rename kwant-spectrum to kwantspectrum

.coveragerc

@@ -2,8 +2,8 @@
 omit =
     *tests*
     *__init__*
-    kwant_spectrum/_kwant_spectrum_version.py
-    kwant_spectrum/version.py
+    kwantspectrum/_kwant_spectrum_version.py
+    kwantspectrum/version.py
 branch = True
 [report]
 exclude_lines =

.gitignore

@@ -4,4 +4,5 @@ __pycache__/
 /doc/build/
 *~
 .coverage
+*.egg-info/
 

AUTHORS.rst

-The Kwant-Spectrum authors can be reached at tkwant-authors@kwant-project.org.
-
-Kwant-Spectrum has been developed by
-
-* Thomas Kloss (CEA Grenoble)
-
-Contributors
-
-* Christoph Groth (CEA Grenoble)
-* Xavier Waintal (CEA Grenoble)
-
-(CEA = Commissariat à l'énergie atomique et aux énergies alternatives)

INSTALL.rst

-Installation
-============
-
-This section covers the installation of Kwant_Spectrum on a GNU/Linux
-system as Debian and Ubuntu via the command line.
-
-Requirements
-^^^^^^^^^^^^
-
-Kwant_Spectrum has following non-Python dependency:
-
-- `Kwant <https://kwant-project.org/>`_
-
-The non-Python dependencies of Kwant_Spectrum can be installed with the following command::
-
-   sudo apt-add-repository -s ppa:kwant-project/ppa
-   sudo apt-get update
-   sudo apt-get install python3-kwant
-
-Kwant_Spectrum requires at least Python 3.5. The following packages must
-be installed to build Kwant_Spectrum:
-
-- `NumPy <https://numpy.org/>`_
-- `SciPy <https://www.scipy.org/>`_
-
-Most packages can be installed from the command line
-by the standard Python package manager `pip <https://pip.pypa.io/en/stable/>`_ via::
-
-    sudo pip3 install numpy scipy
-
-The *pip* command can be also used within the Anaconda Python distribution,
-see the instructions for `Conda <#conda>`__.
-For version requirements we refer to the *requirements* section in
-:download:`setup.py <../../../setup.py>`.
-
-Testing requirements
---------------------
-The Kwant_Spectrum test suite requires the following Python packages:
-
-- `pytest <https://docs.pytest.org/en/latest/>`_
-- `pytest-cov <https://pytest-cov.readthedocs.io/en/latest/>`_
-- `pytest-flake8 <https://pypi.org/project/pytest-flake8/>`_
-
-
-The packages can be installed by the standard *pip* command::
-
-    sudo pip3 install pytest pytest-cov pytest-flake8
-
-
-Documentation requirements
---------------------------
-The Kwant_Spectrum test suite requires the following Python packages:
-
-- `sphinx <https://www.sphinx-doc.org/en/master/>`_
-- `jupyter-sphinx <https://jupyter-sphinx.readthedocs.io/en/latest/>`_
-
-
-The packages can be installed by the standard *pip* command::
-
-    sudo pip3 install sphinx jupyter-sphinx
-
-
-Installating Kwant_Spectrum
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Kwant_Spectrum can be installed with pip via::
-
-    sudo pip3 install kwant_spectrum
-
-
-Building Kwant_Spectrum for development
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-For development, Kwant_Spectrum should first be cloned from the official repository::
-
-    git clone https://gitlab.kwant-project.org/kwant/spectrum.git
-
-Then, after *cd* into the local repository,
-one can locally build kwant_spectrum with the command::
-
-    python3 setup.py build_ext -i
-
-Conda
-^^^^^
-.. _conda:
-
-Kwant_Spectrum provides no dedicated Anaconda support. It is however possible to
-install packages via *pip* and *git* similarly with conda.
-First, *pip* and *git* must be installed for conda with::
-
-    conda install git pip
-
-Kwant-Spectrum can then be installed with the commands given above.

LICENSE.rst

-======================
-Kwant-Spectrum license
-======================
+=====================
+kwantSpectrum license
+=====================
 
 Copyright 2018-2019 T. Kloss (CEA), C. W. Groth (CEA), X. Waintal (CEA),
 and others.

MANIFEST.in

-include *.rst
-include test_*.py
+include .coveragerc
+include LICENSE.rst
+include MANIFEST.in
+include README.rst
 include doc/Makefile
+include doc/source/about.rst
 include doc/source/conf.py
-include doc/source/*.rst
+include doc/source/index.rst
 include doc/source/kwantdoctheme/static/kwantdoctheme.css
 include doc/source/kwantdoctheme/theme.conf
+include doc/source/reference.rst
+include doc/source/tutorial.rst
+include kwantspectrum/__init__.py
+include kwantspectrum/_kwant_spectrum_version.py
+include kwantspectrum/kwant_spectrum.py
+include kwantspectrum/tests/__init__.py
+include kwantspectrum/tests/test_kwant_spectrum.py
+include kwantspectrum/version.py
+include pytest.ini
+include setup.py

README.rst

-About Kwant-Spectrum
-====================
+About kwantSpectrum
+===================
 
-Kwant-Spectrum is an extension to `Kwant <http://kwant-project.org/>`__ that
+kwantSpectrum is an extension to `Kwant <http://kwant-project.org/>`__ that
 adaptively analyzes band structures of infinite quasi-1d systems.  The
 bandstructure is approximated to an arbitrary precision by piecewise cubic
 polynomials.  Functionality to deal with special points, intervals, and the
 periodic nature of the spectrum is provided.
 
 
-Kwant_Spectrum is distributed under the `2-clause BSD license <https://gitlab.kwant-project.org/kwant/spectrum/-/blob/master/LICENSE.rst>`_
+kwantSpectrum is distributed under the `2-clause BSD license <https://gitlab.kwant-project.org/kwant/kwantspectrum/-/blob/master/LICENSE.rst>`_
 
-Website: https://kwant-project.org/extensions/spectrum
+Website: https://kwant-project.org/extensions/kwantspectrum
 
-Source code: https://gitlab.kwant-project.org/kwant/spectrum
+Source code: https://gitlab.kwant-project.org/kwant/kwantspectrum
 
 
 
 Installation
 ############
 
-This section covers the installation of Kwant_Spectrum on a GNU/Linux
+This section covers the installation of kwantSpectrum on a GNU/Linux
 system as Debian and Ubuntu via the command line.
 
 Requirements
 ^^^^^^^^^^^^
 
-Kwant_Spectrum has following non-Python dependency:
+kwantSpectrum has following non-Python dependency:
 
 - `Kwant <https://kwant-project.org/>`__
 
-The non-Python dependencies of Kwant_Spectrum can be installed with the following command::
+Kwant can be installed with the following command::
 
    sudo apt-add-repository -s ppa:kwant-project/ppa
    sudo apt-get update
    sudo apt-get install python3-kwant
 
-Kwant_Spectrum requires at least Python 3.5. The following packages must
-be installed to build Kwant_Spectrum:
+kwantSpectrum requires at least Python 3.5. The following packages must
+be installed to build kwantSpectrum:
 
 - `NumPy <https://numpy.org/>`_
 - `SciPy <https://www.scipy.org/>`_
@@ -48,7 +48,7 @@ by the standard Python package manager `pip <https://pip.pypa.io/en/stable/>`_ v
 
 Testing requirements
 --------------------
-The Kwant_Spectrum test suite requires the following Python packages:
+The kwantSpectrum test suite requires the following Python packages:
 
 - `pytest <https://docs.pytest.org/en/latest/>`_
 - `pytest-cov <https://pytest-cov.readthedocs.io/en/latest/>`_
@@ -61,35 +61,31 @@ The packages can be installed by the standard *pip* command::
 
 Documentation requirements
 --------------------------
-The Kwant_Spectrum test suite requires the following Python packages:
+Building the documentation requires the following Python packages:
 
+- `matplotlib <https://matplotlib.org/>`_
 - `sphinx <https://www.sphinx-doc.org/en/master/>`_
 - `jupyter-sphinx <https://jupyter-sphinx.readthedocs.io/en/latest/>`_
 
 
 The packages can be installed by the standard *pip* command::
 
-    sudo pip3 install sphinx jupyter-sphinx
+    sudo pip3 install matplotlib sphinx jupyter-sphinx
 
-Building Kwant_Spectrum
-^^^^^^^^^^^^^^^^^^^^^^^
+Building kwantSpectrum
+^^^^^^^^^^^^^^^^^^^^^^
 
-Kwant-Spectrum can be installed from PyPI with::
+kwantSpectrum can be installed from PyPI with::
 
-    sudo pip3 install kwant_spectrum
+    sudo pip3 install kwantspectrum
 
 Alternatively, it can be installed directly from the source code repository::
 
-    sudo pip3 install git+https://gitlab.kwant-project.org/kwant/spectrum.git
+    sudo pip3 install git+https://gitlab.kwant-project.org/kwant/kwantspectrum.git
 
-For development, Kwant_Spectrum should first be cloned from the official repository::
+For development, kwantSpectrum can be cloned from the official repository with::
 
-    git clone https://gitlab.kwant-project.org/kwant/spectrum.git
-
-Then, after *cd* into the local repository,
-one can locally build kwant_spectrum with the command::
-
-    python3 setup.py build
+    git clone https://gitlab.kwant-project.org/kwant/kwantspectrum.git
 
 Test suite
 ----------
@@ -116,7 +112,20 @@ Documentation
 
 Full documentation including a tutorial:
 
-- https://kwant-project.org/extensions/spectrum
+- https://kwant-project.org/extensions/kwantspectrum
+
+Communication
+#############
+
+The kwant-discuss mailing list is the main communication channel for
+questions and discussions around kwantSpectrum. Searching and using the mailing list
+is explained in section
+`mailing list <https://kwant-project.org/community#mailing-list>`_.
+
+- Mailing list: kwant-discuss@kwant-project.org
+
+In addition, the authors can be reached by email, see below.
+
 
 
 Contributing
@@ -132,16 +141,16 @@ a new merge request.
 License
 #######
 
-Kwant_Spectrum distributed under BSD license, see  ``LICENSE.rst`` in the
-project repository.
+kwantSpectrum is distributed under BSD license, see the file ``LICENSE.rst``
+in the project repository.
 
 
 Authors
 #######
 
-The principle developer of Kwant-Spectrum is:
+The principle developer of kwantSpectrum is:
 
-* Thomas Kloss (CEA Grenoble)
+* Thomas Kloss (CEA Grenoble), kloss@itp.uni-frankfurt.de
 
 Contributors to the project are:
 

doc/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = kwant-spectrum
+SPHINXPROJ    = kwantspectrum
 SOURCEDIR     = source
 BUILDDIR      = build
 

doc/source/conf.py

@@ -13,14 +13,16 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'kwant-spectrum'
+project = 'kwantspectrum'
 copyright = '2018-2019, T. Kloss, C. W. Groth, X. Waintal, et al.'
 author = 'T. Kloss, C. W. Groth, X. Waintal, et al.'
 
-# The short X.Y version
-version = ''
-# The full version, including alpha/beta/rc tags
-release = '0.0'
+# The full version, including alpha/beta/rc tags.
+import kwantspectrum
+release = kwantspectrum.__version__
+
+# The short X.Y version.
+version = release[:len(release) - len(release.lstrip('012345679.'))].rstrip('.')
 
 
 # -- General configuration ---------------------------------------------------
@@ -100,7 +102,7 @@ html_static_path = []
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'kwant-spectrumdoc'
+htmlhelp_basename = 'kwantspectrumdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -127,7 +129,7 @@ latex_elements = {
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'kwant-spectrum.tex', 'kwant-spectrum Documentation',
+    (master_doc, 'kwantspectrum.tex', 'kwantspectrum Documentation',
      'T. Kloss, C. W. Groth, X. Waintal, et al.', 'manual'),
 ]
 
@@ -137,7 +139,7 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'kwant-spectrum', 'kwant-spectrum Documentation',
+    (master_doc, 'kwantspectrum', 'kwantspectrum Documentation',
      [author], 1)
 ]
 
@@ -148,8 +150,8 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'kwant-spectrum', 'kwant-spectrum Documentation',
-     author, 'kwant-spectrum', 'One line description of project.',
+    (master_doc, 'kwantspectrum', 'kwantspectrum Documentation',
+     author, 'kwantspectrum', 'One line description of project.',
      'Miscellaneous'),
 ]
 

doc/source/index.rst

-Kwant-Spectrum |release| documentation
-======================================
+kwantSpectrum |release| documentation
+=====================================
 
 .. toctree::
    :maxdepth: 2

doc/source/reference.rst

-:mod:`kwant_spectrum` -- Reference documentation
-================================================
+:mod:`kwantspectrum` -- Reference documentation
+===============================================
 
-.. automodule:: kwant_spectrum
+.. automodule:: kwantspectrum
    :members:

doc/source/tutorial.rst

-Kwant-Spectrum tutorial
-=======================
+kwantSpectrum tutorial
+======================
 
 For many situations we need to calculate and analyze the band structure
 of a semi-infinite lead. In the following we will look at a simple toy
@@ -83,7 +83,7 @@ A much more convenient method for examining the spectrum is the
 
 .. jupyter-execute::
 
-    import kwant_spectrum as ks
+    import kwantspectrum as ks
     
     spec = ks.spectrum(lead)
 
@@ -505,12 +505,6 @@ the number evaluation points used internally.
         print('tolerance= {}, number of points= {}'.format(tol, len(spec.x)))
 
 
-.. parsed-literal::
-
-    tolerance= 0.0001, number of points= 57
-    tolerance= 1e-08, number of points= 533
-
-
 Note that ``tol`` affects both the matching and the interpolation step.
 First, if the tolerance becomes too large, the internally used matching
 algorithm (see ``_match_functions`` below) may no longer be able to

kwant_spectrum/__init__.py → kwantspectrum/__init__.py

-# Copyright 2018-2020 Kwant-Spectrum authors.
+# Copyright 2018-2020 kwantspectrum authors.
 #
-# This file is part of Kwant-Spectrum.  It is subject to the license terms in
+# This file is part of kwantspectrum.  It is subject to the license terms in
 # the file LICENSE.rst found in the top-level directory of this distribution.
 
-from . import version
+__all__ = []
+
+from . import version, kwant_spectrum
 
 version.ensure_python()
 __version__ = version.version
 
-__all__ = []
-
-for module in ('kwant_spectrum', ):
-    exec('from . import {0}'.format(module))
-    __all__.append(module)
-
 available = [
     ('kwant_spectrum', kwant_spectrum.__all__)
 ]
@@ -21,3 +17,4 @@ available = [
 for module, names in available:
     exec('from .{0} import {1}'.format(module, ', '.join(names)))
     __all__.extend(names)
+

kwant_spectrum/kwant_spectrum.py → kwantspectrum/kwant_spectrum.py

-# Copyright 2018-2020 Kwant-Spectrum authors.
+# Copyright 2018-2020 kwantspectrum authors.
 #
-# This file is part of Kwant-Spectrum.  It is subject to the license terms in
+# This file is part of kwantspectrum.  It is subject to the license terms in
 # the file LICENSE.rst found in the top-level directory of this distribution.
 
 from functools import partial, wraps

kwant_spectrum/tests/test_kwant_spectrum.py → kwantspectrum/tests/test_kwant_spectrum.py

-# Copyright 2018-2020 Kwant-Spectrum authors.
+# Copyright 2018-2020 kwantspectrum authors.
 #
-# This file is part of Kwant-Spectrum.  It is subject to the license terms in
+# This file is part of kwantspectrum.  It is subject to the license terms in
 # the file LICENSE.rst found in the top-level directory of this distribution.
 
 from functools import partial

kwant_spectrum/version.py → kwantspectrum/version.py

-# Copyright 2018-2020 Kwant-Spectrum authors.
+# Copyright 2018-2020 kwantspectrum authors.
 #
-# This file is part of Kwant-Spectrum.  It is subject to the license terms in
+# This file is part of kwantspectrum.  It is subject to the license terms in
 # the file LICENSE.rst found in the top-level directory of this distribution.
 
 import sys

pytest.ini

 [pytest]
 # add coverage report, source analyzer, and pep8 compliance checks
-addopts = --cov=kwant_spectrum --cov-config=.coveragerc --flake8
-testpaths = kwant_spectrum
+addopts = --cov=kwantspectrum --cov-config=.coveragerc --flake8
+testpaths = kwantspectrum
 flake8-ignore =
     E501  # lines too long
     W503  # line break before binary operator
-    kwant_spectrum/kwant_spectrum.py E722  # do not use bare 'except'
-    kwant_spectrum/__init__.py ALL # __version__ import confuse flakes
+    kwantspectrum/kwant_spectrum.py E722  # do not use bare 'except'
+    kwantspectrum/__init__.py ALL # __version__ import confuse flakes

setup.py

 #!/usr/bin/env python3
 
-from setuptools import setup, find_packages
+import os
 import importlib
+import subprocess
+from setuptools import setup, find_packages
+from distutils.command.build import build as build_orig
+from setuptools.command.sdist import sdist as sdist_orig
+
+
+STATIC_VERSION_PATH = ('kwantspectrum', '_kwant_spectrum_version.py')
+
+distr_root = os.path.dirname(os.path.abspath(__file__))
+
 
 # Get the long description from the README file.
 with open('README.rst', encoding='utf-8') as f:
     long_description = f.read()
 
+
 def check_versions():
+    global version, version_is_from_git
 
-    # Let kwant-spectrum itself determine its own version.
-    # We cannot simply import kwant-spectrum, as it is not built yet.
-    spec = importlib.util.spec_from_file_location('version', 'kwant_spectrum/version.py')
+    # Let kwantspectrum itself determine its own version.
+    # We cannot simply import kwantspectrum, as it is not built yet.
+    spec = importlib.util.spec_from_file_location('version', 'kwantspectrum/version.py')
     version_module = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(version_module)
 
     version_module.ensure_python()
-    return version_module.version
+    version = version_module.version
+    version_is_from_git = version_module.version_is_from_git
+
+
+def write_version(fname):
+    # This could be a hard link, so try to delete it first.  Is there any way
+    # to do this atomically together with opening?
+    try:
+        os.remove(fname)
+    except OSError:
+        pass
+    with open(fname, 'w') as f:
+        f.write("# This file has been created by setup.py.\n")
+        f.write("version = '{}'\n".format(version))
+
+
+class build(build_orig):
+    def run(self):
+        super().run()
+        write_version(os.path.join(self.build_lib, *STATIC_VERSION_PATH))
+
+
+def git_lsfiles():
+    if not version_is_from_git:
+        return
+
+    try:
+        p = subprocess.Popen(['git', 'ls-files'], cwd=distr_root,
+                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except OSError:
+        return
+
+    if p.wait() != 0:
+        return
+    return p.communicate()[0].decode().split('\n')[:-1]
+
+
+# Make the command "sdist" depend on "build".  This verifies that the
+# distribution in the current state actually builds.  It also makes sure that
+# the Cython-made C files will be up-to-date and included in the source.
+class sdist(sdist_orig):
+    sub_commands = [('build', None)] + sdist_orig.sub_commands
+
+    def run(self):
+        """Create MANIFEST.in from git if possible, otherwise check that
+        MANIFEST.in is present.
+
+        Right now (2015) generating MANIFEST.in seems to be the only way to
+        include files in the source distribution that setuptools does not think
+        should be there.  Setting include_package_data to True makes setuptools
+        include *.pyx and other source files in the binary distribution.
+        """
+        manifest_in_file = 'MANIFEST.in'
+        manifest = os.path.join(distr_root, manifest_in_file)
+        names = git_lsfiles()
+        if names is None:
+            if not (os.path.isfile(manifest) and os.access(manifest, os.R_OK)):
+                print("Error:", manifest_in_file,
+                      "file is missing and Git is not available"
+                      " to regenerate it.", file=sys.stderr)
+                sys.exit(1)
+        else:
+            with open(manifest, 'w') as f:
+                for name in names:
+                    a, sep, b = name.rpartition('/')
+                    if b == '.gitignore':
+                        continue
+                    stem, dot, extension = b.rpartition('.')
+                    f.write('include {}'.format(name))
+                    if extension == 'pyx':
+                        f.write(''.join([' ', a, sep, stem, dot, 'c']))
+                    f.write('\n')
+
+        super().run()
+
+        if names is None:
+            msg = ("Git was not available to generate the list of files to be "
+                   "included in the\nsource distribution. The old {} was used.")
+            msg = msg.format(manifest_in_file)
+            print(banner(' Caution '), msg, banner(), sep='\n', file=sys.stderr)
+
+    def make_release_tree(self, base_dir, files):
+        super().make_release_tree(base_dir, files)
+        write_version(os.path.join(base_dir, *STATIC_VERSION_PATH))
+
 
 def main():
 
-    version = check_versions()
+    check_versions()
 
     setup(
-        name='kwant-spectrum',
+        name='kwantspectrum',
         version=version,
         description='Adaptive band structure analyzer for Kwant leads',
         long_description=long_description,
-        url='https://gitlab.kwant-project.org/kwant/spectrum',
+        url='https://gitlab.kwant-project.org/kwant/kwantspectrum',
         author='T. Kloss, C. W. Groth, X. Waintal, et al.',
         author_email='kloss@itp.uni-frankfurt.de',
         classifiers=[
@@ -41,9 +137,11 @@ def main():
         ],
         keywords='physics kwant bandstructure',
         packages=find_packages('.'),
+        cmdclass={'build': build,
+                  'sdist': sdist},
         python_requires='>=3.5',
         install_requires=['kwant >= 1.4', 'numpy', 'scipy'],
-        extras_require={'test': ['pytest'],},
+        extras_require={'test': ['pytest', 'pytest-cov', 'pytest-flake8'], },
     )
 
 if __name__ == '__main__':