Update source code

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Maia Azubel

unread,

Aug 4, 2022, 2:27:07 PM8/4/22

to EMAN2

I'm using

EMAN 2.99 ( GITHUB: 2021-09-13 10:49 - commit: ba39969d8 )
Your Python version is: 3.7.9

and want to update

I followed instructions

(Full details below)

But for >git pull I'm getting

.....

Already on 'master'

Your branch is behind 'origin/master' by 653 commits, and can be fast-forwarded.

(use "git pull" to update your local branch)

(eman2) [maia2@tomo eman2]$ git pull

warning: Pulling without specifying how to reconcile divergent branches is

discouraged. You can squelch this message by running one of the following

commands sometime before your next pull:

git config pull.rebase false # merge (the default strategy)

git config pull.rebase true # rebase

git config pull.ff only # fast-forward only

You can replace "git config" with "git config --global" to set a default

preference for all repositories. You can also pass --rebase, --no-rebase,

or --ff-only on the command line to override the configured default per

invocation.

Updating ba39969d8..8a24bb112

error: Your local changes to the following files would be overwritten by merge:

.gitignore

...

Aborting

I'd appreacite advice regarding what option to use, or if I need to do something differently.

Thanks,
Maia

-------

(eman2) [maia2@tomo eman2]$ git fetch --all --prune

Fetching origin

From https://github.com/cryoem/eman2

- [deleted] (none) -> origin/binary

- [deleted] (none) -> origin/cmake-boost

- [deleted] (none) -> origin/deps

- [deleted] (none) -> origin/jenkins-/envs

- [deleted] (none) -> origin/refactor-prog-tests

- [deleted] (none) -> origin/relion_tool_integration

- [deleted] (none) -> origin/tapu_transfer

remote: Enumerating objects: 4355, done.

remote: Counting objects: 100% (2562/2562), done.

remote: Compressing objects: 100% (263/263), done.

remote: Total 4355 (delta 2320), reused 2519 (delta 2296), pack-reused 1793

Receiving objects: 100% (4355/4355), 24.44 MiB | 14.68 MiB/s, done.

Resolving deltas: 100% (3210/3210), completed with 249 local objects.

ba39969d8..8a24bb112 master -> origin/master

ea3078b76..98d35247a fix_unittests -> origin/fix_unittests

9db1ac73d..bf8cc9dc8 isac_filament -> origin/isac_filament

* [new branch] new-scaling -> origin/new-scaling

* [new branch] read-write-images-cpp -> origin/read-write-images-cpp

a81e1e046..3d547a343 starfile_integration -> origin/starfile_integration

(eman2) [maia2@tomo eman2]$ git checkout master

M .gitignore

M BSD-3-Clause.txt

M CMakeLists.txt

M Jenkinsfile

M README.md

M TODO

M broken/e22.py

M broken/e2ali2img.py

M broken/e2avg_ffts.py

M broken/e2fileinfo.py

M broken/e2findsubunit.py

M broken/e2flick.py

M broken/e2helical_recons.py

M broken/e2markbadparticles.py

M broken/e2modeleval.py

M broken/e2montecarlorecon.py

M broken/e2plotFSC.py

M broken/e2preferences.py

M broken/e2refine_evenodd.py

M broken/e2refmerge.py

M broken/e2remoted.py

M broken/e2resolution.py

M broken/e2scp.py

M broken/e2tomoaverage.py

M broken/em3Dhelloworld.py

M ci_support/build_no_recipe.sh

M ci_support/build_recipe.sh

M ci_support/constructor-huge/construct.yaml

M ci_support/constructor-mini/construct.yaml

M ci_support/package.sh

M ci_support/post-install-actions.bat

M ci_support/post-install-actions.sh

M ci_support/set_env_vars.sh

M ci_support/setup_conda.sh

M cmake/Boost.cmake

M cmake/FindACML.cmake

M cmake/FindConda.cmake

M cmake/FindDJBFFT.cmake

M cmake/FindFFTW3.cmake

M cmake/FindFTGL.cmake

M cmake/FindNFFT2.cmake

M cmake/FindNosetests.cmake

M cmake/FindNumPy.cmake

M cmake/FindOPTPP.cmake

M cmake/FindPython.cmake

M cmake/FindSZLIB.cmake

M cmake/Freetype.cmake

M cmake/GSL.cmake

M cmake/HDF5.cmake

M cmake/JPEG.cmake

M cmake/OpenGL.cmake

M cmake/PNG.cmake

M cmake/TIFF.cmake

M cmake/find_all.cmake

M cmake/functions.cmake

M cmake/testing.cmake

M doc/CMakeLists.txt

M doc/EMAN2.0.big.jpg

M doc/EMANnonum.big.png

M doc/INSTALL

M doc/adding_processor.html

M doc/coding_style.html

M doc/cvshowto.html

M doc/develop_system_setup.html

M doc/developer-guide.html

M doc/development_policy_faq.html

M doc/doc.html

M doc/doxygen/CMakeLists.txt

M doc/doxygen/Doxyfile

M doc/eman2doc.h

M doc/exception_faq.html

M doc/header_naming.html

M doc/index.html

M doc/latex/CMakeLists.txt

M doc/latex/EMAN2.lot

M doc/latex/EMAN2.tex

M doc/latex/TOC.tex

M doc/latex/abstract.tex

M doc/latex/adding-components.tex

M doc/latex/adding-documentation.tex

M doc/latex/coding-style.tex

M doc/latex/development-policy-faq.tex

M doc/latex/dirs.tex

M doc/latex/e2align3d.tex

M doc/latex/e2aligntest.tex

M doc/latex/e2boxer.tex

M doc/latex/e2cmmtomrc.tex

M doc/latex/e2dumplog.tex

M doc/latex/e2foldfitter.tex

M doc/latex/e2make3d.tex

M doc/latex/e2pdb2mrc.tex

M doc/latex/e2proc2d.tex

M doc/latex/e2proc3d.tex

M doc/latex/e2project3d.tex

M doc/latex/e2scannereval.tex

M doc/latex/e2symbest.tex

M doc/latex/e2tomogram.tex

M doc/latex/exceptions.tex

M doc/latex/factory-classes.tex

M doc/latex/fancyhdr.sty

M doc/latex/fncychap.sty

M doc/latex/frame-work-testing.tex

M doc/latex/goals.tex

M doc/latex/help-opt-prog-inst.tex

M doc/latex/hyperref.perl

M doc/latex/image-header-attribs.tex

M doc/latex/index.tex

M doc/latex/install.tex

M doc/latex/logger.tex

M doc/latex/ltxmarkup.sty

M doc/latex/make3d.tex

M doc/latex/misc-developers-guide.tex

M doc/latex/processors.tex

M doc/latex/project3d.tex

M doc/latex/python-scripts.tex

M doc/latex/reference-manual.tex

M doc/latex/using-cvs.tex

M doc/modular_class_html/CMakeLists.txt

M doc/testing.html

M examples/00README

M examples/CMakeLists.txt

M examples/jsontest.py

M examples/mpi_test.py

M examples/refine_test.sh

M gpl-2.0.txt

M images/Bag.png

M images/CMakeLists.txt

M images/Close.png

M images/Close.txt

M images/EMAN2Icon.png

M images/File.png

M images/Folder.png

M images/FolderFiles.png

M images/Key.png

M images/SirEMAN2.png

M images/black_box.png

M images/boxer_erase.png

M images/boxer_unerase.png

M images/boxhabanosclose.png

M images/classes.png

M images/ctf.png

M images/database.png

M images/desktop.ico

M images/desktop.png

M images/display.ico

M images/display_icon.png

M images/eman.ico

M images/eman.png

M images/eman_idea.png

M images/eman_tomo_plot.png

M images/eman_tomo_raw.png

M images/eman_tomo_recon.png

M images/eman_tomo_seg.png

M images/eman_tomo_spt.png

M images/eulerxplor.png

M images/feather.png

M images/freeze_swirl.png

M images/green_boxes.ico

M images/green_boxes.png

M images/multiple_images.png

M images/multiple_images_3d.png

M images/plot.png

M images/pp_boxer_icon.png

M images/refine.png

M images/single_image.png

M images/single_image_3d.png

M images/sparxicon.png

M images/swarm_icon.png

M images/sxgui.py_main_window_background_image.png

M images/sxgui_background.png

M images/sxgui_icon_sphire.png

M images/sxgui_info.png

M images/sxgui_logo_sphire.png

M images/sxgui_pictograph_cter.png

M images/sxgui_pictograph_info.png

M images/sxgui_pictograph_isac.png

M images/sxgui_pictograph_localres.png

M images/sxgui_pictograph_meridien.png

M images/sxgui_pictograph_movie.png

M images/sxgui_pictograph_project.png

M images/sxgui_pictograph_sort3d.png

M images/sxgui_pictograph_subtract.png

M images/sxgui_pictograph_utilities.png

M images/sxgui_pictograph_viper.png

M images/sxgui_pictograph_window.png

M images/tomo_hunter.png

M images/tomoseg.png

M images/up_arrow.png

M images/white_box.png

M images/workflow.ico

M images/workflow.png

M libEM/CMakeLists.txt

M libEM/aligner.cpp

M libEM/aligner.h

M libEM/analyzer.cpp

M libEM/analyzer.h

M libEM/averager.cpp

M libEM/averager.h

M libEM/boxingtools.cpp

M libEM/boxingtools.h

M libEM/byteorder.cpp

M libEM/byteorder.h

M libEM/cmp.cpp

M libEM/cmp.h

M libEM/ctf.cpp

M libEM/ctf.h

M libEM/cuda/CMakeLists.txt

M libEM/cuda/CudaCMakeExample

M libEM/cuda/CudaDependency.cmake

M libEM/cuda/FindCUDA.cmake

M libEM/cuda/cuda_cmp.cu

M libEM/cuda/cuda_cmp.h

M libEM/cuda/cuda_defs.h

M libEM/cuda/cuda_emfft.cu

M libEM/cuda/cuda_emfft.h

M libEM/cuda/cuda_processor.cu

M libEM/cuda/cuda_processor.h

M libEM/cuda/cuda_projector.cu

M libEM/cuda/cuda_projector.h

M libEM/cuda/cuda_reconstructor.cu

M libEM/cuda/cuda_reconstructor.h

M libEM/cuda/cuda_util.cu

M libEM/cuda/cuda_util.h

M libEM/cuda/empty.depend.in

M libEM/cuda/make2cmake.cmake

M libEM/cuda/parse_cubin.cmake

M libEM/cuda/run_nvcc.cmake

M libEM/emassert.h

M libEM/emcache.cpp

M libEM/emcache.h

M libEM/emdata.cpp

M libEM/emdata.h

M libEM/emdata_core.cpp

M libEM/emdata_core.h

M libEM/emdata_cuda.cpp

M libEM/emdata_cuda.h

M libEM/emdata_io.cpp

M libEM/emdata_io.h

M libEM/emdata_metadata.cpp

M libEM/emdata_metadata.h

M libEM/emdata_modular.cpp

M libEM/emdata_modular.h

M libEM/emdata_transform.cpp

M libEM/emdata_transform.h

M libEM/emfft.cpp

M libEM/emfft.h

M libEM/emftgl.cpp

M libEM/emftgl.h

M libEM/emobject.cpp

M libEM/emobject.h

M libEM/emutil.cpp

M libEM/emutil.h

M libEM/exception.cpp

M libEM/exception.h

M libEM/fonts/CMakeLists.txt

M libEM/fonts/DejaVuSerif.ttf

M libEM/fonts/readme.txt

M libEM/geometry.cpp

M libEM/geometry.h

M libEM/glutil.cpp

M libEM/glutil.h

M libEM/gorgon/CMakeLists.txt

M libEM/gorgon/grid_queue.cpp

M libEM/gorgon/grid_queue.h

M libEM/gorgon/grid_queue2.cpp

M libEM/gorgon/grid_queue2.h

M libEM/gorgon/priority_queue.h

M libEM/gorgon/skeletonizer.cpp

M libEM/gorgon/skeletonizer.h

M libEM/gorgon/volume.cpp

M libEM/gorgon/volume.h

M libEM/gorgon/volume_data.cpp

M libEM/gorgon/volume_data.h

M libEM/interp.cpp

M libEM/interp.h

M libEM/io/all_imageio.h

M libEM/io/amiraio.cpp

M libEM/io/amiraio.h

M libEM/io/df3io.cpp

M libEM/io/df3io.h

M libEM/io/dm3io.cpp

M libEM/io/dm3io.h

M libEM/io/dm4io.cpp

M libEM/io/dm4io.h

M libEM/io/eerio.cpp

M libEM/io/eerio.h

M libEM/io/emio.cpp

M libEM/io/emio.h

M libEM/io/fitsio.cpp

M libEM/io/fitsio.h

M libEM/io/gatan2io.cpp

M libEM/io/gatan2io.h

M libEM/io/hdf_filecache.cpp

M libEM/io/hdf_filecache.h

M libEM/io/hdfio.cpp

M libEM/io/hdfio.h

M libEM/io/hdfio2.cpp

M libEM/io/hdfio2.h

M libEM/io/icosio.cpp

M libEM/io/icosio.h

M libEM/io/imageio.cpp

M libEM/io/imageio.h

M libEM/io/imagicio.cpp

M libEM/io/imagicio.h

M libEM/io/imagicio2.cpp

M libEM/io/imagicio2.h

M libEM/io/jpegio.cpp

M libEM/io/jpegio.h

M libEM/io/lstfastio.cpp

M libEM/io/lstfastio.h

M libEM/io/lstio.cpp

M libEM/io/lstio.h

M libEM/io/mrcio.cpp

M libEM/io/mrcio.h

M libEM/io/omapio.cpp

M libEM/io/omapio.h

M libEM/io/pgmio.cpp

M libEM/io/pgmio.h

M libEM/io/pifio.cpp

M libEM/io/pifio.h

M libEM/io/pngio.cpp

M libEM/io/pngio.h

M libEM/io/salio.cpp

M libEM/io/salio.h

M libEM/io/serio.cpp

M libEM/io/serio.h

M libEM/io/situsio.cpp

M libEM/io/situsio.h

M libEM/io/spiderio.cpp

M libEM/io/spiderio.h

M libEM/io/sspiderio.cpp

M libEM/io/sspiderio.h

M libEM/io/tifio.cpp

M libEM/io/tifio.h

M libEM/io/v4l2io.cpp

M libEM/io/v4l2io.h

M libEM/io/vtkio.cpp

M libEM/io/vtkio.h

M libEM/io/xplorio.cpp

M libEM/io/xplorio.h

M libEM/isosurface.h

M libEM/log.cpp

M libEM/log.h

M libEM/marchingcubes.cpp

M libEM/marchingcubes.h

M libEM/pdbreader.cpp

M libEM/pdbreader.h

M libEM/plugins/aligner_template.cpp

M libEM/plugins/aligner_template.h

M libEM/plugins/averager_template.cpp

M libEM/plugins/averager_template.h

M libEM/plugins/cmp_template.cpp

M libEM/plugins/cmp_template.h

M libEM/plugins/io_template.cpp

M libEM/plugins/io_template.h

M libEM/plugins/processor_template.cpp

M libEM/plugins/processor_template.h

M libEM/plugins/projector_template.cpp

M libEM/plugins/projector_template.h

M libEM/plugins/reconstructor_template.cpp

M libEM/plugins/reconstructor_template.h

M libEM/pmconfig/CMakeLists.txt

M libEM/pmconfig/RCTboxer.json

M libEM/pmconfig/RCTboxergo.json

M libEM/pmconfig/boxer.json

M libEM/pmconfig/boxergo.json

M libEM/pmconfig/breaksym.json

M libEM/pmconfig/buildstacks.json

M libEM/pmconfig/classaverage3d.json

M libEM/pmconfig/coordimport.json

M libEM/pmconfig/ctfautofit.json

M libEM/pmconfig/ctfgo.json

M libEM/pmconfig/ctfsf.json

M libEM/pmconfig/ctftuning.json

M libEM/pmconfig/evalrawdata.json

M libEM/pmconfig/icons.json

M libEM/pmconfig/montecarlo.json

M libEM/pmconfig/particleimport.json

M libEM/pmconfig/ploteulers.json

M libEM/pmconfig/plotfsc.json

M libEM/pmconfig/plottiltvalidation.json

M libEM/pmconfig/rawdata.json

M libEM/pmconfig/rawdataimport.json

M libEM/pmconfig/rct.json

M libEM/pmconfig/relion2d.json

M libEM/pmconfig/relion3d.json

M libEM/pmconfig/runtiltvalidation.json

M libEM/pmconfig/spr.json

M libEM/pmconfig/symaligner.json

M libEM/pmconfig/symsearch.json

M libEM/pmconfig/tomo.json

M libEM/pmconfig/tomo_legacy.json

M libEM/pmconfig/tomoboxer.json

M libEM/pmconfig/tomoimport.json

M libEM/pmconfig/tomores.json

M libEM/pmconfig/tomosegpanel.json

M libEM/pmconfig/wedge.json

M libEM/pointarray.cpp

M libEM/pointarray.h

M libEM/polardata.cpp

M libEM/polardata.h

M libEM/portable_fileio.h

M libEM/processor.cpp

M libEM/processor.h

M libEM/projector.cpp

M libEM/projector.h

M libEM/quaternion.cpp

M libEM/quaternion.h

M libEM/randnum.cpp

M libEM/randnum.h

M libEM/reconstructor.cpp

M libEM/reconstructor.h

M libEM/reconstructor_tools.cpp

M libEM/reconstructor_tools.h

M libEM/sparx/00_README_ADDING_NEW_CODE

M libEM/sparx/CMakeLists.txt

M libEM/sparx/analyzer_sparx.h

M libEM/sparx/cuda/CMakeLists.txt

M libEM/sparx/cuda/cuda_ccf.cu

M libEM/sparx/cuda/cuda_ccf.h

M libEM/sparx/cuda/cuda_kmeans.cu

M libEM/sparx/cuda/cuda_kmeans.h

M libEM/sparx/cuda/cuda_mpi_kmeans.cu

M libEM/sparx/cuda/cuda_mpi_kmeans.h

M libEM/sparx/emarray.h

M libEM/sparx/emconstants.h

M libEM/sparx/emdata_sparx.cpp

M libEM/sparx/emdata_sparx.h

M libEM/sparx/fftpack4.h

M libEM/sparx/fftpack4_precision.h

M libEM/sparx/fourierfilter.cpp

M libEM/sparx/fundamentals.cpp

M libEM/sparx/fundamentals.h

M libEM/sparx/lapackblas.cpp

M libEM/sparx/lapackblas.h

M libEM/sparx/lbfgsb.cpp

M libEM/sparx/lbfgsb.h

M libEM/sparx/mcqd.h

M libEM/sparx/native_fft.cpp

M libEM/sparx/native_fft.h

M libEM/sparx/pca.cpp

M libEM/sparx/pca.h

M libEM/sparx/processor_sparx.h

M libEM/sparx/rsconvolution.cpp

M libEM/sparx/steepest.cpp

M libEM/sparx/steepest.h

M libEM/sparx/temp/HyBR_Cart.cpp

M libEM/sparx/temp/HyBR_Cart.h

M libEM/sparx/temp/Makefile

M libEM/sparx/temp/README

M libEM/sparx/temp/ali3d_d_mpi.cpp

M libEM/sparx/temp/ali3d_d_mpi.h

M libEM/sparx/temp/ali3d_unified_mpi.cpp

M libEM/sparx/temp/ali3d_unified_mpi.h

M libEM/sparx/temp/alignoptions.cpp

M libEM/sparx/temp/alignoptions.h

M libEM/sparx/temp/fgcalc.cpp

M libEM/sparx/temp/fgcalc.h

M libEM/sparx/temp/hybr.h

M libEM/sparx/temp/project3d.cpp

M libEM/sparx/temp/project3d.h

M libEM/sparx/temp/project3d_Cart.cpp

M libEM/sparx/temp/project3d_Cart.h

M libEM/sparx/temp/runali3d_d.cpp

M libEM/sparx/temp/runhybrid.cpp

M libEM/sparx/temp/runsirt.cpp

M libEM/sparx/temp/runsirt_Cart.cpp

M libEM/sparx/temp/rununified.cpp

M libEM/sparx/temp/sirt.cpp

M libEM/sparx/temp/sirt.h

M libEM/sparx/temp/sirt_Cart.cpp

M libEM/sparx/temp/sirt_Cart.h

M libEM/sparx/temp/utilcomm.cpp

M libEM/sparx/temp/utilcomm.h

M libEM/sparx/temp/utilcomm_Cart.cpp

M libEM/sparx/temp/utilcomm_Cart.h

M libEM/sparx/temp/utilnum.cpp

M libEM/sparx/temp/utilnum.h

M libEM/sparx/temp/utilparse.cpp

M libEM/sparx/temp/utilparse.h

M libEM/sparx/temp/voldist/Makefile

M libEM/sparx/temp/voldist/runcartrec.cpp

M libEM/sparx/temp/voldist/utilcomm2d.cpp

M libEM/sparx/util_sparx.cpp

M libEM/sparx/util_sparx.h

M libEM/sparx/varimax.cpp

M libEM/sparx/varimax.h

M libEM/sphire/CMakeLists.txt

M libEM/sphire/emdata_sphire.cpp

M libEM/sphire/emdata_sphire.h

M libEM/sphire/processor_sphire.h

M libEM/sphire/util_sphire.cpp

M libEM/sphire/util_sphire.h

M libEM/symmetry.cpp

M libEM/symmetry.h

M libEM/testutil.cpp

M libEM/testutil.h

M libEM/tomoseg.cpp

M libEM/tomoseg.h

M libEM/transform.cpp

M libEM/transform.h

M libEM/util.cpp

M libEM/util.h

M libEM/vec3.h

M libEM/vecmath.h

M libEM/xydata.cpp

M libEM/xydata.h

M libpyEM/Anneal.py

M libpyEM/CMakeLists.txt

M libpyEM/EMAN2.py

M libpyEM/EMAN2PAR.py

M libpyEM/EMAN2_cppwrap.py

M libpyEM/EMAN2_meta.py.in

M libpyEM/EMAN2_utils.py

M libpyEM/EMAN2db.py

M libpyEM/EMAN2jsondb.py

M libpyEM/EMAN2star.py

M libpyEM/Simplex.py

M libpyEM/emdata_pickle.h

M libpyEM/emdata_wrapitems.cpp

M libpyEM/emdata_wrapitems.h

M libpyEM/libpyAligner2.cpp

M libpyEM/libpyAnalyzer2.cpp

M libpyEM/libpyAverager2.cpp

M libpyEM/libpyBoxingTools2.cpp

M libpyEM/libpyCmp2.cpp

M libpyEM/libpyEMData2.cpp

M libpyEM/libpyEMObject2.cpp

M libpyEM/libpyFundamentals2.cpp

M libpyEM/libpyGLUtils2.cpp

M libpyEM/libpyGeometry2.cpp

M libpyEM/libpyMarchingCubes2.cpp

M libpyEM/libpyPDBReader2.cpp

M libpyEM/libpyPointArray2.cpp

M libpyEM/libpyPolarData2.cpp

M libpyEM/libpyProcessor2.cpp

M libpyEM/libpyProjector2.cpp

M libpyEM/libpyReconstructor2.cpp

M libpyEM/libpyTomoSeg2.cpp

M libpyEM/libpyTransform2.cpp

M libpyEM/libpyTypeConverter2.cpp

M libpyEM/libpyUtils2.cpp

M libpyEM/mpi_eman.py

M libpyEM/qtgui/CMakeLists.txt

M libpyEM/qtgui/__init__.py

M libpyEM/qtgui/boxertools.py

M libpyEM/qtgui/em3Dfonts.py

M libpyEM/qtgui/emanimationutil.py

M libpyEM/qtgui/emapplication.py

M libpyEM/qtgui/emboxerbase.py

M libpyEM/qtgui/embrowser.py

M libpyEM/qtgui/emdataitem3d.py

M libpyEM/qtgui/emdatastorage.py

M libpyEM/qtgui/emdisplayserver.py

M libpyEM/qtgui/emfoldhunterstat.py

M libpyEM/qtgui/emform.py

M libpyEM/qtgui/emglobjects.py

M libpyEM/qtgui/emhist.py

M libpyEM/qtgui/emimage.py

M libpyEM/qtgui/emimage2d.py

M libpyEM/qtgui/emimage3d.py

M libpyEM/qtgui/emimage3diso.py

M libpyEM/qtgui/emimage3dslice.py

M libpyEM/qtgui/emimage3dsym.py

M libpyEM/qtgui/emimage3dvol.py

M libpyEM/qtgui/emimagemx.py

M libpyEM/qtgui/emimageutil.py

M libpyEM/qtgui/emitem3d.py

M libpyEM/qtgui/emlights.py

M libpyEM/qtgui/empdbitem3d.py

M libpyEM/qtgui/empdbvaltool.py

M libpyEM/qtgui/empdbviewer.py

M libpyEM/qtgui/emplot2d.py

M libpyEM/qtgui/emplot3d.py

M libpyEM/qtgui/empmtabwidgets.py

M libpyEM/qtgui/empmwidgets.py

M libpyEM/qtgui/emrctboxergui.py

M libpyEM/qtgui/emrctstrategy.py

M libpyEM/qtgui/emsave.py

M libpyEM/qtgui/emscene3d.py

M libpyEM/qtgui/emselector.py

M libpyEM/qtgui/emshape.py

M libpyEM/qtgui/emshapeitem3d.py

M libpyEM/qtgui/emsprworkflow.py

M libpyEM/qtgui/emtprworkflow.py

M libpyEM/qtgui/matching.py

M libpyEM/qtgui/pmicons.py

M libpyEM/qtgui/valslider.py

M libpyEM/sparx.cpp

M libpyEM/sparx.h

M libpyEM/typeconverter.cpp

M libpyEM/typeconverter.h

M programs/CMakeLists.txt

M programs/e2compress.py

M programs/e2fsc_real_local.py

M programs/e2gmm_refine.py

M programs/e2simmx.py

M programs/e2spt_align_subtlt.py

M programs/e2spt_simulation.py

M programs/e2spt_subtlt_local.py

M programs/e2tomo_ctfraw.py

M programs/e2tomo_tiltstacker.py

M programs/e3.py

M recipe/bld.bat

M recipe/build.sh

M recipe/cross-linux.cmake

M recipe/meta.yaml

M rt/CMakeLists.txt

M rt/demo/align.py

M rt/demo/averager.py

M rt/demo/cmp.py

M rt/demo/model.tcp

M rt/demo/processor1.py

M rt/demo/processor2.py

M rt/demo/processor3.py

M rt/demo/project.py

M rt/demo/reconstruction.py

M rt/demo/reconstructor.py

M rt/demo/scene3d_test.py

M rt/demo/test_image.py

M rt/demo/tomrc.py

M rt/emdata/CMakeLists.txt

M rt/emdata/blankimg.cpp

M rt/emdata/ccf1.cpp

M rt/emdata/ccf2.cpp

M rt/emdata/ccf3.cpp

M rt/emdata/emdata_api.cpp

M rt/emdata/exception1.py

M rt/emdata/fft.cpp

M rt/emdata/fft_test.cpp

M rt/emdata/imagic_ctf_test.cpp

M rt/emdata/mem_test.cpp

M rt/emdata/memtest.cpp

M rt/emdata/memtest2.cpp

M rt/emdata/projector_test.cpp

M rt/emdata/randnum_test.cpp

M rt/emdata/rotate.cpp

M rt/emdata/rotate1.cpp

M rt/emdata/rotate_phi.cpp

M rt/emdata/rotate_translate.cpp

M rt/emdata/storage_order_test.cpp

M rt/emdata/storage_order_test.py

M rt/emdata/test_emobject.cpp

M rt/emdata/test_inplace_clip.cpp

M rt/emdata/testalign.cpp

M rt/emdata/testpolardata.cpp

M rt/emdata/testprocessor.cpp

M rt/emdata/transform.cpp

M rt/imageio/CMakeLists.txt

M rt/imageio/basic.cpp

M rt/imageio/imageio.cpp

M rt/imageio/test_eer.cpp

M rt/pyem/CMakeLists.txt

M rt/pyem/no_test_emdata_cuda.py

M rt/pyem/rt.py

M rt/pyem/test_aligner.py

M rt/pyem/test_averager.py

M rt/pyem/test_cmp.py

M rt/pyem/test_emdata.py

M rt/pyem/test_imageio.py

M rt/pyem/test_misc.py

M rt/pyem/test_processor.py

M rt/pyem/test_reconstructor.py

M rt/pyem/test_transform.py

M rt/pyem/test_typeconverter.py

M rt/pyem/test_utils.py

M rt/pyem/test_vec.py

M rt/pyem/test_xydata.py

M rt/pyem/testlib.py

M rt/timetests/test_times.py

M sparx/CMakeLists.txt

M sparx/README

M sparx/__init__.py

M sparx/bin/CMakeLists.txt

M sparx/bin/sx.py

M sparx/bin/sx3dvariability.py

M sparx/bin/sx_real.py

M sparx/bin/sxali2d.py

M sparx/bin/sxali2d_mref.py

M sparx/bin/sxali3d.py

M sparx/bin/sxali_vol.py

M sparx/bin/sxave_ali.py

M sparx/bin/sxbatch.py

M sparx/bin/sxcenter_projections.py

M sparx/bin/sxchains.py

M sparx/bin/sxcompute_isac_avg.py

M sparx/bin/sxconsistency.py

M sparx/bin/sxcopyfromtif.py

M sparx/bin/sxcpy.py

M sparx/bin/sxcter.py

M sparx/bin/sxctf.py

M sparx/bin/sxfactcoords.py

M sparx/bin/sxfilrecons3d.py

M sparx/bin/sxfilterlocal.py

M sparx/bin/sxfind_struct.py

M sparx/bin/sxfit_error.py

M sparx/bin/sxgenbuf.py

M sparx/bin/sxgui.py

M sparx/bin/sxgui_cter.py

M sparx/bin/sxgui_meridien.py

M sparx/bin/sxgui_unblur.py

M sparx/bin/sxhac_averages.py

M sparx/bin/sxhac_clustering.py

M sparx/bin/sxheader.py

M sparx/bin/sxhelical_demo.py

M sparx/bin/sxhelicon.py

M sparx/bin/sxhelicon_utils.py

M sparx/bin/sxheliconlocal.py

M sparx/bin/sxhelixboxer.py

M sparx/bin/sxihrsr.py

M sparx/bin/sximgstat.py

M sparx/bin/sxisac2.py

M sparx/bin/sxk_means.py

M sparx/bin/sxk_means_groups.py

M sparx/bin/sxk_means_stable.py

M sparx/bin/sxlocal_ali2d.py

M sparx/bin/sxlocal_ali3d.py

M sparx/bin/sxlocal_ali3dm.py

M sparx/bin/sxlocres.py

M sparx/bin/sxmask.py

M sparx/bin/sxmeridien.py

M sparx/bin/sxmontage.py

M sparx/bin/sxmref_ali2d.py

M sparx/bin/sxmref_ali3d.py

M sparx/bin/sxmref_alignment.py

M sparx/bin/sxmulti_ali2d.py

M sparx/bin/sxmulti_assign.py

M sparx/bin/sxparams_2D_to_3D.py

M sparx/bin/sxparams_3D_to_2D.py

M sparx/bin/sxpca.py

M sparx/bin/sxpdb2em.py

M sparx/bin/sxpipe.py

M sparx/bin/sxplot_projs_distrib.py

M sparx/bin/sxprepare_2d_forPCA.py

M sparx/bin/sxprocess.py

M sparx/bin/sxproj_compare.py

M sparx/bin/sxproj_stability.py

M sparx/bin/sxproject3d.py

M sparx/bin/sxrealignment.py

M sparx/bin/sxrecons3d_f.py

M sparx/bin/sxrecons3d_n.py

M sparx/bin/sxrelion2sphire.py

M sparx/bin/sxreproducibility.py

M sparx/bin/sxresample.py

M sparx/bin/sxrewindow.py

M sparx/bin/sxrot_sym.py

M sparx/bin/sxrsort3d.py

M sparx/bin/sxrviper.py

M sparx/bin/sxshiftali.py

M sparx/bin/sxsort3d_depth.py

M sparx/bin/sxsphire2relion.py

M sparx/bin/sxspliteigen.py

M sparx/bin/sxssnr3d.py

M sparx/bin/sxstability.py

M sparx/bin/sxsummovie.py

M sparx/bin/sxtransform2d.py

M sparx/bin/sxunblur.py

M sparx/bin/sxvar.py

M sparx/bin/sxvarimax.py

M sparx/bin/sxviper.py

M sparx/bin/sxwindow.py

M sparx/doc/3dvariability.txt

M sparx/doc/README.txt

M sparx/doc/batch.txt

M sparx/doc/compute_isac_avg.txt

M sparx/doc/cter.txt

M sparx/doc/e2bdb.txt

M sparx/doc/e2boxer.txt

M sparx/doc/e2boxer_old.txt

M sparx/doc/e2display.txt

M sparx/doc/e2proc3d.txt

M sparx/doc/filterlocal.txt

M sparx/doc/gui_cter.txt

M sparx/doc/gui_meridien.txt

M sparx/doc/gui_unblur.txt

M sparx/doc/header.txt

M sparx/doc/isac2.txt

M sparx/doc/locres.txt

M sparx/doc/mask.txt

M sparx/doc/meridien.txt

M sparx/doc/pdb2em.txt

M sparx/doc/pipe_angular_distribution.txt

M sparx/doc/pipe_isac_substack.txt

M sparx/doc/pipe_moon_eliminator.txt

M sparx/doc/pipe_organize_micrographs.txt

M sparx/doc/pipe_resample_micrographs.txt

M sparx/doc/pipe_restacking.txt

M sparx/doc/process.txt

M sparx/doc/proj_compare.txt

M sparx/doc/relion2sphire.txt

M sparx/doc/rewindow.txt

M sparx/doc/rviper.txt

M sparx/doc/sort3d.txt

M sparx/doc/sort3d_depth.txt

M sparx/doc/summovie.txt

M sparx/doc/unblur.txt

M sparx/doc/viper.txt

M sparx/doc/window.txt

M sparx/libpy/CMakeLists.txt

M sparx/libpy/alignment.py

M sparx/libpy/applications.py

M sparx/libpy/development.py

M sparx/libpy/filter.py

M sparx/libpy/fundamentals.py

M sparx/libpy/global_def.py

M sparx/libpy/isac.py

M sparx/libpy/logger.py

M sparx/libpy/morphology.py

M sparx/libpy/multi_shc.py

M sparx/libpy/pap_statistics.py

M sparx/libpy/pixel_error.py

M sparx/libpy/projection.py

M sparx/libpy/reconstruction.py

M sparx/libpy/sparx.py

M sparx/libpy/user_functions.py

M sparx/libpy/utilities.py

M sparx/templates/import_SPIDER_320.py

M sparx/test/1MNF.pdb.gz

M sparx/test/I0_1.75.out

M sparx/test/I0_backft_1.75.out

M sparx/test/I0fft_1.75.out

M sparx/test/I0filt_1.75.out

M sparx/test/I0img_1.75.out

M sparx/test/NOTES

M sparx/test/aac.py

M sparx/test/b01.mol

M sparx/test/bootstrap/bs_efg0.job

M sparx/test/bootstrap/documentation.h

M sparx/test/bootstrap/mympimodule.c

M sparx/test/doapmd.cpp

M sparx/test/doapmq.cpp

M sparx/test/dpw2_close_b.hrs

M sparx/test/main_example.py

M sparx/test/model001.tcp

M sparx/test/model1_var2a.pdb

M sparx/test/pdb_1.py

M sparx/test/pw2_close_b.hrs

M sparx/test/sinh_1.75.out

M sparx/test/sinh_disc_1.75.out

M sparx/test/spidfft.cpp

M sparx/test/spidfft.h

M sparx/test/spidutil.cpp

M sparx/test/spidutil.h

M sparx/test/test.spi

M sparx/test/test30.spi

M sparx/test/test_pw.py

M sparx/test/testc.cpp

M sparx/test/tests.cpp

M sparx/test/tf2d0001.tfc

M sparx/test/vol001.tfc

M sparx/tests/test_Util.py

M sparx/tests/test_fundamentals.py

M sparx/tests/test_pixel_error.py

M sphire/CMakeLists.txt

M sphire/MANIFEST.in

M sphire/README

M sphire/README.md

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M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_cryolo_train.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_ctf_refine.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_filterlocal.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_gui.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_meridien.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_meridien_alpha.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_pdb2em.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_pipe.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_process.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_proj_compare.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_real.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_recons3d_n.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_rviper.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_separate_class.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_unblur_old.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_viper.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/bin/sp_window.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_alignment.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_global_def.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_isac.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_logger.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_morphology.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_multi_shc.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_pixel_error.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_projection.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_reconstruction.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_sparx.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_statistics.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_user_functions.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_user_functions_meridien.py

M sphire/archive/utils/03_SPHIRE_IMPORTS/libpy/sp_utilities.py

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M sphire/archive/utils/03_SPHIRE_IMPORTS/templates/wikiparser.py

M sphire/archive/utils/03_final_finish.py

M sphire/archive/utils/SPHIRE/__init__.py

M sphire/archive/utils/SPHIRE/bin/__init__.py

M sphire/archive/utils/SPHIRE/bin/sp_3dvariability.py

M sphire/archive/utils/SPHIRE/bin/sp_auto.py

M sphire/archive/utils/SPHIRE/bin/sp_batch.py

M sphire/archive/utils/SPHIRE/bin/sp_cinderella_pred.py

M sphire/archive/utils/SPHIRE/bin/sp_compute_isac_avg.py

M sphire/archive/utils/SPHIRE/bin/sp_cpy.py

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M sphire/archive/utils/SPHIRE/bin/sp_cryolo_predict.py

M sphire/archive/utils/SPHIRE/bin/sp_cryolo_train.py

M sphire/archive/utils/SPHIRE/bin/sp_cter.py

M sphire/archive/utils/SPHIRE/bin/sp_ctf_refine.py

M sphire/archive/utils/SPHIRE/bin/sp_filterlocal.py

M sphire/archive/utils/SPHIRE/bin/sp_gui.py

M sphire/archive/utils/SPHIRE/bin/sp_gui_cter.py

M sphire/archive/utils/SPHIRE/bin/sp_gui_meridien.py

M sphire/archive/utils/SPHIRE/bin/sp_gui_unblur.py

M sphire/archive/utils/SPHIRE/bin/sp_header.py

M sphire/archive/utils/SPHIRE/bin/sp_isac2.py

M sphire/archive/utils/SPHIRE/bin/sp_locres.py

M sphire/archive/utils/SPHIRE/bin/sp_mask.py

M sphire/archive/utils/SPHIRE/bin/sp_meridien_alpha.py

M sphire/archive/utils/SPHIRE/bin/sp_pdb2em.py

M sphire/archive/utils/SPHIRE/bin/sp_pipe.py

M sphire/archive/utils/SPHIRE/bin/sp_process.py

M sphire/archive/utils/SPHIRE/bin/sp_proj_compare.py

M sphire/archive/utils/SPHIRE/bin/sp_real.py

M sphire/archive/utils/SPHIRE/bin/sp_recons3d_n.py

M sphire/archive/utils/SPHIRE/bin/sp_relion2sphire.py

M sphire/archive/utils/SPHIRE/bin/sp_rewindow.py

M sphire/archive/utils/SPHIRE/bin/sp_separate_class.py

M sphire/archive/utils/SPHIRE/bin/sp_sort3d_depth.py

M sphire/archive/utils/SPHIRE/bin/sp_sphire2relion.py

M sphire/archive/utils/SPHIRE/bin/sp_summovie.py

M sphire/archive/utils/SPHIRE/bin/sp_sx.py

M sphire/archive/utils/SPHIRE/bin/sp_unblur.py

M sphire/archive/utils/SPHIRE/bin/sp_unblur_old.py

M sphire/archive/utils/SPHIRE/bin/sp_window.py

M sphire/archive/utils/SPHIRE/libpy/__init__.py

M sphire/archive/utils/SPHIRE/libpy/sp_alignment.py

M sphire/archive/utils/SPHIRE/libpy/sp_applications.py

M sphire/archive/utils/SPHIRE/libpy/sp_ctf_refine_io.py

M sphire/archive/utils/SPHIRE/libpy/sp_ctf_refine_plotting.py

M sphire/archive/utils/SPHIRE/libpy/sp_development.py

M sphire/archive/utils/SPHIRE/libpy/sp_filter.py

M sphire/archive/utils/SPHIRE/libpy/sp_fundamentals.py

M sphire/archive/utils/SPHIRE/libpy/sp_global_def.py

M sphire/archive/utils/SPHIRE/libpy/sp_isac.py

M sphire/archive/utils/SPHIRE/libpy/sp_logger.py

M sphire/archive/utils/SPHIRE/libpy/sp_morphology.py

M sphire/archive/utils/SPHIRE/libpy/sp_multi_shc.py

M sphire/archive/utils/SPHIRE/libpy/sp_pixel_error.py

M sphire/archive/utils/SPHIRE/libpy/sp_projection.py

M sphire/archive/utils/SPHIRE/libpy/sp_reconstruction.py

M sphire/archive/utils/SPHIRE/libpy/sp_sparx.py

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M sphire/archive/utils/SPHIRE/templates/install_sxpatch.py

M sphire/archive/utils/SPHIRE/templates/sxgui_template.py

M sphire/archive/utils/SPHIRE/templates/wikiparser.py

M sphire/archive/utils/__init__.py

M sphire/archive/utils/remove_unused.py

M sphire/archive/utils/rename_it.py

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M sphire/bin_py2/SPHIRE_LOG_HISTORY/2019-10-18_14-45-54_applications.log

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M sphire/bin_py2/sp_meridien_alpha.py

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M sphire/bin_py2/sp_meridien_sort.py

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M sphire/bin_py3/sp_cinderella_pred.py

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M sphire/bin_py3/sp_compute_isac_avg.py

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M sphire/bin_py3/sp_cter.py

M sphire/bin_py3/sp_ctf_refine.py

M sphire/bin_py3/sp_eval_isac.py

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M sphire/bin_py3/sp_gui_meridien.py

M sphire/bin_py3/sp_gui_unblur.py

M sphire/bin_py3/sp_header.py

M sphire/bin_py3/sp_locres.py

M sphire/bin_py3/sp_mask.py

M sphire/bin_py3/sp_meridien_alpha.py

M sphire/bin_py3/sp_pdb2em.py

M sphire/bin_py3/sp_pipe.py

M sphire/bin_py3/sp_process.py

M sphire/bin_py3/sp_proj_compare.py

M sphire/bin_py3/sp_real.py

M sphire/bin_py3/sp_recons3d_n.py

M sphire/bin_py3/sp_relion2sphire.py

M sphire/bin_py3/sp_rewindow.py

M sphire/bin_py3/sp_rviper.py

M sphire/bin_py3/sp_signalsubtract.py

M sphire/bin_py3/sp_sort3d_depth.py

M sphire/bin_py3/sp_sphire2relion.py

M sphire/bin_py3/sp_summovie.py

M sphire/bin_py3/sp_sx.py

M sphire/bin_py3/sp_unblur.py

M sphire/bin_py3/sp_unblur_old.py

M sphire/bin_py3/sp_viper.py

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M sphire/images/sxgui_pictograph_info.png

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M sphire/libpy_py2/sp_alignment.py

M sphire/libpy_py2/sp_applications.py

M sphire/libpy_py2/sp_ctf_refine_io.py

M sphire/libpy_py2/sp_ctf_refine_plotting.py

M sphire/libpy_py2/sp_development.py

M sphire/libpy_py2/sp_filter.py

M sphire/libpy_py2/sp_fundamentals.py

M sphire/libpy_py2/sp_global_def.py

M sphire/libpy_py2/sp_isac.py

M sphire/libpy_py2/sp_logger.py

M sphire/libpy_py2/sp_morphology.py

M sphire/libpy_py2/sp_multi_shc.py

M sphire/libpy_py2/sp_pixel_error.py

M sphire/libpy_py2/sp_projection.py

M sphire/libpy_py2/sp_reconstruction.py

M sphire/libpy_py2/sp_sparx.py

M sphire/libpy_py2/sp_statistics.py

M sphire/libpy_py2/sp_user_functions.py

M sphire/libpy_py2/sp_user_functions_meridien.py

M sphire/libpy_py2/sp_utilities.py

M sphire/libpy_py3/sp_alignment.py

M sphire/libpy_py3/sp_applications.py

M sphire/libpy_py3/sp_ctf_refine_io.py

M sphire/libpy_py3/sp_development.py

M sphire/libpy_py3/sp_filter.py

M sphire/libpy_py3/sp_fundamentals.py

M sphire/libpy_py3/sp_global_def.py

M sphire/libpy_py3/sp_isac.py

M sphire/libpy_py3/sp_logger.py

M sphire/libpy_py3/sp_morphology.py

M sphire/libpy_py3/sp_multi_shc.py

M sphire/libpy_py3/sp_pixel_error.py

M sphire/libpy_py3/sp_projection.py

M sphire/libpy_py3/sp_reconstruction.py

M sphire/libpy_py3/sp_sparx.py

M sphire/libpy_py3/sp_statistics.py

M sphire/libpy_py3/sp_user_functions.py

M sphire/libpy_py3/sp_user_functions_meridien.py

M sphire/libpy_py3/sp_utilities.py

M sphire/setup.py

M sphire/sphire/__init__.py

M sphire/sphire/bin/__init__.py

M sphire/sphire/bin/sp_compare2d.py

M sphire/sphire/bin/sp_eval_isac.py

M sphire/sphire/bin/sp_meridien.py

M sphire/sphire/bin/sp_meridien_alpha2.py

M sphire/sphire/bin/sp_meridien_beta.py

M sphire/sphire/bin/sp_meridien_sort.py

M sphire/sphire/bin/sp_micrograh_selection.py

M sphire/sphire/bin/sp_signalsubtract.py

M sphire/sphire/libpy/__init__.py

M sphire/sphire/libpy/prior_calculation/__init__.py

M sphire/sphire/libpy/sp_ctf_refine_plotting.py

M sphire/sphire/libpy/sp_sparx.py

M sphire/templates/install_sxpatch.py

M sphire/templates/sxgui_template.py

M sphire/templates/wikiparser.py

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M sphire/test/bootstrap/documentation.h

M sphire/test/bootstrap/mympimodule.c

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M sphire/test/test_pw.py

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M sphire/tests/test_bdb_rdwr.py

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M tests/programs_no_test.txt

M tests/run_prog_tests.sh

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M tests/test_EMAN2DIR.py

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M tests/test_binary_installation.sh

M tests/test_git_hash.sh

M tests/test_imports.py

M utils/CMakeLists.txt

M utils/replace_shebang.sh

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ci_support/build_no_recipe.sh

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ci_support/constructor-huge/construct.yaml

ci_support/constructor-mini/construct.yaml

ci_support/post-install-actions.bat

ci_support/post-install-actions.sh

ci_support/set_env_vars.sh

ci_support/setup_conda.sh

cmake/Boost.cmake

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doc/CMakeLists.txt

doc/INSTALL

doc/coding_style.html

doc/cvshowto.html

doc/develop_system_setup.html

doc/developer-guide.html

doc/development_policy_faq.html

doc/doc.html

doc/doxygen/CMakeLists.txt

doc/doxygen/Doxyfile

doc/eman2doc.h

doc/exception_faq.html

doc/header_naming.html

doc/index.html

doc/latex/CMakeLists.txt

doc/latex/EMAN2.lot

doc/latex/EMAN2.tex

doc/latex/TOC.tex

doc/latex/abstract.tex

doc/latex/adding-components.tex

doc/latex/adding-documentation.tex

doc/latex/coding-style.tex

doc/latex/development-policy-faq.tex

doc/latex/dirs.tex

doc/latex/e2align3d.tex

doc/latex/e2aligntest.tex

doc/latex/e2boxer.tex

doc/latex/e2cmmtomrc.tex

doc/latex/e2dumplog.tex

doc/latex/e2foldfitter.tex

doc/latex/e2make3d.tex

doc/latex/e2pdb2mrc.tex

doc/latex/e2proc2d.tex

doc/latex/e2proc3d.tex

doc/latex/e2project3d.tex

doc/latex/e2scannereval.tex

doc/latex/e2symbest.tex

doc/latex/e2tomogram.tex

doc/latex/exceptions.tex

doc/latex/factory-classes.tex

doc/latex/fancyhdr.sty

doc/latex/fncychap.sty

doc/latex/frame-work-testing.tex

doc/latex/goals.tex

doc/latex/help-opt-prog-inst.tex

doc/latex/hyperref.perl

doc/latex/image-header-attribs.tex

doc/latex/index.tex

doc/latex/install.tex

doc/latex/logger.tex

doc/latex/ltxmarkup.sty

doc/latex/make3d.tex

doc/latex/misc-developers-guide.tex

doc/latex/processors.tex

doc/latex/project3d.tex

doc/latex/python-scripts.tex

doc/latex/reference-manual.tex

doc/latex/using-cvs.tex

doc/modular_class_html/CMakeLists.txt

doc/testing.html

libEM/CMakeLists.txt

libEM/averager.cpp

libEM/cmp.cpp

libEM/cmp.h

libEM/emdata.cpp

libEM/emdata.h

libEM/emdata_io.cpp

libEM/emutil.cpp

libEM/glutil.cpp

libEM/glutil.h

libEM/io/df3io.cpp

libEM/io/df3io.h

libEM/io/eerio.cpp

libEM/io/hdfio2.cpp

libEM/io/hdfio2.h

libEM/io/imagicio.cpp

libEM/io/jpegio.cpp

libEM/io/jpegio.h

libEM/io/lstfastio.cpp

libEM/io/mrcio.cpp

libEM/io/mrcio.h

libEM/io/pgmio.cpp

libEM/io/pgmio.h

libEM/io/pngio.cpp

libEM/io/pngio.h

libEM/io/tifio.cpp

libEM/io/tifio.h

libEM/pmconfig/tomo.json

libEM/pmconfig/tomo_legacy.json

libEM/processor.cpp

libEM/processor.h

libEM/sparx/lapackblas.cpp

libEM/sparx/util_sparx.cpp

libEM/symmetry.cpp

libEM/transform.cpp

libEM/util.cpp

libpyEM/EMAN2.py

libpyEM/EMAN2PAR.py

libpyEM/EMAN2_utils.py

libpyEM/EMAN2db.py

libpyEM/EMAN2jsondb.py

libpyEM/libpyEMData2.cpp

libpyEM/libpyGLUtils2.cpp

libpyEM/libpyTypeConverter2.cpp

libpyEM/qtgui/boxertools.py

libpyEM/qtgui/emapplication.py

libpyEM/qtgui/embrowser.py

libpyEM/qtgui/emdataitem3d.py

libpyEM/qtgui/emdisplayserver.py

libpyEM/qtgui/emimage2d.py

libpyEM/qtgui/emimagemx.py

libpyEM/qtgui/emplot2d.py

libpyEM/qtgui/emplot3d.py

libpyEM/qtgui/empmwidgets.py

libpyEM/qtgui/emsave.py

libpyEM/qtgui/emscene3d.py

libpyEM/qtgui/emselector.py

libpyEM/qtgui/emshape.py

libpyEM/qtgui/emshapeitem3d.py

libpyEM/qtgui/emsprworkflow.py

libpyEM/qtgui/emtprworkflow.py

libpyEM/typeconverter.cpp

libpyEM/typeconverter.h

programs/CMakeLists.txt

programs/e2gmm_refine.py

programs/e2simmx.py

programs/e2spt_align_subtlt.py

programs/e2spt_subtlt_local.py

programs/e2tomo_tiltstacker.py

recipe/bld.bat

recipe/build.sh

recipe/meta.yaml

rt/CMakeLists.txt

rt/demo/align.py

rt/demo/averager.py

rt/demo/cmp.py

rt/demo/model.tcp

rt/demo/processor1.py

rt/demo/processor2.py

rt/demo/processor3.py

rt/demo/project.py

rt/demo/reconstruction.py

rt/demo/reconstructor.py

rt/demo/scene3d_test.py

rt/demo/tomrc.py

rt/emdata/CMakeLists.txt

rt/emdata/blankimg.cpp

rt/emdata/ccf1.cpp

rt/emdata/ccf2.cpp

rt/emdata/ccf3.cpp

rt/emdata/emdata_api

Aborting

Ludtke, Steven J.

unread,

Aug 4, 2022, 2:37:18 PM8/4/22

to em...@googlegroups.com

This should be fine:

git config --global pull.rebase false

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor
 College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technical Cores                   and Molecular Biology
Academic Director, CryoEM Core
Co-Director CIBR Center

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Maia Azubel

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Aug 4, 2022, 2:50:32 PM8/4/22

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Thanks for the prompt response.

Unfortunately I'm still encountering problems

(eman2) [maia2@tomo eman2]$ git config --global pull.rebase false

(eman2) [maia2@tomo eman2]$ git pull

Updating ba39969d8..8a24bb112

error: Your local changes to the following files would be overwritten by merge:

.gitignore

CMakeLists.txt

...

Aborting

Maia

From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Ludtke, Steven J. <slu...@bcm.edu>
Sent: Thursday, August 4, 2022 11:37 AM
To: em...@googlegroups.com <em...@googlegroups.com>
Subject: Re: [EMAN2] Update source code

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/580563E0-A6E1-48DD-8B51-AAE0FDF8C169%40bcm.edu.

Colin Gauvin

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Aug 4, 2022, 3:19:45 PM8/4/22

to EMAN2

I ran into this today when updating as well, and I had to run:

git reset --hard

git pull

to get it to work.

Maia Azubel

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Aug 4, 2022, 4:36:47 PM8/4/22

to em...@googlegroups.com

Many thanks! It worked for me too.

Maia

From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Colin Gauvin <ccgau...@gmail.com>
Sent: Thursday, August 4, 2022 12:19 PM
To: EMAN2 <em...@googlegroups.com>

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/54ccf2db-b17a-407d-b445-e08c2981f418n%40googlegroups.com.

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