Merge pull request #48 from bacpop/fix-pipepines

Fix Compatibility issues (fix Pipeline)

.github/workflows/python-package-conda.yml

@@ -4,10 +4,11 @@ on: [push]
 
 jobs:
   build-linux:
-    runs-on: ubuntu-22.04
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.10"]
+        os: [ubuntu-latest, ubuntu-22.04]
+        python-version: ["3.9", "3.13"]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -28,8 +29,13 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Install and run_test.py
+    - name: Install
       shell: bash -l {0}
       run: |
         python -m pip install --no-deps --ignore-installed -v .
-        cd test && python run_test.py
+    - name: Test
+      shell: bash -l {0}
+      working-directory: test
+      run: |
+        python run_test.py
+      

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.19)
 project(SCE)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 14 CACHE STRING "C++ version selection") 
 cmake_policy(SET CMP0104 OLD) # Can't get CUDA_ARCHITECTURES to work with NEW
 
 # Variable definitions
@@ -19,7 +19,7 @@ set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
 
 if(UNIX AND NOT APPLE)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS")
-    set(CMAKE_LD_FLAGS "${CMAKE_LDFLAGS} -Wl,--as-needed")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--as-needed")
 endif()
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -ffast-math -funroll-loops -m64")
 
@@ -29,13 +29,14 @@ if(DEFINED ENV{CONDA_PREFIX})
     link_directories($ENV{CONDA_PREFIX}/lib)
     link_directories($ENV{CONDA_PREFIX}/lib/intel64)
 else()
-  find_package(OpenMP)
+    find_package(OpenMP)
 endif()
 
 # Add libraries
-find_package(ZLIB)
+find_package(ZLIB REQUIRED)
+find_package(Boost REQUIRED)
 find_package(pybind11 REQUIRED)
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/vendor)
+include_directories(${Boost_INCLUDE_DIRS})
 
 # Check for CUDA and compiles GPU library
 include(CheckLanguage)
@@ -46,7 +47,7 @@ if(CMAKE_CUDA_COMPILER)
     enable_language(CUDA)
     set(CUDA_OPTS "-Wreorder -Xcompiler -fPIC -Xcompiler -Wall -Xcompiler -fopenmp -Xptxas -dlcm=ca --cudart static --relocatable-device-code=false")
     if(NOT DEFINED CMAKE_CUDA_ARCHITECTURES)
-        set(CMAKE_CUDA_ARCHITECTURES 80 86 90)
+        set(CMAKE_CUDA_ARCHITECTURES "80;86;90" CACHE STRING "CUDA architectures")
     endif()
     if(CMAKE_BUILD_TYPE MATCHES Debug)
         string(APPEND CUDA_OPTS " -G")

environment.yml

@@ -22,3 +22,4 @@ dependencies:
   - libgomp
   - tqdm
   - ffmpeg
+  - boost-cpp

mandrake/__init__.py

@@ -3,4 +3,4 @@
 
 '''Visualisation of pathogen population structure'''
 
-__version__ = '1.2.3'
+__version__ = '1.2.4'

mandrake/sce.py

@@ -9,7 +9,6 @@
 from functools import partial
 import numpy as np
 import pandas as pd
-
 # C++ extensions
 from SCE import wtsne
 try:
@@ -31,8 +30,9 @@ def save_input(I, J, dists, names, output_prefix):
         sys.stderr.write("Distances calculated, but not running SCE\n")
         sys.exit(1)
 
-    pd.Series(names).to_csv(output_prefix + '.names.txt',
-                            sep='\n', header=False, index=False)
+    pd.Series(names).to_csv(
+        output_prefix + ".names.txt", header=False, index=False
+    )
 
     _saveDists(output_prefix, I, J, dists, names)
 

src/kseq.h

@@ -115,7 +115,7 @@ typedef struct __kstring_t {
 				for (i = ks->begin; i < ks->end; ++i)					\
 					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
 			} else i = 0; /* never come to here! */						\
-			if (str->m - str->l < i - ks->begin + 1) {					\
+			if (str->m - str->l < (size_t)(i - ks->begin + 1)) {					\
 				str->m = str->l + (i - ks->begin) + 1;					\
 				kroundup32(str->m);										\
 				str->s = (char*)realloc(str->s, str->m);				\

src/pairsnp.hpp

@@ -5,6 +5,7 @@
 #include <stdio.h>
 #include <string>
 #include <zlib.h>
+#include <omp.h>
 
 #include "kseq.h"
 #include "progress.hpp"
@@ -196,7 +197,7 @@ pairsnp(const char *fasta, int n_threads, int dist, int knn) {
 #pragma omp parallel for schedule(static) reduction(+:len) num_threads(n_threads)
   for (uint64_t i = 0; i < n_seqs; i++) {
     // Cannot throw in an openmp block, short circuit instead
-    if (interrupt || PyErr_CheckSignals() != 0) {
+    if (interrupt || (omp_get_thread_num() == 0 && PyErr_CheckSignals() != 0)) {
       interrupt = true;
     } else {
       std::vector<int> comp_snps(n_seqs);

src/wtsne.hpp

@@ -73,8 +73,8 @@ std::vector<double> conditional_probabilities(const std::vector<uint64_t> &I,
 // https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/manifold/_utils.pyx
 #pragma omp parallel for schedule(static) num_threads(n_threads)
     for (uint64_t sample_idx = 0; sample_idx < n_samples; ++sample_idx) {
-      real_t beta_min = -std::numeric_limits<real_t>::infinity();
-      real_t beta_max = std::numeric_limits<real_t>::infinity();
+      real_t beta_min = -std::numeric_limits<real_t>::max();
+      real_t beta_max = std::numeric_limits<real_t>::max();
       real_t beta = 1.0;
       real_t sum_Pi, sum_disti_Pi, entropy, entropy_diff;
       for (int l = 0; l < n_steps; ++l) {
@@ -105,14 +105,14 @@ std::vector<double> conditional_probabilities(const std::vector<uint64_t> &I,
 
         if (entropy_diff > 0.0) {
           beta_min = beta;
-          if (beta_max == std::numeric_limits<real_t>::infinity()) {
+          if (beta_max == std::numeric_limits<real_t>::max()) {
             beta *= 2.0;
           } else {
             beta = (beta + beta_max) * 0.5;
           }
         } else {
           beta_max = beta;
-          if (beta_min == -std::numeric_limits<real_t>::infinity()) {
+          if (beta_min == -std::numeric_limits<real_t>::max()) {
             beta *= 0.5;
           } else {
             beta = (beta + beta_min) * 0.5;