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Bug #2840

open

Remove EMAN1 functions from Appion

Added by Neil Voss over 10 years ago. Updated about 9 years ago.

Status:
Assigned
Priority:
High
Assignee:
Category:
-
Target version:
-
Start date:
07/15/2014
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:

Description

EMAN1 is deprecated, so it is our best interest to remove any code using EMAN1 programs, such as proc2d, proc3d, etc.

Code to get program counts:

PROGRAM=proc2d; pyfiles=`find . -name '*.py' -type f`; filecount=`grep $PROGRAM $pyfiles | egrep -v ':\s*\#' | cut -d':' -f1 | sort | uniq | wc -l`; instance=`grep $PROGRAM $pyfiles | egrep -v ':\s*\#' | wc -l`; echo $PROGRAM: $instance instances in $filecount files

proc2d: 158 instances in 57 files
proc3d: 105 instances in 32 files
make3d: 45 instances in 8 files
project3d: 13 instances in 4 files
refine2d: 6 instances in 3 files
applyctf: 6 instances in 2 files
startAny: 5 instances in 2 files
batchboxer: 4 instances in 3 files
classalign: 3 instances in 2 files
startcsym: 3 instances in 1 files
startoct: 3 instances in 1 files
pdb2mrc: 3 instances in 1 files
starticos: 3 instances in 1 files
iminfo: 2 instances in 2 files
runpar: 1 instances in 1 files

Related issues 4 (4 open0 closed)

Related to Appion - Bug #2939: Appion Developers Conference Call NotesNew09/24/2014

Actions
Blocked by Appion - Bug #2981: Make a highpass filter for AppionIn Code ReviewAnchi Cheng11/19/2014

Actions
Blocked by Appion - Bug #3327: Remove proc2d from makestack2.pyIn Code ReviewSargis Dallakyan07/23/2015

Actions
Blocked by Appion - Feature #2997: create an Appion alternative to EMAN1 proc2dAssignedNeil Voss12/15/2014

Actions
Actions #1

Updated by Neil Voss almost 10 years ago

  • Related to Bug #2939: Appion Developers Conference Call Notes added
Actions #2

Updated by Neil Voss almost 10 years ago

  • Status changed from New to Assigned
  • Assignee set to Scott Stagg

Goal to write a proc2d.py

Actions #3

Updated by Neil Voss almost 10 years ago

  • Blocked by Bug #2981: Make a highpass filter for Appion added
Actions #4

Updated by Clint Potter almost 10 years ago

Discussed during Appion call. proc2d will not work anymore. Scott says we don't want to rely on eman2.  Want our old proc2d. Neil found all instances. 158 instances. Can do this with pyami. Need to create a proc2d.py. Scott will take stab at it.

Actions #5

Updated by Neil Voss over 9 years ago

  • Blocked by Bug #3327: Remove proc2d from makestack2.py added
Actions #6

Updated by Neil Voss over 9 years ago

  • Blocked by Feature #2997: create an Appion alternative to EMAN1 proc2d added
Actions #7

Updated by Anchi Cheng about 9 years ago

Is there a plan for proc3d replacement ?

Actions

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