IsoSpecPy 2.3.0.dev4__tar.gz → 2.3.0.dev11__tar.gz

isospecpy-2.3.0.dev11/PKG-INFO

@@ -0,0 +1,43 @@
+Metadata-Version: 2.4
+Name: IsoSpecPy
+Version: 2.3.0.dev11
+Summary: IsoSpecPy is a Python library for computing isotopic distributions of molecules.
+Keywords: isotopic distribution,mass spectrometry,chemistry,isotopic envelope,isotopologues
+Author: Michał Startek, Mateusz Łącki
+License-Expression: BSD-2-Clause
+License-File: LICENCE
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Operating System :: OS Independent
+Project-URL: Homepage, https://github.com/MatteoLacki/IsoSpec
+Project-URL: Repository, https://github.com/MatteoLacki/IsoSpec
+Requires-Python: >=3.6
+Requires-Dist: cffi
+Provides-Extra: testing
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: OldIsoSpecPy; extra == "testing"
+Description-Content-Type: text/markdown
+
+IsoSpec, the isotopic fine structure calculator
+===============================================
+
+The main purpose of this software package is to be used as a library, 
+mostly in mass spectrometry software. We do not provide any standalone
+programs, except for those in Examples directory which are intended to
+showcase the usage of the library.
+
+Please see the code in Examples directory for example usage.
+
+The software is publically available under a 2-clause BSD licence. If 
+you require other licensing terms, please contact the authors. See 
+LICENCE file for more details.
+
+More details about the program may be found in the following Analytical
+Chemistry publications:
+
+https://pubs.acs.org/doi/10.1021/acs.analchem.0c00959
+https://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01459
+
+See especially the Supporting Information for details about the algorithm.

isospecpy-2.3.0.dev11/pyproject.toml

@@ -0,0 +1,58 @@
+[build-system]
+requires = ["setuptools", "scikit-build-core"]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build]
+cmake.source-dir = "skbuild"
+
+[project]
+name = "IsoSpecPy"
+dependencies = ["cffi"]
+description = "IsoSpecPy is a Python library for computing isotopic distributions of molecules."
+version = "2.3.0dev11"
+license = "BSD-2-Clause"
+license-files = ["LICENCE"]
+authors = [{name = "Michał Startek"}, {name = "Mateusz Łącki"}]
+readme = "README.md"
+requires-python = ">=3.6"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Development Status :: 5 - Production/Stable",
+    "Operating System :: OS Independent",
+]
+keywords = ["isotopic distribution", "mass spectrometry", "chemistry", "isotopic envelope", "isotopologues"]
+
+[project.urls]
+Homepage = "https://github.com/MatteoLacki/IsoSpec"
+Repository = "https://github.com/MatteoLacki/IsoSpec"
+
+
+
+[project.optional-dependencies]
+testing = ["pytest", "OldIsoSpecPy"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests/Python"]
+
+[tool.cibuildwheel]
+enable = ["pypy"]
+skip = ["cp36-*", "cp37-*", "pp37-*"]
+test-command = "python -m pytest {project}/tests/Python"
+#test-sources = ["tests/Python"]
+test-extras = ["testing"]
+
+[tool.scikit-build.sdist]
+exclude = ["**/*"]
+include = [
+    "/src/IsoSpecPy/*.py",
+    "/src/IsoSpec++/*.c",
+    "/src/IsoSpec++/*.h",
+    "/src/IsoSpec++/*.hpp",
+    "/src/IsoSpec++/*.cpp",
+    "/LICENCE",
+    "/README.md",
+    "/pyproject.toml",
+    "/skbuild/CMakeLists.txt"
+]

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11}/skbuild/CMakeLists.txt

@@ -2,13 +2,17 @@ cmake_minimum_required(VERSION 3.15)
 
 project(IsoSpecPy CXX)
 
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
 #find_package(PythonExtensions REQUIRED)
 #find_package(Python COMPONENTS Interpreter Development REQUIRED)
 
-add_library(IsoSpecCppPy SHARED ../IsoSpec++/unity-build.cpp)
+add_library(IsoSpecCppPy SHARED ../src/IsoSpec++/unity-build.cpp)
 target_compile_features(IsoSpecCppPy PRIVATE cxx_std_17)
 #python_extension_module(IsoSpecCppPy)
 install(TARGETS IsoSpecCppPy LIBRARY DESTINATION IsoSpecPy)
-install(DIRECTORY ../IsoSpec++/ DESTINATION IsoSpecPy/IsoSpec++
+install(DIRECTORY ../src/IsoSpec++/ DESTINATION IsoSpecPy/IsoSpec++
         FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp" PATTERN "*.hxx"
 )

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/cwrapper.h

@@ -16,6 +16,8 @@
 
 #pragma once
 
+#include "platform.h"
+
 #define ISOSPEC_ALGO_LAYERED 0
 #define ISOSPEC_ALGO_ORDERED 1
 #define ISOSPEC_ALGO_THRESHOLD_ABSOLUTE 2
@@ -50,22 +52,6 @@ ISOSPEC_C_API double* getMarginalLogSizeEstimates(void* iso, double target_total
 
 ISOSPEC_C_API void deleteIso(void* iso);
 
-#define ISOSPEC_C_FN_HEADER(generatorType, dataType, method)\
-ISOSPEC_C_API dataType method##generatorType(void* generator);
-
-#define ISOSPEC_C_FN_HEADER_GET_CONF_SIGNATURE(generatorType)\
-ISOSPEC_C_API void method##generatorType(void* generator);
-
-#define ISOSPEC_C_FN_HEADERS(generatorType)\
-ISOSPEC_C_FN_HEADER(generatorType, double, mass) \
-ISOSPEC_C_FN_HEADER(generatorType, double, lprob) \
-ISOSPEC_C_FN_HEADER(generatorType, double, prob) \
-ISOSPEC_C_FN_HEADER_GET_CONF_SIGNATURE(generatorType) \
-ISOSPEC_C_FN_HEADER(generatorType, bool, advanceToNextConfiguration) \
-ISOSPEC_C_FN_HEADER(generatorType, void, delete)
-
-
-
 
 // ______________________________________________________THRESHOLD GENERATOR
 ISOSPEC_C_API void* setupIsoThresholdGenerator(void* iso,
@@ -74,7 +60,12 @@ ISOSPEC_C_API void* setupIsoThresholdGenerator(void* iso,
                                  int _tabSize,
                                  int _hashSize,
                                  bool reorder_marginals);
-ISOSPEC_C_FN_HEADERS(IsoThresholdGenerator)
+ISOSPEC_C_API double massIsoThresholdGenerator(void* generator);
+ISOSPEC_C_API double lprobIsoThresholdGenerator(void* generator);
+ISOSPEC_C_API double probIsoThresholdGenerator(void* generator);
+ISOSPEC_C_API void get_conf_signatureIsoThresholdGenerator(void* generator, int* space);
+ISOSPEC_C_API bool advanceToNextConfigurationIsoThresholdGenerator(void* generator);
+ISOSPEC_C_API void deleteIsoThresholdGenerator(void* generator);
 
 
 // ______________________________________________________LAYERED GENERATOR
@@ -83,20 +74,35 @@ ISOSPEC_C_API void* setupIsoLayeredGenerator(void* iso,
                                int _hashSize,
                                bool reorder_marginals,
                                double t_prob_hint);
-ISOSPEC_C_FN_HEADERS(IsoLayeredGenerator)
+ISOSPEC_C_API double massIsoLayeredGenerator(void* generator);
+ISOSPEC_C_API double lprobIsoLayeredGenerator(void* generator);
+ISOSPEC_C_API double probIsoLayeredGenerator(void* generator);
+ISOSPEC_C_API void get_conf_signatureIsoLayeredGenerator(void* generator, int* space);
+ISOSPEC_C_API bool advanceToNextConfigurationIsoLayeredGenerator(void* generator);
+ISOSPEC_C_API void deleteIsoLayeredGenerator(void* generator);
 
 // ______________________________________________________ORDERED GENERATOR
 ISOSPEC_C_API void* setupIsoOrderedGenerator(void* iso,
                                int _tabSize,
                                int _hashSize);
-ISOSPEC_C_FN_HEADERS(IsoOrderedGenerator)
-
+ISOSPEC_C_API double massIsoOrderedGenerator(void* generator);
+ISOSPEC_C_API double lprobIsoOrderedGenerator(void* generator);
+ISOSPEC_C_API double probIsoOrderedGenerator(void* generator);
+ISOSPEC_C_API void get_conf_signatureIsoOrderedGenerator(void* generator, int* space);
+ISOSPEC_C_API bool advanceToNextConfigurationIsoOrderedGenerator(void* generator);
+ISOSPEC_C_API void deleteIsoOrderedGenerator(void* generator);
+
+// ______________________________________________________STOCHASTIC GENERATOR
 ISOSPEC_C_API void* setupIsoStochasticGenerator(void* iso,
                                    size_t no_molecules,
                                    double precision,
                                    double beta_bias);
-ISOSPEC_C_FN_HEADERS(IsoStochasticGenerator)
-
+ISOSPEC_C_API double massIsoStochasticGenerator(void* generator);
+ISOSPEC_C_API double lprobIsoStochasticGenerator(void* generator);
+ISOSPEC_C_API double probIsoStochasticGenerator(void* generator);
+ISOSPEC_C_API void get_conf_signatureIsoStochasticGenerator(void* generator, int* space);
+ISOSPEC_C_API bool advanceToNextConfigurationIsoStochasticGenerator(void* generator);
+ISOSPEC_C_API void deleteIsoStochasticGenerator(void* generator);
 
 ISOSPEC_C_API void* setupThresholdFixedEnvelope(void* iso,
                               double threshold,
@@ -143,7 +149,7 @@ ISOSPEC_C_API double orientedWassersteinDistance(void* tabulator1, void* tabulat
 ISOSPEC_C_API double abyssalWassersteinDistance(void* tabulator1, void* tabulator2, double abyss_depth, double other_scale);
 //ISOSPEC_C_API double abyssalWassersteinDistanceGrad(void* const* envelopes, const double* scales, double* ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the);
 
-ISOSPEC_C_API struct ws_match_res{
+struct ws_match_res{
 double res1;
 double res2;
 double flow;

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/element_tables.cpp

@@ -23,7 +23,7 @@ namespace IsoSpec
 extern "C" {
 #endif
 
-const size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES;
+const ::size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES;
 
 const int elem_table_ID [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {
 1,

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/element_tables.h

@@ -18,6 +18,8 @@
 
 #include <stddef.h>
 
+#include "platform.h"
+
 namespace IsoSpec
 {
 

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/fixedEnvelopes.cpp

@@ -16,6 +16,7 @@
 
 #include "fixedEnvelopes.h"
 #include <limits>
+#include <cassert>
 #include "isoMath.h"
 
 namespace IsoSpec

{isospecpy-2.3.0.dev4 → isospecpy-2.3.0.dev11/src}/IsoSpec++/marginalTrek++.cpp

@@ -737,4 +737,7 @@ SingleAtomMarginal<add_guards>::SingleAtomMarginal(Marginal&& m, int, int)
         guarded_lProbs = lProbs.data();
 }
 
+template class SingleAtomMarginal<true>;
+template SingleAtomMarginal<false>::SingleAtomMarginal(IsoSpec::Marginal&&, int, int);
+
 }  // namespace IsoSpec

{isospecpy-2.3.0.dev4 → isospecpy-2.3.0.dev11/src}/IsoSpec++/misc.cpp

@@ -25,7 +25,7 @@
 namespace IsoSpec
 {
 
-void* quickselect(void ** array, int n, int start, int end)
+void* quickselect(void ** array, size_t n, size_t start, size_t end)
 {
     if(start == end)
         return array[start];
@@ -33,9 +33,9 @@ void* quickselect(void ** array, int n, int start, int end)
     while(true)
     {
         // Partition part
-        int len = end - start;
+        size_t len = end - start;
 #if ISOSPEC_BUILDING_R
-        int pivot = len/2 + start;
+        size_t pivot = len/2 + start;
 #else
         size_t pivot = random_gen() % len + start;  // Using Mersenne twister directly - we don't
                                                     // need a very uniform distribution just for pivot
@@ -44,8 +44,8 @@ void* quickselect(void ** array, int n, int start, int end)
         void* pval = array[pivot];
         double pprob = getLProb(pval);
         std::swap(array[pivot], array[end-1]);
-        int loweridx = start;
-        for(int i = start; i < end-1; i++)
+        size_t loweridx = start;
+        for(size_t i = start; i < end-1; i++)
         {
             if(getLProb(array[i]) < pprob)
             {

{isospecpy-2.3.0.dev4 → isospecpy-2.3.0.dev11/src}/IsoSpec++/misc.h

@@ -82,11 +82,11 @@ inline double calc_mass(const int* conf, const double* masses, int dim)
 
 
 
-template<typename T> void printArray(const T* array, int size, const char* prefix = "")
+template<typename T> void printArray(const T* array, size_t size, const char* prefix = "")
 {
     if (strlen(prefix) > 0)
         std::cout << prefix << " ";
-    for (int i = 0; i < size; i++)
+    for (size_t i = 0; i < size; i++)
         std::cout << array[i] << " ";
     std::cout << std::endl;
 }
@@ -101,34 +101,34 @@ template<typename T> void printVector(const pod_vector<T>& vec)
     printArray<T>(vec.data(), vec.size());
 }
 
-template<typename T> void printOffsets(const T** array, int size, const T* offset, const char* prefix = "")
+template<typename T> void printOffsets(const T** array, size_t size, const T* offset, const char* prefix = "")
 {
     if (strlen(prefix) > 0)
         std::cout << prefix << " ";
-    for (int i = 0; i < size; i++)
+    for (size_t i = 0; i < size; i++)
         std::cout << array[i] - offset << " ";
     std::cout << std::endl;
 }
 
-template<typename T> void printNestedArray(const T** array, const int* shape, int size)
+template<typename T> void printNestedArray(const T** array, const int* shape, size_t size)
 {
-    for (int i = 0; i < size; i++)
+    for (size_t i = 0; i < size; i++)
         printArray(array[i], shape[i]);
     std::cout << std::endl;
 }
 
 //! Quickly select the n'th positional statistic, including the weights.
-void* quickselect(const void** array, int n, int start, int end);
+void* quickselect(const void** array, size_t n, size_t start, size_t end);
 
 
-template <typename T> inline static T* array_copy(const T* A, int size)
+template <typename T> inline static T* array_copy(const T* A, size_t size)
 {
     T* ret = new T[size];
     memcpy(ret, A, size*sizeof(T));
     return ret;
 }
 
-template <typename T> static T* array_copy_nptr(const T* A, int size)
+template <typename T> static T* array_copy_nptr(const T* A, size_t size)
 {
     if(A == nullptr)
         return nullptr;
@@ -159,7 +159,7 @@ template<typename T> size_t* get_order(T* order_array, size_t N)
     for(size_t ii = 0; ii < N; ii++)
         arr[ii] = ii;
 
-    std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] < order_array[j]; });
+    std::sort(arr, arr + N, [&](size_t i, size_t j) { return order_array[i] < order_array[j]; });
 
     return arr;
 }
@@ -170,7 +170,7 @@ template<typename T> size_t* get_inverse_order(T* order_array, size_t N)
     for(size_t ii = 0; ii < N; ii++)
         arr[ii] = ii;
 
-    std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] > order_array[j]; });
+    std::sort(arr, arr + N, [&](size_t i, size_t j) { return order_array[i] > order_array[j]; });
 
     return arr;
 }

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/operators.h

@@ -126,7 +126,7 @@ template<typename T> class TableOrder
         const T* tbl;
  public:
         inline explicit TableOrder(const T* _tbl) : tbl(_tbl) {}
-        inline bool operator()(unsigned int i, unsigned int j) { return tbl[i] < tbl[j]; }
+        inline bool operator()(size_t i, size_t j) { return tbl[i] < tbl[j]; }
 };
 
 }  // namespace IsoSpec
@@ -143,7 +143,7 @@ template<typename T> class OrderMarginalsBySizeDecresing
     T const* const* const MT;
  public:
     explicit OrderMarginalsBySizeDecresing(T const* const * const MT_) : MT(MT_) {};
-    inline bool operator()(int m1, int m2) { return MT[m1]->get_no_confs() > MT[m2]->get_no_confs(); }
+    inline bool operator()(size_t m1, size_t m2) { return MT[m1]->get_no_confs() > MT[m2]->get_no_confs(); }
 };
 
 

{isospecpy-2.3.0.dev4/aaa/isospecpy-2.3.0.dev1 → isospecpy-2.3.0.dev11/src}/IsoSpec++/platform.h

@@ -64,7 +64,7 @@
 #define ISOSPEC_IMPOSSIBLE(condition) __assume(!(condition));
 #define ISOSPEC_LIKELY(condition) condition
 #define ISOSPEC_UNLIKELY(condition) condition
-#define ISOSPEC_FORCE_INLINE __forceinline inline
+#define ISOSPEC_FORCE_INLINE __forceinline
 #else
 #define ISOSPEC_IMPOSSIBLE(condition)
 #define ISOSPEC_LIKELY(condition) condition
@@ -96,7 +96,11 @@
 #define ISOSPEC_EXPORT_SYMBOL
 #endif
 
+#if defined(_WIN32) || defined(_WIN64)
+#define ISOSPEC_C_API __declspec(dllexport)
+#else
 #define ISOSPEC_C_API
+#endif
 
 #if !defined(__cpp_if_constexpr)
 #define constexpr_if if

{isospecpy-2.3.0.dev4 → isospecpy-2.3.0.dev11/src}/IsoSpecPy/IsoSpecPy.py

@@ -9,11 +9,11 @@
 #
 #   IsoSpec is distributed in the hope that it will be useful,
 #   but WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 #
 #   You should have received a copy of the Simplified BSD Licence
 #   along with IsoSpec.  If not, see <https://opensource.org/licenses/BSD-2-Clause>.
-# 
+#
 
 from .isoFFI import isoFFI
 import re
@@ -39,7 +39,7 @@ def ParseFormula(formula):
 
     Args:
         formula (str): a chemical formula, e.g. "C2H6O1" or "C2H6O"
-    
+
     Returns:
         A tuple containing element symbols and atomCounts of elements in the parsed formula.
     """
@@ -110,6 +110,19 @@ def IsoParamsFromDict(formula, use_nominal_masses = False):
     return ParsedFormula(atomCounts, masses, probs, symbols)
 
 
+def IsoParamsFromFormula(formula, use_nominal_masses = False):
+    """Produces a set of IsoSpec parameters from a chemical formula.
+
+    Args:
+        formula (str): a chemical formula, e.g. "C2H6O1" or "C2H6O"
+        use_nominal_masses (boolean): use masses of elements rounded to integer numbers (nominal masses)
+
+    Returns:
+        ParsedFormula: a tuple containing atomCounts, masses and marginal probabilities of elements in the parsed formula.
+    """
+    parsed = ParseFormula(formula)
+    return IsoParamsFromDict(parsed, use_nominal_masses = use_nominal_masses)
+
 
 class Iso(object):
     """Virtual class representing an isotopic distribution."""
@@ -699,7 +712,7 @@ class IsoGenerator(Iso):
 
     def __del__(self):
         super(IsoGenerator, self).__del__()
-        
+
 
 class IsoThresholdGenerator(IsoGenerator):
     """Class alowing memory-efficient iteration over the isotopic distribution up till some probability threshold.

{isospecpy-2.3.0.dev4 → isospecpy-2.3.0.dev11/src}/IsoSpecPy/isoFFI.py

@@ -1,12 +1,11 @@
 import cffi
-import os
 import platform
 import sys
 import glob
+from pathlib import Path
 if False:
     import IsoSpecCppPy
 
-
 class IsoFFI:
     def __init__(self):
         self.ffi = cffi.FFI()
@@ -37,7 +36,12 @@ class IsoFFI:
                                          int _tabSize,
                                          int _hashSize,
                                          bool reorder_marginals);
-        double massIsoThresholdGenerator(void* generator); double lprobIsoThresholdGenerator(void* generator); double probIsoThresholdGenerator(void* generator); void methodIsoThresholdGenerator(void* generator); bool advanceToNextConfigurationIsoThresholdGenerator(void* generator); void deleteIsoThresholdGenerator(void* generator); void get_conf_signatureIsoThresholdGenerator(void* generator, int* space);
+        double massIsoThresholdGenerator(void* generator);
+        double lprobIsoThresholdGenerator(void* generator);
+        double probIsoThresholdGenerator(void* generator);
+        bool advanceToNextConfigurationIsoThresholdGenerator(void* generator);
+        void deleteIsoThresholdGenerator(void* generator);
+        void get_conf_signatureIsoThresholdGenerator(void* generator, int* space);
 
 
 
@@ -46,19 +50,34 @@ class IsoFFI:
                                        int _hashSize,
                                        bool reorder_marginals,
                                        double t_prob_hint);
-        double massIsoLayeredGenerator(void* generator); double lprobIsoLayeredGenerator(void* generator); double probIsoLayeredGenerator(void* generator); void methodIsoLayeredGenerator(void* generator); bool advanceToNextConfigurationIsoLayeredGenerator(void* generator); void deleteIsoLayeredGenerator(void* generator); void get_conf_signatureIsoLayeredGenerator(void* generator, int* space);
+        double massIsoLayeredGenerator(void* generator);
+        double lprobIsoLayeredGenerator(void* generator);
+        double probIsoLayeredGenerator(void* generator);
+        bool advanceToNextConfigurationIsoLayeredGenerator(void* generator);
+        void deleteIsoLayeredGenerator(void* generator);
+        void get_conf_signatureIsoLayeredGenerator(void* generator, int* space);
 
 
         void* setupIsoOrderedGenerator(void* iso,
                                        int _tabSize,
                                        int _hashSize);
-        double massIsoOrderedGenerator(void* generator); double lprobIsoOrderedGenerator(void* generator); double probIsoOrderedGenerator(void* generator); void methodIsoOrderedGenerator(void* generator); bool advanceToNextConfigurationIsoOrderedGenerator(void* generator); void deleteIsoOrderedGenerator(void* generator); void get_conf_signatureIsoOrderedGenerator(void* generator, int* space);
+        double massIsoOrderedGenerator(void* generator);
+        double lprobIsoOrderedGenerator(void* generator);
+        double probIsoOrderedGenerator(void* generator);
+        bool advanceToNextConfigurationIsoOrderedGenerator(void* generator);
+        void deleteIsoOrderedGenerator(void* generator);
+        void get_conf_signatureIsoOrderedGenerator(void* generator, int* space);
 
         void* setupIsoStochasticGenerator(void* iso,
                                    size_t no_molecules,
                                    double precision,
                                    double beta_bias);
-        double massIsoStochasticGenerator(void* generator); double lprobIsoStochasticGenerator(void* generator); double probIsoStochasticGenerator(void* generator); void methodIsoStochasticGenerator(void* generator); bool advanceToNextConfigurationIsoStochasticGenerator(void* generator); void deleteIsoStochasticGenerator(void* generator); void get_conf_signatureIsoStochasticGenerator(void* generator, int* space);
+        double massIsoStochasticGenerator(void* generator);
+        double lprobIsoStochasticGenerator(void* generator);
+        double probIsoStochasticGenerator(void* generator);
+        bool advanceToNextConfigurationIsoStochasticGenerator(void* generator);
+        void deleteIsoStochasticGenerator(void* generator);
+        void get_conf_signatureIsoStochasticGenerator(void* generator, int* space);
 
         void* setupThresholdFixedEnvelope(void* iso,
                                     double threshold,
@@ -140,9 +159,9 @@ class IsoFFI:
         extern const bool elem_table_Radioactive[NUMBER_OF_ISOTOPIC_ENTRIES];
                         ''');
 
-        mod_dir = os.path.dirname(os.path.abspath(__file__))
+        mod_dir = Path(__file__).resolve().parent
 
-        if os.path.exists(os.path.join(mod_dir, '..', 'setup.py')):
+        if (mod_dir.parent / 'setup.py').exists():
             raise ImportError('''Attempted to load IsoSpecPy module from its build directory. This usually
 won't work and is generally a Bad Idea. Please cd somewhere else, or, if you're really
 sure you want to do that, edit the source and disable this check.''')
@@ -168,19 +187,20 @@ sure you want to do that, edit the source and disable this check.''')
             return res
 
         paths_to_check = cprod(prebuilt, cprod(libprefix, cprod(libnames, extension)))
-
         dpc = []
 
-        for dirpath in [mod_dir, mod_dir + '/..']:
-            dpc.extend([os.path.join(dirpath, p) for p in paths_to_check])
+        for dirpath in [mod_dir, mod_dir.parent, mod_dir.parent / 'bin', mod_dir.parent / 'lib']:
+            dpc.extend([dirpath / p for p in paths_to_check])
 
         paths_to_check = dpc
-
-        paths_to_check = sum(map(glob.glob, paths_to_check), [])
-
+        # expand glob patterns using pathlib (keep only actual matches, like glob.glob did)
+        expanded = []
+        for p in paths_to_check:
+            expanded.extend(p.parent.glob(p.name))
+        paths_to_check = expanded
         try:
             import importlib
-            paths_to_check.insert(0, importlib.util.find_spec("IsoSpecCppPy").origin)
+            paths_to_check.insert(0, Path(importlib.util.find_spec("IsoSpecCppPy").origin))
         except (ImportError, AttributeError):
             pass
 
@@ -189,7 +209,7 @@ sure you want to do that, edit the source and disable this check.''')
         self.clib = None
         for libpath in set(paths_to_check):
             try:
-                self.clib = self.ffi.dlopen(libpath)
+                self.clib = self.ffi.dlopen(str(libpath))
                 self.libpath = libpath
                 break
             except (IndexError, OSError) as e:

isospecpy-2.3.0.dev4/.github/workflows/build_wheels.yml

@@ -1,40 +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: ${{ matrix.os }}
-    strategy:
-      matrix:
-        #os: [ubuntu-20.04, windows-2019, macos-10.15]
-        os: [ubuntu-22.04, windows-latest, macos-13, macos-14, macos-15]
-
-    steps:
-      - uses: actions/checkout@v4
-
-      # Used to host cibuildwheel
-      - uses: actions/setup-python@v5
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel
-
-      - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-        # to supply options, put them in 'env', like:
-        env:
-          GITHUB_BUILDING_WHEELS: 1
-          CIBW_SKIP: pp*-* cp36-* cp37-*
-
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl

isospecpy-2.3.0.dev4/.vscode/settings.json

@@ -1,48 +0,0 @@
-{
-    "files.associations": {
-        "__bit_reference": "cpp",
-        "__hash_table": "cpp",
-        "__locale": "cpp",
-        "__node_handle": "cpp",
-        "__split_buffer": "cpp",
-        "__verbose_abort": "cpp",
-        "array": "cpp",
-        "bitset": "cpp",
-        "cctype": "cpp",
-        "clocale": "cpp",
-        "cmath": "cpp",
-        "cstdarg": "cpp",
-        "cstdint": "cpp",
-        "cstdio": "cpp",
-        "cstdlib": "cpp",
-        "cstring": "cpp",
-        "ctime": "cpp",
-        "cwchar": "cpp",
-        "cwctype": "cpp",
-        "deque": "cpp",
-        "execution": "cpp",
-        "initializer_list": "cpp",
-        "iomanip": "cpp",
-        "ios": "cpp",
-        "iosfwd": "cpp",
-        "iostream": "cpp",
-        "istream": "cpp",
-        "limits": "cpp",
-        "locale": "cpp",
-        "mutex": "cpp",
-        "new": "cpp",
-        "optional": "cpp",
-        "print": "cpp",
-        "queue": "cpp",
-        "ratio": "cpp",
-        "stdexcept": "cpp",
-        "streambuf": "cpp",
-        "string": "cpp",
-        "string_view": "cpp",
-        "typeinfo": "cpp",
-        "unordered_map": "cpp",
-        "variant": "cpp",
-        "vector": "cpp",
-        "algorithm": "cpp"
-    }
-}