Merge branch 'master' into development

.github/workflows/conda-build.yml

@@ -0,0 +1,46 @@
+name: Conda Build
+
+on:
+  push:
+    branches:
+      - development
+
+jobs:
+  build-linux:
+    name: CondaBuild (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.11"]
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+
+      - name: Display Conda Settings
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Build Conda Package
+        shell: bash -el {0}
+        run: |
+          mamba install conda-build boa
+          cd conda-recipe
+          curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
+          # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
+          conda mambabuild .

.github/workflows/conda-release.yml

@@ -0,0 +1,56 @@
+
+name: Build and Upload Conda Packages
+
+on:
+#  push:
+#    branches:
+#      - develop
+  release:
+    types: ['released', 'prereleased']
+
+jobs:
+  build:
+    name: CondaBuild (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+
+      - name: Display Conda Settings
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Build Conda Package
+        shell: bash -el {0}
+        run: |
+          mamba install conda-build boa anaconda-client
+          cd conda-recipe
+          # Use older conda_build_config -> boost-cpp 1.78
+          curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
+          # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
+          conda mambabuild conda-recipe --output-folder conda-bld
+
+      - name: Upload Conda Package
+        shell: bash -el {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u tpeulen --force conda-bld/**/*.tar.bz2
+

.github/workflows/gitlab-sync.yml

@@ -0,0 +1,22 @@
+name: GitlabSync
+
+on:
+  - push
+  - delete
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    name: Git Repo Sync
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - uses: wangchucheng/[email protected]
+        with:
+          # Such as https://github.com/wangchucheng/git-repo-sync.git
+          target-url: ${{ secrets.TARGET_URL }}
+          # Such as wangchucheng
+          target-username: ${{ secrets.TARGET_USERNAME }}
+          # You can store token in your project's 'Setting > Secrets' and reference the name here. Such as ${{ secrets.ACCESS\_TOKEN }}
+          target-token: ${{ secrets.TARGET_TOKEN }}

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.13.0 FATAL_ERROR)
 SET(PROJECT_NAME fit2x)
 PROJECT(${PROJECT_NAME})
 ENABLE_LANGUAGE(CXX)
-SET(CMAKE_CXX_STANDARD 11)
+SET(CMAKE_CXX_STANDARD 17)
 ADD_DEFINITIONS(-D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES)
 
 ################################################################################
@@ -40,32 +40,37 @@ IF (CMAKE_BUILD_TYPE STREQUAL "Debug")
     endif()
 ENDIF (CMAKE_BUILD_TYPE STREQUAL "Debug")
 
-if(LINUX)
-    STRING(APPEND CMAKE_CXX_FLAGS " -Ofast -ffast-math -funroll-loops")
-    STRING(APPEND CMAKE_C_FLAGS " -Ofast -ffast-math -funroll-loops")
-endif()
-if(APPLE)
+# SIMD
+###########################
+IF(NOT APPLE)
+    IF(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/dependency)
+        INCLUDE(simd)
+        IF(${AVX_FOUND})
+            MESSAGE("BUILD WITH SIMD")
+            add_compile_definitions(WITH_AVX)
+            IF (MSVC)
+                # https://devblogs.microsoft.com/cppblog/simd-extension-to-c-openmp-in-visual-studio/
+                # /Oi is for intrinsics
+                SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX -openmp:experimental /Oi")
+            ELSE(MSVC)
+                STRING(APPEND CMAKE_CXX_FLAGS " -Ofast -mavx -mfma -ffast-math -funroll-loops")
+            ENDIF (MSVC)
+        ELSE(${AVX_FOUND})
+            UNSET(WITH_AVX)
+        ENDIF(${AVX_FOUND})
+    ENDIF()
+ENDIF()
+
+# MACOSX
+##############
+if (APPLE)
     FIND_PACKAGE(Threads)
     # explicit link to libc++ for recent osx versions
     MESSAGE(STATUS "Explicitly link to libc++ on modern osx versions")
     ADD_DEFINITIONS(-stdlib=libc++)
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
     SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pthread")
-    # Requires AVX and FMA
-    STRING(APPEND CMAKE_CXX_FLAGS " -Ofast -ffast-math -funroll-loops")
-    STRING(APPEND CMAKE_C_FLAGS " -Ofast -ffast-math -funroll-loops")
-endif()
-if (MSVC)
-    ADD_DEFINITIONS(-DMS_WIN64)
-    ADD_DEFINITIONS(-D_USE_MATH_DEFINES)
-    # https://devblogs.microsoft.com/cppblog/simd-extension-to-c-openmp-in-visual-studio/
-    # /Oi is for intrinsics
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX -openmp:experimental /Oi /O2")
-endif (MSVC)
-
-# MACOSX
-##############
-if (APPLE)
     # Don't set MACOSX_RPATH by default
     # https://github.com/conda/conda/issues/3624
     if(DEFINED ENV{CONDA_PREFIX})
@@ -101,6 +106,13 @@ ENDIF (CMAKE_BUILD_TYPE STREQUAL "Release")
 ###### INCLUDES AND LIBRARIES
 ################################################################################
 
+# third party includes/code
+FILE(GLOB_RECURSE SRC_files_thirdparty "${CMAKE_CURRENT_SOURCE_DIR}/thirdparty/*.cpp")
+LIST(APPEND SRC_files ${SRC_files_thirdparty})
+INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/thirdparty)
+
+## CONDA
+###########################
 FIND_PACKAGE(Conda)
 LINK_LIBRARIES(tttrlib)
 

src/fsconv.cpp

@@ -187,6 +187,7 @@ void fconv_per(double *fit, double *x, double *lamp, int numexp, int start, int
 // fast convolution, high repetition rate, AVX
 void fconv_per_avx(double *fit, double *x, double *lamp, int numexp, int start, int stop,
                    int n_points, double period, double dt) {
+
 #ifdef __AVX2__
 #if VERBOSE_FIT2X
     std::clog << "fconv_per_avx" << std::endl;
@@ -493,7 +494,7 @@ void fconv_per_cs_time_axis(
         double period
 ){
     double dt = time_axis[1] - time_axis[0];
-#ifdef __AVX2__
+#ifdef WITH_AVX
     fconv_per_avx(
             model,
             lifetime_spectrum,
@@ -504,7 +505,7 @@ void fconv_per_cs_time_axis(
             period, dt
     );
 #endif
-#ifndef __AVX2__
+#ifndef WITH_AVX
     fconv_per(
             model, lifetime_spectrum, instrument_response_function, (int) n_lifetime_spectrum / 2,
             convolution_start, convolution_stop, n_model, period, dt
@@ -523,7 +524,7 @@ void fconv_cs_time_axis(
         int convolution_stop
 ){
     double dt = time_axis[1] - time_axis[0];
-#ifdef __AVX2__
+#ifdef WITH_AVX
     fconv_avx(
             output,
             lifetime_spectrum,
@@ -532,7 +533,7 @@ void fconv_cs_time_axis(
             convolution_start, convolution_stop, dt
     );
 #endif
-#ifndef __AVX2__
+#ifndef WITH_AVX
     fconv(
             output,
             lifetime_spectrum,

test/test_fsconv.py

@@ -131,7 +131,6 @@ def test_fconv(self):
             np.allclose(model_ref, model_fconv), True
         )
 
-        # AVX wont be supported on Apple -> M1
         if platform != "darwin":
             model_fconv_avx = np.zeros_like(irf)
             fit2x.fconv_avx(
@@ -140,9 +139,7 @@ def test_fconv(self):
                 x=lifetime_spectrum,
                 dt=dt
             )
-            self.assertEqual(
-                np.allclose(model_fconv_avx, model_fconv), True
-            )
+            np.testing.assert_allclose(model_fconv_avx, model_fconv)
 
     def test_fconv_per(self):
         period = 13.0
@@ -190,7 +187,7 @@ def test_fconv_per(self):
             np.allclose(model_fconv_per, ref), True
         )
 
-        # AVX wont be supported on Apple -> M1
+        # AVX won't be supported on Apple -> M1
         if platform != "darwin":
             model_fconv_avx = np.zeros_like(irf)
             fit2x.fconv_per_avx(
@@ -248,9 +245,7 @@ def test_fconv_per_cs(self):
         # plt.semilogy(irf)
         # plt.show()
 
-        self.assertEqual(
-            np.allclose(ref, model_fconv_per_cs), True
-        )
+        np.testing.assert_allclose(ref, model_fconv_per_cs)
 
     # def test_sconv(self):
     #     period = 12.0