tick.tick_cpp import \ ModelLinRegWithInterceptsDouble as _ModelLinRegWithIntercepts __author__ = 'Stephane Gaiffas' diff --git a/tick/robust/model_modified_huber.py b/tick/robust/model_modified_huber.py index 3c7f2c83e..df2275673 100644 --- a/tick/robust/model_modified_huber.py +++ b/tick/robust/model_modified_huber.py @@ -4,7 +4,7 @@ from numpy.linalg import svd from tick.base_model import ModelGeneralizedLinear, ModelFirstOrder, \ ModelLipschitz -from .build.robust import ModelModifiedHuberDouble as _ModelModifiedHuber +from tick.tick_cpp import ModelModifiedHuberDouble as _ModelModifiedHuber __author__ = 'Stephane Gaiffas' diff --git a/tick/solver/__init__.py b/tick/solver/__init__.py index 7862bd37e..f6bb108e5 100644 --- a/tick/solver/__init__.py +++ b/tick/solver/__init__.py @@ -1,8 +1,8 @@ # License: BSD 3 clause import tick.base -import tick.linear_model.build.linear_model -import tick.robust.build.robust + + from .gd import GD from .agd import AGD diff --git a/tick/solver/adagrad.py b/tick/solver/adagrad.py index a5108ec7c..a82615a67 100644 --- a/tick/solver/adagrad.py +++ b/tick/solver/adagrad.py @@ -3,8 +3,8 @@ import numpy as np from .base import SolverFirstOrderSto -from .build.solver import AdaGradDouble as _AdaGradDouble -from .build.solver import AdaGradFloat as _AdaGradFloat +from tick.tick_cpp import AdaGradDouble as _AdaGradDouble +from tick.tick_cpp import AdaGradFloat as _AdaGradFloat __author__ = "Søren Vinther Poulsen" diff --git a/tick/solver/base/sto.py b/tick/solver/base/sto.py index 5e9b4989c..29b32a1c9 100644 --- a/tick/solver/base/sto.py +++ b/tick/solver/base/sto.py @@ -6,8 +6,8 @@ from tick.base_model import Model from tick.prox.base import Prox -from ..build.solver import RandType_perm as perm -from ..build.solver import RandType_unif as unif +from tick.tick_cpp import RandType_perm as perm +from tick.tick_cpp import RandType_unif as unif class SolverSto(Base): diff --git a/tick/solver/build/__init__.py b/tick/solver/build/__init__.py deleted file mode 100644 index ecd9b515e..000000000 --- a/tick/solver/build/__init__.py +++ /dev/null @@ -1,23 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand -# As observed here both "base_model" and "linear_model" are required - -from tick.base.opsys import add_to_path_if_windows - - -def required(): - import os, sys - root = os.path.dirname(os.path.realpath(os.path.join(__file__, "../.."))) - - deps = ["base_model", "linear_model", "robust"] - - for dep in deps: - if "tick." + dep + ".build" not in sys.modules: - p = os.path.realpath(os.path.join(root, dep + "/build")) - os.environ["PATH"] = p + os.pathsep + os.environ["PATH"] - - -add_to_path_if_windows(__file__, [required]) diff --git a/tick/solver/saga.py b/tick/solver/saga.py index 6477456a4..19bb1f677 100644 --- a/tick/solver/saga.py +++ b/tick/solver/saga.py @@ -7,15 +7,15 @@ from tick.base_model import ModelGeneralizedLinear from tick.solver.base import SolverFirstOrderSto, SolverSto -from tick.solver.build.solver import SAGADouble as _SAGADouble -from tick.solver.build.solver import SAGAFloat as _SAGAFloat +from tick.tick_cpp import SAGADouble as _SAGADouble +from tick.tick_cpp import SAGAFloat as _SAGAFloat dtype_class_mapper = { np.dtype('float32'): _SAGAFloat, np.dtype('float64'): _SAGADouble } -from tick.solver.build.solver import AtomicSAGADouble as _ASAGADouble -from tick.solver.build.solver import AtomicSAGAFloat as _ASAGAFloat +from tick.tick_cpp import AtomicSAGADouble as _ASAGADouble +from tick.tick_cpp import AtomicSAGAFloat as _ASAGAFloat dtype_atomic_mapper = { np.dtype('float32'): _ASAGAFloat, np.dtype('float64'): _ASAGADouble diff --git a/tick/solver/sdca.py b/tick/solver/sdca.py index ea55f218c..221b7a4a8 100644 --- a/tick/solver/sdca.py +++ b/tick/solver/sdca.py @@ -2,8 +2,8 @@ from .base import SolverFirstOrderSto -from .build.solver import SDCADouble as _SDCADouble -from .build.solver import SDCAFloat as _SDCAFloat +from tick.tick_cpp import SDCADouble as _SDCADouble +from tick.tick_cpp import SDCAFloat as _SDCAFloat import numpy as np diff --git a/tick/solver/sgd.py b/tick/solver/sgd.py index 0af296429..ff653a32d 100644 --- a/tick/solver/sgd.py +++ b/tick/solver/sgd.py @@ -3,8 +3,8 @@ import numpy as np from .base import SolverFirstOrderSto -from .build.solver import SGDDouble as _SGDDouble -from .build.solver import SGDFloat as _SGDFloat +from tick.tick_cpp import SGDDouble as _SGDDouble +from tick.tick_cpp import SGDFloat as _SGDFloat __author__ = "Stephane Gaiffas" diff --git a/tick/solver/svrg.py b/tick/solver/svrg.py index 68c7cd527..76e7eed2d 100644 --- a/tick/solver/svrg.py +++ b/tick/solver/svrg.py @@ -6,16 +6,16 @@ from tick.base_model import Model from .base import SolverFirstOrderSto -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Last -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Average -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Random +from tick.tick_cpp import SVRG_VarianceReductionMethod_Last +from tick.tick_cpp import SVRG_VarianceReductionMethod_Average +from tick.tick_cpp import SVRG_VarianceReductionMethod_Random -from tick.solver.build.solver import SVRG_StepType_Fixed -from tick.solver.build.solver import SVRG_StepType_BarzilaiBorwein +from tick.tick_cpp import SVRG_StepType_Fixed +from tick.tick_cpp import SVRG_StepType_BarzilaiBorwein -from .build.solver import SVRGDouble as _SVRGDouble -from .build.solver import SVRGFloat as _SVRGFloat -from .build.solver import MultiSVRGDouble as MultiSVRG, SVRGDoublePtrVector +from tick.tick_cpp import SVRGDouble as _SVRGDouble +from tick.tick_cpp import SVRGFloat as _SVRGFloat +from tick.tick_cpp import MultiSVRGDouble as MultiSVRG, SVRGDoublePtrVector __author__ = "Stephane Gaiffas" diff --git a/tick/solver/tests/saga_test.py b/tick/solver/tests/saga_test.py index bb06d93ef..af5e30d57 100644 --- a/tick/solver/tests/saga_test.py +++ b/tick/solver/tests/saga_test.py @@ -6,7 +6,7 @@ from tick.prox import ProxElasticNet from tick.solver import SAGA from tick.solver.tests import TestSolver -from tick.solver.build.solver import SAGADouble as _SAGA +from tick.tick_cpp import SAGADouble as _SAGA from tick.linear_model import ModelLogReg, SimuLogReg from tick.survival import SimuCoxReg, ModelCoxRegPartialLik from tick.simulation import weights_sparse_gauss diff --git a/tick/solver/tests/svrg_test.py b/tick/solver/tests/svrg_test.py index 615489667..8421798f3 100644 --- a/tick/solver/tests/svrg_test.py +++ b/tick/solver/tests/svrg_test.py @@ -16,12 +16,12 @@ from tick.solver import SVRG from tick.solver.tests import TestSolver -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Last -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Average -from tick.solver.build.solver import SVRG_VarianceReductionMethod_Random +from tick.tick_cpp import SVRG_VarianceReductionMethod_Last +from tick.tick_cpp import SVRG_VarianceReductionMethod_Average +from tick.tick_cpp import SVRG_VarianceReductionMethod_Random -from tick.solver.build.solver import SVRG_StepType_Fixed -from tick.solver.build.solver import SVRG_StepType_BarzilaiBorwein +from tick.tick_cpp import SVRG_StepType_Fixed +from tick.tick_cpp import SVRG_StepType_BarzilaiBorwein from tick.simulation import weights_sparse_gauss @@ -247,7 +247,7 @@ def test_dense_and_sparse_match(self): solver_sparse.solve() solver_dense.solve() places = 7 - if self.dtype is "float32": + if self.dtype == "float32": places = 3 np.testing.assert_array_almost_equal(solver_sparse.solution, solver_dense.solution, diff --git a/tick/survival/__init__.py b/tick/survival/__init__.py index 68c11a039..04318bdf7 100644 --- a/tick/survival/__init__.py +++ b/tick/survival/__init__.py @@ -1,7 +1,7 @@ # License: BSD 3 clause import tick.base -import tick.base_model.build.base_model + from .cox_regression import CoxRegression diff --git a/tick/survival/build/__init__.py b/tick/survival/build/__init__.py deleted file mode 100644 index 29f51d054..000000000 --- a/tick/survival/build/__init__.py +++ /dev/null @@ -1,21 +0,0 @@ -# License: BSD 3 clause - -# Templating update - 19/02/2018 -# Importing DLLs has gotten a bit strange and now requires -# updating the path for DLLs to be found before hand -# As observed here both "base_model" and "linear_model" are required - -from tick.base.opsys import add_to_path_if_windows - -def required(): - import os, sys - root = os.path.dirname(os.path.realpath(os.path.join(__file__, "../.."))) - - deps = ["base_model", "linear_model", "solver"] - - for dep in deps: - if "tick." + dep + ".build" not in sys.modules: - p = os.path.realpath(os.path.join(root, dep + "/build")) - os.environ["PATH"] = p + os.pathsep + os.environ["PATH"] - -add_to_path_if_windows(__file__, [required]) diff --git a/tick/survival/model_coxreg_partial_lik.py b/tick/survival/model_coxreg_partial_lik.py index 1b7ff5dd3..b2e5a8e63 100644 --- a/tick/survival/model_coxreg_partial_lik.py +++ b/tick/survival/model_coxreg_partial_lik.py @@ -4,10 +4,8 @@ from tick.base_model import Model, ModelFirstOrder from tick.preprocessing.utils import safe_array -from .build.survival import ModelCoxRegPartialLikDouble \ - as _ModelCoxRegPartialLik_d -from .build.survival import ModelCoxRegPartialLikFloat \ - as _ModelCoxRegPartialLik_f +from tick.tick_cpp import ModelCoxRegPartialLikDouble as _ModelCoxRegPartialLik_d +from tick.tick_cpp import ModelCoxRegPartialLikFloat as _ModelCoxRegPartialLik_f dtype_class_mapper = { np.dtype('float32'): _ModelCoxRegPartialLik_f, diff --git a/tick/survival/model_sccs.py b/tick/survival/model_sccs.py index c2ba34f7d..caddb1dea 100644 --- a/tick/survival/model_sccs.py +++ b/tick/survival/model_sccs.py @@ -2,7 +2,7 @@ import numpy as np from tick.base_model import ModelFirstOrder, ModelLipschitz -from .build.survival import ModelSCCS as _ModelSCCS +from tick.tick_cpp import ModelSCCS as _ModelSCCS from tick.preprocessing.utils import check_longitudinal_features_consistency, \ check_censoring_consistency diff --git a/tick/tick_cpp/.gitignore b/tick/tick_cpp/.gitignore new file mode 100644 index 000000000..9d6e0df1d --- /dev/null +++ b/tick/tick_cpp/.gitignore @@ -0,0 +1 @@ +tick_cpp.py \ No newline at end of file diff --git a/tick/tick_cpp/__init__.py b/tick/tick_cpp/__init__.py new file mode 100644 index 000000000..1afc1a5d7 --- /dev/null +++ b/tick/tick_cpp/__init__.py @@ -0,0 +1 @@ +from .tick_cpp import *