Adding gitlab-ci + cleaning Dockerfiles + applying debian patches

.gitignore

@@ -65,6 +65,10 @@ ltfatpy.egg-info/
 .project
 .pydevproject
 
+# PyCharm #
+###########
+.idea
+
 # Ipython files #
 #################
 
@@ -84,8 +88,9 @@ pytests_results.txt
 .coverage
 .html
 .png
-htmlcov/
+.eggs
 LtfatPyt.egg-info/
 .cache/
 dist/
 MANIFEST
+

.gitlab-ci.yml

+# CI Config for ltaftpy / gitlab
+
+# nosetests template
+.nose: &nose
+  script:
+    - pip3 install -e .
+    - nosetests3
+  artifacts:
+    paths:
+      - build
+    expire_in: 8d
+
+# doc template
+.doc: &doc
+  script:
+    - pip3 install -e .
+    - python3 setup.py build_sphinx
+    - cp -r build/sphinx/html public
+  artifacts:
+    paths:
+      - public
+
+# Tests on X86_64 ubuntu
+unbutu:X86_64:
+  <<: *nose
+  image: registry.gitlab.lif.univ-mrs.fr:5005/dev/ltfatpy/ubuntu:X86_64
+  tags:
+    - docker
+
+# Tests on i686 ubuntu
+ubuntu:i686:
+  <<: *nose
+  image: registry.gitlab.lif.univ-mrs.fr:5005/dev/ltfatpy/ubuntu:i686
+  tags:
+    - docker
+
+# Doc Generation
+pages:
+  <<: *doc
+  image: registry.gitlab.lif.univ-mrs.fr:5005/dev/ltfatpy/ubuntu:X86_64
+  tags:
+    - docker
+  only:
+    - master

MANIFEST.in

@@ -3,7 +3,7 @@ recursive-include ltfatpy/comp *.c *.pyx
 recursive-include doc *.rst *.py *.png *.bib
 prune ltfat_C_kernel/tests
 prune ltfat_C_kernel/lib
-prune ltfatpy/tests
+#prune ltfatpy/tests
 graft cmake-modules
 include *.txt
 include *.rst

doc/conf.py

@@ -44,7 +44,7 @@ extensions = [
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
-    'sphinx.ext.pngmath',
+    'sphinx.ext.imgmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
     'sphinxcontrib.bibtex'

docker/Dockerfile

-FROM debian:jessie
-MAINTAINER Denis Arrivault
-WORKDIR /
-RUN apt-get update && apt-get install -y \
-    cmake \
-    libfftw3-dev \
-    liblapack-dev \
-    python \
-    python-dev \
-    python-pip \
-    python-matplotlib \
-    gfortran
-RUN pip install scipy coverage Sphinx sphinxcontrib-bibtex 
-ADD ltfatpy-1.0.0.tar.gz /
-RUN pip install ltfatpy-1.0.0/ && pip uninstall ltfatpy
-RUN cd ltfatpy-1.0.0/ && python setup.py build_sphinx

docker/Dockerfile_X86_64

+FROM ubuntu:latest
+MAINTAINER Denis Arrivault
+WORKDIR /
+RUN apt-get update && apt-get install -y \
+    cmake \
+    libfftw3-dev \
+    liblapack-dev \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-tk \
+    python3-matplotlib
+RUN pip3 install --upgrade pip
+RUN pip3 install scipy nose coverage pytest pytest-cov Sphinx sphinxcontrib-bibtex
+
+# Copy the ltfatpy sdist in the docker directory and uncomment the following line
+# if you want to include ltfatpy sources in the docker image :
+# ADD ltfatpy-1.0.8.tar.gz /
+
+# cleanup
+RUN apt-get -qy autoremove
\ No newline at end of file

docker/Dockerfile_cython

-FROM debian:jessie
-MAINTAINER Denis Arrivault
-WORKDIR /
-RUN apt-get update && apt-get install -y \
-    cmake \
-    libfftw3-dev \
-    liblapack-dev \
-    python \
-    python-pip \
-    cython \
-    python-matplotlib \
-    gfortran
-RUN pip install scipy coverage
-ADD ltfatpy-1.0.0.tar.gz /
-RUN pip install ltfatpy-1.0.0/
\ No newline at end of file

docker/Dockerfile_cython_X86_64

+FROM ubuntu:latest
+MAINTAINER Denis Arrivault
+WORKDIR /
+RUN apt-get update && apt-get install -y \
+    cmake \
+    libfftw3-dev \
+    liblapack-dev \
+    python3 \
+    python3-dev \
+    python3-pip \
+    cython \
+    python3-tk \
+    python3-matplotlib
+RUN pip3 install --upgrade pip
+RUN pip3 install scipy nose coverage pytest pytest-cov Sphinx sphinxcontrib-bibtex
+
+# Copy the ltfatpy sdist in the docker directory and uncomment the following line
+# if you want to include ltfatpy sources in the docker image :
+# ADD ltfatpy-1.0.8.tar.gz /
+
+# cleanup
+RUN apt-get -qy autoremove
\ No newline at end of file

docker/Dockerfile_i686

+FROM ioft/i386-ubuntu
+MAINTAINER Denis Arrivault
+WORKDIR /
+RUN apt-get update && apt-get install -y \
+    cmake \
+    libfftw3-dev \
+    liblapack-dev \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-tk \
+    python3-matplotlib
+RUN pip3 install --upgrade pip
+RUN pip3 install scipy nose coverage pytest pytest-cov Sphinx sphinxcontrib-bibtex
+
+# Copy the ltfatpy sdist in the docker directory and uncomment the following line
+# if you want to include ltfatpy sources in the docker image :
+# ADD ltfatpy-1.0.8.tar.gz /
+
+# cleanup
+RUN apt-get -qy autoremove
\ No newline at end of file

setup.cfg

 [nosetests]
 #verbosity=1
 where=./ltfatpy
+with-xunit=1
+xunit-file=./build/nosetests.xml
 with-coverage=1
 cover-package=ltfatpy
 cover-erase=1
 cover-html=1
-cover-html-dir=../htmlcov
+cover-html-dir=../build/htmlcov
 
 [pytest]
 # Specifies a minimal pytest version required for running tests.
@@ -19,4 +21,5 @@ norecursedirs = .git bin build cmake-modules ltfat_C_kernel sandboxes .settings
 source=./ltfatpy
 omit = ./ltfatpy/tests/*
 [coverage html]
-directory=../htmlcov
\ No newline at end of file
+directory=../build/htmlcov
+

setup.py

@@ -66,14 +66,9 @@ import distutils.spawn as ds
 import distutils.dir_util as dd
 
 # Always prefer setuptools over distutils
-try:
-    from setuptools import setup, Extension
-    from setuptools.command.clean import clean
-    from setuptools.command.sdist import sdist
-except ImportError:
-    from distutils.core import setup, Extension
-    from distutils.command.clean import clean
-    from distutils.command.sdist import sdist
+from setuptools import setup, find_packages, Extension
+from distutils.command.clean import clean
+from distutils.command.sdist import sdist
 
 # Test if Cython is installed
 USE_CYTHON = True
@@ -134,7 +129,7 @@ def run_cmake(root_dir):
     except ds.DistutilsExecError:
         print("Error while running cmake")
         print("run 'setup.py build --help' for build options")
-        print("You may also try editing the settings in CMakeLists.txt file " +
+        print("You may also try editing the settings in CMakeLists.txt file " + 
               "and re-running setup")
         sys.exit(-1)
 
@@ -152,7 +147,7 @@ def run_make(root_dir):
     except ds.DistutilsExecError:
         print("Error while running make")
         print("run 'setup.py build --help' for build options")
-        print("You may also try editing the settings in CMakeLists.txt file " +
+        print("You may also try editing the settings in CMakeLists.txt file " + 
               "and re-running setup")
         sys.exit(-1)
 
@@ -171,7 +166,7 @@ def run_make_install(root_dir):
     except ds.DistutilsExecError:
         print("Error while running make install")
         print("run 'setup.py build --help' for build options")
-        print("You may also try editing the settings in CMakeLists.txt file " +
+        print("You may also try editing the settings in CMakeLists.txt file " + 
               "and re-running setup")
         sys.exit(-1)
 
@@ -189,7 +184,7 @@ def run_uninstall(root_dir):
     except ds.DistutilsExecError:
         print("Error while running make uninstall")
         print("run 'setup.py build --help' for build options")
-        print("You may also try editing the settings in CMakeLists.txt file " +
+        print("You may also try editing the settings in CMakeLists.txt file " + 
               "and re-running setup")
         sys.exit(-1)
 
@@ -214,7 +209,8 @@ class m_build_ext(build_ext):
 ##########################
 def read(*paths):
     """Build a file path from *paths* and return the contents."""
-    with open(os.path.join(*paths), 'r') as f:
+    from io import open
+    with open(os.path.join(*paths), 'r', encoding='utf-8') as f:
         return f.read()
 
 
@@ -317,22 +313,21 @@ def setup_package():
     setup(name="ltfatpy",
           version=VERSION,
           description='The Large Time-Frequency Toolbox (LTFAT) in Python',
-          long_description=(read('README.rst') + '\n\n' +
-                            read('HISTORY.rst') + '\n\n' +
+          long_description=(read('README.rst') + '\n\n' + 
+                            read('HISTORY.rst') + '\n\n' + 
                             read('AUTHORS.rst')),
-          packages=["ltfatpy", "ltfatpy.comp", "ltfatpy.fourier",
-                    "ltfatpy.gabor", "ltfatpy.signals", "ltfatpy.sigproc",
-                    "ltfatpy.tools"],
+          packages=find_packages(),
           package_data={'ltfatpy.signals': ['*.wav'],
-                        'ltfatpy.comp': ['*.pxd']},
+                        'ltfatpy.comp': ['*.pxd'],
+                        'ltfatpy.tests.datasets': ['*.mat']},
           url="https://gitlab.lif.univ-mrs.fr/dev/ltfatpy",
           license='GNU GPL V3',
           author='Denis Arrivault and Florent Jaillet',
-          author_email='denis.arrivault@lif.univ-mrs.fr ' +
+          author_email='denis.arrivault@lif.univ-mrs.fr ' + 
                        'florent.jaillet@lif.univ-mrs.fr',
-          # install_requires=['numpy'],
           ext_modules=extensions,
-          tests_require=['pytest'],
+          test_suite='nose.collector',
+          tests_require=['nose', 'coverage'],
           cmdclass={'build_ext': m_build_ext,
                     'clean': m_clean, 'sdist': m_sdist},
           classifiers=['Development Status :: 5 - Production/Stable',
@@ -349,7 +344,7 @@ def setup_package():
                        'Topic :: Scientific/Engineering :: Mathematics',
                        'Topic :: Scientific/Engineering'
                        ],
-          install_requires=['numpy>=1.8', 'matplotlib>=1.4', 'six>=1.10'],
+          install_requires=['scipy>=0.18', 'numpy>=1.8', 'matplotlib>=1.4', 'six>=1.10'],
           )