pull

.gitlab-ci.yml

-image: "python:3.5"
-
-before_script:
-  # Check and print Python version
-  - python --version
-  # Create SSH configuration directory if necessary (also parents with -p, mode: read/write/exec):
-  - mkdir -p --mode=700 ~/.ssh/
-  # Add SSH key for jutil:
-  - echo "$ID_RSA_JUTIL_PRIVATE" > ~/.ssh/id_rsa_jutil
-  # Provide read access to owner (octal value code: 400) to jutil key and known_hosts with chmod:
-  - chmod 400 ~/.ssh/id_rsa_jutil
-  # Configure SSH to use ~/.ssh/jutil_key for iffgit.fz-juelich.de (-e allows \n):
-  - echo -e "Host iffgit.fz-juelich.de\n\tIdentityFile ~/.ssh/id_rsa_jutil\n" > ~/.ssh/config
-  # Add iffgit.fz-juelich.de to known_hosts (not the same key as Jutil!):
-  - echo iffgit.fz-juelich.de,134.94.161.83 "$ID_RSA_IFFGIT_PUBLIC" > ~/.ssh/known_hosts
-  # Provide read access to owner (octal value code: 400) to known_hosts with chmod:
-  - chmod 400 ~/.ssh/known_hosts
-  # Install jutil via secure ssh connection:
-  - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
-
 stages:
   - test
 
-test:
+before_script:
+    # Create SSH configuration directory if necessary (also parents with -p, mode: read/write/exec):
+    - mkdir -p --mode=700 ~/.ssh/
+    # Add SSH key for jutil:
+    - echo "$ID_RSA_JUTIL_PRIVATE" > ~/.ssh/id_rsa_jutil
+    # Provide read access to owner (octal value code: 400) to jutil key and known_hosts with chmod:
+    - chmod 400 ~/.ssh/id_rsa_jutil
+    # Configure SSH to use ~/.ssh/jutil_key for iffgit.fz-juelich.de (-e allows \n):
+    - echo -e "Host iffgit.fz-juelich.de\n\tIdentityFile ~/.ssh/id_rsa_jutil\n" > ~/.ssh/config
+    # Add iffgit.fz-juelich.de to known_hosts (not the same key as Jutil!):
+    - echo iffgit.fz-juelich.de,134.94.161.83 "$ID_RSA_IFFGIT_PUBLIC" > ~/.ssh/known_hosts
+    # Provide read access to owner (octal value code: 400) to known_hosts with chmod:
+    - chmod 400 ~/.ssh/known_hosts
+    # Install necessary apps like git and mesa-utils (needed for GL):
+    # TODO: Check if this is still needed after removing mayavi!?
+    - apt-get update
+    - apt-get install -y curl bzip2 git mesa-utils
+
+test_miniconda:
   stage: test
+  image: continuumio/miniconda3
   script:
-    # TODO: Different jobs with custom develop arguments? extra_requires (hyperspy, plotting)?
-    # TODO: Use pip install -e .[hyperspy], etc.
-    # Install requirements:
-    # - pip install -r requirements.txt  # TODO: DOES NOT WORK (because mayavi and stuff...)
-    - pip install -e .['tests']
+    # Install requirements for pyramid:
+    - conda info --envs
+    - conda env create -q # -q: quiet/ no progressbar, because it spams the log!
+    - source activate pyramid
+    - conda info --envs
+    - conda uninstall mayavi vtk -y  # TODO: necessary, because mayavi does not play nice with qt5!
+    - conda install pyqt=5  # TODO: This is needed for tests to run, but breaks mayavi (not used)!
+    # Install jutil via secure ssh connection:
+    - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
+    # Execute tests:
     - python setup.py test
+    # Create coverage report:
     - coverage html
   artifacts:
     paths:
       - htmlcov/
+
+test_conda_ubuntu:
+  stage: test
+  image: ubuntu:16.04
+  script:
+    # Install miniconda:
+    - curl -O -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    - chmod +x Miniconda3-latest-Linux-x86_64.sh
+    - ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
+    - export PATH="/opt/miniconda3/bin:${PATH}"
+    # Install requirements for pyramid:
+    - conda info --envs
+    - conda env create -q # -q: quiet/ no progressbar, because it spams the log!
+    - source activate pyramid
+    - conda info --envs
+    - conda uninstall mayavi vtk -y  # TODO: necessary, because mayavi does not play nice with qt5!
+    - conda install pyqt=5  # TODO: This is needed for tests to run, but breaks mayavi (not used)!
+    # Install jutil via secure ssh connection:
+    - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
+    # Execute tests:
+    - python setup.py test
+
+test_pip_minimal:
+  stage: test
+  image: python:3.5
+  script:
+    # TODO: Different jobs with custom develop arguments? extra_requires (hyperspy, plotting)?
+    # TODO: Use pip install -e .[hyperspy], etc.
+    # Install requirements:
+    - pip install -e .['tests']  # TODO: other case with ['all']? After getting rid of mayavi...
+    # Install jutil via secure ssh connection:
+    - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
+    # Execute tests:
+    - python setup.py test
+
+test_pip_requirements:
+  stage: test
+  image: python:3.5
+  script:
+    # Install requirements:
+    - pip install -r requirements.txt  # TODO: mayavi/pyfftw commented out by hand to make work!
+    # Install jutil via secure ssh connection:
+    - pip install git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git
+    # Execute tests:
+    - python setup.py test
+
+# TODO: What about windows? Better have one test (miniconda?) for windows/max/linux, each!

environment.yml

@@ -2,6 +2,7 @@
 # This file contains the top level dependencies of the pyramid project!
 # requirements.txt also contains sub-dependencies, generated by "pip freeze > requirements.txt"!
 # Add new dependencies here, then "conda env update", then "pip freeze > requirements.txt"!
+# To see if compatible upgrades are available for the current packages, use "conda upgrade --all"!
 # When packages are deprecated/deleted, it may be best to recreate the environment from scratch!
 
 name: pyramid
@@ -23,13 +24,13 @@ dependencies:
   # File IO:
   - hyperspy=1.3
   - hyperspy-gui-ipywidgets=1.0
-  - hyperspy-gui-traitsui=1.0  # TODO: Optional! Delete when mayavi is gone!
+  # - 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  # Only works with qt4 from conda-forge channel!
+  - matplotlib=2.0  # Only conda-forge channel has working version for qt4!
   - Pillow=4.1
   - cmocean=1.1
-  - qt=4.8  # Necessary because of traits in mayavi...
+  - qt=4.8  # Necessary because of traits in mayavi... On server, pyqt=5.6 is needed!
   - mayavi=4.5  # TODO: Get rid of!
   #- colorspacious  # TODO: NOT USED?
   #- visvis  # TODO: NOT USED?
@@ -50,9 +51,3 @@ dependencies:
 #  - 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/analytic.py

@@ -164,8 +164,7 @@ def phase_mag_sphere(dim, a, phi, center, radius, b_0=1):
         r = np.hypot(x - x0, y - y0)
         result = coeff * R ** 3 / (r + 1E-30) ** 2 * (
             (y - y0) * np.cos(phi) - (x - x0) * np.sin(phi))
-        # TODO: During testing: "RuntimeWarning: invalid value encountered in power":
-        result *= np.where(r > R, 1, (1 - (1 - (r / R) ** 2) ** (3. / 2.)))
+        result *= 1 - np.clip(1 - (r / R) ** 2, 0, 1) ** (3. / 2.)
         return result
 
     # Process input parameters:

pyramid/file_io/io_vectordata.py

@@ -155,11 +155,15 @@ def _load_from_ovf(filename, a):
         field = np.asarray((x_mag, y_mag, z_mag)) * float(header.get('valuemultiplier', 1))
         if a is None:
             # TODO: If transferred to HyperSpy, this has to stay in Pyramid reader!
-            if not header.get('xstepsize') == header.get('ystepsize') == header.get('zstepsize'):
-                _log.warning('Grid spacing is not equal in x, y and z (x will be used)!')
-            a = float(header.get('xstepsize', 1.))
-            meshunit = header.get('meshunit', 'nm')
-            a *= {'m': 1e9, 'mm': 1e6, 'µm': 1e3, 'nm': 1}[meshunit]  # Conversion to nm
+            xstep = float(header.get('xstepsize'))
+            ystep = float(header.get('ystepsize'))
+            zstep = float(header.get('zstepsize'))
+            if not np.allclose(xstep, ystep) and np.allclose(xstep, zstep):
+                _log.warning('Grid spacing is not equal in x, y and z (x will be used)!\n'
+                             'Found step sizes are x:{}, y:{}, z:{} (all in {})!'.format(
+                                xstep, ystep, zstep, header.get('meshunit')))
+            # Extract grid spacing from xstepsize and convert according to meshunit:
+            a = xstep * {'m': 1e9, 'mm': 1e6, 'µm': 1e3, 'nm': 1}[header.get('meshunit', 'nm')]
         return VectorData(a, field)
 
 

pyramid/kernel.py

@@ -101,15 +101,18 @@ class Kernel(object):
         u = np.linspace(-(u_dim - 1), u_dim - 1, num=2 * u_dim - 1)
         v = np.linspace(-(v_dim - 1), v_dim - 1, num=2 * v_dim - 1)
         uu, vv = np.meshgrid(u, v)
+        # TODO: u, v are coordinates, rename self.u/v to self.kern_u/v!
         self.u = np.empty(self.dim_kern, dtype=dtype)
         self.v = np.empty(self.dim_kern, dtype=dtype)
         self.u[...] = coeff * self._get_elementary_phase(geometry, uu, vv, a)
+        # TODO: The minus sign belongs into the phasemapper (debatable)!
         self.v[...] = coeff * -self._get_elementary_phase(geometry, vv, uu, a)
         # Include perturbed reference wave:
         if prw_vec is not None:
             uu += prw_vec[1]
             vv += prw_vec[0]
             self.u[...] -= coeff * self._get_elementary_phase(geometry, uu, vv, a)
+            # TODO: The minus sign belongs into the phasemapper (debatable)!
             self.v[...] -= coeff * -self._get_elementary_phase(geometry, vv, uu, a)
         # Calculate Fourier trafo of kernel components:
         self.u_fft = fft.rfftn(self.u, self.dim_pad)
@@ -128,6 +131,7 @@ class Kernel(object):
 
     def _get_elementary_phase(self, geometry, n, m, a):
         self._log.debug('Calling _get_elementary_phase')
+        # TODO: Rename n m to p q ?
         if geometry == 'disc':
             in_or_out = ~ np.logical_and(n == 0, m == 0)
             return m / (n ** 2 + m ** 2 + 1E-30) * in_or_out

pyramid/plottools.py

@@ -28,13 +28,14 @@ FIGSIZE_DEFAULT = (6.7, 5)  # TODO: Apparently does not fit as well as before...
 FONTSIZE_DEFAULT = 20
 STROKE_DEFAULT = None
 
-
+# TODO: Replace by matplotlib styles!
 def pretty_plots(figsize=None, fontsize=None, stroke=None):
     """Set IPython formats (for interactive and PDF output) and set pretty matplotlib font."""
     from IPython.display import set_matplotlib_formats
     set_matplotlib_formats('png', 'pdf')  # png for interactive, pdf, for PDF output!
     mpl.rcParams['mathtext.fontset'] = 'stix'  # Mathtext in $...$!
     mpl.rcParams['font.family'] = 'STIXGeneral'  # Set normal text to look the same!
+    # TODO: set 'font.size' = FONTSIZE! Does this change everything relative to this value???
     mpl.rcParams['figure.max_open_warning'] = 0  # Disable Max Open Figure warning!
     if figsize is not None:
         global FIGSIZE_DEFAULT

setup.cfg

@@ -32,7 +32,7 @@ test=pytest
 branch = True
 source = pyramid
 omit =
- pyramid/tests/*
+    tests/*
 
 [tool:pytest]
 addopts = --cov --flake8

setup.py

@@ -7,7 +7,7 @@ import re
 import subprocess
 import sys
 import itertools
-from distutils.command.build import build
+#from distutils.command.build import build
 
 #import numpy
 from setuptools import setup, find_packages
@@ -150,8 +150,8 @@ extras_require["all"] = list(itertools.chain(*list(extras_require.values())))
 
 
 print('\n-------------------------------------------------------------------------------')
-print('checking requirements')
-check_requirements()
+# print('checking requirements')  # TODO: Get rid of!
+# check_requirements()
 print('write version.py')
 write_version_py()
 setup(name=DISTNAME,
@@ -168,6 +168,6 @@ setup(name=DISTNAME,
       #tests_require=['pytest', 'pytest-cov', 'pytest-flake8'],
       install_requires=install_requires,
       extras_require=extras_require,
-      cmdclass={'build': build}  # TODO: necessary?
+      #cmdclass={'build': build}  # TODO: necessary?
     )
 print('-------------------------------------------------------------------------------\n')