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mobiusklein · Nov 4, 2023 · 7226550 · 7226550
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diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,8 @@
 [build-system]
 requires = ["setuptools",
             "wheel",
-            "Cython"]
+            "Cython"]
+
+[tool.ruff]
+target-version = "py38"
+line-length = 120
diff --git a/setup.py b/setup.py
@@ -123,7 +123,7 @@ def run_setup(include_cext=True):
         packages=find_packages(where='src'),
         package_dir={"": "src"},
         description="Fast and efficient theoretical isotopic profile generation",
-        long_description='''
+        long_description="""
 :mod:`brainpy` is a small Python library implementing the *B* afflingly *R* ecursive
 *A* lgorithm for *I* sotopic Patter *N* generation [Dittwald2014]_. It includes three implementations,
 a pure-Python object oriented implementation, a :title-reference:`Cython` accelerated
@@ -163,7 +163,7 @@ def run_setup(include_cext=True):
     H. Hu, P. Dittwald, J. Zaia, and D. Valkenborg,
     "Comment on 'Computation of isotopic peak center-mass distribution by fourier transform'.",
     Anal. Chem., vol. 85, no. 24, pp. 12189–92, Dec. 2013.
-    ''',
+    """,
         long_description_content_type='text/markdown',
         author=', '.join(["Joshua Klein", "Han Hu"]),
         author_email="[email protected]",
@@ -190,7 +190,7 @@ def run_setup(include_cext=True):
 if __name__ == '__main__':
     try:
         run_setup(True)
-    except Exception as exc:
+    except Exception:
         run_setup(False)
 
         status_msgs(

diff --git a/src/brainpy/__init__.py b/src/brainpy/__init__.py
@@ -1,11 +1,12 @@
-'''
-A Python Implementation of the Baffling Recursive Algorithm for Isotopic cluster distributioN
-'''
+"""
+A Python Implementation of the
+Baffling Recursive Algorithm for Isotopic cluster distributioN
+"""
 import os
 
 from .brainpy import (isotopic_variants, IsotopicDistribution, periodic_table,
                       max_variants, calculate_mass, neutral_mass, mass_charge_ratio,
-                      PROTON, _has_c, Peak)
+                      PROTON, _has_c, Peak, max_variants_approx)
 
 from .composition import parse_formula, PyComposition
 
@@ -14,20 +15,23 @@
 
 
 def get_include():
-    """Retrieve the path to compiled C extensions' source files to make linking simple.
-
-    This module contains two variants of the algorithm reimplimented using C and the Python-C API.
+    """
+    Retrieve the path to compiled C extensions' source files to make linking simple.
 
-    The `_speedup` module is a direct translation of the pure Python implementation using Cython,
-    using static typing and `cdef class` versions of the existing classes. As this implementation still
-    spends a substantial amount of time in Python-space, it is slower than the option below, but is more
-    straight-forward to manipulate from Python.
+    This module contains two variants of the algorithm reimplimented using C and the
+    Python-C API.
 
-    The `_c` module is a complete rewrite of the algorithm directly in C, using Python only to load
-    mass configuration information and is fully usable. It exports an entrypoint function to Python
-    which replaces the :func:`isotopic_variants` function when available. Because almost all of the
-    action happens in C here, it's not possible to run individual parts of the process directly from
+    The `_speedup` module is a direct translation of the pure Python implementation
+    using Cython, using static typing and `cdef class` versions of the existing classes.
+    As this implementation still spends a substantial amount of time in Python-space,
+    it is slower than the option below, but is more straight-forward to manipulate from
     Python.
+
+    The `_c` module is a complete rewrite of the algorithm directly in C, using Python
+    only to load mass configuration information and is fully usable. It exports an
+    entrypoint function to Python which replaces the :func:`isotopic_variants` function
+    when available. Because almost all of the action happens in C here, it's not
+    possible to run individual parts of the process directly from Python.
     """
     return os.path.join(__path__[0], "_c")
 
@@ -41,7 +45,7 @@ def get_include():
 __all__ = [
     "isotopic_variants", "IsotopicDistribution", "periodic_table",
     "max_variants", "calculate_mass", "neutral_mass", "mass_charge_ratio",
-    "PROTON", "_has_c", "Peak",
+    "PROTON", "_has_c", "Peak", "max_variants_approx",
 
     "parse_formula", "PyComposition", "SimpleComposition",
 

diff --git a/src/brainpy/_c/composition.pyx b/src/brainpy/_c/composition.pyx
@@ -507,9 +507,9 @@ def show_element(str element):
 # Composition Methods
 
 cdef Composition* make_composition() nogil:
-    '''
+    """
     Create a new, empty Composition struct
-    '''
+    """
     cdef:
         Composition* composition
     composition = <Composition*>malloc(sizeof(Composition))
@@ -521,9 +521,9 @@ cdef Composition* make_composition() nogil:
     return composition
 
 cdef int composition_eq(Composition* composition_1, Composition* composition_2) nogil:
-    '''
+    """
     Test two Composition instances for element-wise equality
-    '''
+    """
     cdef:
         int status
         size_t i
@@ -548,10 +548,10 @@ cdef int composition_eq(Composition* composition_1, Composition* composition_2)
     return 1
 
 cdef Composition* copy_composition(Composition* composition) nogil:
-    '''
+    """
     Create a new Composition instance whose element counts are copied from
     `composition`
-    '''
+    """
     cdef:
         Composition* result
         int status
@@ -600,14 +600,14 @@ cdef void print_composition(Composition* composition) nogil:
     printf("}\n\n")
 
 cdef int composition_set_element_count(Composition* composition, char* element, count_type count) nogil:
-    '''
+    """
     Set the count for `element` in `composition`
 
     Return Values:
     0: Success
     1: General Failure
     -1: Failure due to Out-of-Memory
-    '''
+    """
     cdef:
         size_t i
         int status
@@ -633,13 +633,13 @@ cdef int composition_set_element_count(Composition* composition, char* element,
     return 1
 
 cdef int composition_get_element_count(Composition* composition, char* element, count_type* count) nogil:
-    '''
+    """
     Get the count of `element` in `composition`. The count is 0 if `element` is not in `composition`
 
     Return Values:
     0: Success
     1: Not Found
-    '''
+    """
     cdef:
         size_t i
         int status
@@ -658,14 +658,14 @@ cdef int composition_get_element_count(Composition* composition, char* element,
     return 1
 
 cdef int composition_inc_element_count(Composition* composition, char* element, count_type increment) nogil:
-    '''
+    """
     Increase the count for `element` in `composition` by `increment`.
 
     Return Values:
     0: Success
     1: General Failure
     -1: Failure due to Out-of-Memory
-    '''
+    """
     cdef:
         size_t i
         int status
@@ -691,13 +691,13 @@ cdef int composition_inc_element_count(Composition* composition, char* element,
     return 1
 
 cdef int composition_resize(Composition* composition) nogil:
-    '''
+    """
     Increases the size of the parallel arrays in `composition`, doubling them in length
 
     Return Values:
     0: Success
     -1: Failure due to Out-of-Memory
-    '''
+    """
     composition.elements = <char**>realloc(composition.elements, sizeof(char*) * composition.size * 2)
     composition.counts = <count_type*>realloc(composition.counts, sizeof(count_type) * composition.size * 2)
     composition.size *= 2
@@ -706,13 +706,13 @@ cdef int composition_resize(Composition* composition) nogil:
     return 0
 
 cdef int composition_resize_to(Composition* composition, size_t size) nogil:
-    '''
+    """
     Increases the size of the parallel arrays in `composition`, doubling them in length
 
     Return Values:
     0: Success
     -1: Failure due to Out-of-Memory
-    '''
+    """
     composition.elements = <char**>realloc(composition.elements, sizeof(char*) * size)
     composition.counts = <count_type*>realloc(composition.counts, sizeof(count_type) * size)
     composition.size = size
@@ -721,9 +721,9 @@ cdef int composition_resize_to(Composition* composition, size_t size) nogil:
     return 0
 
 cdef double composition_mass(Composition* composition) nogil:
-    '''
+    """
     Calculates the monoisotopic mass of `composition`
-    '''
+    """
     cdef:
         double mass
         Element* element
@@ -983,13 +983,14 @@ def isotope_parse_test(str element_symbol):
 
 
 cdef class PyComposition(object):
-    '''A mapping representing a chemical composition.
+    """
+    A mapping representing a chemical composition.
 
     Implements arithmetic operations, +/- is defined
     between a :class:`PyComposition` and a :class:`Mapping`-like
     object, and * is defined between a :class:`PyComposition` and
     an integer.
-    '''
+    """
 
     @staticmethod
     cdef PyComposition _create(Composition* base):
@@ -1306,12 +1307,13 @@ cdef class PyComposition(object):
         return iter(self.keys())
 
     cpdef double mass(self):
-        '''Calculate the monoisotopic mass of this chemical composition
+        """
+        Calculate the monoisotopic mass of this chemical composition
 
         Returns
         -------
         float
-        '''
+        """
         if self._clean:
             return self.cached_mass
         else:

diff --git a/src/brainpy/_c/isotopic_distribution.pyx b/src/brainpy/_c/isotopic_distribution.pyx
@@ -674,7 +674,7 @@ cdef int guess_npeaks(Composition* composition_struct, size_t max_npeaks, Elemen
 
 def pyisotopic_variants(object composition not None, object npeaks=None, int charge=0,
                         double charge_carrier=PROTON):
-    '''
+    """
     Compute a peak list representing the theoretical isotopic cluster for `composition`.
 
     Parameters
@@ -695,12 +695,12 @@ def pyisotopic_variants(object composition not None, object npeaks=None, int cha
     Returns
     -------
     list of TheoreticalPeak
-    '''
+    """
     return _isotopic_variants(composition, npeaks, charge, charge_carrier)
 
 
 cpdef list _isotopic_variants(object composition, object npeaks=None, int charge=0, double charge_carrier=PROTON):
-    '''
+    """
     Compute a peak list representing the theoretical isotopic cluster for `composition`.
 
     Parameters
@@ -721,7 +721,7 @@ cpdef list _isotopic_variants(object composition, object npeaks=None, int charge
     Returns
     -------
     list of TheoreticalPeak
-    '''
+    """
     cdef:
         Composition* composition_struct
         list peaklist
@@ -889,7 +889,7 @@ def test(object composition, int max_npeaks=300):
 
 cdef size_t max_variants_approx(double mass, double lambda_factor=1800.0, size_t maxiter=255,
                                 double threshold=0.9999) nogil:
-    '''Approximate the maximum number of isotopic peaks to include in an isotopic distribution
+    """Approximate the maximum number of isotopic peaks to include in an isotopic distribution
     approximation for biomolecules using the Poisson distribution, using the method described
     in Bellew et al [1].
 
@@ -920,7 +920,7 @@ cdef size_t max_variants_approx(double mass, double lambda_factor=1800.0, size_t
     [1] Bellew, M., Coram, M., Fitzgibbon, M., Igra, M., Randolph, T., Wang, P., May, D., Eng, J., Fang, R., Lin, C., Chen, J.,
         Goodlett, D., Whiteaker, J., Paulovich, A., & Mcintosh, M. (2006). A suite of algorithms for the comprehensive analysis
         of complex protein mixtures using high-resolution LC-MS. 22(15), 1902–1909. https://doi.org/10.1093/bioinformatics/btl276
-    '''
+    """
     cdef:
         double lmbda = mass / lambda_factor
         double p_i = 1.0

diff --git a/src/brainpy/_speedup.pyx b/src/brainpy/_speedup.pyx
@@ -122,7 +122,7 @@ cdef class PhiConstants(object):
 
 
 cdef class Isotope(object):
-    '''
+    """
     Isotope represents an elenent with an integer number of neutrons specified.
 
     Attributes
@@ -134,7 +134,7 @@ cdef class Isotope(object):
     neutron_shift: int
         The number of neutrons different between this isotope and the "normal" form. May be 0
         if this represents that normal form.
-    '''
+    """
     cdef:
         public double mass
         public double abundance
@@ -607,11 +607,11 @@ cdef class IsotopicDistribution(object):
         return mass_vector
 
     def aggregated_isotopic_variants(self, int charge=0, double charge_carrier=PROTON):
-        '''
+        """
         Compute the m/z (or neutral mass when `charge` == 0) for each
         aggregated isotopic peak and their intensity relative to
         the monoisotopic peak.
-        '''
+        """
         cdef:
             list probability_vector
             list center_mass_vector