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Document current help formatting
2015-06-04
Teemu Murtol
a
Docu
m
ent
cur
r
ent help for
m
atti
n
g
commit
|
commitdiff
|
tree
2015-06-04
Tee
m
u Murtola
Bas
i
c sup
p
ort fo
r
t
itles wit
h
i
n
tool help
commit
|
commitdiff
|
tree
2015-06-04
Teemu M
u
r
tola
S
u
pport rst tables
in t
o
ol help te
x
ts
commit
|
commitdiff
|
tree
2015-05-28
Teemu Murtola
I
m
pr
o
ve lis
t
s in use
r
g
u
ide
for
s
e
l
ectio
n
s
commit
|
commitdiff
|
tree
2015-05-28
Teemu M
u
rtola
Additio
n
al selection examples
commit
|
commitdiff
|
tree
2015-05-25
Tee
m
u Murtola
Over
v
ie
w
doc
s
for analysis
nbsear
c
h
commit
|
commitdiff
|
tree
2015-05-24
T
eemu Murtola
I
n
clude
selection keyword details in
u
ser
guid
e
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Allow a
n
y
o
rder for sections in 'gmx help -ex
p
ort'
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Base
t
o get all
'
gmx he
l
p' content
s
to user
guide
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Merge
r
elease-5-0 into master
commit
|
commitdiff
|
tree
2015-05-22
Teemu
M
urtol
a
Avoid crash with empty refere
n
ce for 'same as' selection
commit
|
commitdiff
|
tree
2015-05-22
Teemu Murtola
Add subsection depth to HelpWriterContext
commit
|
commitdiff
|
tree
2015-05-22
Te
e
mu Murto
l
a
Ad
d
n
o
te ab
o
u
t
atom order in
selections
commit
|
commitdiff
|
tree
2015-05-21
Teemu Murtola
Restru
c
tu
r
e CommandLineModuleManag
e
r tests
commit
|
commitdiff
|
tree
2015-05-20
T
eemu
Murtola
Fix handlin
g
of real
-
valued 'to' select
i
on ranges
commit
|
commitdiff
|
tree
2015-05-20
Teemu M
u
rtola
F
ix de
p
endenci
e
s for regression test custom target
commit
|
commitdiff
|
tree
2015-05-20
Teemu
Murto
l
a
Some tests f
o
r 'gmx h
e
lp -export rst'
commit
|
commitdiff
|
tree
2015-05-18
T
eemu Murtola
Merge
"Merge
b
ranc
h
origin/release-5-0"
commit
|
commitdiff
|
tree
2015-05-17
Tee
m
u
M
u
rt
o
la
Move a
few defines
t
o buildinfo
.
h
commit
|
commitdiff
|
tree
2015-05-13
T
e
emu
M
urtola
Remov
e
rem
a
ini
n
g
ol
d
-
h
t
ml
content
commit
|
commitdiff
|
tree
2015-05-11
T
eem
u
Murt
o
la
U
s
e single va
r
iable
for expected Doxygen
version
commit
|
commitdiff
|
tree
2015-05-10
Teemu M
u
r
t
ol
a
Mov
e
some
testutils
and overview
d
o
cs to
d
ev guide
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtola
Pr
i
nt correct o
r
der for in
c
lude order/sty
l
e issu
e
s
commit
|
commitdiff
|
tree
2015-05-10
Teemu Murtola
Improv
e
build system
f
o
r
Sphinx
commit
|
commitdiff
|
tree
2015-05-10
Teem
u
Murtola
Con
v
e
rt devel
o
per ma
n
ua
l
to rst
commit
|
commitdiff
|
tree
2015-05-05
Te
e
mu Murtola
Avoid rounding errors affecting result
s
i
n
one
t
es
t
commit
|
commitdiff
|
tree
2015-04-24
Teemu Mur
t
ola
Add sectio
n
on naming
convent
i
ons to dev manual
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Replace mo
r
e
[BR] with rst bullet lists
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Re
p
l
a
ce some [BR
]
i
n help texts with rs
t
l
iterals
commit
|
commitdiff
|
tree
2015-02-13
T
e
emu
M
urtola
Move flow chart fr
o
m old
-
html to Sphinx
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Make (m
o
s
t)
HTML lin
k
s to file formats
w
ork a
g
ain
commit
|
commitdiff
|
tree
2015-02-13
Teemu Murtola
Co
n
vert fil
e
format descriptions to
r
st
commit
|
commitdiff
|
tree
2015-02-13
Te
e
mu
Murt
o
l
a
Generate man page
s
through Sph
i
nx
commit
|
commitdiff
|
tree
2015-02-13
Te
e
mu Murtola
Repla
c
e
t
o
ol
HTM
L
help with Sphinx-generated docs
commit
|
commitdiff
|
tree
2015-02-07
Te
e
m
u Mur
t
ola
Support more comp
l
ex fixed position
s
e
l
ect
i
ons
commit
|
commitdiff
|
tree
2015-01-29
Teem
u
Murtola
Add input file options
t
hat
a
ccept missing files
commit
|
commitdiff
|
tree
2015-01-24
Teemu Murtola
R
e
move old selection parser error handling
code
commit
|
commitdiff
|
tree
2015-01-24
Tee
m
u
M
u
r
tola
Impro
v
e selec
t
ion error
messages (
u
s
e exc
e
p
tions)
commit
|
commitdiff
|
tree
2015-01-23
Teemu M
u
rtol
a
Ignore test-only
depen
d
ency
c
ycles
commit
|
commitdiff
|
tree
2015-01-20
Teemu
M
u
rtola
Make
d
ata f
i
l
e path s
e
arch mo
r
e reusable
commit
|
commitdiff
|
tree
2015-01-20
Teemu Murtol
a
C
onve
r
t
f
orcefiel
d
search to C++
commit
|
commitdiff
|
tree
2015-01-19
Teemu M
u
rtola
Remov
e
Ana
l
ysisNeighborhood::setU
s
eBou
n
d
i
n
g
B
o
x
(
)
commit
|
commitdiff
|
tree
2015-01-17
Teemu
Murtola
Mer
g
e
"
M
erge bra
n
ch rel
e
ase-5-0"
commit
|
commitdiff
|
tree
2015-01-08
Teemu M
u
rtola
Refa
c
tor lo
g
ic for finding
shar
e
/
t
op/ files
commit
|
commitdiff
|
tree
2015-01-08
Teemu Murtol
a
Cl
o
sed some
.
x
vg
f
i
les tha
t
wer
e
being left open
commit
|
commitdiff
|
tree
2015-01-07
Te
e
mu Murtola
Cu
s
tom program c
o
ntext for unit tests
commit
|
commitdiff
|
tree
2015-01-07
Teemu M
u
rto
l
a
S
p
lit unit test init from
t
e
s
toptions
.
cpp
commit
|
commitdiff
|
tree
2015-01-06
Tee
m
u Mur
t
ola
Use analysis nbsearch for surfac
e
a
r
ea calculatio
n
commit
|
commitdiff
|
tree
2015-01-06
Teem
u
Murtola
Use xvgrclose() fo
r
files op
e
ned with xvg
r
open()
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Suppor
t
subset of
rv
e
c
a
rray as
i
nput f
o
r
a
nalysis
.
.
.
commit
|
commitdiff
|
tree
2015-01-05
Teemu Mur
t
o
l
a
Minimal
C
++ replacement for rvec
commit
|
commitdiff
|
tree
2015-01-05
Teemu Murtola
Clar
i
fy GMX_MPI manag
e
ment
commit
|
commitdiff
|
tree
2015-01-03
Teemu Murtola
Minor se
l
ection clarifications
commit
|
commitdiff
|
tree
2015-01-03
T
eem
u
Mur
t
ola
Fix crash with
'
z of
.
.
.
' within an express
i
on
commit
|
commitdiff
|
tree
2015-01-02
Teemu Murtola
Update co
p
y
right year in copyr
i
te
.
cpp
commit
|
commitdiff
|
tree
2014-12-28
Teemu Murtola
Conv
e
rt gmx-insert-m
o
l
e
cules
i
nto prop
e
r C++ module
commit
|
commitdiff
|
tree
2014-12-28
Teemu Murtola
Ad
d
helper fo
r
generic C
+
+
c
om
m
and-line m
o
d
u
l
e
s
commit
|
commitdiff
|
tree
2014-12-18
T
eemu Murtola
Rework gmx-solvate
t
o
use analysis nbsea
r
c
h
commit
|
commitdiff
|
tree
2014-12-17
Teemu
M
urtola
Make 'gmx sasa' c
a
lculation thread-safe
commit
|
commitdiff
|
tree
2014-12-17
T
e
em
u
Mur
t
o
l
a
Remove s
o
me bac
k
w
a
rds-compatibility glue for Je
n
kins
commit
|
commitdiff
|
tree
2014-12-16
Teem
u
Murtola
Mak
e
'gm
x
s
a
sa' vo
l
ume c
o
mput
a
tion translation-in
v
ariant
commit
|
commitdiff
|
tree
2014-12-15
Teemu Murtola
Use new XML format with cppcheck
commit
|
commitdiff
|
tree
2014-12-14
T
e
emu Murtola
C++ interface for
s
urface area calcu
l
ation
commit
|
commitdiff
|
tree
2014-12-11
Teemu M
u
rtola
Co
n
vert gm
x
r
df to
the C++ fr
a
m
ework
commit
|
commitdiff
|
tree
2014-12-10
Teemu
Mur
t
ola
Fi
x
misc
.
analysi
s
neighbor
h
ood search iss
u
es
commit
|
commitdiff
|
tree
2014-12-09
Teemu
M
urtola
Trac
k
locati
o
ns for sele
c
tio
n
parsing products
commit
|
commitdiff
|
tree
2014-12-08
Teemu
Mu
r
tola
R
e
ctangular grid for ana
l
ysis nbsearch
commit
|
commitdiff
|
tree
2014-12-06
Teemu Murtola
S
i
mpli
f
y
analysisda
t
a para
l
le
l
ism model
commit
|
commitdiff
|
tree
2014-12-05
Teemu Murtola
I
mprove sel
e
ction p
a
rsing er
r
or r
e
porti
n
g
commit
|
commitdiff
|
tree
2014-12-05
T
eemu Murtola
No
n
-period
i
c
nbs
e
ar
c
h
w
ith
g
rid based on boundin
g
b
o
x
commit
|
commitdiff
|
tree
2014-12-04
T
e
emu Murtola
Move/add uncrust
i
f
y
d
ocum
e
ntatio
n
to dev manual
commit
|
commitdiff
|
tree
2014-12-02
Teemu Murtola
Add 'gmx pai
r
di
s
t' tool as
p
ar
t
i
a
l g_mindist replac
e
ment
commit
|
commitdiff
|
tree
2014-12-02
Teem
u
Murt
o
la
Analysis grid
nbsearch for mo
r
e
c
a
s
e
s
commit
|
commitdiff
|
tree
2014-11-29
T
eemu Mu
r
tola
B
a
sic support for 'z of
.
.
.
' selection
s
commit
|
commitdiff
|
tree
2014-11-28
T
eemu
M
urtola
C
l
a
rify memory manag
e
ment for
selection values
commit
|
commitdiff
|
tree
2014-11-28
Teemu Murtola
Helper function for grouping selectio
n
positions
commit
|
commitdiff
|
tree
2014-11-27
Te
e
mu Murtola
Cle
a
n up
g
m
x
solv
a
te
commit
|
commitdiff
|
tree
2014-11-27
Teemu
M
ur
t
o
l
a
Port gmx-solvate tes
t
s to us
e
Command
L
in
e
T
estB
a
se
commit
|
commitdiff
|
tree
2014-11-27
Teemu Mur
t
o
la
More contr
o
l over file b
a
ckups
commit
|
commitdiff
|
tree
2014-11-27
Teemu
Murtol
a
Furth
e
r ins
e
rt-molecul
e
s cleanu
p
commit
|
commitdiff
|
tree
2014-11-26
Teem
u
Murt
o
l
a
Convert surface
area calculati
o
n to C++
commit
|
commitdiff
|
tree
2014-11-26
T
e
em
u
Murtola
A
dd some u
n
it test
s
for surface area calculat
i
on
commit
|
commitdiff
|
tree
2014-11-23
Tee
m
u Murtola
Rename doc-*
t
a
r
gets to
b
e less
generic
commit
|
commitdiff
|
tree
2014-11-21
Tee
m
u Mur
t
ol
a
Descr
i
be
d
oc-check in d
e
veloper manual
commit
|
commitdiff
|
tree
2014-11-21
Teemu Murtola
S
k
eleton for a developer manual
commit
|
commitdiff
|
tree
2014-11-14
T
eemu Mur
t
ola
Refactor p
o
s
it
i
on
-
evaluated se
l
ection keyword ha
n
dli
n
g
commit
|
commitdiff
|
tree
2014-10-30
T
eem
u
M
u
rtola
A
d
d
more selection unit tes
t
s
commit
|
commitdiff
|
tree
2014-10-30
Tee
m
u Mu
r
to
l
a
Fix more memory
l
eaks in default gro
u
p creation
commit
|
commitdiff
|
tree
2014-10-30
Teemu Mu
r
tola
Fix memory leak
i
n default
i
n
d
e
x grou
p
c
reation
commit
|
commitdiff
|
tree
2014-10-29
Te
e
mu
M
urtola
Me
r
g
e
relea
s
e-5-0 into master
commit
|
commitdiff
|
tree
2014-10-29
Teemu
M
u
r
to
l
a
I
m
prove analysis nbsearch
grid
mapping
commit
|
commitdiff
|
tree
2014-10-28
Teemu Murtola
Avoid commo
n
.
h
i
ncl
u
si
o
n
i
n
CUDA code
commit
|
commitdiff
|
tree
2014-10-23
Teemu Murtola
Mov
e
t
runcate() wrapper to futil
.
h
commit
|
commitdiff
|
tree
2014-10-23
Teem
u
Mur
t
ola
Encapsulate
u
se
o
f nice()
commit
|
commitdiff
|
tree
2014-10-22
Teemu Murtola
C
o
llect more
p
latform-specif
i
c co
d
e to s
y
s
i
n
fo
.
h
commit
|
commitdiff
|
tree
2014-10-22
Teemu Murtola
Rena
m
e comm
o
n
.
h to
classhelpers
.
h
commit
|
commitdiff
|
tree
2014-10-22
Teemu Mur
t
ola
Move
basic
m
acro
s
f
r
om common
.
h to basedefi
n
itions
.
h
commit
|
commitdiff
|
tree
2014-10-14
Teemu Murtola
Check confi
g
.
h usage in d
o
c
-check
commit
|
commitdiff
|
tree
2014-10-14
Tee
m
u Mu
r
tola
Use
ana
l
ysis nbsearch
i
n inser
t
-molecules
commit
|
commitdiff
|
tree
2014-10-11
Teemu Murtola
C
lean up
g
mx insert-molecules
commit
|
commitdiff
|
tree
next