Added environment.yml and requirement.txt.
GitLab should now produce html coverage artifacts.
io_vectordata: now warns if grid spacing is not equal in all directions.

cmocean, hyperspy to yml file.

Signed-off-by: Jan Caron <j.caron@fz-juelich.de>

Smooth_vortex now can have a homogeneous core with radius larger 1.
Hacky solution for PyQt4/5, change later!

Changed ignore files.

docs: moved up one level.
plottools: added some default label sizes.
version: added to VCS and added a TODO (switch to Git)
fielddata: added rot90 for ScalarData, lot of small changes.

Started working on reader for binary ovf files (WIP).
utils.pm now works with PhaseMapperFDFC.

fielddata and phasemap: Now use the new plottools module, cleanup of arguments
                        and documentation.
plottools: New module for pretty plotting and different annotations like text,
           colorwheels and colorbars.
colors: Colorbar now has a black circle outline and arrows pointing in cardinal
        directions.
diagnostics: Small documentation fixes and naming 'avg' --> 'avrg'.
docs: Renewed documentation.

diagnostics: now takes magdata as input instead of a vector.
             Plotting routines for diagnostics added.
fielddata: Added quiverkey if b_0 is provided.
phasemap: If appropriate unit is provided, will be labeled as "Gain Map".
scalebar: Cleaned up and clipping added.

reconstruction: jutil.TakeTime is now used here.
scalebars: Module which allows nice scalebars to be displayed in all plots.
           This is the new default and can be turned off.
ramp: Now stores everything from the dataset directly to self, instead of
      keeping a reference to the DataSet (construct without Dataset in future!).
projector: tqdm now uses tqdm_notebook if used in IPython Notebook!
magcreator: Added functionality for smooth vortices (see de Graef et al.).
kernel: Corrected behaviour of slab geometry (u and v were still switched!).
dataset: phasemappers now accessable as dictionary or list. The append function
         now also takes lists (but projectors and phasemappers can in turn not
         set directly anymore). Se_inv will be updated automatically.
diagnostics: Functionality to access total, directional and magnitude error,
             according to Kemp et al.

dataset: implemented save/load features in io_dataset.py
h5py: copied data from hdf5 files to make sure they exist after file is closed.
projector/phasemap/dataset: force dim/dim_uv to be tuples.

Projectors now have tqdm options to show progress.

phasemap: Now supports flips, rotations and shifts with ndimage.
          Added plot_phase_with_hist to plot histograms (for difference plots).
fielddata: FieldData now properly plots contours and masks (new).
dataset: set_3d_mask now uses the new mask capability of FieldData.
         Default is no longer "logical backprojection".
io_phasemap: Now includes .tif (although that does not always work).
setup.py: Deleted deprecated depencencies.
Renamed a few plot commands to plot_...
Rollback to RdBu as colormap (back from Spectral).

fielddata: slices now include z-component which will be plotted in plot_field.
colors: Minor tweaks. Mainly for Rec. 601/709 input.
phasemap: Now uses 'Spectral' as a colormap.

Now uses an improved cubehelix colorwheel for most purposes.
Other variants are also provided.
Removed hue_mode.

fielddata: Added plot_quiver_field convenience function.
io_phasemap: Added functionality for images separately from HyperSpy.
phasemap: Automatically normalise confidence.
projector: Quaternion for tilt around x-axis corrected (was falsely around y).
reconstruction: Added verbose option (True by default).
reconstruction_2d_from_phasemap: Plotting optimised.

Renaming of variables in PhaseMapperRDFC.jac_T_dot to make more sense...

phasemapper: PhasemapperRDFC: Now the adjoint is calculated correctly (switched
        slicing order, took conjugate of kernel FFTs, deleted superfluous minus
        sign). Results are the same, but calculation is now CORRECT!
fft: Correction of numpy rfftn_adj.
fielddata: Added option for uniform color specification.

kernel: u and v are switched and now finally correct.
        get_elementary_phase is also switched and corrected.
phasemapper: added PhaseMapperCharge from Feng Shan.
forward_model: now uses y instead of phase_vec/Se_inv and now direct properties.
costfunction: corrected some docstrings and documentation comments.
fielddata: corrected some missing integer divisions (// instead of /),
        added plot_streamline().

Addition of plot_field for FieldData as alternative to quiver plots.
PhaseMap phase plot now has an option to cut outliers (e.g. difference plots).
IO of PhaseMaps now can handle different file extensions in one loading.
Phasemap creator GUI now uses IO loading.
Replaced flatten with ravel (memory efficiency).
Renamed non constant variables to lower case (not UPPER CASE anymore).

fielddata: Now takes figsize as argument
phasemap: phase_plot now uses imshow (much faster)
Removed API (to determine later...)

New API module unclutters the namespace (import pyramid.api as pr).