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Fix error wrapping in interactive selection input
2015-07-04
Teemu Murtola
Fix err
o
r wrapping in interactive se
l
ection input
commit
|
commitdiff
|
tree
2015-07-04
Teemu
M
ur
t
ola
Tests for inter
a
cti
v
e selec
t
ion input
commit
|
commitdiff
|
tree
2015-07-04
Teem
u
Mur
t
ola
R
e
facto
r
f
o
r testing in
t
er
a
ctive sele
c
tion input
commit
|
commitdiff
|
tree
2015-07-04
Teemu
M
urtola
Remo
v
e gmx::File
(
except
f
or File::exists())
commit
|
commitdiff
|
tree
2015-07-04
Te
e
mu Murtola
R
eplace direct uses of gmx::File
with streams
commit
|
commitdiff
|
tree
2015-07-04
Teemu M
u
rtol
a
Bu
m
p
v
a
r
iou
s
version numbers
commit
|
commitdiff
|
tree
2015-07-04
Teemu Murtola
Make some unit t
e
sts use mock file ou
t
put
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murtola
Convert
gm
x
fio to C++
commit
|
commitdiff
|
tree
2015-07-02
Teemu Mur
t
ola
C
l
ea
n
up gmx
f
io includes
commit
|
commitdiff
|
tree
2015-07-02
Teemu Murt
o
la
Reorder c
o
de within gmxfio
commit
|
commitdiff
|
tree
2015-07-02
Te
e
mu M
u
r
t
o
l
a
Fur
t
her gm
x
fio clean
u
p re
l
ated t
o
xdr handling
commit
|
commitdiff
|
tree
2015-07-02
Teem
u
Murto
l
a
Minor inc
l
ude sorti
n
g chang
e
s
commit
|
commitdiff
|
tree
2015-07-01
T
eemu M
u
rtol
a
C
l
e
a
n
up
u
n
u
s
ed co
d
e from gmx
f
io
commit
|
commitdiff
|
tree
2015-06-29
Te
e
mu Mu
r
tol
a
Only accept exact
m
atches for
sel
e
ction keyw
o
rds
commit
|
commitdiff
|
tree
2015-06-29
Te
e
mu Murtola
Make so
m
e unit
t
es
t
s s
k
ip
file
s
yste
m
acce
s
s
commit
|
commitdiff
|
tree
2015-06-27
Teemu Murtola
D
oc
u
men
t
to
o
l chang
e
s in 5
.
1
commit
|
commitdiff
|
tree
2015-06-25
Teemu M
u
r
t
ola
Move documentation on
tool ch
a
nges
f
r
om wik
i
commit
|
commitdiff
|
tree
2015-06-17
Teemu M
u
rtola
M
inor clean up for refdata
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teemu Murto
l
a
I
m
p
r
ove lo
g
ic fo
r
automati
c
sel
e
ctio
n
names
commit
|
commitdiff
|
tree
2015-06-16
Teemu Murt
o
la
F
i
x
broken l
i
n
ks from the ol
d
flow chart
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtol
a
Upda
t
e
help output
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
I
m
prove uncrustify Jenki
n
s bu
i
l
d
s
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtol
a
Initial docs
f
or
J
e
n
ki
n
s i
n
t
egration
commit
|
commitdiff
|
tree
2015-06-12
Teemu M
u
rtola
Ini
t
ial
build s
y
stem
d
o
c
umentation in dev gui
d
e
commit
|
commitdiff
|
tree
2015-06-12
Teem
u
Murtol
a
I
m
pro
v
e J
e
nkins
d
ocs build
commit
|
commitdiff
|
tree
2015-06-12
Teemu Murtola
Extend
source layo
u
t d
e
s
cription in dev guid
e
commit
|
commitdiff
|
tree
2015-06-11
Teemu Mu
r
tol
a
Script for Jenki
n
s docume
n
tat
i
on bui
l
d
commit
|
commitdiff
|
tree
2015-06-09
Te
e
mu
M
urtola
Misc
.
improve
m
ents
t
o
docs bu
i
l
d system
commit
|
commitdiff
|
tree
2015-06-09
Teemu Murto
l
a
Add des
c
r
i
pti
o
n o
f
r
e
locatable
b
i
n
aries
commit
|
commitdiff
|
tree
2015-06-09
Teemu Mu
r
tola
Resolve
o
ne TODO for command
l
i
ne help tests
commit
|
commitdiff
|
tree
2015-06-09
Teem
u
Murto
l
a
Improve u
s
er guide t
e
xt for com
m
and line interface
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Fix p
o
ten
t
ial FP
E
in selection tes
t
s
commit
|
commitdiff
|
tree
2015-06-04
Tee
m
u Murtola
Refactor rst par
s
ing for console
output
commit
|
commitdiff
|
tree
2015-06-04
Teem
u
Murtola
Repla
c
e gromacs
.
7 man page wit
h
gmx
.
1
commit
|
commitdiff
|
tree
2015-06-04
T
e
emu Mu
r
tola
Doc
u
ment c
u
rr
e
nt h
e
lp formatting
commit
|
commitdiff
|
tree
2015-06-04
T
e
emu Murt
o
l
a
Ba
s
ic sup
p
o
rt for titles within tool help
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Su
p
p
ort
rst tables in tool help texts
commit
|
commitdiff
|
tree
2015-05-28
Teemu Mur
t
ola
Imp
r
ove lists in
use
r
guid
e
for se
l
e
ctio
n
s
commit
|
commitdiff
|
tree
2015-05-28
Teemu Murtol
a
A
d
ditional selec
t
ion examples
commit
|
commitdiff
|
tree
2015-05-25
Teemu Murtola
Overview
d
ocs for analys
i
s nb
s
ea
r
ch
commit
|
commitdiff
|
tree
2015-05-24
Teemu Murtola
Include s
e
lection key
w
or
d
details in user
guide
commit
|
commitdiff
|
tree
2015-05-22
Teem
u
Murtol
a
A
llow
a
n
y order for
se
c
tions in 'gmx help
-
export'
commit
|
commitdiff
|
tree
2015-05-22
T
eemu Murtola
Base to
get al
l
'gmx help' c
o
ntents
to user guide
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtol
a
Merge rel
e
ase-5-0 into master
commit
|
commitdiff
|
tree
2015-05-22
T
eemu Murtola
Avoid crash with emp
t
y reference
for 'same as' sel
e
ct
i
on
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Add subs
e
ction depth to HelpWriterContext
commit
|
commitdiff
|
tree
2015-05-22
T
eemu Mu
r
tola
A
d
d
n
o
te about
atom order in sel
e
ctions
commit
|
commitdiff
|
tree
2015-05-21
Teemu Murtola
R
e
structure CommandL
i
ne
M
odul
e
M
a
nager tests
commit
|
commitdiff
|
tree
2015-05-20
Teemu
M
urtola
Fi
x
handl
i
ng of real-va
l
ued 'to' selection r
a
n
ges
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murtol
a
F
i
x d
e
pendenc
i
es for reg
r
es
s
io
n
tes
t
custo
m
t
arget
commit
|
commitdiff
|
tree
2015-05-20
T
e
emu Murtol
a
S
o
m
e te
s
ts for
'gmx hel
p
-export
r
st'
commit
|
commitdiff
|
tree
2015-05-18
Teemu
Murtola
Merge
"Merge br
a
nch
o
r
igin/
r
elease-5-0"
commit
|
commitdiff
|
tree
2015-05-17
Teemu
Murtola
Move
a
few defines to bui
l
din
f
o
.
h
commit
|
commitdiff
|
tree
2015-05-13
T
e
e
mu Mu
r
t
ola
Re
m
ove remaining old-
h
tml content
commit
|
commitdiff
|
tree
2015-05-11
Teemu Mu
r
tola
U
se sin
g
le variable for expected Doxy
g
en
v
e
rsion
commit
|
commitdiff
|
tree
2015-05-10
Teemu M
u
rtola
M
ove som
e
tes
t
uti
l
s and overvi
e
w
d
ocs to dev
g
uide
commit
|
commitdiff
|
tree
2015-05-10
Teemu
Murtola
Print correct order for include order/style issues
commit
|
commitdiff
|
tree
2015-05-10
T
eemu Murto
l
a
Impr
o
ve build
sys
t
em for Sphin
x
commit
|
commitdiff
|
tree
2015-05-10
Teem
u
Murtol
a
Conver
t
devel
o
per manual to rst
commit
|
commitdiff
|
tree
2015-05-05
Teemu Murt
o
la
A
v
o
id rounding error
s
affect
i
n
g results in one t
e
st
commit
|
commitdiff
|
tree
2015-04-24
Teemu Murtola
A
d
d section on naming conventions to
dev man
u
al
commit
|
commitdiff
|
tree
2015-02-13
T
e
emu Murtol
a
R
e
p
la
c
e
more [
B
R] with rst b
u
llet
lis
t
s
commit
|
commitdiff
|
tree
2015-02-13
Teem
u
Murtola
R
eplace som
e
[
BR] in help t
e
xts w
i
t
h rst lit
e
rals
commit
|
commitdiff
|
tree
2015-02-13
Teemu M
u
rtola
Move flow chart from old-html to Sphinx
commit
|
commitdiff
|
tree
2015-02-13
T
eemu Murtola
Mak
e
(most) HTML l
i
n
k
s
to file formats
work again
commit
|
commitdiff
|
tree
2015-02-13
T
eem
u
Murtol
a
Convert fil
e
form
a
t descriptions to
rst
commit
|
commitdiff
|
tree
2015-02-13
T
e
emu
Murtola
Generate man pages through
Sph
i
nx
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtol
a
Replace tool
H
TML he
l
p with Sph
i
nx-generated docs
commit
|
commitdiff
|
tree
2015-02-07
Teemu M
u
rt
o
la
Support more complex fixed
p
osition se
l
ect
i
ons
commit
|
commitdiff
|
tree
2015-01-29
Te
e
mu
M
urtola
Add
i
n
put fil
e
options that accept mis
s
i
ng files
commit
|
commitdiff
|
tree
2015-01-24
Teemu Mu
r
tola
R
e
m
ove old selection parser er
r
or handling cod
e
commit
|
commitdiff
|
tree
2015-01-24
Teemu Mur
t
ola
Improve s
e
le
c
t
i
on
e
r
ror mess
a
ges (use except
i
ons)
commit
|
commitdiff
|
tree
2015-01-23
T
e
e
m
u Murtola
Ig
n
ore
t
e
st-on
l
y
dep
e
ndency cycles
commit
|
commitdiff
|
tree
2015-01-20
T
e
e
m
u M
u
rtola
Make data file path se
a
rch more reusable
commit
|
commitdiff
|
tree
2015-01-20
Teemu M
u
rtola
Convert forcefield se
a
r
c
h to C++
commit
|
commitdiff
|
tree
2015-01-19
Teemu Murtola
Remove An
a
lysisNei
g
hborhood
:
:se
t
UseBoundin
g
Bo
x
()
commit
|
commitdiff
|
tree
2015-01-17
T
e
emu
M
urtola
Me
r
ge "Merge b
r
anc
h
r
e
l
ease-5-0"
commit
|
commitdiff
|
tree
2015-01-08
Te
e
mu Murtola
R
e
fac
t
or logi
c
fo
r
findin
g
share/t
o
p/ fi
l
es
commit
|
commitdiff
|
tree
2015-01-08
T
e
emu Murt
o
la
C
l
osed some
.
xvg file
s
that were be
i
n
g
left open
commit
|
commitdiff
|
tree
2015-01-07
Teemu Murto
l
a
Cus
t
om p
r
ogr
a
m contex
t
for unit tests
commit
|
commitdiff
|
tree
2015-01-07
Te
e
mu Murtola
Split un
i
t
t
est init from t
e
st
o
p
tions
.
cpp
commit
|
commitdiff
|
tree
2015-01-06
Teem
u
Murto
l
a
Use
a
nalysi
s
nbs
e
a
r
ch for surf
a
c
e
area calculation
commit
|
commitdiff
|
tree
2015-01-06
Teemu M
u
rtola
Use xvgrc
l
o
s
e() for files opened w
i
th xvgr
o
pen()
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Support subset o
f
r
v
ec arr
a
y
a
s input fo
r
analysis
.
.
.
commit
|
commitdiff
|
tree
2015-01-05
Teemu M
u
rtola
M
i
n
imal
C++ replacement
f
o
r
rve
c
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Clarify GMX_MP
I
managem
e
nt
commit
|
commitdiff
|
tree
2015-01-03
Teemu Murtola
Minor selection clarificatio
n
s
commit
|
commitdiff
|
tree
2015-01-03
Tee
m
u Mur
t
o
la
Fix
c
rash with 'z o
f
.
.
.
' within an
exp
r
e
s
s
i
o
n
commit
|
commitdiff
|
tree
2015-01-02
Teemu Murtola
Update c
o
pyright year in c
o
pyrite
.
cpp
commit
|
commitdiff
|
tree
2014-12-28
T
eemu Murtola
Conve
r
t g
m
x
-in
s
ert-molecule
s
i
n
to prop
e
r C++ module
commit
|
commitdiff
|
tree
2014-12-28
Teemu
M
urtola
Add helper f
o
r generic C++ com
m
and-line modules
commit
|
commitdiff
|
tree
2014-12-18
Teemu Murtola
Rework
gmx-solvate
t
o use
a
nalysis nbs
e
arch
commit
|
commitdiff
|
tree
2014-12-17
Teemu Murtola
Mak
e
'
g
mx sasa' cal
c
u
lation th
r
ead-s
a
fe
commit
|
commitdiff
|
tree
2014-12-17
T
e
emu Murt
o
la
Remove s
o
me
b
ackwa
r
ds-
c
ompatib
i
l
i
ty glue for Jenkins
commit
|
commitdiff
|
tree
2014-12-16
Teemu
M
u
r
t
ola
M
ak
e
'gm
x
sasa' volu
m
e
c
o
mputation translat
i
on-in
v
aria
n
t
commit
|
commitdiff
|
tree
2014-12-15
Teemu Murt
o
la
Use
n
ew XML f
o
r
m
at with cppcheck
commit
|
commitdiff
|
tree
2014-12-14
Tee
m
u
Mur
t
ola
C
++ interface fo
r
surface a
r
ea calculation
commit
|
commitdiff
|
tree
2014-12-11
Teemu Murtola
Con
v
ert gm
x
rdf
t
o the C++ framew
o
rk
commit
|
commitdiff
|
tree
2014-12-10
Te
e
mu Murtol
a
Fi
x
m
isc
.
analysis neigh
b
orhood search
i
ssues
commit
|
commitdiff
|
tree
2014-12-09
Teemu Mu
r
tola
Track locations for selection p
a
rsi
n
g products
commit
|
commitdiff
|
tree
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