Add newer pythons to github actions (#483)

* Updates for python3.10 / LGTM warnings

.github/workflows/build_nix.yml

@@ -9,7 +9,8 @@ on:
 
 env:
   TICK_DEBUG: 0
-
+  TICK_WERROR: 0
+  MKN_GCC_PREFERRED: 1
 
 jobs:
   build:
@@ -20,25 +21,43 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.7', '3.9', '3.10'] # '3.8' has "'tp_print' is deprecated [-Werror,-Wdeprecated-declarations]"
 
     steps:
     - uses: actions/checkout@v2
       with:
         submodules: true
 
-    - name: install swig
-      run: |
-        git clone https://github.com/swig/swig -b rel-4.0.2 swig
-        cd swig && ./autogen.sh && ./configure --without-pcre
-        make && sudo make install && cd .. && rm -rf swig
-
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
 
-    - run: |
+
+
+
+
+    - name: info
+      run: |
+        python3 -V
+        gcc -v
+        swig -version
+
+    - name: pip
+      run: |
         python3 -m pip install wheel pip --upgrade
         python3 -m pip install -r requirements.txt
-        python3 setup.py build_ext --inplace cpptest pytest
+
+    - 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
+
+    - name: cpptest
+      run: |
+        PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh
+
+    - name: pytest
+      run: |
+        python3 setup.py pytest

.github/workflows/build_osx.yml.off

@@ -11,6 +11,7 @@ env:
   TICK_DEBUG: 0
   TICK_WERROR: 0
 
+
 jobs:
   build:
     name: Python ${{ matrix.python-version }}
@@ -20,30 +21,43 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.9', '3.10'] # '3.8' has "'tp_print' is deprecated [-Werror,-Wdeprecated-declarations]"
 
     steps:
     - uses: actions/checkout@v2
       with:
         submodules: true
 
-    - name: install swig
-      run: |
-        brew update
-        brew install automake m4
-        git clone https://github.com/swig/swig -b rel-4.0.2 swig
-        cd swig && ./autogen.sh && ./configure --without-pcre
-        make && make install && cd .. && rm -rf swigkey
-
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
 
-    - run: |
-        pip install pip --upgrade
-        pip install wheel
-        pip install -r requirements.txt
-        python setup.py build_ext --inplace cpptest
-        python -m unittest discover -v . "*_test.py"
 
+
+
+
+    - name: info
+      run: |
+        python3 -V
+        clang -v
+        swig -version
+
+    - name: pip
+      run: |
+        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
+
+    - name: cpptest
+      run: |
+        PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh
+
+    - name: pytest
+      run: |
+        python -m unittest discover -v . "*_test.py"

.github/workflows/build_win.yml

@@ -9,7 +9,8 @@ on:
 
 env:
   TICK_DEBUG: 0
-#  TICK_CMAKE_GENERATOR: Visual Studio 16 2022
+  TICK_WERROR: 0
+  MKN_CL_PREFERRED: 1
 
 jobs:
   build:
@@ -20,24 +21,43 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.7'] # '3.8', '3.9', '3.10',  have dll init issues
 
     steps:
     - uses: actions/checkout@v2
       with:
         submodules: true
 
-    - uses: actions/setup-python@v1
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         architecture: x64
 
-    - run: |
+    - uses: ilammy/msvc-dev-cmd@v1 # setup vcvars for cl.exe
+      with:
+        arch: amd64
+
+    - name: info
+      run: |
+        python3 -V
         swig -version
-        pip install pip --upgrade
-        pip install wheel
-        pip install -r requirements.txt
-        python setup.py build_ext --inplace
-        python -m unittest discover -v . "*_test.py"
+        cl
 
+    - name: pip
+      run: |
+        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'
+
+    - name: cpptest
+      run: |
+        bash -c 'PATH=$PWD:$PATH KLOG=3 ./sh/gtest.sh'
+
+    - name: pytest
+      run: |
+        python -m unittest discover -v . "*_test.py"

.github/workflows/pythonpublish-linux.yml

@@ -19,7 +19,7 @@ jobs:
         submodules: true
 
     - run: |
-          git clone https://github.com/swig/swig -b rel-4.0.0 swig
+          git clone https://github.com/swig/swig -b rel-4.0.2 swig
           cd swig && ./autogen.sh && ./configure --without-pcre
           make && make install && cd .. && rm -rf swig
 
@@ -38,6 +38,11 @@ jobs:
         $PYTHON39/bin/python -m pip install wheel -r requirements.txt
         $PYTHON39/bin/python setup.py bdist_wheel
 
+    - run: |
+        $PYTHON310/bin/python -m pip install twine pip --upgrade
+        $PYTHON310/bin/python -m pip install wheel -r requirements.txt
+        $PYTHON310/bin/python setup.py bdist_wheel
+
     - run: for wheel in $(ls dist); do auditwheel repair dist/$wheel; done
 
     - env:

.github/workflows/pythonpublish-osx.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     name: Python ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v2
@@ -29,7 +29,7 @@ jobs:
     - run: |
         brew update
         brew install automake m4
-        git clone https://github.com/swig/swig -b rel-4.0.0 swig
+        git clone https://github.com/swig/swig -b rel-4.0.2 swig
         cd swig && ./autogen.sh && ./configure --without-pcre
         make && make install && cd .. && rm -rf swigkey
 

.github/workflows/pythonpublish-win.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     name: Python ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v2

examples/plot_2d_linear_regression.py

@@ -25,7 +25,6 @@
 from sklearn.metrics import mean_squared_error, r2_score
 from sklearn.utils import shuffle
 from sklearn.datasets import load_boston
-from mpl_toolkits.mplot3d import axes3d
 from matplotlib import cm
 
 # Load the Boston Housing Dataset

examples/plot_conv_sccs_cv_results.py

@@ -8,7 +8,6 @@
 and compare the estimated coefficients to the relative incidences used for
 the simulation.
 """
-from time import time
 import numpy as np
 from scipy.sparse import csr_matrix, hstack
 from matplotlib import cm

lib/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.7)
 project(tick)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -ffast-math")
@@ -95,8 +95,8 @@ if (${GTEST_FOUND})
     message(STATUS "Testing in C++ enabled")
 
     find_package(Threads REQUIRED)
-    find_package(PythonInterp 3 REQUIRED)
-    find_package(PythonLibs 3 REQUIRED)
+    find_package(PythonInterp 3.7 REQUIRED)
+    find_package(PythonLibs 3.7 REQUIRED)
 
     include_directories(${GTEST_INCLUDE_DIRS})
 

lib/cpp-test/array/array_gtest.cpp

@@ -37,7 +37,7 @@ class ArrayTest : public ::testing::Test {
 typedef ::testing::Types<ArrayFloat, ArrayDouble, ArrayShort, ArrayUShort,
                          ArrayInt, ArrayUInt, ArrayLong, ArrayULong>
     MyArrayTypes;
-TYPED_TEST_CASE(ArrayTest, MyArrayTypes);
+TYPED_TEST_SUITE(ArrayTest, MyArrayTypes);
 
 template <typename ArrType>
 class Array2dTest : public ::testing::Test {
@@ -49,7 +49,7 @@ typedef ::testing::Types<ArrayFloat2d, ArrayDouble2d, ArrayShort2d,
                          ArrayUShort2d, ArrayInt2d, ArrayUInt2d, ArrayLong2d,
                          ArrayULong2d>
     MyArray2dTypes;
-TYPED_TEST_CASE(Array2dTest, MyArray2dTypes);
+TYPED_TEST_SUITE(Array2dTest, MyArray2dTypes);
 
 TYPED_TEST(ArrayTest, InitToZero) {
   TypeParam arr{TICK_TEST_DATA_SIZE};
@@ -195,6 +195,10 @@ TYPED_TEST(ArrayTest, Contains) {
 
   typename TypeParam::value_type value_3 = arrA[3] + 0.;
   typename TypeParam::value_type new_value = 7032;
+
+  int retries = 0;
+  while(retries++ < 5 && arrA.contains(new_value)) arrA = ::GenerateRandomArray<TypeParam>();
+
   EXPECT_TRUE(arrA.contains(value_3));
   EXPECT_FALSE(arrA.contains(new_value));
   arrA[3] = new_value;

lib/cpp-test/array/atomic_array_gtest.cpp

@@ -163,7 +163,7 @@ class AtomicArrayTest : public ::testing::Test {
 };
 
 typedef ::testing::Types<Array<float>, Array<double>> MyArrayTypes;
-TYPED_TEST_CASE(AtomicArrayTest, MyArrayTypes);
+TYPED_TEST_SUITE(AtomicArrayTest, MyArrayTypes);
 
 TYPED_TEST(AtomicArrayTest, InitToZero) {
   TypeParam arr{TICK_TEST_DATA_SIZE};

lib/cpp-test/array/linear_system_gtest.cpp

@@ -25,7 +25,7 @@ class LinearSystemTest : public ::testing::Test {
 };
 
 typedef ::testing::Types<ArrayFloat, ArrayDouble> MyArrayTypes;
-TYPED_TEST_CASE(LinearSystemTest, MyArrayTypes);
+TYPED_TEST_SUITE(LinearSystemTest, MyArrayTypes);
 
 
 

lib/cpp-test/base/utils_gtest.cpp

@@ -234,7 +234,7 @@ TEST_P(ParallelTest, MapArray) {
   }
 }
 
-INSTANTIATE_TEST_CASE_P(AllParallelTests, ParallelTest,
+INSTANTIATE_TEST_SUITE_P(AllParallelTests, ParallelTest,
                         ::testing::Values(1, 2, 4, 8, 16));
 
 TEST(ParallelTest, CPUCount) {

lib/cpp/hawkes/inference/hawkes_em.cpp

@@ -151,10 +151,11 @@ void HawkesEM::compute_intensities_ur(
   const ulong node_u = r_u % n_nodes;
 
   ArrayDouble2d kernel_norms = *get_kernel_norms(kernels);
-  double marginal_int_intensity = 0;
-  for (ulong node_v = 0; node_v < n_nodes; ++node_v) {
-    marginal_int_intensity += kernel_norms(node_v, node_u);
-  }
+  // ?
+  // double marginal_int_intensity = 0;
+  // for (ulong node_v = 0; node_v < n_nodes; ++node_v) {
+  //   marginal_int_intensity += kernel_norms(node_v, node_u);
+  // }
 
   // Fetch corresponding data
   SArrayDoublePtrList1D &realization = timestamps_list[r];

lib/cpp/random/rand.cpp

@@ -100,8 +100,7 @@ void Rand::reseed(const int seed) {
     std::seed_seq seed_seq{r(), r(), r(), r(), r(), r(), r(), r()};
     generator = std::mt19937_64(seed_seq);
   } else {
-    unsigned int useed = seed < 0 ? 0 : static_cast<unsigned int>(seed);
-    generator = std::mt19937_64(useed);
+    generator = std::mt19937_64(seed);
   }
 
   Rand::seed = seed;

lib/include/tick/base/parallel/parallel_utils.h

@@ -18,6 +18,11 @@ namespace tick {
  */
 template <typename T, typename S, typename... Args>
 using FuncResultType = typename std::result_of<T(S, ulong, Args...)>::type;
+/*
+// this in future will be for C++17
+using FuncResultType = typename std::result_of<T(S, ulong, Args...)>::type;
+*/
+
 
 /**
  * Determine if return type of function call is a Python primitive or not

lib/include/tick/hawkes/simulation/hawkes_kernels/hawkes_kernel_sum_exp.h

@@ -80,7 +80,7 @@ class DLL_PUBLIC HawkesKernelSumExp : public HawkesKernel {
    * @param intensities: Array of the intensities of the kernel
    * @param decay: Array of the decays of the kernel
    */
-  explicit HawkesKernelSumExp(const ArrayDouble &intensities, const ArrayDouble &decays);
+  HawkesKernelSumExp(const ArrayDouble &intensities, const ArrayDouble &decays);
 
   /**
    * Copy constructor