IsoSpecPy 2.2.0__tar.gz → 2.2.2__tar.gz

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/.github/workflows/build_wheels.yml

@@ -3,7 +3,7 @@ name: Build
 on:
   push:
     branches:
-      - version_2_2
+#      - version_2_2
       - ci_wheels
     tags:
       - v*
@@ -15,25 +15,23 @@ jobs:
     strategy:
       matrix:
         #os: [ubuntu-20.04, windows-2019, macos-10.15]
-        os: [windows-2019]
+        os: [windows-latest, macos-14]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-#      - name: Install Visual C++ for Python 2.7
-#        if: runner.os == 'Windows'
-#        run: choco install vcpython27 -f -y
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v3
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel
 
       - name: Build wheels
-        uses: joerick/cibuildwheel@v1.10.0
+        run: python -m cibuildwheel --output-dir wheelhouse
         # to supply options, put them in 'env', like:
-        # env:
-        #   CIBW_SOME_OPTION: value
         env:
-          CIBW_SKIP: cp27-* pp27-*
           GITHUB_BUILDING_WHEELS: 1
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl
-

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/Makefile

@@ -1,6 +1,6 @@
 OPTFLAGS=-O3 -march=native -mtune=native
 DEBUGFLAGS=-O0 -g -Werror -DISOSPEC_DEBUG -DDEBUG -D_GLIBCXX_DEBUG
-CXXFLAGS=-std=c++17 -Wall -pedantic -Wextra -Wshadow -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wmissing-include-dirs -Wno-old-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wno-sign-conversion -Wsign-promo -Wswitch-default -Wundef -Werror
+CXXFLAGS=-std=c++11 -Wall -pedantic -Wextra -Wshadow -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wmissing-include-dirs -Wno-old-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wno-sign-conversion -Wsign-promo -Wswitch-default -Wundef
 SRCFILES=cwrapper.cpp allocator.cpp  dirtyAllocator.cpp  isoSpec++.cpp  isoMath.cpp  marginalTrek++.cpp  operators.cpp element_tables.cpp misc.cpp mman.cpp fixedEnvelopes.cpp fasta.cpp
 
 all: unitylib
@@ -22,11 +22,11 @@ clean:
 
 windows:
 	#g++ -O3 -std=gnu++1z -O3 -shared -static -static-libstdc++ -static-libgcc unity-build.cpp -o ../IsoSpecPy/IsoSpec++.dll
-	x86_64-w64-mingw32-g++.exe -std=c++17 -O3 -shared -static -static-libstdc++ unity-build.cpp -o ../IsoSpecPy/IsoSpecPy/prebuilt-libIsoSpec++-2.1.0-x64.dll
-	i686-w64-mingw32-g++.exe -std=c++17 -O3 -shared -static -static-libstdc++ unity-build.cpp -o ../IsoSpecPy/IsoSpecPy/prebuilt-libIsoSpec++-2.1.0-x32.dll
+	x86_64-w64-mingw32-g++.exe -std=c++11 -O3 -shared -static -static-libstdc++ unity-build.cpp -o ../IsoSpecPy/IsoSpecPy/prebuilt-libIsoSpec++-2.1.0-x64.dll
+	i686-w64-mingw32-g++.exe -std=c++11 -O3 -shared -static -static-libstdc++ unity-build.cpp -o ../IsoSpecPy/IsoSpecPy/prebuilt-libIsoSpec++-2.1.0-x32.dll
 check:
 	cpplint *.cpp *.h
-	#cppcheck --std=c++17 --language=c++ --enable=style,portability,missingInclude,performance -q --force *.cpp *.h --suppress=memleakOnRealloc:*:* --inline-suppr --template={file}:{line}\ \({severity}\)\ \<{id}\>:\ {message}
+	#cppcheck --std=c++11 --language=c++ --enable=style,portability,missingInclude,performance -q --force *.cpp *.h --suppress=memleakOnRealloc:*:* --inline-suppr --template={file}:{line}\ \({severity}\)\ \<{id}\>:\ {message}
 
 check11:
 	$(CXX) -std=c++11 -Wall -pedantic -Wextra -Wshadow -fsyntax-only unity-build.cpp

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/cwrapper.cpp

@@ -357,10 +357,10 @@ double abyssalWassersteinDistanceGrad(void* const* envelopes, const double* scal
 struct ws_match_res wassersteinMatch(void* tabulator1, void* tabulator2, double flow_dist, double other_scale)
 {
     struct ws_match_res res;
-    auto [t1, t2, t3] = reinterpret_cast<FixedEnvelope*>(tabulator1)->WassersteinMatch(*reinterpret_cast<FixedEnvelope*>(tabulator2), flow_dist, other_scale);
-    res.res1 = t1;
-    res.res2 = t2;
-    res.flow = t3;
+    auto tuple = reinterpret_cast<FixedEnvelope*>(tabulator1)->WassersteinMatch(*reinterpret_cast<FixedEnvelope*>(tabulator2), flow_dist, other_scale);
+    res.res1 = std::get<0>(tuple);
+    res.res2 = std::get<1>(tuple);
+    res.flow = std::get<2>(tuple);
     return res;
 }
 

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/fixedEnvelopes.cpp

@@ -153,11 +153,11 @@ template<typename T> void reorder_array(T* arr, size_t* order, size_t size, bool
 
 void FixedEnvelope::sort_by(double* order)
 {
-    size_t* indices = new size_t[_confs_no];
-
     if(_confs_no <= 1)
         return;
 
+    size_t* indices = new size_t[_confs_no];
+
     for(size_t ii = 0; ii < _confs_no; ii++)
         indices[ii] = ii;
 
@@ -443,7 +443,9 @@ double FixedEnvelope::AbyssalWassersteinDistance(FixedEnvelope& other, double ab
 
     while(!finished())
     {
-        auto [m, p] = next();
+        auto pair = next();
+        double m = pair.first;
+        double p = pair.second;
         if(!carried.empty() && carried[0].second * p > 0.0)
         {
             carried.emplace_back(m, p);
@@ -452,7 +454,8 @@ double FixedEnvelope::AbyssalWassersteinDistance(FixedEnvelope& other, double ab
 
         while(!carried.empty())
         {
-            auto& [cm, cp] = carried.back();
+            double cm = carried.back().first;
+            double cp = carried.back().second;
             if(m - cm >= abyss_depth)
             {
                 for(auto it = carried.cbegin(); it != carried.cend(); it++)

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/isoSpec++.h

@@ -64,7 +64,7 @@ class ISOSPEC_EXPORT_SYMBOL Iso {
     int*            isotopeNumbers; /*!< A table with numbers of isotopes for each element. */
     int*            atomCounts;     /*!< A table with numbers of isotopes for each element. */
     unsigned int    confSize;       /*!< The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. */
-    int             allDim;         /*!< The total number of isotopes of elements present in a chemical formula, e.g. for H20 it is 2+3=5. */
+    int             allDim;         /*!< The total number of isotopes of elements present in a chemical formula, e.g. for H2O (water) it is 2+3=5. */
     Marginal**      marginals;      /*!< The table of pointers to the distributions of individual subisotopologues. */
 
     bool doMarginalsNeedSorting() const;

{IsoSpecPy-2.2.0/IsoSpecR/src → IsoSpecPy-2.2.2/IsoSpec++}/marginalTrek++.cpp

@@ -329,14 +329,20 @@ Marginal(std::move(m)),
 current_count(0),
 orderMarginal(atom_lProbs, isotopeNo),
 pq(),
-allocator(isotopeNo, tabSize)
+allocator(isotopeNo, tabSize),
+min_lprob(*std::min_element(atom_lProbs, atom_lProbs+isotopeNo))
 {
     int* initialConf = allocator.makeCopy(mode_conf);
 
-    pq.push({unnormalized_logProb(mode_conf), initialConf});
+    pq.push({mode_lprob, initialConf});
 
     current_count = 0;
 
+    fringe.resize_and_wipe(1);
+
+    current_bucket = 0;
+    initialized_until = 1;
+
     add_next_conf();
 }
 
@@ -347,9 +353,25 @@ bool MarginalTrek::add_next_conf()
     Add next configuration.
     If visited all, return false.
     */
-    if(pq.size() < 1) return false;
+    if(pq.empty())
+    {
+        current_bucket++;
+        while(current_bucket < initialized_until && fringe[current_bucket].empty())
+        {
+//            std::cout << "EMPTY bucket, id: " << current_bucket << std::endl;
+            current_bucket++;
+        }
+
+//        std::cout << "Entering bucket, size: " << fringe[current_bucket].size() << std::endl;
 
-    double logprob = pq.top().first + loggamma_nominator;
+        if(current_bucket >= initialized_until)
+            return false;
+
+    //    std::cout << "Fringe size at pop: " << fringe[current_bucket].size() << std::endl;
+        pq = std::priority_queue<ProbAndConfPtr, pod_vector<ProbAndConfPtr> >(std::less<ProbAndConfPtr>(), pod_vector<ProbAndConfPtr>(std::move(fringe[current_bucket])));
+    };
+
+    double logprob = pq.top().first;
     Conf topConf = pq.top().second;
 
     pq.pop();
@@ -379,9 +401,22 @@ bool MarginalTrek::add_next_conf()
                     ++acceptedCandidate[i];
                     --acceptedCandidate[j];
 
-                    double new_prob = unnormalized_logProb(acceptedCandidate);
+                    double new_prob = logProb(acceptedCandidate);
+                    size_t bucket_nr = bucket_no(new_prob);
+
+                    if(bucket_nr >= initialized_until)
+                    {
+                    //    std::cout << "Extending to: " << bucket_nr << std::endl;
+                        initialized_until = bucket_nr+1;
+                        fringe.resize_and_wipe(initialized_until);
+                    }
+
+                    ISOSPEC_IMPOSSIBLE(bucket_nr < current_bucket);
+                    if(bucket_nr == current_bucket)
+                        pq.push({new_prob, acceptedCandidate});
+                    else
+                        fringe[bucket_nr].push_back({new_prob, acceptedCandidate});
 
-                    pq.push({new_prob, acceptedCandidate});
                 }
 
                 if( topConf[i] > mode_conf[i] )
@@ -398,6 +433,9 @@ bool MarginalTrek::add_next_conf()
 
 MarginalTrek::~MarginalTrek()
 {
+    const size_t fringe_size = fringe.size();
+    for(size_t ii = 0; ii < fringe_size; ii++)
+        fringe[ii].clear();
 }
 
 

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/marginalTrek++.h

@@ -178,14 +178,21 @@ class MarginalTrek : public Marginal
     int current_count;
     const ConfOrderMarginal orderMarginal;
     std::priority_queue<ProbAndConfPtr, pod_vector<ProbAndConfPtr> > pq;
+    pod_vector<unsafe_pod_vector<ProbAndConfPtr> > fringe;
     Allocator<int> allocator;
     pod_vector<double> _conf_lprobs;
     pod_vector<double> _conf_masses;
     pod_vector<int*> _confs;
 
+    const double min_lprob;
+    size_t current_bucket;
+    size_t initialized_until;
+
     //! Proceed to the next configuration and memoize it (as it will be surely needed).
     bool add_next_conf();
 
+    size_t bucket_no(double lprob) { return static_cast<size_t>( (mode_lprob - lprob) * 100.0 ); }
+
  public:
     //! Move constructor: specializes the Marginal class.
     /*!

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/mman.cpp

@@ -26,7 +26,7 @@
 #endif /* FILE_MAP_EXECUTE */
 
 
-static int __map_mman_error(const DWORD err, const int deferr)
+static int __map_mman_error(const DWORD err, const int /* deferr */)
 {
     if (err == 0)
         return 0;
@@ -72,7 +72,7 @@ static DWORD __map_mmap_prot_file(const int prot)
     return desiredAccess;
 }
 
-void* mmap(void *addr, size_t len, int prot, int flags, int fildes, OffsetType off)
+void* mmap(void * /* addr */, size_t len, int prot, int flags, int fildes, OffsetType off)
 {
     HANDLE fm, h;
 
@@ -143,7 +143,7 @@ void* mmap(void *addr, size_t len, int prot, int flags, int fildes, OffsetType o
     return map;
 }
 
-int munmap(void *addr, size_t len)
+int munmap(void *addr, size_t /* len */)
 {
     if (UnmapViewOfFile(addr))
         return 0;
@@ -153,6 +153,10 @@ int munmap(void *addr, size_t len)
     return -1;
 }
 
+#if 0
+// Unused by IsoSpec
+
+
 int _mprotect(void *addr, size_t len, int prot)
 {
     DWORD newProtect = __map_mmap_prot_page(prot);
@@ -166,7 +170,7 @@ int _mprotect(void *addr, size_t len, int prot)
     return -1;
 }
 
-int msync(void *addr, size_t len, int flags)
+int msync(void *addr, size_t len, int /* flags */)
 {
     if (FlushViewOfFile(addr, len))
         return 0;
@@ -195,6 +199,6 @@ int munlock(const void *addr, size_t len)
 
     return -1;
 }
-
+#endif
 
 #endif

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpec++/pod_vector.h

@@ -18,10 +18,12 @@
 
 #include <type_traits>
 #include <cstdlib>
+#include <cstddef>
 #include <utility>
 #include <new>
 #include <algorithm>
 #include "platform.h"
+#include "conf.h"
 
 
 
@@ -29,10 +31,6 @@ template<typename T> class unsafe_pod_vector;
 
 template<typename T> class pod_vector
 {
-#if !ISOSPEC_BUILDING_R
-    static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
-#endif
-
     T* backend_past_end;
     T* first_free;
     T* store;
@@ -40,6 +38,10 @@ template<typename T> class pod_vector
  public:
     explicit pod_vector(size_t initial_size = 16)
     {
+    #if !ISOSPEC_BUILDING_R
+        static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
+    #endif
+
         store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size));
         if(store == NULL)
             throw std::bad_alloc();
@@ -49,6 +51,15 @@ template<typename T> class pod_vector
 
     pod_vector(const pod_vector<T>& other) = delete;
     pod_vector& operator=(const pod_vector<T>& other) = delete;
+    pod_vector& operator=(pod_vector<T>&& other)
+    {
+        free(store);
+        backend_past_end = other.backend_past_end;
+        first_free = other.first_free;
+        store = other.store;
+        other.backend_past_end = other.first_free = other.store = NULL;
+        return *this;
+    }
 
     pod_vector(pod_vector<T>&& other)
     {
@@ -58,22 +69,24 @@ template<typename T> class pod_vector
         other.backend_past_end = other.first_free = other.store = NULL;
     }
 
-    ~pod_vector() { free(store); }
+    ~pod_vector() { free(store); backend_past_end = first_free = store = NULL; }
 
     explicit pod_vector(unsafe_pod_vector<T>&& other)
     {
         backend_past_end = other.backend_past_end;
         first_free = other.first_free;
         store = other.store;
+       other.backend_past_end = other.first_free = other.store = NULL;
     }
 
     void fast_reserve(size_t n)
     {
         ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store));
+        const std::ptrdiff_t store_used_size = first_free - store;
         T* new_store = reinterpret_cast<T*>(realloc(store, n * sizeof(T)));
         if(new_store == NULL)
             throw std::bad_alloc();
-        first_free = new_store + (first_free - store);
+        first_free = new_store + store_used_size;
         backend_past_end = new_store + n;
         store = new_store;
     }
@@ -84,6 +97,28 @@ template<typename T> class pod_vector
             fast_reserve(n);
     }
 
+    void resize(size_t new_size)
+    {
+        ISOSPEC_IMPOSSIBLE(static_cast<std::ptrdiff_t>(new_size) < first_free - store);
+        size_t cap = capacity();
+        if(cap < new_size)
+        {
+            do {
+            cap = cap * 2;
+            } while(cap < new_size);
+            fast_reserve(cap);
+        }
+        first_free = store + new_size;
+    }
+
+    void resize_and_wipe(size_t new_size)
+    {
+        size_t old_size = size();
+        ISOSPEC_IMPOSSIBLE(new_size <= old_size);
+        resize(new_size);
+        memset(store+old_size, 0, (new_size-old_size) * sizeof(T));
+    }
+
     ISOSPEC_FORCE_INLINE void nocheck_push_back(const T& val) noexcept
     {
         ISOSPEC_IMPOSSIBLE(first_free >= backend_past_end);
@@ -188,10 +223,6 @@ template<typename T> class pod_vector
 
 template<typename T> class unsafe_pod_vector
 {
-#if !ISOSPEC_BUILDING_R
-    static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
-    static_assert(std::is_trivially_copyable<unsafe_pod_vector<T> >::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
-#endif
 
     T* backend_past_end;
     T* first_free;
@@ -200,10 +231,20 @@ template<typename T> class unsafe_pod_vector
  public:
     unsafe_pod_vector() = default;
 
-    void init() { memset(this, 0, sizeof(*this)); }
+    void init() {
+    #if !ISOSPEC_BUILDING_R
+        static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
+        static_assert(std::is_trivially_copyable<unsafe_pod_vector<T> >::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
+    #endif
+        memset(this, 0, sizeof(*this));
+    }
 
     void init(size_t initial_size)
     {
+    #if !ISOSPEC_BUILDING_R
+        static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
+        static_assert(std::is_trivially_copyable<unsafe_pod_vector<T> >::value, "Cannot use a pod_vector with a non-Plain Old Data type.");
+    #endif
         store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size));
         if(store == NULL)
             throw std::bad_alloc();
@@ -213,16 +254,10 @@ template<typename T> class unsafe_pod_vector
 
     unsafe_pod_vector(const pod_vector<T>& other) = delete;  // NOLINT(runtime/explicit) - seriously? Deleted constructors have to be marked explicit?
     unsafe_pod_vector& operator=(const pod_vector<T>& other) = delete;
-
-    unsafe_pod_vector(unsafe_pod_vector<T>&& other)
-    {
-        memcpy(this, *other, sizeof(*this));
-    }
+    //unsafe_pod_vector(unsafe_pod_vector<T>&& other) = default;
 
     ~unsafe_pod_vector() = default;
 
-    void free() { free(store); }
-
     void fast_reserve(size_t n)
     {
         ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store));
@@ -257,7 +292,7 @@ template<typename T> class unsafe_pod_vector
     void resize_and_wipe(size_t new_size)
     {
         size_t old_size = size();
-        ISOSPEC_IMPOSSIBLE(new_size < old_size);
+        ISOSPEC_IMPOSSIBLE(new_size <= old_size);
         resize(new_size);
         memset(store+old_size, 0, (new_size-old_size) * sizeof(T));
     }
@@ -362,4 +397,3 @@ template<typename T> class unsafe_pod_vector
 
     friend class pod_vector<T>;
 };
-

IsoSpecPy-2.2.2/IsoSpec++/test.cpp

@@ -0,0 +1,6 @@
+#include "isoSpec++.h"
+
+int main() {
+    auto orderedGenerator = IsoSpec::IsoOrderedGenerator("H2O1");
+    orderedGenerator.advanceToNextConfiguration();
+}

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecPy/Formulas.py

@@ -14,7 +14,7 @@ cholesterol = "C27H46O1"
 caffeine = "C8H10N4O2"
 water = "H2O1"
 glucose = "C6H12O6"
-surcose = "C12H22O11"
+sucrose = "C12H22O11"
 horse_myoglobin = "C769H1212N210O218S2"
 oxygen = "O2"
 

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecPy/__init__.py

@@ -1,7 +1,7 @@
 from .IsoSpecPy import *
 
 
-__version__ = "2.2.0"
+__version__ = "2.2.2"
 
 # Old, deprecated name, for compatibility with 1.9.X only
 IsoLayered = IsoTotalProb

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecPy/isoFFI.py

@@ -152,9 +152,9 @@ sure you want to do that, edit the source and disable this check.''')
         extension = ['.so', '.dylib', '.dll']
         try:
             if platform.system() == 'Linux':
-                extension = ['.so']
+                extension = ['.so', 'pyd']
             elif platform.system() == 'Windows':
-                extension = ['.dll']
+                extension = ['.dll', '.pyd']
         except:
             pass
 

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecPy.egg-info/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.1
 Name: IsoSpecPy
-Version: 2.2.0
+Version: 2.2.2
 Summary: Python interface to IsoSpec++ isotopic envelope calculator library
 Home-page: http://matteolacki.github.io/IsoSpec/
 Author: Mateusz Lacki & Michal Startek
 Author-email: matteo.lacki@gmail.com
 License: 2-clause BSD
 Keywords: isotopic envelope mass spectrometry
-Platform: UNKNOWN
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Chemistry
@@ -23,8 +22,10 @@ Classifier: Programming Language :: Python :: 3.6
 Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
-Provides-Extra: test
 License-File: LICENCE
+Requires-Dist: cffi
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: numpy; extra == "test"
 
 Python interface to IsoSpec++ isotopic envelope calculator library
-

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecPy.egg-info/SOURCES.txt

@@ -65,6 +65,7 @@ IsoSpec++/platform_incl.h
 IsoSpec++/pod_vector.h
 IsoSpec++/python-build.cpp
 IsoSpec++/summator.h
+IsoSpec++/test.cpp
 IsoSpec++/unity-build.cpp
 IsoSpecPy/Advanced.py
 IsoSpecPy/Distributions.py
@@ -194,6 +195,7 @@ tests/C++/marginal-test.cpp
 tests/C++/mass_range.cpp
 tests/C++/nr_conf.cpp
 tests/C++/tabulator_test.cpp
+tests/C++/test_marginal_ordered.cpp
 tests/C++/titin-test.cpp
 tests/C++/wasserstein_matching.cpp
 tests/Python/test_IsoSpecPy.py

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecR/src/cwrapper.cpp

@@ -357,10 +357,10 @@ double abyssalWassersteinDistanceGrad(void* const* envelopes, const double* scal
 struct ws_match_res wassersteinMatch(void* tabulator1, void* tabulator2, double flow_dist, double other_scale)
 {
     struct ws_match_res res;
-    auto [t1, t2, t3] = reinterpret_cast<FixedEnvelope*>(tabulator1)->WassersteinMatch(*reinterpret_cast<FixedEnvelope*>(tabulator2), flow_dist, other_scale);
-    res.res1 = t1;
-    res.res2 = t2;
-    res.flow = t3;
+    auto tuple = reinterpret_cast<FixedEnvelope*>(tabulator1)->WassersteinMatch(*reinterpret_cast<FixedEnvelope*>(tabulator2), flow_dist, other_scale);
+    res.res1 = std::get<0>(tuple);
+    res.res2 = std::get<1>(tuple);
+    res.flow = std::get<2>(tuple);
     return res;
 }
 

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecR/src/fixedEnvelopes.cpp

@@ -153,11 +153,11 @@ template<typename T> void reorder_array(T* arr, size_t* order, size_t size, bool
 
 void FixedEnvelope::sort_by(double* order)
 {
-    size_t* indices = new size_t[_confs_no];
-
     if(_confs_no <= 1)
         return;
 
+    size_t* indices = new size_t[_confs_no];
+
     for(size_t ii = 0; ii < _confs_no; ii++)
         indices[ii] = ii;
 
@@ -443,7 +443,9 @@ double FixedEnvelope::AbyssalWassersteinDistance(FixedEnvelope& other, double ab
 
     while(!finished())
     {
-        auto [m, p] = next();
+        auto pair = next();
+        double m = pair.first;
+        double p = pair.second;
         if(!carried.empty() && carried[0].second * p > 0.0)
         {
             carried.emplace_back(m, p);
@@ -452,7 +454,8 @@ double FixedEnvelope::AbyssalWassersteinDistance(FixedEnvelope& other, double ab
 
         while(!carried.empty())
         {
-            auto& [cm, cp] = carried.back();
+            double cm = carried.back().first;
+            double cp = carried.back().second;
             if(m - cm >= abyss_depth)
             {
                 for(auto it = carried.cbegin(); it != carried.cend(); it++)

{IsoSpecPy-2.2.0 → IsoSpecPy-2.2.2}/IsoSpecR/src/isoSpec++.h

@@ -64,7 +64,7 @@ class ISOSPEC_EXPORT_SYMBOL Iso {
     int*            isotopeNumbers; /*!< A table with numbers of isotopes for each element. */
     int*            atomCounts;     /*!< A table with numbers of isotopes for each element. */
     unsigned int    confSize;       /*!< The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. */
-    int             allDim;         /*!< The total number of isotopes of elements present in a chemical formula, e.g. for H20 it is 2+3=5. */
+    int             allDim;         /*!< The total number of isotopes of elements present in a chemical formula, e.g. for H2O (water) it is 2+3=5. */
     Marginal**      marginals;      /*!< The table of pointers to the distributions of individual subisotopologues. */
 
     bool doMarginalsNeedSorting() const;