[med-svn] [Git][med-team/phyx][master] 7 commits: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Thu Dec 12 11:52:21 GMT 2019
Steffen Möller pushed to branch master at Debian Med / phyx
Commits:
38be0d09 by Steffen Moeller at 2019-11-10T18:01:50Z
New upstream version
- - - - -
a8d0bf71 by Steffen Moeller at 2019-11-10T18:01:51Z
New upstream version 1.01+ds
- - - - -
1e77d02c by Steffen Moeller at 2019-11-10T18:01:54Z
Update upstream source from tag 'upstream/1.01+ds'
Update to upstream version '1.01+ds'
with Debian dir a06ce99fef5d84de1ebbe9a0cb32427fdc53632f
- - - - -
6f60e5d5 by Steffen Moeller at 2019-12-12T11:24:49Z
Preparing for 1.01
- - - - -
e4ac43eb by Steffen Moeller at 2019-12-12T11:25:41Z
New upstream version 1.01+ds
- - - - -
887f364c by Steffen Moeller at 2019-12-12T11:25:44Z
Update upstream source from tag 'upstream/1.01+ds'
Update to upstream version '1.01+ds'
with Debian dir 636f327b6401bb1182e59168ab115be9652ccc8d
- - - - -
609c5d94 by Steffen Moeller at 2019-12-12T11:50:45Z
Clean-up prior to upload
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/manpages
- − debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- − src/Phyx_Gui.py
- − src/configure
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+phyx (1.01+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Removed obsolete 2to3 patch
+ * Adjusted cleanup after build
+ * Not having upstream's auto-generated src/configure in source tree
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 12 Dec 2019 12:50:28 +0100
+
phyx (1.0+ds-1) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
libnlopt-dev,
libatlas-cpp-0.6-dev,
libarmadillo-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/phyx
Vcs-Git: https://salsa.debian.org/med-team/phyx.git
Homepage: https://github.com/FePhyFoFum/phyx
=====================================
debian/copyright
=====================================
@@ -3,6 +3,7 @@ Upstream-Name: phyx
Source: https://github.com/FePhyFoFum/phyx/releases
Files-Excluded:
deps
+ src/configure
Files: *
Copyright: 2014-2017 Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith
=====================================
debian/manpages
=====================================
@@ -1 +1 @@
-debian/mans/*.1
+#debian/mans/*.1
=====================================
debian/patches/2to3.patch deleted
=====================================
@@ -1,220 +0,0 @@
-Description: port from python2 to python3
-Author: Shayan Doust <hello at shayandoust.me>
-Bug-Debian: https://bugs.debian.org/937285
-Last-Update: 2019-09-11
----
-
-Index: phyx/src/Phyx_Gui.py
-===================================================================
---- phyx.orig/src/Phyx_Gui.py 2019-09-13 02:52:54.301623771 +0100
-+++ phyx/src/Phyx_Gui.py 2019-09-13 02:52:54.285623836 +0100
-@@ -1,5 +1,5 @@
--import Tkinter,os,sys
--from Tkinter import *
-+import tkinter,os,sys
-+from tkinter import *
-
-
- class GUI:
-@@ -12,7 +12,7 @@
- #self.label.pack()
-
- global a
-- a = Tkinter.StringVar()
-+ a = tkinter.StringVar()
- self.a_seq = Entry(master, bd=5, textvariable=a).grid(row=0,column=1)
- #self.aa_seq.pack(side = LEFT)
-
-@@ -20,7 +20,7 @@
- #self.label.pack(side = LEFT)
-
- global b
-- b = Tkinter.StringVar()
-+ b = tkinter.StringVar()
- self.b_seq = Entry(master, bd=5, textvariable=b).grid(row=0,column=3)
- #self.b_seq.pack(side = LEFT)
-
-@@ -28,7 +28,7 @@
- #self.label.pack(side = LEFT)
-
- global c
-- c = Tkinter.StringVar()
-+ c = tkinter.StringVar()
- self.c_seq = Entry(master, bd=5, textvariable=c).grid(row=0,column=5)
- #self.c_seq.pack(side = LEFT)
-
-@@ -36,118 +36,118 @@
- #self.label.pack(side = LEFT)
-
- global d
-- d = Tkinter.StringVar()
-+ d = tkinter.StringVar()
- self.d_seq = Entry(master, bd=5, textvariable=d).grid(row=0,column=7)
- #self.d_seq.pack(side = LEFT)
-
- self.label = Label(master, text="Path to -e").grid(row=1,column=0)
- global e
-- e = Tkinter.StringVar()
-+ e = tkinter.StringVar()
- self.e_seq = Entry(master, bd=5, textvariable=e).grid(row=1,column=1)
-
- self.label = Label(master, text="Path to -f").grid(row=1,column=2)
- global f
-- f = Tkinter.StringVar()
-+ f = tkinter.StringVar()
- self.f_seq = Entry(master, bd=5, textvariable=f).grid(row=1,column=3)
-
- self.label = Label(master, text="Path to -g").grid(row=1,column=4)
- global g
-- g = Tkinter.StringVar()
-+ g = tkinter.StringVar()
- self.g_seq = Entry(master, bd=5, textvariable=g).grid(row=1,column=5)
-
- self.label = Label(master, text="Path to -h").grid(row=1,column=6)
- global h
-- h = Tkinter.StringVar()
-+ h = tkinter.StringVar()
- self.h_seq = Entry(master, bd=5, textvariable=h).grid(row=1,column=7)
-
- self.label = Label(master, text="Path to -i").grid(row=2,column=0)
- global i
-- i = Tkinter.StringVar()
-+ i = tkinter.StringVar()
- self.i_seq = Entry(master, bd=5, textvariable=i).grid(row=2,column=1)
-
- self.label = Label(master, text="Path to -j").grid(row=2,column=2)
- global j
-- j = Tkinter.StringVar()
-+ j = tkinter.StringVar()
- self.j_seq = Entry(master, bd=5, textvariable=j).grid(row=2,column=3)
-
- self.label = Label(master, text="Path to -k").grid(row=2,column=4)
- global k
-- k = Tkinter.StringVar()
-+ k = tkinter.StringVar()
- self.k_seq = Entry(master, bd=5, textvariable=k).grid(row=2,column=5)
-
- self.label = Label(master, text="Path to -l").grid(row=2,column=6)
- global l
-- l = Tkinter.StringVar()
-+ l = tkinter.StringVar()
- self.l_seq = Entry(master, bd=5, textvariable=l).grid(row=2,column=7)
-
- self.label = Label(master, text="Path to -m").grid(row=3,column=0)
- global m
-- m = Tkinter.StringVar()
-+ m = tkinter.StringVar()
- self.m_seq = Entry(master, bd=5, textvariable=m).grid(row=3,column=1)
-
- self.label = Label(master, text="Path to -n").grid(row=3,column=2)
- global n
-- n = Tkinter.StringVar()
-+ n = tkinter.StringVar()
- self.n_seq = Entry(master, bd=5, textvariable=n).grid(row=3,column=3)
-
- self.label = Label(master, text="Path to -o").grid(row=3,column=4)
- global o
-- o = Tkinter.StringVar()
-+ o = tkinter.StringVar()
- self.o_seq = Entry(master, bd=5, textvariable=o).grid(row=3,column=5)
-
- self.label = Label(master, text="Path to -p").grid(row=3,column=6)
- global p
-- p = Tkinter.StringVar()
-+ p = tkinter.StringVar()
- self.p_seq = Entry(master, bd=5, textvariable=p).grid(row=3,column=7)
-
- self.label = Label(master, text="Path to -q").grid(row=4,column=0)
- global q
-- q = Tkinter.StringVar()
-+ q = tkinter.StringVar()
- self.q_seq = Entry(master, bd=5, textvariable=q).grid(row=4,column=1)
-
- self.label = Label(master, text="Path to -r").grid(row=4,column=2)
- global r
-- r = Tkinter.StringVar()
-+ r = tkinter.StringVar()
- self.r_seq = Entry(master, bd=5, textvariable=r).grid(row=4,column=3)
-
- self.label = Label(master, text="Path to -s").grid(row=4,column=4)
- global s
-- s = Tkinter.StringVar()
-+ s = tkinter.StringVar()
- self.s_seq = Entry(master, bd=5, textvariable=s).grid(row=4,column=5)
-
- self.label = Label(master, text="Path to -t").grid(row=4,column=6)
- global t
-- t = Tkinter.StringVar()
-+ t = tkinter.StringVar()
- self.t_seq = Entry(master, bd=5, textvariable=t).grid(row=4,column=7)
-
- self.label = Label(master, text="Path to -u").grid(row=5,column=0)
- global u
-- u = Tkinter.StringVar()
-+ u = tkinter.StringVar()
- self.u_seq = Entry(master, bd=5, textvariable=u).grid(row=5,column=1)
-
- self.label = Label(master, text="Path to -v").grid(row=5,column=2)
- global v
-- v = Tkinter.StringVar()
-+ v = tkinter.StringVar()
- self.v_seq = Entry(master, bd=5, textvariable=v).grid(row=5,column=3)
-
- self.label = Label(master, text="Path to -w").grid(row=5,column=4)
- global w
-- w = Tkinter.StringVar()
-+ w = tkinter.StringVar()
- self.w_seq = Entry(master, bd=5, textvariable=w).grid(row=5,column=5)
-
- self.label = Label(master, text="Path to -x").grid(row=5,column=6)
- global x
-- x = Tkinter.StringVar()
-+ x = tkinter.StringVar()
- self.x_seq = Entry(master, bd=5, textvariable=x).grid(row=5,column=7)
-
- self.label = Label(master, text="Path to -y").grid(row=6,column=0)
- global y
-- y = Tkinter.StringVar()
-+ y = tkinter.StringVar()
- self.y_seq = Entry(master, bd=5, textvariable=y).grid(row=6,column=1)
-
- self.label = Label(master, text="Path to -z").grid(row=6,column=2)
- global z
-- z = Tkinter.StringVar()
-+ z = tkinter.StringVar()
- self.z_seq = Entry(master, bd=5, textvariable=z).grid(row=6,column=3)
- """
- self.label = Label(master, text="Path to -n")
-@@ -648,19 +648,19 @@
- cmd += " -o " + o.get()
- os.system(cmd)
- def h(self):
-- print "========================================================="
-- print "This is GUI for PHYX designed to make input easier"
-- print "Type the location of the file or value into the box"
-- print "For help on a program, type anything into the help box"
-- print "and click the program you want help with. Not all options are"
-- print "needed for all programs so only fill in boxes used for "
-- print "the program of interest. Anything extra filled in will be"
-- print "ignored if it is not an option for the program"
-- print "If the programs option does not require an argument"
-- print "simply type something into the box and it will activate"
-- print "that argument"
-- print "Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)"
-- print "========================================================="
-+ print("=========================================================")
-+ print("This is GUI for PHYX designed to make input easier")
-+ print("Type the location of the file or value into the box")
-+ print("For help on a program, type anything into the help box")
-+ print("and click the program you want help with. Not all options are")
-+ print("needed for all programs so only fill in boxes used for ")
-+ print("the program of interest. Anything extra filled in will be")
-+ print("ignored if it is not an option for the program")
-+ print("If the programs option does not require an argument")
-+ print("simply type something into the box and it will activate")
-+ print("that argument")
-+ print("Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)")
-+ print("=========================================================")
-
-
- root = Tk()
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
-2to3.patch
link_lnlopt.patch
=====================================
debian/rules
=====================================
@@ -16,8 +16,14 @@ endif
override_dh_auto_install:
mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
dh_auto_install -- prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
- echo "#!/usr/bin/python3" > $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
- cat src/Phyx_Gui.py >> $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+ #echo "#!/usr/bin/python3" > $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+ #cat src/Phyx_Gui.py >> $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
override_dh_compress:
dh_compress --exclude=.pdf
+
+override_dh_auto_clean:
+ rm -rf src/phyx.logfile
+ if [ -r src/Makefile ]; then \
+ $(MAKE) -C src distclean; \
+ fi
=====================================
src/Phyx_Gui.py deleted
=====================================
@@ -1,668 +0,0 @@
-import Tkinter,os,sys
-from Tkinter import *
-
-
-class GUI:
- def __init__(self, master):
-
- self.master = master
- master.title("PHYX GUI")
-
- self.label = Label(master, text="Path to -a").grid(row=0,column=0)
- #self.label.pack()
-
- global a
- a = Tkinter.StringVar()
- self.a_seq = Entry(master, bd=5, textvariable=a).grid(row=0,column=1)
- #self.aa_seq.pack(side = LEFT)
-
- self.label = Label(master, text="Path to -b").grid(row=0,column=2)
- #self.label.pack(side = LEFT)
-
- global b
- b = Tkinter.StringVar()
- self.b_seq = Entry(master, bd=5, textvariable=b).grid(row=0,column=3)
- #self.b_seq.pack(side = LEFT)
-
- self.label = Label(master, text="Path to -c").grid(row=0,column=4)
- #self.label.pack(side = LEFT)
-
- global c
- c = Tkinter.StringVar()
- self.c_seq = Entry(master, bd=5, textvariable=c).grid(row=0,column=5)
- #self.c_seq.pack(side = LEFT)
-
- self.label = Label(master, text="Path to -d").grid(row=0,column=6)
- #self.label.pack(side = LEFT)
-
- global d
- d = Tkinter.StringVar()
- self.d_seq = Entry(master, bd=5, textvariable=d).grid(row=0,column=7)
- #self.d_seq.pack(side = LEFT)
-
- self.label = Label(master, text="Path to -e").grid(row=1,column=0)
- global e
- e = Tkinter.StringVar()
- self.e_seq = Entry(master, bd=5, textvariable=e).grid(row=1,column=1)
-
- self.label = Label(master, text="Path to -f").grid(row=1,column=2)
- global f
- f = Tkinter.StringVar()
- self.f_seq = Entry(master, bd=5, textvariable=f).grid(row=1,column=3)
-
- self.label = Label(master, text="Path to -g").grid(row=1,column=4)
- global g
- g = Tkinter.StringVar()
- self.g_seq = Entry(master, bd=5, textvariable=g).grid(row=1,column=5)
-
- self.label = Label(master, text="Path to -h").grid(row=1,column=6)
- global h
- h = Tkinter.StringVar()
- self.h_seq = Entry(master, bd=5, textvariable=h).grid(row=1,column=7)
-
- self.label = Label(master, text="Path to -i").grid(row=2,column=0)
- global i
- i = Tkinter.StringVar()
- self.i_seq = Entry(master, bd=5, textvariable=i).grid(row=2,column=1)
-
- self.label = Label(master, text="Path to -j").grid(row=2,column=2)
- global j
- j = Tkinter.StringVar()
- self.j_seq = Entry(master, bd=5, textvariable=j).grid(row=2,column=3)
-
- self.label = Label(master, text="Path to -k").grid(row=2,column=4)
- global k
- k = Tkinter.StringVar()
- self.k_seq = Entry(master, bd=5, textvariable=k).grid(row=2,column=5)
-
- self.label = Label(master, text="Path to -l").grid(row=2,column=6)
- global l
- l = Tkinter.StringVar()
- self.l_seq = Entry(master, bd=5, textvariable=l).grid(row=2,column=7)
-
- self.label = Label(master, text="Path to -m").grid(row=3,column=0)
- global m
- m = Tkinter.StringVar()
- self.m_seq = Entry(master, bd=5, textvariable=m).grid(row=3,column=1)
-
- self.label = Label(master, text="Path to -n").grid(row=3,column=2)
- global n
- n = Tkinter.StringVar()
- self.n_seq = Entry(master, bd=5, textvariable=n).grid(row=3,column=3)
-
- self.label = Label(master, text="Path to -o").grid(row=3,column=4)
- global o
- o = Tkinter.StringVar()
- self.o_seq = Entry(master, bd=5, textvariable=o).grid(row=3,column=5)
-
- self.label = Label(master, text="Path to -p").grid(row=3,column=6)
- global p
- p = Tkinter.StringVar()
- self.p_seq = Entry(master, bd=5, textvariable=p).grid(row=3,column=7)
-
- self.label = Label(master, text="Path to -q").grid(row=4,column=0)
- global q
- q = Tkinter.StringVar()
- self.q_seq = Entry(master, bd=5, textvariable=q).grid(row=4,column=1)
-
- self.label = Label(master, text="Path to -r").grid(row=4,column=2)
- global r
- r = Tkinter.StringVar()
- self.r_seq = Entry(master, bd=5, textvariable=r).grid(row=4,column=3)
-
- self.label = Label(master, text="Path to -s").grid(row=4,column=4)
- global s
- s = Tkinter.StringVar()
- self.s_seq = Entry(master, bd=5, textvariable=s).grid(row=4,column=5)
-
- self.label = Label(master, text="Path to -t").grid(row=4,column=6)
- global t
- t = Tkinter.StringVar()
- self.t_seq = Entry(master, bd=5, textvariable=t).grid(row=4,column=7)
-
- self.label = Label(master, text="Path to -u").grid(row=5,column=0)
- global u
- u = Tkinter.StringVar()
- self.u_seq = Entry(master, bd=5, textvariable=u).grid(row=5,column=1)
-
- self.label = Label(master, text="Path to -v").grid(row=5,column=2)
- global v
- v = Tkinter.StringVar()
- self.v_seq = Entry(master, bd=5, textvariable=v).grid(row=5,column=3)
-
- self.label = Label(master, text="Path to -w").grid(row=5,column=4)
- global w
- w = Tkinter.StringVar()
- self.w_seq = Entry(master, bd=5, textvariable=w).grid(row=5,column=5)
-
- self.label = Label(master, text="Path to -x").grid(row=5,column=6)
- global x
- x = Tkinter.StringVar()
- self.x_seq = Entry(master, bd=5, textvariable=x).grid(row=5,column=7)
-
- self.label = Label(master, text="Path to -y").grid(row=6,column=0)
- global y
- y = Tkinter.StringVar()
- self.y_seq = Entry(master, bd=5, textvariable=y).grid(row=6,column=1)
-
- self.label = Label(master, text="Path to -z").grid(row=6,column=2)
- global z
- z = Tkinter.StringVar()
- self.z_seq = Entry(master, bd=5, textvariable=z).grid(row=6,column=3)
- """
- self.label = Label(master, text="Path to -n")
- self.label.pack(padx=10)
-
- global test2
- test2 = Tkinter.StringVar()
- self.nuc_seq = Entry(master, bd=5, textvariable=test2)
- self.nuc_seq.pack(padx=10)
-
- self.label = Label(master, text="Outfile -o")
- self.label.pack()
-
- global test3
- test3 = ""
- test3 = Tkinter.StringVar()
- self.out_seq = Entry(master, bd=5, textvariable=test3)
- self.out_seq.pack()
-
- self.label = Label(master, text="help -h")
- self.label.pack()
-
- global help_me
- help_me = ""
- help_me = Tkinter.StringVar()
- self.help_seq = Entry(master, bd=5, textvariable=help_me)
- self.help_seq.pack()
- """
- self.aa_button = Button(master, text="Run pxaatocdn", command=self.aa).grid(row=7,column=0)
- #self.aa_button.pack()
-
- self.bdfit_button = Button(master, text="Run pxbdfit", command=self.bdfit).grid(row=7,column=1)
-
- self.bdsim_button = Button(master, text="Run pxbdsim", command=self.bdsim).grid(row=7,column=2)
-
- self.boot_button = Button(master, text="Run pxboot", command=self.boot).grid(row=7,column=3)
-
- self.bp_button = Button(master, text="Run pxbp", command=self.bp).grid(row=7,column=4)
-
- self.bpseq_button = Button(master, text="Run pxbpseq", command=self.bpseq).grid(row=7,column=5)
-
- self.cat_button = Button(master, text="Run pxcat", command=self.cat).grid(row=7,column=6)
-
- self.clsq_button = Button(master, text="Run pxclsq", command=self.clsq).grid(row=7,column=7)
-
- self.conseq_button = Button(master, text="Run pxconseq", command=self.conseq).grid(row=8,column=0)
-
- self.contrates_button = Button(master, text="Run pxcontrates", command=self.contrates).grid(row=8,column=1)
-
- self.fqfilt_button = Button(master, text="Run pxfqfilt", command=self.fqfilt).grid(row=8,column=2)
-
- self.lsseq_button = Button(master, text="Run pxlsseq", command=self.lsseq).grid(row=8,column=3)
-
- self.lstr_button = Button(master, text="Run pxlstr", command=self.lstr).grid(row=8,column=4)
-
- self.mrca_button = Button(master, text="Run pxmrca", command=self.mrca).grid(row=8,column=5)
-
- self.mrcacut_button = Button(master, text="Run pxmrcacut", command=self.mrcacut).grid(row=8,column=6)
-
- self.mrcaname_button = Button(master, text="Run pxmrcaname", command=self.mrcaname).grid(row=8,column=7)
-
- self.nj_button = Button(master, text="Run pxnj", command=self.nj).grid(row=9,column=0)
-
- self.nni_button = Button(master, text="Run pxnni", command=self.nni).grid(row=9,column=1)
-
- self.nw_button = Button(master, text="Run pxnw", command=self.nw).grid(row=9,column=2)
-
- self.recode_button = Button(master, text="Run pxrecode", command=self.recode).grid(row=9,column=3)
-
- self.revcomp_button = Button(master, text="Run pxrevcomp", command=self.revcomp).grid(row=9,column=4)
-
- self.rms_button = Button(master, text="Run pxrms", command=self.rms).grid(row=9,column=5)
-
- self.rmt_button = Button(master, text="Run pxrmt", command=self.rmt).grid(row=9,column=6)
-
- self.rr_button = Button(master, text="Run pxrr", command=self.rr).grid(row=9,column=7)
-
- self.seqgen_button = Button(master, text="Run pxseqgen", command=self.seqgen).grid(row=10,column=0)
-
- self.stofa_button = Button(master, text="Run pxstofa", command=self.stofa).grid(row=10,column=1)
-
- self.stonex_button = Button(master, text="Run pxstonex", command=self.stonex).grid(row=10,column=2)
-
- self.stophy_button = Button(master, text="Run pxstophy", command=self.stophy).grid(row=10,column=3)
-
- self.strec_button = Button(master, text="Run pxstrec", command=self.strec).grid(row=10,column=4)
-
- self.sw_button = Button(master, text="Run pxsw", command=self.sw).grid(row=10,column=5)
-
- self.tlate_button = Button(master, text="Run pxtlate", command=self.tlate).grid(row=10,column=6)
-
- self.upgma_button = Button(master, text="Run pxupgma", command=self.upgma).grid(row=10,column=7)
-
- #self.seqgen_button.pack()
-
- self.h_button = Button(master, text="print help menu", command=self.h).grid(row=11,column=3)
- #self.h_button.pack()
- #global help_on
- #help_on = ""
- #help_on = Tkinter.StringVar()
-
- self.close_button = Button(master, text="Close program", command=master.quit).grid(row=11,column=4)
- #self.close_button.pack()
- def aa(self):
- if (h.get() != ""):
- cmd = "pxaatocdn -h"
- else:
- cmd = "pxaatocdn -a " + a.get() + " -n " + n.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def bdfit(self):
- if (h.get() != ""):
- cmd = "pxbdfit -h"
- else:
- cmd = "pxbdfit -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def bdsim(self):
- if (h.get() != ""):
- cmd = "pxbdsim -h"
- else:
- cmd = "pxbdsim "
- if (e.get() != ""):
- cmd += " -e " + e.get()
- if (t.get() != ""):
- cmd += " -t " + t.get()
- if (b.get() != ""):
- cmd += " -b " + b.get()
- if (d.get() != ""):
- cmd += " -d " + d.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (s.get() != ""):
- cmd += " -s " + s.get()
- if (x.get() != ""):
- cmd += " -x " + x.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def boot(self):
- if (h.get() != ""):
- cmd = "pxboot -h"
- else:
- cmd = "pxboot "
- if (s.get() != ""):
- cmd += " -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- if (p.get() != ""):
- cmd += " -p " + p.get()
- if (f.get() != ""):
- cmd += " -f " + f.get()
- if (x.get() != ""):
- cmd += " -x " + x.get()
- os.system(cmd)
- def bp(self):
- if (h.get() != ""):
- cmd = "pxbp -h"
- else:
- cmd = "pxbp -t" + t.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def bpseq(self):
- if (h.get() != ""):
- cmd = "pxbpseq -h"
- else:
- cmd = "pxbpseq -t" + t.get() + " -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def cat(self):
- if (h.get() != ""):
- cmd = "pxcat -h"
- else:
- cmd = "pxcat -s " + s.get()
- if (p.get() != ""):
- cmd += " -p " + p.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def clsq(self):
- if (h.get() != ""):
- cmd = "pxclsq -h"
- else:
- cmd = "pxclsq -s " + s.get()
- if (p.get() != ""):
- cmd += " -p " + p.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def conseq(self):
- if (h.get() != ""):
- cmd = "pxconseq -h"
- else:
- cmd = "pxconseq -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def contrates(self):
- if (h.get() != ""):
- cmd = "pxcontrates -h"
- else:
- cmd = "pxcontrates -s " + s.get()
- if (c.get() != ""):
- cmd += " -c " + c.get()
- if (t.get() != ""):
- cmd += " -t " + t.get()
- if (a.get() != ""):
- cmd += " -a " + a.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def fqfilt(self):
- if (h.get() != ""):
- cmd = "pxfqfilt -h"
- else:
- cmd = "pxfqfilt -s " + s.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (s.get() != ""):
- cmd += " -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def lsseq(self):
- if (h.get() != ""):
- cmd = "pxlsseq -h"
- else:
- cmd = "pxlsseq -s " + s.get()
- if (a.get() != ""):
- cmd += " -a "
- if (p.get() != ""):
- cmd += " -p "
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def lstr(self):
- if (h.get() != ""):
- cmd = "pxlstr -h"
- else:
- cmd = "pxlstr -t " + t.get()
- if (a.get() != ""):
- cmd += " -a "
- if (r.get() != ""):
- cmd += " -r "
- if (b.get() != ""):
- cmd += " -b "
- if (u.get() != ""):
- cmd += " -u "
- if (n.get() != ""):
- cmd += " -n "
- if (l.get() != ""):
- cmd += " -l "
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def mrca(self):
- if (h.get() != ""):
- cmd = "pxmrca -h"
- else:
- cmd = "pxmrca -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def mrcacut(self):
- if (h.get() != ""):
- cmd = "pxmrcacut -h"
- else:
- cmd = "pxmrcacut -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def mrcaname(self):
- if (h.get() != ""):
- cmd = "pxmrcaname -h"
- else:
- cmd = "pxmrcaname -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def nj(self):
- if (h.get() != ""):
- cmd = "pxnj -h"
- else:
- cmd = "pxnj -s " + s.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def nni(self):
- if (h.get() != ""):
- cmd = "pxnni -h"
- else:
- cmd = "pxnni -t " + t.get()
- if (x.get() != ""):
- cmd += " -x " + x.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def nw(self):
- if (h.get() != ""):
- cmd = "pxnw -h"
- else:
- cmd = "pxnw -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- if (a.get() != ""):
- cmd += " -a " + a.get()
- if (t.get() != ""):
- cmd += " -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (v.get() != ""):
- cmd += " -v " + v.get()
- os.system(cmd)
- def recode(self):
- if (h.get() != ""):
- cmd = "pxrecode -h"
- else:
- cmd = "pxrecode -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def revcomp(self):
- if (h.get() != ""):
- cmd = "pxrevcomp -h"
- else:
- cmd = "pxrevcomp -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def rms(self):
- if (h.get() != ""):
- cmd = "pxrms -h"
- else:
- cmd = "pxrms -s " + s.get()
- if (r.get() != ""):
- cmd += " -r " + r.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def rmt(self):
- if (h.get() != ""):
- cmd = "pxrmt -h"
- else:
- cmd = "pxrmt -t " + t.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (f.get() != ""):
- cmd += " -f " + f.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def rr(self):
- if (h.get() != ""):
- cmd = "pxrr -h"
- else:
- cmd = "pxrr -t " + t.get()
- if (f.get() != ""):
- cmd += " -f " + f.get()
- if (u.get() != ""):
- cmd += " -u " + u.get()
- if (s.get() != ""):
- cmd += " -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def seqgen(self):
- if (h.get() != ""):
- cmd = "pxseqgen -h"
- else:
- cmd = "pxseqgen -t " + t.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- if (l.get() != ""):
- cmd += " -l " + l.get()
- if (c.get() != ""):
- cmd += " -c "
- if (b.get() != ""):
- cmd += " -b " + b.get()
- if (w.get() != ""):
- cmd += " -w " + w.get()
- if (q.get() != ""):
- cmd += " -q " + q.get()
- if (g.get() != ""):
- cmd += " -g " + g.get()
- if (r.get() != ""):
- cmd += " -r " + r.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (x.get() != ""):
- cmd += " -x " + x.get()
- if (a.get() != ""):
- cmd += " -a "
- if (p.get() != ""):
- cmd += " -p "
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (k.get() != ""):
- cmd += " -k " + k.get()
- os.system(cmd)
- def stofa(self):
- if (h.get() != ""):
- cmd = "pxstofa -h"
- else:
- cmd = "pxstofa -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def stonex(self):
- if (h.get() != ""):
- cmd = "pxstonex -h"
- else:
- cmd = "pxstonex -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def stophy(self):
- if (h.get() != ""):
- cmd = "pxstophy -h"
- else:
- cmd = "pxstophy -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def strec(self):
- if (h.get() != ""):
- cmd = "pxstrec -h"
- else:
- cmd = "pxstrec -d" + d.get()
- if (w.get() != ""):
- cmd += " -w "
- if (z.get() != ""):
- cmd += " -z "
- if (t.get() != ""):
- cmd += " -t " + t.get()
- if (c.get() != ""):
- cmd += " -c " + c.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (a.get() != ""):
- cmd += " -a " + a.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (p.get() != ""):
- cmd += " -p " + p.get()
- if (l.get() != ""):
- cmd += " -l " + l.get()
- os.system(cmd)
- def sw(self):
- if (h.get() != ""):
- cmd = "pxsw -h"
- else:
- cmd = "pxsw -s" + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- if (a.get() != ""):
- cmd += " -a " + a.get()
- if (t.get() != ""):
- cmd += " -t " + t.get()
- if (m.get() != ""):
- cmd += " -m " + m.get()
- if (n.get() != ""):
- cmd += " -n " + n.get()
- if (v.get() != ""):
- cmd += " -v " + v.get()
- os.system(cmd)
- def tlate(self):
- if (h.get() != ""):
- cmd = "pxtlate -h"
- else:
- cmd = "pxtlate -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def upgma(self):
- if (h.get() != ""):
- cmd = "pxupgma -h"
- else:
- cmd = "pxupgma -s " + s.get()
- if (o.get() != ""):
- cmd += " -o " + o.get()
- os.system(cmd)
- def h(self):
- print "========================================================="
- print "This is GUI for PHYX designed to make input easier"
- print "Type the location of the file or value into the box"
- print "For help on a program, type anything into the help box"
- print "and click the program you want help with. Not all options are"
- print "needed for all programs so only fill in boxes used for "
- print "the program of interest. Anything extra filled in will be"
- print "ignored if it is not an option for the program"
- print "If the programs option does not require an argument"
- print "simply type something into the box and it will activate"
- print "that argument"
- print "Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)"
- print "========================================================="
-
-
-root = Tk()
-my_gui = GUI(root)
-root.mainloop()
=====================================
src/configure deleted
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/1b018fd27bfb7cb632358ee53edc7de3cd66e7a1...609c5d942fb7e6ba40af2a66de50152729261300
--
View it on GitLab: https://salsa.debian.org/med-team/phyx/compare/1b018fd27bfb7cb632358ee53edc7de3cd66e7a1...609c5d942fb7e6ba40af2a66de50152729261300
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