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Use LegacyInput.
2020-06-26
M
.
Eric Irrg
a
ng
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
Constraint
s
P
aram
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrg
a
ng
Move Profili
n
g parame
t
er out o
f
simulator
b
uilder
.
buil
d
(
)
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irr
g
ang
Use SimulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
I
m
ple
m
ent r
e
main
i
ng SimulatorBuilder
.
a
d
d
() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgan
g
Int
e
rface fo
r
remaining Simulato
r
Builder
.
ad
d
() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Sim
u
latorBuilder
.
add() for StopHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrgang
Implemen
t
SimulatorBuild
e
r
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Reformat p
a
irs
.
c
p
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric
I
rrgang
Use Grom
a
cs::gmx
targ
e
t to hint gmx
a
pi
tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eri
c
I
rrgang
Rem
o
ve worka
r
ound for gcc b
u
g 5826
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgan
g
Imp
r
ove pytest output handlin
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
ic
Irrgang
Compartmentali
z
e job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Impro
v
e usage of Python logging module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused
(a
n
d
brok
e
n
) image from Doc
k
er i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrga
n
g
D
ocker image b
u
ilds
:
simplify
d
o
xygen version handlin
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image builds: mo
v
e do
x
y
g
en h
a
ndlin
g
to
a
se
p
a
rate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
Irrgang
Extend MPI ensem
b
le
t
e
s
ting for
g
mxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
i
c Ir
r
gang
En
a
b
le MPI ensemb
l
e testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irr
g
ang
Ma
k
e sure images
have
/usr/b
i
n/pyth
o
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrga
n
g
Update docker im
a
ge
bui
l
d scr
i
pts
for mast
e
r branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make
sure CI scr
i
pt can c
a
ll
/
bin/en
v
python
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Minor clean up to buildall
.
s
h
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Allo
w
llvm option already used in bui
l
dall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Update head
e
r s
o
rti
n
g
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic Irrgan
g
Require C++17 sta
n
dar
d
and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Apply more
gran
u
la
r
CTest ti
m
e-out po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
E
ric Irrgang
Note CUDA builds
i
n jo
b
name
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
O
n
ly set GMX_PYTHON_PACKAGE=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Irrgang
Change
default CMa
k
e v
e
rsion to 3
.
13
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
R
eq
u
ire CMa
k
e >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eri
c
Ir
r
gang
Explicitly set
U
TF-8 encoding for
g
mxa
p
i CLI in
t
eraction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eri
c
Irrg
a
ng
Avoi
d
accidentally initializing pyenv in CI image
s
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Er
i
c Irrgang
Mock hpccm import s
o
infrastructure docs
b
uild easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrga
n
g
Ex
t
ract logic for w
h
e
n
CI
jobs execut
e
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
I
rrgang
Normalize so
m
e more j
o
b names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
ang
S
i
mpli
f
y archive
.
gitlab-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrgang
Remove redun
d
a
nt jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Fix duplicate va
r
iab
l
es pa
r
amet
e
r
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
Add required Infrastructure for Gitla
b
m
erges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Ir
r
gang
Normalize naming for gromacs build/testing jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgang
Remove some unnecessar
y
ind
i
rect
i
on
i
n jo
b
d
efinitio
n
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Consolidate
.
use-clangX CI job mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Consolidate
.
use-gccX CI j
o
b
m
ix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgan
g
A
d
opt CI job
n
aming gui
d
elines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
Normalize GitL
a
b
-
CI *
c
ach
e
*
p
arameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
M
e
rge enviro
n
ment support into
glo
b
al
.
gi
t
lab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
I
r
rga
n
g
Move
.
build-te
m
p
late
.
yml def
i
ni
t
ions closer to point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
Merg
e
*-test-te
m
plate
.
yml into testing-matrix
.
g
i
t
lab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Merge
.
test-runner-temp
l
ate
.
yml in
t
o testing-matr
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
r
g
ang
Mer
g
e
.
te
s
t-scri
p
t-temp
l
ate
.
yml into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
regressiontest-
t
e
mp
l
ate
.
yml into a
r
chive
c
onfig
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Consolidat
e
documen
t
ation templates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrg
a
ng
Reo
r
g
a
nize relea
s
e templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
ric I
r
r
gang
Remove c
o
nf
u
sing an
d
duplicated
v
a
r
iables assignme
n
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Irrgang
C
o
n
solid
a
te global m
i
x-
i
ns
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip] Remove indirection for
d
efault tags parameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
r
i
c
Irrgang
[
c
i
skip]
Reor
g
anize
.
git
l
ab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Ir
r
ga
n
g
Document
CI varia
b
le and remove unused template
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Ir
r
gang
D
i
s
able sp
h
inx
.
e
xt
.
view
c
od
e
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Add stub Variables d
o
cume
n
t
ation to Gi
t
Lab
CI
d
oc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric
I
rrgang
Remove duplicated YAML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eri
c
I
r
r
gang
Add docume
n
t for con
t
aineriz
a
t
i
on infrastruc
t
ur
e
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Alphabetize lis
t
for rea
d
abi
l
ity
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrg
a
ng
Reformat arguments for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic Irrgang
Defi
n
e
a
n
ar
g
pars
e
pare
n
t pa
r
s
e
r
for c
o
ntainer
i
m
ag
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eri
c
Irr
g
ang
Build MPI in Do
c
ke
r
file
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Merge conf
.
p
y
and con
f
-va
r
s
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
E
r
ic
Irrgang
Distinguish
Docker images
f
or different re
l
e
as
e
requirem
e
nts
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
ric
I
rr
g
ang
Free
up D
o
c
k
er image
t
ag namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Remo
v
e
duplicated GitLab-CI jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Reformat
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrga
n
g
Consolidate
l
o
gic
f
or whether to use ModularSim
u
l
ato
r
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Manage t
h
e list of
i
mage ta
g
s in Docker bu
i
ld scr
i
p
t
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eri
c
Irrga
n
g
Manage the l
i
st of image ta
g
s in Docker build script
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
r
ic Irrgang
Resolve a Python
linting
e
rror
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric
I
rrgang
Fix
b
roken
Python err
o
r check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
E
ric Irrgang
Remove cruft and reso
l
ve depreca
t
ion warnings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgan
g
Fix docstring
b
ugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irrg
a
ng
Fix sphinx-build option
typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Let commandline_operati
o
n accept stdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Ir
r
gan
g
Make gmxapi
.
vers
i
on
.
has_feature wa
r
ning more useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
rgang
U
se subprocess
.
run instead of
su
b
proces
s
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Improve
g
m
xapi
.
operation error hand
l
ing
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
C
l
arify annota
t
ion
a
bout GitLab CI
D
ocker
i
m
age
s
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Er
i
c
Irrgang
Simpl
i
fy
Gi
t
Lab
CI Dockerfile
s
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Ir
r
g
ang
E
stablish
stub
s
f
o
r
d
o
c
u
m
e
nting GitLab configuration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric Irrgan
g
Reformat
.
git
l
a
b
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
E
r
ic Irrga
n
g
U
se
e
num
for
g
m
xapi
.
testsupport fi
x
ture options
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
E
r
ic
I
rrgang
Further consolidate gmxapi
.
testsuppo
r
t
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Update gmxapi Pyt
h
o
n p
a
ckage versio
n
and
v
ersionin
g
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric Irrgang
Remove st
r
ay "to do
"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eri
c
I
r
rgang
Remove transitional links for online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Ir
r
g
ang
Add Flake
8
linting
t
o
g
mxapi
tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eri
c
Irrgang
Us
e
`t
o
do` Sphin
x
dir
e
ctive
m
ore
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Add
tracking for a
d
ocumente
d
actio
n
item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Link some "to do"s in the dev ma
n
ual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
E
ric I
r
rgang
Make
gmxapi
.
tes
t
suppo
r
t usable a
s
a pytes
t
plugin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
E
r
ic Irrga
n
g
Resolve CMake
a
m
biguities for gmx
a
pi Python p
a
ckage
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric
Irrg
a
ng
Update intersphin
x
co
n
figuratio
n
.
commit
|
commitdiff
|
tree
next