biotite 1.1.0__tar.gz → 1.3.0__tar.gz

{biotite-1.1.0 → biotite-1.3.0}/PKG-INFO

@@ -1,46 +1,16 @@
 Metadata-Version: 2.4
 Name: biotite
-Version: 1.1.0
+Version: 1.3.0
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
 Project-URL: documentation, https://www.biotite-python.org
 Author: The Biotite contributors
-License: BSD 3-Clause License
-        --------------------
-        
-        Copyright 2017, The Biotite contributors
-        All rights reserved.
-        
-        Redistribution and use in source and binary forms, with or without modification,
-        are permitted provided that the following conditions are met:
-        
-        1. Redistributions of source code must retain the above copyright notice, this
-        list of conditions and the following disclaimer.
-        
-        2. Redistributions in binary form must reproduce the above copyright notice,
-        this list of conditions and the following disclaimer in the documentation and/or
-        other materials provided with the distribution.
-        
-        3. Neither the name of the copyright holder nor the names of its contributors
-        may be used to endorse or promote products derived from this software without
-        specific prior written permission.
-        
-        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-        ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-        WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-        ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-        (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-        LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-        ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-        (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-Expression: BSD-3-Clause
 License-File: LICENSE.rst
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
@@ -48,14 +18,16 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Requires-Dist: biotraj<2.0,>=1.0
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
 Requires-Dist: numpy>=1.25
+Requires-Dist: packaging>=24.0
 Requires-Dist: requests>=2.12
 Provides-Extra: lint
-Requires-Dist: ruff==0.6.9; extra == 'lint'
+Requires-Dist: numpydoc==1.8.0; extra == 'lint'
+Requires-Dist: ruff==0.9.7; extra == 'lint'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-codspeed; extra == 'test'
@@ -186,5 +158,5 @@ Contribution
 
 Interested in improving *Biotite*?
 Have a look at the
-`contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
+`contribution guidelines <https://www.biotite-python.org/latest/contribution/index.html>`_.
 Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

{biotite-1.1.0 → biotite-1.3.0}/README.rst

@@ -123,5 +123,5 @@ Contribution
 
 Interested in improving *Biotite*?
 Have a look at the
-`contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
+`contribution guidelines <https://www.biotite-python.org/latest/contribution/index.html>`_.
 Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

{biotite-1.1.0 → biotite-1.3.0}/pyproject.toml

@@ -1,15 +1,15 @@
 [project]
 name = "biotite"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 description = "A comprehensive library for computational molecular biology"
 readme = "README.rst"
 authors = [{name = "The Biotite contributors"}]
-license = {"file" = "LICENSE.rst"}
+license = "BSD-3-Clause"
+license-files = ["LICENSE.rst"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS",
@@ -27,7 +27,7 @@ dependencies = [
   "requests >= 2.12",
   "msgpack >= 0.5.6",
   "networkx >= 2.0",
-  "requests >= 2.12",
+  "packaging >= 24.0",
 ]
 dynamic = ["version"]
 
@@ -37,7 +37,8 @@ test = [
   "pytest-codspeed",
 ]
 lint = [
-  "ruff == 0.6.9"
+  "ruff == 0.9.7",
+  "numpydoc == 1.8.0",
 ]
 
 [project.urls]
@@ -63,6 +64,8 @@ ignore = [
 "doc/conf.py" = ["E402"]
 # Due to `from .module import *` imports in `__init__.py` modules
 "__init__.py" = ["F403", "TID252"]
+# Due to package existence check before other modules are imported
+"src/biotite/interface/**/__init__.py" = ["E402"]
 # Due to pymol scripts that are evaluated in other example scripts
 "doc/examples/**/*_pymol.py" = ["F821"]
 # Due to 'Table' class used as parametrized argument in test functions
@@ -83,6 +86,53 @@ no-lines-before = [
 order-by-type = true
 known-first-party = ["biotite"]
 
+[tool.numpydoc_validation]
+# The description of each rule is documented at
+# https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks
+checks = [
+  "all",
+  # ... except:
+  "GL08",  # Properties do not have a docstring
+  "SS03",  # Sometimes the citation comes after the period
+  "SS05",  # Too error-prone; classes do not use infinite verbs
+  "SS06",  # Sometimes summaries are a bit longer
+  "ES01",  # Some functions are simple enough to not need an extended summary
+  "PR06",  # The types are quite descriptive (include shape, dtype, etc.)
+  "RT02",  # In Biotite all return values have names
+  # Intentionally not all docstrings contain these sections
+  "YD01",
+  "SA01",
+  "EX01",
+]
+exclude = [
+  '__init__$', # Subpackage descriptions are not Numpydoc formatted
+  '\._[_a-z0-9]+$',  # Do not validate private or special methods
+  # Dataclasses: Numpydoc complains about additional constructor parameters,
+  # but the constructor is absent
+  'sdf.Metadata\.Key',
+  'header.Header',
+  'throttle.ThrottleStatus',
+  # Numpydoc does not accept the parameters of inherited constructors
+  "query.DepositGrouping",
+  "query.UniprotGrouping",
+  # Function uses args/kwargs, but docstring describes parameter
+  'geometry.index_',
+  'query.FieldQuery',
+  'query.SimilarityQuery',
+  'query.IdentityQuery',
+  'query.StructureQuery',
+  'query.SuperOrSubstructureQuery',
+  'query.SuperstructureQuery',
+  'query.SubstructureQuery',
+  # Numpydoc expects a return value for decorators
+  'application.requires_state',
+  'version.requires_version',
+  'object.validate',
+  # Usage of the return value is not intended
+  'display.show',
+  'display.play',
+]
+
 [tool.pytest.ini_options]
 testpaths = [
   "tests",
@@ -102,7 +152,6 @@ filterwarnings = [
   "ignore:Input structure has no associated 'BondList'",
 ]
 
-
 [tool.hatch.build.targets.sdist]
 exclude = [
   "tests",

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/application.py

@@ -157,7 +157,7 @@ class Application(metaclass=abc.ABCMeta):
             if timeout is not None and time.time() - self._start_time > timeout:
                 self.cancel()
                 raise TimeoutError(
-                    f"The application expired its timeout " f"({timeout:.1f} s)"
+                    f"The application expired its timeout ({timeout:.1f} s)"
                 )
             else:
                 time.sleep(self.wait_interval())
@@ -214,7 +214,7 @@ class Application(metaclass=abc.ABCMeta):
         Returns
         -------
         finished : bool
-            True of the application has finished, false otherwise
+            True of the application has finished, false otherwise.
         """
         pass
 
@@ -230,7 +230,7 @@ class Application(metaclass=abc.ABCMeta):
         -------
         interval : float
             Time (in seconds) between calls of :func:`is_finished()` in
-            :func:`join()`
+            :func:`join()`.
         """
         pass
 

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/autodock/app.py

@@ -153,7 +153,7 @@ class VinaApp(LocalApp):
 
         Parameters
         ----------
-        number : float
+        energy_range : float
             The energy range (kcal/mol).
         """
         self._energy_range = energy_range

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/blast/webapp.py

@@ -46,7 +46,7 @@ class BlastWebApp(WebApp):
     obey_rules : bool, optional
         If true, the application raises an :class:`RuleViolationError`,
         if the server is contacted too often, based on the NCBI BLAST
-        usage rules. (Default: True)
+        usage rules.
     mail : str, optional
         If a mail address is provided, it will be appended in the
         HTTP request. This allows the NCBI to contact you in case

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/clustalo/app.py

@@ -172,7 +172,7 @@ class ClustalOmegaApp(MSAApp):
         """
         if self._mbed:
             raise ValueError(
-                "Getting the distance matrix requires " "'full_matrix_calculation()'"
+                "Getting the distance matrix requires 'full_matrix_calculation()'"
             )
         return self._dist_matrix
 

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/localapp.py

@@ -178,7 +178,7 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         Returns
         -------
         process : Popen
-            The `Popen` instance
+            The `Popen` instance.
         """
         return self._process
 
@@ -279,7 +279,7 @@ class LocalApp(Application, metaclass=abc.ABCMeta):
         if exit_code != 0:
             err_msg = self.get_stderr().replace("\n", " ")
             raise SubprocessError(
-                f"'{self._bin_path}' returned with exit code {exit_code}: " f"{err_msg}"
+                f"'{self._bin_path}' returned with exit code {exit_code}: {err_msg}"
             )
 
     def clean_up(self):

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/msaapp.py

@@ -68,7 +68,7 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         # Check matrix symmetry
         if matrix is not None and not matrix.is_symmetric():
             raise ValueError(
-                "A symmetric matrix is required for " "multiple sequence alignments"
+                "A symmetric matrix is required for multiple sequence alignments"
             )
 
         # Check whether the program supports the alignment for the given
@@ -274,12 +274,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports nucleotide sequences for
         alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -290,12 +290,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports nucleotide sequences for
         alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -306,12 +306,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports custom substitution matrices
         for protein sequence alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -322,12 +322,12 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Check whether this class supports custom substitution matrices
         for nucleotide sequence alignment.
 
+        PROTECTED: Override when inheriting.
+
         Returns
         -------
         support : bool
             True, if the class has support, false otherwise.
-
-        PROTECTED: Override when inheriting.
         """
         pass
 
@@ -342,7 +342,7 @@ class MSAApp(LocalApp, metaclass=abc.ABCMeta):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default
             path will be used.

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/muscle/app3.py

@@ -29,9 +29,9 @@ class MuscleApp(MSAApp):
     matrix : SubstitutionMatrix, optional
         A custom substitution matrix.
 
-    See also
+    See Also
     --------
-    Muscle5App
+    Muscle5App : Interface to MUSCLE version ``>=5``.
 
     Examples
     --------
@@ -197,7 +197,7 @@ class MuscleApp(MSAApp):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default path
             will be used.

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/muscle/app5.py

@@ -22,9 +22,9 @@ class Muscle5App(MSAApp):
     bin_path : str, optional
         Path of the MUSCLE binary.
 
-    See also
+    See Also
     --------
-    MuscleApp
+    MuscleApp : Interface to MUSCLE version ``<5``.
 
     Notes
     -----
@@ -147,7 +147,7 @@ class Muscle5App(MSAApp):
         Parameters
         ----------
         sequences : iterable object of Sequence
-            The sequences to be aligned
+            The sequences to be aligned.
         bin_path : str, optional
             Path of the MSA software binary. By default, the default path
             will be used.

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/sra/app.py

@@ -45,11 +45,6 @@ class _DumpApp(Application, metaclass=abc.ABCMeta):
     prefetch_path, fasterq_dump_path : str, optional
         Path to the ``prefetch_path`` and ``fasterq-dump`` binary,
         respectively.
-    offset : int or {'Sanger', 'Solexa', 'Illumina-1.3', 'Illumina-1.5', 'Illumina-1.8'}, optional
-        This value is subtracted from the FASTQ ASCII code to obtain the
-        quality score.
-        Can either be directly the value, or a string that indicates
-        the score format.
     """
 
     def __init__(

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/util.py

@@ -17,6 +17,16 @@ def map_sequence(sequence):
     Map a sequence with an arbitrary alphabet into a
     :class:`ProteinSequence`, in order to support arbitrary sequence
     types in software that can handle protein sequences.
+
+    Parameters
+    ----------
+    sequence : Sequence
+        The sequence to be mapped.
+
+    Returns
+    -------
+    mapped_sequence : ProteinSequence
+        The mapped sequence.
     """
     if len(sequence.alphabet) > len(ProteinSequence.alphabet):
         # Cannot map into a protein sequence if the alphabet
@@ -40,10 +50,20 @@ def map_matrix(matrix):
     class:`SubstitutionMatrix` for protein sequences, in order to support
     arbitrary sequence types in software that can handle protein
     sequences.
+
+    Parameters
+    ----------
+    matrix : SubstitutionMatrix
+        The substitution matrix to be mapped.
+
+    Returns
+    -------
+    mapped_matrix : SubstitutionMatrix
+        The mapped substitution matrix.
     """
     if matrix is None:
         raise TypeError(
-            "A substitution matrix must be provided for custom " "sequence types"
+            "A substitution matrix must be provided for custom sequence types"
         )
     # Create a protein substitution matrix with the values taken
     # from the original matrix

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/viennarna/rnaalifold.py

@@ -167,15 +167,15 @@ class RNAalifoldApp(LocalApp):
         free_energy : float
             The free energy.
 
+        See Also
+        --------
+        get_covariance_energy : Get the energy of the artificial covariance term.
+
         Notes
         -----
         The total energy of the secondary structure regarding the
         minimization objective is the sum of the free energy and the
         covariance term.
-
-        See also
-        --------
-        get_covariance_energy
         """
         return self._free_energy
 
@@ -190,15 +190,15 @@ class RNAalifoldApp(LocalApp):
         covariance_energy : float
             The energy of the covariance term.
 
+        See Also
+        --------
+        get_free_energy : Get the free energy.
+
         Notes
         -----
         The total energy of the secondary structure regarding the
         minimization objective is the sum of the free energy and the
         covariance term.
-
-        See also
-        --------
-        get_free_energy
         """
         return self._covariance_energy
 

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/viennarna/rnaplot.py

@@ -28,15 +28,15 @@ class RNAplotApp(LocalApp):
 
     Parameters
     ----------
-    dot_bracket : str, optional (default: None)
+    dot_bracket : str, optional
         The structure in dot bracket notation.
-    base_pairs : ndarray, shape=(n,2), optional (default: None)
+    base_pairs : ndarray, shape=(n,2), optional
         Each row corresponds to the positions of the bases in the
         strand. This parameter is mutually exclusive to ``dot_bracket``.
-    length : int, optional (default: None)
+    length : int, optional
         The number of bases in the strand. This parameter is required if
         ``base_pairs`` is given.
-    layout_type : RNAplotApp.Layout, optional (default: RNAplotApp.Layout.NAVIEW)
+    layout_type : RNAplotApp.Layout, optional
         The layout type according to the *RNAplot* documentation.
     bin_path : str, optional
         Path of the *RNAplot* binary.
@@ -124,7 +124,7 @@ class RNAplotApp(LocalApp):
 
         Parameters
         ----------
-        type : RNAplotApp.Layout
+        layout_type : RNAplotApp.Layout
             The layout type.
         """
         self._layout_type = str(layout_type)
@@ -176,15 +176,17 @@ class RNAplotApp(LocalApp):
 
         Parameters
         ----------
-        dot_bracket : str, optional (default: None)
+        dot_bracket : str, optional
             The structure in dot bracket notation.
-        base_pairs : ndarray, shape=(n,2), optional (default: None)
+        base_pairs : ndarray, shape=(n,2), optional
             Each row corresponds to the positions of the bases in the
             strand. This parameter is mutually exclusive to
             ``dot_bracket``.
-        length : int, optional (default: None)
+        length : int, optional
             The number of bases in the strand. This parameter is
             required if ``base_pairs`` is given.
+        layout_type : Layout
+            The desired layout of the plot.
         bin_path : str, optional
             Path of the *RNAplot* binary.
 

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/viennarna/util.py

@@ -39,7 +39,7 @@ def build_constraint_string(
     Returns
     -------
     constraints : str
-        The constraint string
+        The constraint string.
     """
     constraints = np.full(sequence_length, ".", dtype="U1")
 

{biotite-1.1.0 → biotite-1.3.0}/src/biotite/application/webapp.py

@@ -29,7 +29,7 @@ class WebApp(Application, metaclass=abc.ABCMeta):
         URL of the web app.
     obey_rules : bool, optional
         If true, the application raises an :class:`RuleViolationError`, if
-        the server rules are violated. (Default: True)
+        the server rules are violated.
     """
 
     def __init__(self, app_url, obey_rules=True):

biotite-1.3.0/src/biotite/database/afdb/__init__.py

@@ -0,0 +1,12 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+A subpackage for downloading predicted protein structures from the AlphaFold DB.
+"""
+
+__name__ = "biotite.database.afdb"
+__author__ = "Alex Carlin"
+
+from .download import *