Merge branch 'master' of https://github.com/PyWavelets/pywt into bug_cwt_complex_conjugate

Author: pavle256

.coveragerc

@@ -5,6 +5,7 @@ include = */pywt/*
 omit =
     */version.py
     */pywt/tests/*
+    */pywt/_doc_utils.py*
     */pywt/data/create_dat.py
     *.pxd
     stringsource

.github/FUNDING.yml

@@ -0,0 +1 @@
+tidelift: "pypi/PyWavelets"

.mailmap

@@ -0,0 +1,13 @@
+Aaron O'Leary <aaron.oleary@gmail.com> <eeaol@leeds.ac.uk>
+Alexandre Saint <snt.alex@gmail.com> asnt <snt.alex@gmail.com>
+Arthur Roullier <36152494+0-tree@users.noreply.github.com> 0-tree <36152494+0-tree@users.noreply.github.com>
+Daniel M. Pelt <d.m.pelt@cwi.nl> Daniel M Pelt <dmpelt@lbl.gov>
+Gregory R. Lee <grlee77@gmail.com> Gregory R. Lee <gregory.lee@cchmc.org>
+Gregory R. Lee <grlee77@gmail.com> Gregory Lee <grlee77@gmail.com>
+Helder Oliveira <heldercro@gmail.com> Helder <heldercro@gmail.com>
+Holger Nahrstaedt <holgernahrstaedt@gmx.de> Holger Nahrstaedt <holgern@users.noreply.github.com>
+Kai Wohlfahrt <kai.wohlfahrt@gmail.com> <kai.scorpio@gmail.com>
+Kai Wohlfahrt <kai.wohlfahrt@gmail.com> <kjw53@cam.ac.uk>
+Kai Wohlfahrt <kai.wohlfahrt@gmail.com> Kai <kai.scorpio@gmail.com>
+Ralf Gommers <ralf.gommers@gmail.com> <ralf.gommers@googlemail.com>
+Sylvain Lannuzel <sylvain.lannuzel@student.ecp.fr> SylvainLan <sylvain.lannuzel@student.ecp.fr>

.travis.yml

@@ -16,25 +16,32 @@ matrix:
       env:
         - NUMPYSPEC=numpy
         - MATPLOTLIBSPEC=matplotlib
+        - CYTHONSPEC=cython
         - USE_WHEEL=1
     - os: linux
-      python: 3.7-dev
+      python: 3.7
+      dist: xenial # travis-ci/travis-ci/issues/9815
+      sudo: true
       env:
         - NUMPYSPEC=numpy
         - MATPLOTLIBSPEC=matplotlib
+        - CYTHONSPEC=cython
         - USE_SDIST=1
+        - USE_SCIPY=1
     - os: linux
       python: 3.5
       env:
         - NUMPYSPEC="numpy==1.13.3"
         - MATPLOTLIBSPEC=matplotlib
+        - CYTHONSPEC="cython==0.23.5"
         - REFGUIDE_CHECK=1  # run doctests only
     - os: osx
       osx_image: xcode7.3
       language: objective-c
       env:
         - NUMPYSPEC=numpy
         - MATPLOTLIBSPEC=matplotlib
+        - CYTHONSPEC=cython
         - TRAVIS_PYTHON_VERSION=3.5
 
 cache: pip
@@ -51,9 +58,11 @@ before_install:
   # Set numpy version first, other packages link against it
   - pip install $NUMPYSPEC
   - pip install $MATPLOTLIBSPEC
-  - pip install Cython nose coverage codecov futures
+  - pip install $CYTHONSPEC
+  - pip install pytest pytest-cov coverage codecov futures
   - set -o pipefail
   - if [ "${USE_WHEEL}" == "1" ]; then pip install wheel; fi
+  - if [ "${USE_SCIPY}" == "1" ]; then pip install scipy; fi
   - |
     if [ "${REFGUIDE_CHECK}" == "1" ]; then
         pip install sphinx numpydoc
@@ -67,21 +76,26 @@ script:
         pip wheel . -v
         pip install PyWavelets*.whl -v
         pushd demo
-        nosetests pywt
+        pytest --pyargs pywt
+        python ../pywt/tests/test_doc.py
         popd
     elif [ "${USE_SDIST}" == "1" ]; then
         python setup.py sdist
         # Move out of source directory to avoid finding local pywt
         pushd dist
         pip install PyWavelets* -v
-        nosetests pywt
+        pytest --pyargs pywt
+        python ../pywt/tests/test_doc.py
         popd
     elif [ "${REFGUIDE_CHECK}" == "1" ]; then
         pip install -e . -v
         python util/refguide_check.py --doctests
     else
         CFLAGS="--coverage" python setup.py build --build-lib build/lib/ --build-temp build/tmp/
-        nosetests build/lib/ --tests pywt/tests
+        CFLAGS="--coverage" pip install -e . -v
+        pushd demo
+        pytest --pyargs pywt --cov=pywt
+        popd
     fi
 
 after_success:

LICENSE

@@ -1,5 +1,5 @@
 Copyright (c) 2006-2012 Filip Wasilewski <http://en.ig.ma/>
-Copyright (c) 2012-2017 The PyWavelets Developers <https://github.com/PyWavelets/pywt>
+Copyright (c) 2012-2019 The PyWavelets Developers <https://github.com/PyWavelets/pywt>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

LICENSES_bundled.txt

@@ -0,0 +1,10 @@
+The PyWavelets repository and source distributions bundle some code that is
+adapted from compatibly licensed projects. We list these here.
+
+Name: NumPy
+Files:  pywt/_pytesttester.py
+License: 3-clause BSD
+
+Name: SciPy
+Files:  setup.py, util/*
+License: 3-clause BSD

MANIFEST.in

@@ -15,7 +15,7 @@ recursive-include demo *
 include cythonize.dat
 
 # Add build and testing tools
-include tox.ini
+include tox.ini pytest.ini
 recursive-include util *
 
 # Exclude what we don't want to include

README.rst

@@ -65,9 +65,11 @@ For more usage examples see the `demo`_ directory in the source package.
 Installation
 ------------
 
-PyWavelets supports `Python`_ >=3.5, and is only dependent on `Numpy`_
+PyWavelets supports `Python`_ >=3.5, and is only dependent on `NumPy`_
 (supported versions are currently ``>= 1.13.3``). To pass all of the tests,
-`Matplotlib`_ is also required.
+`Matplotlib`_ is also required. `SciPy`_ is also an optional dependency. When
+present, FFT-based continuous wavelet transforms will use FFTs from SciPy
+rather than NumPy.
 
 There are binary wheels for Intel Linux, Windows and macOS / OSX on PyPi.  If
 you are on one of these platforms, you should get a binary (precompiled)
@@ -116,29 +118,43 @@ All contributions including bug reports, bug fixes, new feature implementations
 and documentation improvements are welcome.  Moreover, developers with an
 interest in PyWavelets are very welcome to join the development team!
 
+As of 2019, PyWavelets development is supported in part by Tidelift.
+`Help support PyWavelets with the Tidelift Subscription <https://tidelift.com/subscription/pkg/pypi-pywavelets?utm_source=pypi-pywavelets&utm_medium=referral&utm_campaign=readme>`_
+
 
 Contact
 -------
 
 Use `GitHub Issues`_ or the `mailing list`_ to post your comments or questions.
 
+**Report a security vulnerability:** https://tidelift.com/security
+
 License
 -------
 
 PyWavelets is a free Open Source software released under the MIT license.
 
-If you wish to cite PyWavelets in a publication, you may use the following DOI.
+If you wish to cite PyWavelets in a publication, please use the following
+JOSS publication.
+
+.. image:: http://joss.theoj.org/papers/10.21105/joss.01237/status.svg
+   :target: https://doi.org/10.21105/joss.01237
+
+Specific releases can also be cited via Zenodo. The DOI below will correspond
+to the most recent release. DOIs for past versions can be found by following
+the link in the badge below to Zenodo:
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1407172.svg
-   :target: https://doi.org/10.5281/zenodo.1407172
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1407171.svg
+   :target: https://doi.org/10.5281/zenodo.1407171
 
 .. _built-in wavelet filters: http://wavelets.pybytes.com/
 .. _Cython: http://cython.org/
 .. _demo: https://github.com/PyWavelets/pywt/tree/master/demo
 .. _Anaconda: https://www.continuum.io
 .. _GitHub: https://github.com/PyWavelets/pywt
 .. _GitHub Issues: https://github.com/PyWavelets/pywt/issues
-.. _Numpy: http://www.numpy.org
+.. _NumPy: https://www.numpy.org
+.. _SciPy: https://www.scipy.org
 .. _original developer: http://en.ig.ma
 .. _Python: http://python.org/
 .. _Python Package Index: http://pypi.python.org/pypi/PyWavelets/

appveyor.yml

@@ -23,11 +23,13 @@ install:
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install
      numpy --cache-dir c:\\tmp\\pip-cache"
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install
-     Cython nose coverage matplotlib futures --cache-dir c:\\tmp\\pip-cache"
+     Cython pytest coverage matplotlib futures --cache-dir c:\\tmp\\pip-cache"
 
 test_script:
-  - "util\\appveyor\\build.cmd %PYTHON%\\python.exe setup.py build --build-lib build\\lib\\"
-  - "%PYTHON%\\Scripts\\nosetests build\\lib --tests pywt\\tests"
+  - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install -e . -v"
+  - "cd demo"
+  - "%PYTHON%\\Scripts\\pytest --pyargs pywt"
+  - "cd .."
 
 after_test:
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe setup.py bdist_wheel"

benchmarks/README.rst

@@ -32,7 +32,7 @@ To record the results use:
 
     asv publish
 
-And to see the results via a web broweser, run:
+And to see the results via a web browser, run:
 
     asv preview