biotite 0.38.0__tar.gz → 0.40.0__tar.gz

{biotite-0.38.0/src/biotite.egg-info → biotite-0.40.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biotite
-Version: 0.38.0
+Version: 0.40.0
 Summary: A comprehensive library for computational molecular biology
 Author: The Biotite contributors
 License: BSD 3-Clause License
@@ -52,7 +52,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 Requires-Dist: requests>=2.12
-Requires-Dist: numpy>=1.14.5
+Requires-Dist: numpy<=2.0,>=1.14.5
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
 Provides-Extra: test

{biotite-0.38.0 → biotite-0.40.0}/pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 # this should be manually updated as the minimum python version increases
 dependencies = [
   "requests >= 2.12",
-  "numpy >= 1.14.5",
+  "numpy >= 1.14.5, <= 2.0",
   "msgpack >= 0.5.6",
   "networkx >= 2.0",
 ]

{biotite-0.38.0 → biotite-0.40.0}/setup.py

@@ -39,17 +39,21 @@ try:
     )
 except ValueError:
     # This is a source distribution and the directory already contains
-    # only C files
+    # only C/C++ files
     pass
 
 
 def get_extensions():
     ext_sources = []
-    for dirpath, dirnames, filenames in os.walk(normpath("src/biotite")):
-        for filename in fnmatch.filter(filenames, '*.c'):
+    for dirpath, _, filenames in os.walk(normpath("src/biotite")):
+        for filename in (
+            fnmatch.filter(filenames, "*.c") +
+            fnmatch.filter(filenames, "*.cpp")
+        ):
             ext_sources.append(os.path.join(dirpath, filename))
     ext_names = [source
                  .replace("src"+normpath("/"), "")
+                 .replace(".cpp", "")
                  .replace(".c", "")
                  .replace(normpath("/"), ".")
                  for source in ext_sources]
@@ -64,23 +68,26 @@ setup(
     zip_safe = False,
     packages = find_packages("src"),
     package_dir = {"" : "src"},
-    
+
     ext_modules = get_extensions(),
-    
+
     # Including additional data
     package_data = {
-        # Substitution matrices
-        "biotite.sequence.align"    : ["matrix_data/*.mat"],
+        "biotite.sequence.align"    : [
+            # Substitution matrices
+            "matrix_data/*.mat",
+            # Prime hash table sizes
+            "primes.txt"
+        ],
         # Color schmemes
         "biotite.sequence.graphics" : ["color_schemes/*.json"],
         # Codon tables
         "biotite.sequence"          : ["codon_tables.txt"],
         # Structure data (masses, bonds, etc.)
-        "biotite.structure.info"    : ["*.json", "*.msgpack"]
+        "biotite.structure.info"    : ["atom_masses.json", "ccd/*"]
     },
 )
 
 
 # Return to original directory
 os.chdir(original_wd)
-

{biotite-0.38.0 → biotite-0.40.0}/src/biotite/__init__.py

@@ -9,11 +9,11 @@ it does provide utilities and base classes used by a lot of *Biotite*'s
 modules.
 """
 
-__version__ = "0.38.0"
+__version__ = "0.40.0"
 __name__ = "biotite"
 __author__ = "Patrick Kunzmann"
 
 from .file import *
 from .temp import *
-from .copyable import * 
-from .visualize import * 
+from .copyable import *
+from .visualize import *

{biotite-0.38.0 → biotite-0.40.0}/src/biotite/application/application.py

@@ -15,7 +15,7 @@ from enum import Flag, auto
 
 class AppState(Flag):
     """
-    This enum type represents the app states of an application. 
+    This enum type represents the app states of an application.
     """
     CREATED = auto()
     RUNNING = auto()
@@ -30,17 +30,17 @@ def requires_state(app_state):
     raises an :class:`AppStateError` in case the method is called, when
     the :class:`Application` is not in the specified :class:`AppState`
     `app_state`.
-    
+
     Parameters
     ----------
     app_state : AppState
         The required app state.
-    
+
     Examples
     --------
     Raises :class:`AppStateError` when `function` is called,
     if :class:`Application` is not in one of the specified states:
-    
+
     >>> @requires_state(AppState.RUNNING | AppState.FINISHED)
     ... def function(self):
     ...     pass
@@ -49,7 +49,12 @@ def requires_state(app_state):
         @wraps(func)
         def wrapper(*args, **kwargs):
             # First parameter of method is always 'self'
-            instance = args[0]
+            try:
+                instance = args[0]
+            except IndexError:
+                raise TypeError(
+                    "This method must be called from a class instance"
+                )
             if not instance._state & app_state:
                 raise AppStateError(
                     f"The application is in {instance.get_app_state()} state, "
@@ -66,7 +71,7 @@ class Application(metaclass=abc.ABCMeta):
     software in any sense. Subclasses of this abstract base class
     specify the respective kind of software and the way of interacting
     with it.
-    
+
     Every :class:`Application` runs through a different app states
     (instances of enum :class:`AppState`) from its creation until its
     termination:
@@ -95,15 +100,15 @@ class Application(metaclass=abc.ABCMeta):
     accessible results.
     If a method is called in an unsuitable app state, an
     :class:`AppStateError` is called.
-    
+
     The application run behaves like an additional thread: Between the
     call of :func:`start()` and :func:`join()` other Python code can be
     executed, while the application runs in the background.
     """
-    
+
     def __init__(self):
         self._state = AppState.CREATED
-    
+
     @requires_state(AppState.CREATED)
     def start(self):
         """
@@ -113,17 +118,17 @@ class Application(metaclass=abc.ABCMeta):
         self.run()
         self._start_time = time.time()
         self._state = AppState.RUNNING
-    
+
     @requires_state(AppState.RUNNING | AppState.FINISHED)
     def join(self, timeout=None):
         """
         Conclude the application run and set its state to *JOINED*.
         This can only be done from the *RUNNING* or *FINISHED* state.
-        
+
         If the application is *FINISHED* the joining process happens
         immediately, if otherwise the application is *RUNNING*, this
         method waits until the application is *FINISHED*.
-        
+
         Parameters
         ----------
         timeout : float, optional
@@ -132,7 +137,7 @@ class Application(metaclass=abc.ABCMeta):
             out.
             After this time is exceeded a :class:`TimeoutError` is
             raised and the application is cancelled.
-        
+
         Raises
         ------
         TimeoutError
@@ -159,7 +164,7 @@ class Application(metaclass=abc.ABCMeta):
         else:
             self._state = AppState.JOINED
         self.clean_up()
-    
+
     @requires_state(AppState.RUNNING | AppState.FINISHED)
     def cancel(self):
         """
@@ -167,11 +172,11 @@ class Application(metaclass=abc.ABCMeta):
         """
         self._state = AppState.CANCELLED
         self.clean_up()
-    
+
     def get_app_state(self):
         """
         Get the current app state.
-        
+
         Returns
         -------
         app_state : AppState
@@ -181,38 +186,38 @@ class Application(metaclass=abc.ABCMeta):
             if self.is_finished():
                 self._state = AppState.FINISHED
         return self._state
-    
+
     @abc.abstractmethod
     def run(self):
         """
         Commence the application run. Called in :func:`start()`.
-        
+
         PROTECTED: Override when inheriting.
         """
         pass
-    
+
     @abc.abstractmethod
     def is_finished(self):
         """
         Check if the application has finished.
-        
+
         PROTECTED: Override when inheriting.
-        
+
         Returns
         -------
         finished : bool
             True of the application has finished, false otherwise
         """
         pass
-    
+
     @abc.abstractmethod
     def wait_interval(self):
         """
         The time interval of :func:`is_finished()` calls in the joining
         process.
-        
+
         PROTECTED: Override when inheriting.
-        
+
         Returns
         -------
         interval : float
@@ -220,20 +225,20 @@ class Application(metaclass=abc.ABCMeta):
             :func:`join()`
         """
         pass
-    
+
     @abc.abstractmethod
     def evaluate(self):
         """
         Evaluate application results. Called in :func:`join()`.
-        
+
         PROTECTED: Override when inheriting.
         """
         pass
-    
+
     def clean_up(self):
         """
         Do clean up work after the application terminates.
-        
+
         PROTECTED: Optionally override when inheriting.
         """
         pass

{biotite-0.38.0 → biotite-0.40.0}/src/biotite/application/dssp/app.py

@@ -9,7 +9,7 @@ __all__ = ["DsspApp"]
 from tempfile import NamedTemporaryFile
 from ..localapp import LocalApp, cleanup_tempfile
 from ..application import AppState, requires_state
-from ...structure.io.pdbx.file import PDBxFile
+from ...structure.io.pdbx.cif import CIFFile
 from ...structure.io.pdbx.convert import set_structure
 import numpy as np
 
@@ -18,13 +18,13 @@ class DsspApp(LocalApp):
     r"""
     Annotate the secondary structure of a protein structure using the
     *DSSP* software.
-    
+
     Internally this creates a :class:`Popen` instance, which handles
     the execution.
-    
+
     DSSP differentiates between 8 different types of secondary
     structure elements:
-    
+
        - C: loop, coil or irregular
        - H: :math:`{\alpha}`-helix
        - B: :math:`{\beta}`-bridge
@@ -32,15 +32,15 @@ class DsspApp(LocalApp):
        - G: 3 :sub:`10`-helix
        - I: :math:`{\pi}`-helix
        - T: hydrogen bonded turn
-       - S: bend 
-    
+       - S: bend
+
     Parameters
     ----------
     atom_array : AtomArray
         The atom array to be annotated.
     bin_path : str, optional
         Path of the *DDSP* binary.
-    
+
     Examples
     --------
 
@@ -51,7 +51,7 @@ class DsspApp(LocalApp):
     ['C' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'T' 'T' 'G' 'G' 'G' 'G' 'T' 'C' 'C' 'C'
      'C' 'C']
     """
-    
+
     def __init__(self, atom_array, bin_path="mkdssp"):
         super().__init__(bin_path)
 
@@ -77,15 +77,15 @@ class DsspApp(LocalApp):
         self._out_file = NamedTemporaryFile("r", suffix=".dssp", delete=False)
 
     def run(self):
-        in_file = PDBxFile()
-        set_structure(in_file, self._array, data_block="DSSP_INPUT")
+        in_file = CIFFile()
+        set_structure(in_file, self._array)
         in_file.write(self._in_file)
         self._in_file.flush()
         self.set_arguments(
             ["-i", self._in_file.name, "-o", self._out_file.name]
         )
         super().run()
-    
+
     def evaluate(self):
         super().evaluate()
         lines = self._out_file.read().split("\n")
@@ -106,17 +106,17 @@ class DsspApp(LocalApp):
         for i, line in enumerate(lines):
             self._sse[i] = line[16]
         self._sse[self._sse == " "] = "C"
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._in_file)
         cleanup_tempfile(self._out_file)
-    
+
     @requires_state(AppState.JOINED)
     def get_sse(self):
         """
         Get the resulting secondary structure assignment.
-        
+
         Returns
         -------
         sse : ndarray, dtype="U1"
@@ -124,22 +124,22 @@ class DsspApp(LocalApp):
             corresponding to the residues in the input atom array.
         """
         return self._sse
-    
+
     @staticmethod
     def annotate_sse(atom_array, bin_path="mkdssp"):
         """
         Perform a secondary structure assignment to an atom array.
-        
+
         This is a convenience function, that wraps the :class:`DsspApp`
         execution.
-        
+
         Parameters
         ----------
         atom_array : AtomArray
             The atom array to be annotated.
         bin_path : str, optional
             Path of the DDSP binary.
-        
+
         Returns
         -------
         sse : ndarray, dtype="U1"

{biotite-0.38.0 → biotite-0.40.0}/src/biotite/application/sra/__init__.py

@@ -5,6 +5,11 @@
 """
 A subpackage for obtaining sequencing data from the *NCBI*
 *sequence read archive* (SRA).
+
+It comprises two central classes:
+:class:`FastqDumpApp` downloads sequence reads in FASTQ format.
+If only sequences (and no scores) are required :class:`FastaDumpApp`
+writes sequence reads into FASTA format.
 """
 
 __name__ = "biotite.application.sra"