From 352242aefec28dad411e893bacc9270d5a1924ed Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Tue, 18 Jul 2017 10:03:03 +0200
Subject: [PATCH] Got rid of nose in all tests. Finished environment.yml.
---
.gitignore | 2 ++
environment.yml | 56 ++++++++++++++++++++++++++---
pyramid/fft.py | 2 +-
pyramid/tests/test_analytic.py | 5 ---
pyramid/tests/test_costfunction.py | 5 ---
pyramid/tests/test_dataset.py | 5 ---
pyramid/tests/test_fielddata.py | 5 ---
pyramid/tests/test_forwardmodel.py | 5 ---
pyramid/tests/test_kernel.py | 5 ---
pyramid/tests/test_magcreator.py | 5 ---
pyramid/tests/test_phasemap.py | 5 ---
pyramid/tests/test_phasemapper.py | 5 ---
pyramid/tests/test_pm.py | 5 ---
pyramid/tests/test_projector.py | 4 ---
pyramid/tests/test_regularisator.py | 5 ---
requirements.txt | 2 +-
setup.py | 39 +++++++++++---------
17 files changed, 78 insertions(+), 82 deletions(-)
diff --git a/.gitignore b/.gitignore
index ff052d9..c9a869b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,8 @@ desktop.ini
.idea
+.coverage
+
*.egg-info
.DS_Store
diff --git a/environment.yml b/environment.yml
index c45b555..156ba42 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,53 @@
+# 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
diff --git a/pyramid/fft.py b/pyramid/fft.py
index f87fa44..1ab7ce4 100644
--- a/pyramid/fft.py
+++ b/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
diff --git a/pyramid/tests/test_analytic.py b/pyramid/tests/test_analytic.py
index c5b5485..e318a6b 100644
--- a/pyramid/tests/test_analytic.py
+++ b/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__)
diff --git a/pyramid/tests/test_costfunction.py b/pyramid/tests/test_costfunction.py
index 44d44f7..21015f2 100644
--- a/pyramid/tests/test_costfunction.py
+++ b/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__)
diff --git a/pyramid/tests/test_dataset.py b/pyramid/tests/test_dataset.py
index cbc5e47..1e8646b 100644
--- a/pyramid/tests/test_dataset.py
+++ b/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__)
diff --git a/pyramid/tests/test_fielddata.py b/pyramid/tests/test_fielddata.py
index 39cc04f..8ca3b77 100644
--- a/pyramid/tests/test_fielddata.py
+++ b/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__)
diff --git a/pyramid/tests/test_forwardmodel.py b/pyramid/tests/test_forwardmodel.py
index 1ca4fc4..3604e71 100644
--- a/pyramid/tests/test_forwardmodel.py
+++ b/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__)
diff --git a/pyramid/tests/test_kernel.py b/pyramid/tests/test_kernel.py
index c16e603..7aac1dc 100644
--- a/pyramid/tests/test_kernel.py
+++ b/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__)
diff --git a/pyramid/tests/test_magcreator.py b/pyramid/tests/test_magcreator.py
index 75686bd..5ab8000 100644
--- a/pyramid/tests/test_magcreator.py
+++ b/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__)
diff --git a/pyramid/tests/test_phasemap.py b/pyramid/tests/test_phasemap.py
index 2af8a33..5ff1e70 100644
--- a/pyramid/tests/test_phasemap.py
+++ b/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__)
diff --git a/pyramid/tests/test_phasemapper.py b/pyramid/tests/test_phasemapper.py
index a134945..164d865 100644
--- a/pyramid/tests/test_phasemapper.py
+++ b/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__)
diff --git a/pyramid/tests/test_pm.py b/pyramid/tests/test_pm.py
index 061d5c5..dfc839c 100644
--- a/pyramid/tests/test_pm.py
+++ b/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__)
diff --git a/pyramid/tests/test_projector.py b/pyramid/tests/test_projector.py
index b87d447..72635a7 100644
--- a/pyramid/tests/test_projector.py
+++ b/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__)
diff --git a/pyramid/tests/test_regularisator.py b/pyramid/tests/test_regularisator.py
index 3ed52ea..53c7eb9 100644
--- a/pyramid/tests/test_regularisator.py
+++ b/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__)
diff --git a/requirements.txt b/requirements.txt
index d6e1198..26f4c20 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1 @@
--e .
+-e .['all']
diff --git a/setup.py b/setup.py
index d36cd31..7085106 100644
--- a/setup.py
+++ b/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')
--
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