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Reformat pairs.cpp
2020-06-22
M
.
Eric Irrgang
R
e
format pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Gro
m
acs
:
:gmx ta
r
get
to
hint gmx
a
pi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Remove workar
o
u
n
d for gcc
bug 582
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Er
i
c
Ir
r
gang
Improve pytest output
h
andling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
Irrg
a
n
g
Comp
a
rt
m
enta
l
ize job
rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic Irrgan
g
Imp
r
ove usage of Pyt
h
on
lo
g
ging module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irr
g
ang
Remo
v
e unu
s
ed (and
b
roken) image from Doc
k
e
r
i
m
ag
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric I
r
rgan
g
Docker ima
g
e builds
:
simpli
f
y doxygen version ha
n
dling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Ir
r
gang
Docker
i
mage
b
uilds: move doxygen handli
n
g to a se
p
ar
a
te
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
E
x
ten
d
MPI ensemble testing f
o
r gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irr
g
ang
Enable MPI ensemble test
i
n
g
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
E
ric Ir
r
gang
Make sure im
a
ges have /usr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
Upd
a
te d
o
cker
i
mage build s
c
ripts for master br
a
nch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgang
M
ak
e
sure CI script can
c
all /bin/env
p
ytho
n
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
r
g
ang
Minor c
l
ean up to
b
uildall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrg
a
ng
Allo
w
llvm opt
i
on al
r
ead
y
used in b
u
ildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic Irrgan
g
Update head
e
r so
r
ting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic
I
rrgang
Require C++17 stan
d
ar
d
and STL featur
e
s
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Apply mo
r
e gr
a
nular CTest time-ou
t
po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrgang
N
ote CUDA b
u
il
d
s in job name
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Ir
r
gang
O
nly se
t
G
M
X_PYTHON_PA
C
KAGE=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric
I
rrg
a
ng
Cha
n
g
e
default CMake vers
i
on to 3
.
13
.
0 for CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
ric
I
r
r
gang
R
e
quir
e
CMake >=
3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eri
c
Ir
r
gang
Exp
l
ic
i
t
ly set UTF-8 enc
o
ding for
g
mxapi
C
LI interacti
o
n
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Er
i
c Irrga
n
g
Avoid accidental
l
y initializi
n
g
pyenv in CI images
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrgang
Mock hpc
c
m im
p
o
r
t s
o
i
n
f
rastr
u
cture docs build easi
l
y
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgang
Ex
t
r
act logic for
w
h
en CI jo
b
s exec
u
te
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Norma
l
ize
s
ome more job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Simplify ar
c
hi
v
e
.
gitlab-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove red
u
nd
a
nt jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
Fix dupli
c
ate
v
ariables para
m
eter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c Irr
g
ang
Add
required Infrastructure for
G
i
tlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
N
o
rmalize naming for g
r
omacs
bui
l
d/tes
t
in
g
job
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Ir
r
g
a
ng
Remove some unnece
s
sary indirection in job def
i
n
itions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c
Irr
g
ang
Consolidat
e
.
us
e
-
clan
g
X CI job m
i
x-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
ang
Conso
l
idate
.
use-gccX
C
I
jo
b
mi
x
-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
Adopt CI
job na
m
ing gu
i
delines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrg
a
ng
Nor
m
alize Gi
t
Lab-CI
*cache* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rg
a
n
g
Me
r
ge
e
nv
i
ronment support
into global
.
gitlab-c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
an
g
Move
.
build-template
.
yml definitio
n
s clo
s
er
to point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge *-test-template
.
yml into testing-matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Merge
.
te
s
t-runner-template
.
yml i
n
t
o testi
n
g
-mat
r
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrgang
Me
r
ge
.
test-scr
i
pt-template
.
yml into t
e
sting-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
Me
r
ge
.
regressiontest
-
template
.
yml int
o
a
r
chive config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
C
onsoli
d
ate
d
o
cume
n
tation
templates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Reorg
a
nize rel
e
ase templat
e
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irr
g
ang
Re
m
ove con
f
using
and duplicated vari
a
bles assignment
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
Irrg
a
ng
Consoli
d
ate
gl
o
bal mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
Irrgang
[ci skip] R
e
move indirection
for default
tag
s
parame
t
er
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Ir
r
gang
[ci skip]
R
eorganize
.
gitlab-
c
i
.
y
ml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Docume
n
t
C
I
va
r
iabl
e
and remove unused
t
e
mplat
e
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Disable sphinx
.
ext
.
viewcode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
I
rr
g
a
ng
Add stub Variables docum
e
ntation to GitLab CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric
I
rrgang
Remove duplica
t
e
d
YAML
ke
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eri
c
I
r
rgang
A
dd docum
e
nt for containerization infrastru
c
ture
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eri
c
I
r
rga
n
g
Alphabetize
list fo
r
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c
Irrgang
Reformat arguments for reada
b
ility
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic
I
r
rgang
Define an argparse parent parser for contai
n
er i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
ric
Ir
r
gang
B
u
ild MPI in Docker
f
i
l
e
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Me
r
ge c
o
nf
.
py and
c
onf-v
a
rs
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric
Irrgang
Disti
n
guish Docker images for different rele
a
se require
m
ents
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
I
rrga
n
g
Fre
e
u
p
D
o
ck
e
r image ta
g
namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irr
g
a
n
g
R
e
mo
v
e
duplicated Gi
t
Lab-CI jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
R
eformat
.
gitlab-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Ir
r
gang
Consolidate lo
g
ic for whet
h
er to use Modu
l
arSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
M
a
n
age the li
s
t of image ta
g
s in Docker build script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
M
an
a
ge
t
he list of image tags in Docker build script
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Ir
r
gang
Resolve
a
Python
l
i
n
ting error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
r
i
c
Irrgang
F
i
x
bro
k
en Pyth
o
n error check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
E
ric Irr
g
ang
Remov
e
cruft and r
e
solve deprecation warnings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irrgang
Fix docst
r
in
g
b
u
gs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix sphinx-
b
u
i
ld option typ
o
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Let com
m
andline_o
p
erat
i
on acce
p
t stdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrga
n
g
Make gmxapi
.
version
.
has
_
feature w
a
rning more usefu
l
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Use sub
p
rocess
.
r
u
n i
n
stead o
f
s
ubpr
o
cess
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eri
c
Ir
r
gang
Improv
e
gmxapi
.
operation error hand
l
ing
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic I
r
rgang
Clarify
a
n
n
otat
i
o
n about GitLab CI Docke
r
im
a
ges
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric Irrgang
S
i
mplify GitLab CI Do
c
ke
r
f
i
les
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Irrgang
Establ
i
sh stubs
f
o
r do
c
u
menting G
i
tLab con
f
iguration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric
Ir
r
g
a
ng
Refor
m
at
.
g
itlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Use enum for gmxapi
.
testsuppor
t
fixture opti
o
ns
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric I
r
rgang
Further c
o
nsolidate gmxapi
.
testsuppor
t
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric I
r
rgang
Update gm
x
ap
i
Python package versio
n
a
n
d versioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
E
ric Irrgang
Remove
s
tray "to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrga
n
g
R
emove transi
t
ional
l
i
n
k
s for online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrg
a
ng
Add
F
l
ake
8
lintin
g
to gmxapi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
Use `todo`
S
p
h
inx directive
m
or
e
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric I
r
r
g
ang
Add tracking
for a documented action item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irr
g
ang
Lin
k
s
o
me "to do"
s
in the dev manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Ir
r
gang
M
a
k
e
gmxap
i
.
testsupport u
s
abl
e
a
s a p
y
tes
t
plugin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irrgang
Res
o
lv
e
CMake
a
mb
i
g
uities for gmxa
p
i Pytho
n
package
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric Irrgang
Upd
a
te intersph
i
n
x
con
f
igu
r
ation
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Let GMX
_
DEV
E
LOPE
R
_BUI
L
D t
r
igger a "
t
o
d
o
"
list in the
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Set S
p
hinx default role
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eri
c
Irr
g
a
ng
Fix external web link
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
ic Irrgang
Enable
Sphinx todo direct
i
v
e for GMX_DEVE
L
OPER_BU
I
LD
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric
I
rrgang
Clea
n
up Sphinx interpreted text in t
h
e d
e
f
ault ro
l
e
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric Irrgang
A
dd
i
ssue tracking for
deprecatio
n
s
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eric Ir
r
g
ang
U
pdate reference to
u
nc
r
usti
f
y and clang-format
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
Eric
Irr
g
ang
Be
m
ore spe
c
ifi
c
with clang-format s
u
ggestion
s
.
commit
|
commitdiff
|
tree
next