… >= 0.17, 1.0.0 tested. Linux tests will be performed after numpy version is updated.

… skip]

… [ci skip]

Set NumPy version: 1.9, test Jenkins PR Builder [ci skip]

This reverts commit d33f745.

…tack

- sxpipe.py --isac_substack
  Added header import of xform.projections into ISAC or Beautifier substack
- pipe_isac_substack.txt & wikiparser.py
  Reflected above interface changes of sxpipe.py --isac_substack to the Wiki Document.
- sxgui.py
  Reflected above interface changes of sxpipe.py --isac_substack to GUI.
- sxcompute_isac_avg.py
  Fixed extraction of ISAC shrink ratio.
  Fixed missing n_object header entries from some images (depended on MPI proc).
  Added subdirectories for ali2d_local_params_avg and params_avg.
- NOTE: Same commit is pushed to master branch.

New Sort3D for release

Fixed 3D angular distribution representation

linux: 1.6.17
osx:   1.6.32

… [ci skip]

- wikiparser.py & sxgui_template.py
  Added support for reversed default value in GUI.
- 3dvariability.txt
  Correctly reversed default value of --CTF option in GUI.
- relion2sphire.txt
  Minor correction of help strings.
- sxgui.py
  Reflected all above changes to GUI.
- sxpipe.py isac_substack
  Fixed typos in standard output/error.
  Added error handling for inconsistency of input datasets.
  Added counts of default ISAC class averages (ordered_class_averages.hdf).
- sxrelion2sphire.py
  Fixed an import error.
- sxsort3d_depth.py
  Fixed an typo fatal error.

Fixed a bug related to reversed default value in GUI.

- sxrviper (rviper.txt)
  moon_elimination
- sxviper (viper.txt)
  moon_elimination
- sxprocess.py --combinemaps of halfset vols (wikiparser.py)
  fsc_adj, B_start, B_stop, aa
- sxprocess.py --combinemaps of cluster vols (wikiparser.py)
  aa
- sxprocess.py --angular_distribution (wikiparser.py)
  pixel_size, box_size, cylinder_width, cylinder_length
- Reflected all above changes to sxgui.py.

- sxsort3d_depth.py (sort3d_depth.txt)
  Reflected Zhong explanation of --swap_ratio to the help string
  Also, moved --swap_ratio under --do_swap_au.
- sxpipe.py isac_substack (wikiparser.py)
  Corrected type of input_bdb_stack_path argument in GUI (from "image" to "bdb").
- sxprocess.py adaptive_mask (process.txt)
  Fixed typo in help string of --nsigma.
- Reflected all above changes to GUI (sxgui.py)
- sxmeridien.py
  Reflected change in master branch.
- sxpipe.py isac_substack
  Removed xform from output file name & standard outputs upon Pawel's request.
  Fixed typo from "paramter" to "parameter".

…checkout [ci skip]

This reverts commit 629aa6c.

Pin openmpi to 2.0.2 in constructor

- Reflected Zhong's recent modifications of in sx3dvariability.py.
  Also, corrected Zhong's reversion from resolution [A] to abs freq [1/Pixel].
- Reflected Zhong's recent modifications of sxcompute_isac_avg.py.
  Changed low pass filter related parameters.
- Reflected Zhong's recent modifications of sxcter.py.
  Also, changed "frequency" to "resolution" of --f_start & --f_stop.
- Reflected Zhong's recent modifications of sxprocess.py.
- Reflected Zhong's recent modifications of 3dvariability.txt.
  Also, added minor edition of help strings.
- Reflected Zhong's recent modifications of compute_isac_avg.txt.
  Also, corrected the default value of --fl option.
  Additionally edited help strings.
- Reflected Zhong's recent modifications of cter.txt.
- Reflected Zhong's recent modifications of locres.txt.
  Also, corrected the description of --cutoff option.
  Also, edited help string of --res_overall option.
- Reflected Zhong's recent modifications of process.txt.
  Also, fixed typo in help string of --nsigma of sxprocess.py adaptive_mask.

…elease/2.21

  merge before push

- This commit merges GUI update in master to release.
- Also reflected recent modifications to wikiparser.py.
  Zhong's recent modifications of compute_isac_avg.txt.
    Edited short info of "Beautifier - No Adjust" mode.
    (i.e. sxcompute_isac_avg.py --no_adjustment)
  Zhong's recent modifications of process.txt.
    help string of --fl option of sxprocess.py --combinemaps.
- Reflected all above changes to GUI (sxgui.py)

- For isac_substack, especially tuple to list.
- This commmit merges master and release branch.

- process.txt & wikiparser.py.
  Added --symmetry option to process.txt --angular_distribution.
- Reflected all above changes to GUI (sxgui.py).
- This commit merges master and release branches.

…lready in place, but this

should fix it permanently I believe.

…rrectly as 2d

…nor bugfix for LST support

- All Pawel's commits between 2018/01/24-28 in master
- Updated symclass
- Added tet suppport

…elease/2.21

…elease/2.21

This reverts commit 2d90d18.

…elease/2.21

…elease/2.21

merge before push