Got rid of nose in all tests. Finished environment.yml.

.gitignore

@@ -4,6 +4,8 @@ desktop.ini
 
 .idea
 
+.coverage
+
 *.egg-info
 
 .DS_Store

environment.yml

+# Create environment with "conda env create", update with "conda env update"!
+
 name: pyramid
+
+channels:
+  - defaults
+  - conda-forge  # Used for hyperspy, pyFFTW (linux-64/osx-64) and more!
+  - ccpi  # Used for pyFFTW on win-64!
+
 dependencies:
-- python=3.5
-- numpy
-- pip
-- pip:
-    - pypi-package-name
+  # Basic:
+  - python=3.5  # TODO: upgrade to 3.6!
+  - numpy=1.11
+  - scipy=0.19
+  - tqdm=4.14
+  - scikit-image=0.13
+  # Fast computation:
+  - pyFFTW=0.10
+  # File IO:
+  - hyperspy=1.3
+  - hyperspy-gui-ipywidgets=1.0
+  - hyperspy-gui-traitsui=1.0  # TODO: Optional! Delete when mayavi is gone!
+  - h5py=2.7
+  # Plotting and colors:  # TODO: Shift to plotting package?
+  - matplotlib=2.0
+  - Pillow=4.1
+  - cmocean=1.1
+  - qt=4.8  # Necessary because of traits in mayavi...
+  - mayavi=4.5  # TODO: Get rid of!
+  #- colorspacious  # TODO: NOT USED?
+  #- visvis  # TODO: NOT USED?
+  # Testing:
+  - pytest=3.1
+  - pytest-cov=2.5
+  - pytest-flake8=0.8
+  - pytest-runner=2.11
+  - coverage=4.4
+  # IPython and notebooks:
+  - ipython=5.3
+  - jupyter=1.0
+  # TODO: Add back GUI dependencies!
+  # TODO: Get Jutil from gitlab (currently doesn't work, git and cygwin don't play nice,...
+  # TODO: ...because one is Unix, ond is Windows).
+#  - pip=9.0
+#  - pip:
+#    # ALSO NEEDS JUTIL!
+#    - "git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git"
+#
+#    # FOLLOWING NOT USED ANYMORE, CONDA WORKS, TOO (with appropriate channels):
+#    # Install pyFFTW=0.10 from wheel:
+#    - http://www.lfd.uci.edu/~gohlke/pythonlibs/pyFFTW‑0.10.4‑cp35‑cp35m‑win_amd64.whl
+#    # Install mayavi=4.5 and VTK from wheel:
+#    - http://www.lfd.uci.edu/~gohlke/pythonlibs/mayavi‑4.5.0+vtk71‑cp35‑cp35m‑win_amd64.whl

pyramid/fft.py

@@ -10,7 +10,7 @@ pack will be used. FFTW objects are saved in a cache after creation which speeds
 FFT operations.
 
 """
-
+# TODO: is this still in use or deprecated by jutil???
 
 import pickle
 import logging

pyramid/tests/test_analytic.py

@@ -54,8 +54,3 @@ class TestCaseAnalytic(unittest.TestCase):
         reference = np.load(os.path.join(self.path, 'ref_phase_vort.npy'))
         assert_allclose(phase, reference, atol=1E-10,
                         err_msg='Unexpected behavior in phase_mag_vortex()')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_costfunction.py

@@ -74,8 +74,3 @@ class TestCaseCostfunction(unittest.TestCase):
     def test_hess_diag(self):
         assert_allclose(self.cost.hess_diag(None), np.ones(self.cost.n),
                         err_msg='Unexpected behaviour in hess_diag()!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_dataset.py

@@ -88,8 +88,3 @@ class TestCaseDataSet(unittest.TestCase):
         mask_ref[1:-1, 1:-1, 1:-1] = True
         np.testing.assert_equal(self.data.mask, mask_ref,
                                 err_msg='Unexpected behaviour in set_3d_mask')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_fielddata.py

@@ -116,8 +116,3 @@ class TestCaseVectorData(unittest.TestCase):
                         err_msg='Unexpected behavior in load_from_hdf5()!')
         assert_allclose(magdata.a, self.magdata.a,
                         err_msg='Unexpected behavior in load_from_hdf5()!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_forwardmodel.py

@@ -67,8 +67,3 @@ class TestCaseForwardModel(unittest.TestCase):
         jac_T_ref = np.load(os.path.join(self.path, 'jac.npy')).T
         assert_allclose(jac_T, jac_T_ref, atol=1E-7,
                         err_msg='Unexpected behaviour in the the transposed jacobi matrix!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_kernel.py

@@ -30,8 +30,3 @@ class TestCaseKernel(unittest.TestCase):
                         err_msg='Unexpected behavior in u_fft')
         assert_allclose(self.kernel.v_fft, ref_v_fft, atol=1E-7,
                         err_msg='Unexpected behavior in v_fft')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_magcreator.py

@@ -78,8 +78,3 @@ class TestCaseMagCreator(unittest.TestCase):
         magnitude = mc.create_mag_dist_vortex(mag_shape)
         assert_allclose(magnitude, np.load(os.path.join(self.path, 'ref_mag_vort.npy')),
                         err_msg='Created vortex magnetic distribution does not match expectation')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_phasemap.py

@@ -72,8 +72,3 @@ class TestCasePhaseMap(unittest.TestCase):
                         err_msg='Unexpected behavior in load_from_netcdf4()!')
         assert_allclose(phasemap.a, self.phasemap.a,
                         err_msg='Unexpected behavior in load_from_netcdf4()!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_phasemapper.py

@@ -201,8 +201,3 @@ class TestCasePhaseMapperCharge(unittest.TestCase):
 
     def test_jac_T_dot(self):
         self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_pm.py

@@ -26,8 +26,3 @@ class TestCasePM(unittest.TestCase):
         assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
                         err_msg='Unexpected behavior in pm()!')
         assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in pm()!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_projector.py

@@ -256,7 +256,3 @@ class TestCaseYTiltProjector(unittest.TestCase):
 
 
 # TODO: Test RotTiltProjector!!!
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

pyramid/tests/test_regularisator.py

@@ -128,8 +128,3 @@ class TestCaseFirstOrderRegularisator(unittest.TestCase):
         hess_diag_ref = np.diag(np.load(os.path.join(self.path, 'first_order_jac_ref.npy')))
         assert_allclose(hess_diag, hess_diag_ref, atol=1E-7,
                         err_msg='Unexpected behaviour in hess_diag()!')
-
-
-if __name__ == '__main__':
-    import nose
-    nose.run(defaultTest=__name__)

requirements.txt

--e .
+-e .['all']

setup.py

@@ -6,6 +6,7 @@ import os
 import re
 import subprocess
 import sys
+import itertools
 from distutils.command.build import build
 
 #import numpy
@@ -17,12 +18,13 @@ DESCRIPTION = 'PYthon based Reconstruction Algorithm for MagnetIc Distributions'
 MAINTAINER = 'Jan Caron'
 MAINTAINER_EMAIL = 'j.caron@fz-juelich.de'
 URL = ''
-VERSION = '0.1.0-dev'
-PYTHON_VERSION = (2, 7)
-DEPENDENCIES = {'numpy': (1, 10)}  # TODO: get rid off!!!
+VERSION = '0.1.0.dev0'  # TODO: Better way?
+PYTHON_VERSION = (2, 7)  # TODO: get rid of!!!
+DEPENDENCIES = {'numpy': (1, 10)}  # TODO: get rid of!!!
 LONG_DESCRIPTION = 'long description (TODO!)'  # TODO: Long description! put in (Readme?) file!
 
 
+# TODO: get rid of superfluous functions!
 def get_package_version(package):
     """Return the package version of the specified package.
 
@@ -70,7 +72,7 @@ def check_requirements():
                               % ((package_name,) + min_version))
 
 
-def hg_version():  # TODO: Replace with GIT! Also check build output on GitLab!
+def hg_version():  # TODO: Replace with GIT! Also check build output on GitLab! See numpy setup.py!
     """Get the Mercurial reference identifier.
 
     Returns
@@ -126,13 +128,24 @@ def get_files(rootdir):
     return filepaths
 
 
+
+# TODO: Use requirements.txt? extras_require for optional stuff (hyperspy, plotting)?
+# TODO: After split of Pyramid, comment out and see what really is used (is e.g. scipy?)!
+install_requires = ['numpy>=1.6', 'tqdm', 'scipy', 'matplotlib', 'Pillow', 'h5py',
+                    'hyperspy', 'jutil', 'cmocean']
+
 # TODO: extend extras_require for plotting and IO:
+# TODO: extra: 'pyfftw', 'mayavi' (not easy to install... find a way!)
+# TODO: See https://stackoverflow.com/a/28842733 for extras_require...
+# TODO: ...replace [dev] with [IO] (hyperspy) and [plotting] (separate plotting library)!
 extras_require = {
     # TODO: Test all if really needed! don't use nose, if possible (pure pytest)!
-    "tests": ['pytest', 'pytest-runner', 'pytest-cov', 'pytest-flake8', 'coverage', 'nose']
+    'tests': ['pytest', 'pytest-runner', 'pytest-cov', 'pytest-flake8', 'coverage'],
+    '3Dplot': ['qt==4.8', 'mayavi==4.5']
     # TODO: more for mayavi (plotting in general) and hyperspy, etc (see below)...
 }
 
+extras_require["all"] = list(itertools.chain(*list(extras_require.values())))
 
 
 print('\n-------------------------------------------------------------------------------')
@@ -148,18 +161,12 @@ setup(name=DISTNAME,
       url=URL,
       download_url=URL,
       version=VERSION,
-      packages=find_packages(exclude=['tests', 'doc']),
-      #include_dirs=[numpy.get_include()],
-      # TODO: Use requirements.txt? extras_require for optional stuff (hyperspy, plotting)?
-      # TODO: After split of Pyramid, comment out and see what really is used (is e.g. scipy?)!
+      packages=find_packages(exclude=['tests', 'doc']),  # TODO: necessary?
+      #include_dirs=[numpy.get_include()],  # TODO: Maybe used for sphinx?!
       #setup_requires=['numpy>=1.6', 'pytest', 'pytest-runner'],
       #tests_require=['pytest', 'pytest-cov', 'pytest-flake8'],
-      install_requires=['numpy>=1.6', 'tqdm', 'scipy', 'matplotlib', 'Pillow', 'h5py',
-                        'hyperspy', 'jutil', 'cmocean'],
+      install_requires=install_requires,
       extras_require=extras_require,
-      # TODO: extra: 'pyfftw', 'mayavi' (not easy to install... find a way!)
-      # TODO: See https://stackoverflow.com/a/28842733 for extras_require...
-      # TODO: ...replace [dev] with [IO] (hyperspy) and [plotting] (separate plotting library)!
-      #test_suite='nose.collector',  # TODO: don't use nose!
-      cmdclass={'build': build})
+      cmdclass={'build': build}  # TODO: necessary?
+    )
 print('-------------------------------------------------------------------------------\n')