biotite 0.41.1__tar.gz → 1.0.0__tar.gz

{biotite-0.41.1 → biotite-1.0.0}/.gitignore

@@ -20,10 +20,9 @@ htmlcov
 # Ignore version file created by hatch-vcs
 /src/biotite/version.py
 
-# Ignore autogenerated API reference
+# Ignore autogenerated documentation files
+/doc/static/switcher.json
 /doc/apidoc
-
-# Ignore autogenerated example gallery
 /doc/examples/gallery
 /doc/examples/backreferences
 /doc/sg_execution_times.rst
@@ -40,7 +39,6 @@ htmlcov
 # Ignore all compiled python files (e.g. from running the unit tests)
 *.pyc
 *.pyo
-*.py{}
 *.py-e
 
 # Ignore potential directory created during install
@@ -58,8 +56,9 @@ biotite.egg-info
 *.code-workspace
 .vscode/*
 
-# Ignore fuse_hidden files on Linux systems
+# Ignore hidden OS related files
 *.fuse_hidden*
+.DS_Store
 
 # Ignore temp files created via Jupyter
 **/.ipynb_checkpoints/

{biotite-0.41.1 → biotite-1.0.0}/CONTRIB.rst

@@ -4,6 +4,7 @@ CONTRIBUTORS
 - Fabrice Allain <https://github.com/f-allain>
 - Jacob Marcel Anter <https://github.com/JacobAnter>
 - Daniel Bauer <https://github.com/dnlbauer>
+- Lukas Jarosch <https://github.com/ljarosch>
 - Patrick Kunzmann <https://github.com/padix-key>
 - Tom David Müller <https://github.com/t0mdavid-m>
 - Thomas Nevolianis <https://github.com/thomasnevolianis>
@@ -16,4 +17,5 @@ CONTRIBUTORS
 - Jincai Yang <https://github.com/0ut0fcontrol>
 - Tom Eulenfeld <https://github.com/trichter>
 - Benjamin E. Mayer <https://github.com/entropybit>
-- Natasha Jaffe <https://github.com/tcjaffe>
+- Natasha Jaffe <https://github.com/tcjaffe>
+- Tristen J. Mier  <https://github.com/tjmier>

{biotite-0.41.1 → biotite-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biotite
-Version: 0.41.1
+Version: 1.0.0
 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
@@ -37,7 +37,7 @@ License: BSD 3-Clause License
         (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-File: LICENSE.rst
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
@@ -49,9 +49,10 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
+Requires-Dist: biotraj<2.0,>=1.0
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0
-Requires-Dist: numpy<2.0,>=1.14.5
+Requires-Dist: numpy>=1.25
 Requires-Dist: requests>=2.12
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
@@ -80,7 +81,7 @@ This package bundles popular tasks in computational molecular biology
 into a uniform *Python* library.
 It can handle a major part of the typical workflow
 for sequence and biomolecular structure data:
-   
+
    - Searching and fetching data from biological databases
    - Reading and writing popular sequence/structure file formats
    - Analyzing and editing sequence/structure data
@@ -116,7 +117,6 @@ Installation
 
 Some functions require some extra packages:
 
-   - **mdtraj** - Required for trajetory file I/O operations.
    - **matplotlib** - Required for plotting purposes.
 
 *Biotite* can be installed via *Conda*...
@@ -184,4 +184,4 @@ Contribution
 Interested in improving *Biotite*?
 Have a look at the
 `contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
-Feel free to join or community chat on `Discord <https://discord.gg/cUjDguF>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

{biotite-0.41.1 → biotite-1.0.0}/README.rst

@@ -21,7 +21,7 @@ This package bundles popular tasks in computational molecular biology
 into a uniform *Python* library.
 It can handle a major part of the typical workflow
 for sequence and biomolecular structure data:
-   
+
    - Searching and fetching data from biological databases
    - Reading and writing popular sequence/structure file formats
    - Analyzing and editing sequence/structure data
@@ -57,7 +57,6 @@ Installation
 
 Some functions require some extra packages:
 
-   - **mdtraj** - Required for trajetory file I/O operations.
    - **matplotlib** - Required for plotting purposes.
 
 *Biotite* can be installed via *Conda*...
@@ -125,4 +124,4 @@ Contribution
 Interested in improving *Biotite*?
 Have a look at the
 `contribution guidelines <https://www.biotite-python.org/contribute.html>`_.
-Feel free to join or community chat on `Discord <https://discord.gg/cUjDguF>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

biotite-1.0.0/pyproject.toml

@@ -0,0 +1,121 @@
+[project]
+name = "biotite"
+requires-python = ">=3.10"
+description = "A comprehensive library for computational molecular biology"
+readme = "README.rst"
+authors = [{name = "The Biotite contributors"}]
+license = {"file" = "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",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+  # Wheels compiled with NumPy 2.0 are backward compatible with NumPy 1.x
+  # https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice
+  "numpy >= 1.25",
+  "biotraj >= 1.0, < 2.0",
+  "requests >= 2.12",
+  "msgpack >= 0.5.6",
+  "networkx >= 2.0",
+  "requests >= 2.12",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+]
+
+[project.urls]
+homepage = "https://www.biotite-python.org"
+repository = "https://github.com/biotite-dev/biotite"
+documentation = "https://www.biotite-python.org"
+
+[tool.ruff.lint]
+# pyflakes, pycodestyle isort and varibale naming
+select = ["F", "E", "W", "I", "TID", "N"]
+ignore = [
+    # In docstrings long lines are often intentional
+    # Most other ocassions are caught by the ruff formatter
+    "E501",
+    # Due to constants and class placeholders defined in functions
+    "N806",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# Due to `* import` of BCIF encoding
+"setup_ccd.py" = ["F405", "F403"]
+# Due to imports after the PATH has been adjusted
+"doc/conf.py" = ["E402"]
+# Due to `from .module import *` imports in `__init__.py` modules
+"__init__.py" = ["F403", "TID252"]
+# Due to pymol scripts that are evaluated in other example scripts
+"doc/examples/**/*_pymol.py" = ["F821"]
+
+[tool.ruff.lint.flake8-tidy-imports]
+ban-relative-imports = "all"
+
+[tool.ruff.lint.isort]
+# No separator lines between import sections
+no-lines-before = [
+    "future",
+    "standard-library",
+    "third-party",
+    "first-party",
+    "local-folder",
+]
+order-by-type = true
+known-first-party = ["biotite"]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+  # Appears in loading NetCDF trajectory files
+  "ignore:The 'netCDF4' Python package is not installed.",
+  "ignore:Input structure has no associated 'BondList'",
+]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "tests",
+  "doc",
+  "environment.yml",
+  "setup_ccd.py",
+  # .github, .gitignore, .gitattributes
+  ".git*",
+]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/biotite/version.py"
+
+[tool.hatch.build.targets.wheel.hooks.cython]
+dependencies = ["hatch-cython"]
+
+[tool.hatch.build.targets.wheel.hooks.cython.options]
+include_numpy = true
+compile_py = false
+define_macros = [
+    ["NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"],
+]
+
+[build-system]
+requires = [
+    "hatchling",
+    "hatch-vcs == 0.4",
+    "hatch-cython == 0.5",
+    "numpy >= 2.0",
+    "cython >= 3.0",
+]
+build-backend = "hatchling.build"

{biotite-0.41.1 → biotite-1.0.0}/src/biotite/__init__.py

@@ -12,8 +12,7 @@ modules.
 __name__ = "biotite"
 __author__ = "Patrick Kunzmann"
 
-from .file import *
-from .temp import *
 from .copyable import *
+from .file import *
+from .version import __version__, __version_tuple__  # noqa: F401
 from .visualize import *
-from .version import __version__, __version_tuple__

biotite-1.0.0/src/biotite/application/__init__.py

@@ -0,0 +1,69 @@
+# 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 that provides interfaces for external software in case
+*Biotite*’s integrated functionality is not sufficient for your tasks.
+These interfaces range from locally installed software
+(e.g. MSA software) to web services (e.g. BLAST).
+The interfaces are seamless:
+Writing input files and reading output files is handled internally.
+The user only needs to provide objects like a :class:`Sequence`
+and will receive objects like an :class:`Alignment`.
+
+Note that in order to use an interface in :mod:`biotite.application`
+the corresponding software must be installed or the web server must be
+reachable, respectively.
+These programs are not shipped with the *Biotite* package.
+
+Each application is represented by its respective :class:`Application`
+class.
+Each :class:`Application` instance has a life cycle, starting with its
+creation and ending with the result extraction.
+Each state in this life cycle is described by the value of the
+*enum* :class:`AppState`, that each :class:`Application` contains:
+Directly after its instantiation the app is in the ``CREATED`` state.
+In this state further parameters can be set for the application run.
+After the user calls the :func:`Application.start()` method, the app
+state is set to ``RUNNING`` and the app performs the calculations.
+When the application finishes the AppState
+changes to ``FINISHED``.
+The user can now call the :func:`Application.join()` method, concluding
+the application in the ``JOINED`` state and making the results of the
+application accessible.
+Furthermore, this may trigger cleanup actions in some applications.
+:func:`Application.join()` can even be called in the ``RUNNING`` state:
+This will constantly check if the application has finished and will
+directly go into the ``JOINED`` state as soon as the application reaches
+the ``FINISHED`` state.
+Calling the :func:`Application.cancel()` method while the application is
+``RUNNING`` or ``FINISHED`` leaves the application in the ``CANCELLED``
+state.
+This triggers cleanup, too, but there are no accessible results.
+If a method is called in an unsuitable app state, an
+:class:`AppStateError` is called.
+At each state in the life cycle, :class:`Application` type specific
+methods are called, as shown in the following diagram.
+
+.. figure:: /static/assets/figures/app_lifecycle.png
+    :alt: Application life cycle
+    :scale: 50%
+
+    Taken from
+    `Kunzmann & Hamacher 2018 <https://doi.org/10.1186/s12859-018-2367-z>`_
+    licensed under `CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/>`_.
+
+The execution of an :class:`Application` can run in parallel:
+The time between starting the run and collecting the results can be
+used to run other code, similar to the *Python* :class:`Thread` or
+:class:`Process` classes.
+"""
+
+__name__ = "biotite.application"
+__author__ = "Patrick Kunzmann"
+
+from .application import *
+from .localapp import *
+from .msaapp import *
+from .webapp import *

{biotite-0.41.1 → biotite-1.0.0}/src/biotite/application/application.py

@@ -4,19 +4,26 @@
 
 __name__ = "biotite.application"
 __author__ = "Patrick Kunzmann"
-__all__ = ["Application", "AppStateError", "TimeoutError", "VersionError",
-           "AppState", "requires_state"]
+__all__ = [
+    "Application",
+    "AppStateError",
+    "TimeoutError",
+    "VersionError",
+    "AppState",
+    "requires_state",
+]
 
 import abc
 import time
-from functools import wraps
 from enum import Flag, auto
+from functools import wraps
 
 
 class AppState(Flag):
     """
     This enum type represents the app states of an application.
     """
+
     CREATED = auto()
     RUNNING = auto()
     FINISHED = auto()
@@ -45,6 +52,7 @@ def requires_state(app_state):
     ... def function(self):
     ...     pass
     """
+
     def decorator(func):
         @wraps(func)
         def wrapper(*args, **kwargs):
@@ -52,16 +60,16 @@ def requires_state(app_state):
             try:
                 instance = args[0]
             except IndexError:
-                raise TypeError(
-                    "This method must be called from a class instance"
-                )
+                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, "
                     f"but {app_state} state is required"
                 )
             return func(*args, **kwargs)
+
         return wrapper
+
     return decorator
 
 
@@ -74,7 +82,8 @@ class Application(metaclass=abc.ABCMeta):
 
     Every :class:`Application` runs through a different app states
     (instances of enum :class:`AppState`) from its creation until its
-    termination:
+    termination.
+
     Directly after its instantiation the app is in the *CREATED* state.
     In this state further parameters can be set for the application run.
     After the user calls the :func:`start()` method, the app state is
@@ -145,11 +154,10 @@ class Application(metaclass=abc.ABCMeta):
         """
         time.sleep(self.wait_interval())
         while self.get_app_state() != AppState.FINISHED:
-            if timeout is not None and time.time()-self._start_time > timeout:
+            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 " f"({timeout:.1f} s)"
                 )
             else:
                 time.sleep(self.wait_interval())
@@ -248,6 +256,7 @@ class AppStateError(Exception):
     """
     Indicate that the application lifecycle was violated.
     """
+
     pass
 
 
@@ -255,6 +264,7 @@ class TimeoutError(Exception):
     """
     Indicate that the application's timeout expired.
     """
+
     pass
 
 
@@ -262,4 +272,5 @@ class VersionError(Exception):
     """
     Indicate that the application's version is invalid.
     """
-    pass
+
+    pass

{biotite-0.41.1 → biotite-1.0.0}/src/biotite/application/autodock/__init__.py

@@ -9,4 +9,4 @@ A subpackage for static ligand docking with *Autodock*.
 __name__ = "biotite.application.autodock"
 __author__ = "Patrick Kunzmann"
 
-from .app import *
+from .app import *