IsoSpecPy 2.2.1__tar.gz → 2.2.3__tar.gz

isospecpy-2.2.3/.github/workflows/build_wheels.yml

@@ -0,0 +1,40 @@
+name: Build
+
+on:
+  push:
+    branches:
+#      - version_2_2
+      - ci_wheels
+    tags:
+      - v*
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        #os: [ubuntu-20.04, windows-2019, macos-10.15]
+        os: [windows-latest, macos-13, macos-14, macos-15]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v5
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        # to supply options, put them in 'env', like:
+        env:
+          GITHUB_BUILDING_WHEELS: 1
+          CIBW_SKIP: pp*-*
+
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/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
+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-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/IsoSpecPy/IsoSpecPyOld.py

@@ -34,6 +34,9 @@ except NameError:
 import re
 from .IsoSpecPy import IsoTotalProb, IsoThreshold
 
+DIGIT_PATTERN = re.compile(r"\d+")
+NON_DIGIT_PATTERN = re.compile(r"\D+")
+
 class IsoSpec():
     def __init__(
                     self,
@@ -95,8 +98,8 @@ class IsoSpec():
     def IsoFromFormula(formula, cutoff, tabSize = 1000, hashSize = 1000, classId = None, method = 'threshold_relative', step = 0.25, trim = True):
         # It's much easier to just parse it in python than to use the C parsing function
         # and retrieve back into Python the relevant object sizes
-        symbols = re.findall("\D+", formula)
-        atom_counts = [int(x) for x in re.findall("\d+", formula)]
+        symbols = re.findall(NON_DIGIT_PATTERN, formula)
+        atom_counts = [int(x) for x in re.findall(DIGIT_PATTERN, formula)]
 
         if not len(symbols) == len(atom_counts):
             raise ValueError("Invalid formula")

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/IsoSpecPy/__init__.py

@@ -1,7 +1,7 @@
 from .IsoSpecPy import *
 
 
-__version__ = "2.2.1"
+__version__ = "2.2.3"
 
 # Old, deprecated name, for compatibility with 1.9.X only
 IsoLayered = IsoTotalProb

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/IsoSpecPy.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: IsoSpecPy
-Version: 2.2.1
+Version: 2.2.3
 Summary: Python interface to IsoSpec++ isotopic envelope calculator library
 Home-page: http://matteolacki.github.io/IsoSpec/
-Author: Mateusz Lacki & Michal Startek
+Author: Mateusz Łącki & Michał Startek
 Author-email: matteo.lacki@gmail.com
 License: 2-clause BSD
 Keywords: isotopic envelope mass spectrometry
@@ -22,7 +22,24 @@ 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
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 License-File: LICENCE
+Requires-Dist: cffi
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: numpy; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 Python interface to IsoSpec++ isotopic envelope calculator library

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/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-2.2.1 → isospecpy-2.2.3}/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;

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/LICENCE

@@ -8,7 +8,7 @@ your own software, but you are under no legal obligation to do so.
 -------------------------------------------------------------------------
 
 
-Copyright (c) 2015-2020, Micha� Startek and Mateusz ��cki
+Copyright (c) 2015-2025, Michał Startek and Mateusz Łącki
 
 All rights reserved.
 

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: IsoSpecPy
-Version: 2.2.1
+Version: 2.2.3
 Summary: Python interface to IsoSpec++ isotopic envelope calculator library
 Home-page: http://matteolacki.github.io/IsoSpec/
-Author: Mateusz Lacki & Michal Startek
+Author: Mateusz Łącki & Michał Startek
 Author-email: matteo.lacki@gmail.com
 License: 2-clause BSD
 Keywords: isotopic envelope mass spectrometry
@@ -22,7 +22,24 @@ 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
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 License-File: LICENCE
+Requires-Dist: cffi
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: numpy; extra == "test"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 Python interface to IsoSpec++ isotopic envelope calculator library

{IsoSpecPy-2.2.1 → isospecpy-2.2.3}/setup.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 """A setuptools based setup module.
 
@@ -8,7 +9,6 @@ https://github.com/pypa/sampleproject
 
 # Always prefer setuptools over distutils
 from setuptools import setup, find_packages, Extension
-from distutils import spawn
 # To use a consistent encoding
 from codecs import open
 import os
@@ -28,13 +28,18 @@ here = os.path.abspath(os.path.dirname(__file__))
 #with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
 #    long_description = f.read()
 
+native_ok = not ('darwin' in platform.system().lower())
+
 def get_cflags():
     if 'windows' in platform.system().lower():
         # Assuming MSVC, probably Anaconda
         return ["/O2", "/std:c++17"]
     if use_asan:
         return '-O0 -g -DISOSPEC_DEBUG -std=c++17 -fsanitize=address'.split()
-    return '-mtune=native -march=native -O3 -std=c++17'.split()
+    ret = ['-O3', '-std=c++17']
+    if native_ok:
+        ret.extend(['-mtune=native', '-march=native'])
+    return ret
 
 cmodule = Extension('IsoSpecCppPy',
                 sources = ['IsoSpec++/python-build.cpp'],
@@ -49,7 +54,7 @@ setup_args = {
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    'version': '2.2.1',
+    'version': '2.2.3',
 
     'description': 'Python interface to IsoSpec++ isotopic envelope calculator library',
     'long_description': 'Python interface to IsoSpec++ isotopic envelope calculator library',
@@ -58,7 +63,7 @@ setup_args = {
     'url': 'http://matteolacki.github.io/IsoSpec/',
 
     # Author details
-    'author': 'Mateusz Lacki & Michal Startek',
+    'author': 'Mateusz Łącki & Michał Startek',
     'author_email': 'matteo.lacki@gmail.com',
 
     # Choose your license
@@ -92,6 +97,10 @@ setup_args = {
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
 
     # What does your project relate to?
@@ -148,7 +157,7 @@ if 'cygwin' in platform.system().lower():
         print("You appear to be using CYGWIN, and CFFI was not found. Please use the Cygwin installer to install the cffi-python package for the appropriate Python version.")
         print("Installing CFFI using pip will most likely NOT work. This is *NOT* a bug in IsoSpecPy.")
         sys.exit(1)
-    if spawn.find_executable('clang++') == None:
+    if shutil.which('clang++') is None:
         print("You appear to be using CYGWIN and clang++ executable was not found. Please install the clang++ package using Cygwin installer.")
         sys.exit(1)
     import distutils

IsoSpecPy-2.2.1/.github/workflows/build_wheels.yml

@@ -1,39 +0,0 @@
-name: Build
-
-on:
-  push:
-    branches:
-      - version_2_2
-      - ci_wheels
-    tags:
-      - v*
-
-jobs:
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        #os: [ubuntu-20.04, windows-2019, macos-10.15]
-        os: [windows-2019]
-
-    steps:
-      - uses: actions/checkout@v2
-
-#      - name: Install Visual C++ for Python 2.7
-#        if: runner.os == 'Windows'
-#        run: choco install vcpython27 -f -y
-
-      - name: Build wheels
-        uses: joerick/cibuildwheel@v1.10.0
-        # 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
-        with:
-          path: ./wheelhouse/*.whl
-