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Use IonSwapping parameter.
2020-06-26
M
.
Er
i
c
Irr
g
ang
Use IonSwapping parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Cent
e
rOfMassPu
l
ling
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Use ReplicaEx
c
h
a
nge membe
r
instead of build(
)
arg
u
ment
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use
S
imula
t
orModu
l
es
p
a
r
ameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use In
t
e
r
act
i
veMD Simul
a
torBu
i
l
der parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
an
g
Use Le
g
acyIn
p
ut
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
I
rrgang
Use Co
n
str
a
int
s
P
a
r
a
m
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Move Profiling
parameter out of s
i
mul
a
torbuilder
.
b
uild()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Sim
u
latorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrgang
Imple
m
ent rem
a
ining Simula
t
o
r
Bui
l
der
.
add() meth
o
ds
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Int
e
rf
a
ce for rema
i
ning Sim
u
lat
o
rBuil
d
er
.
add
(
)
m
ethods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c
I
rrgang
Simulat
o
rBuilder
.
add() for
S
topHan
d
lerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Implement SimulatorBuilder
.
bui
l
d()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Reformat pair
s
.
cp
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Gr
o
macs::gmx target to hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric I
r
r
gan
g
Remov
e
workaround for gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric I
r
r
gang
Impr
o
ve pytest out
p
ut
hand
l
ing
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Compartmenta
l
ize job
r
u
l
es
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Im
p
rove
usage of Pyth
o
n
l
og
g
i
n
g
m
odul
e
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (a
n
d broken) imag
e
f
r
om Docker
i
mage
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric
I
rrgang
D
o
cke
r
imag
e
build
s
:
simplify doxygen version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image
bu
i
lds: move doxygen ha
n
dling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
I
r
rgang
Extend MP
I
ensemble testing for
g
mx
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgan
g
Enable MPI ense
m
ble testing for gmxap
i
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Make sure im
a
g
es have /
u
sr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
I
r
rgang
Up
d
a
te docker image build scr
i
pts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make sur
e
C
I script c
a
n call
/
bin/
e
nv python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Minor cle
a
n
up to b
u
il
d
all
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
Allow l
l
vm option already used in bu
i
ldall
.
sh
script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
ri
c
Irrgang
Update header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eri
c
I
rrgang
R
e
quire
C+
+
17 standar
d
and
STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
App
l
y more
granul
a
r CTest time-
o
ut
p
olicy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
E
ri
c
Irrgang
Note CUDA
bui
l
ds in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
O
n
ly
set G
M
X
_
PYTHON_PACKAGE
=
ON whe
r
e n
e
eded
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Ir
r
gang
C
han
g
e
defaul
t
CMake version
t
o
3
.
13
.
0 for CI im
a
ges
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Require CMa
k
e >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric
Irrgan
g
Explicitl
y
s
et UTF-8 enc
o
d
i
ng f
o
r g
m
xapi CL
I
interaction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
E
r
ic I
r
rgang
Av
o
id
a
ccid
e
ntall
y
initi
a
lizing pye
n
v in CI i
m
ag
e
s
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric
Irrgang
Mock h
p
ccm import so in
f
rastructu
r
e
d
ocs build easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c
I
rrg
a
ng
Extract logic for
when CI
jobs
e
x
ecute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
Normal
i
ze some more job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
S
i
mplify archive
.
gitlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove redundant jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
F
i
x duplic
a
te v
a
ria
b
le
s
parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrga
n
g
Add
r
equ
i
red Infrastructure for Gitlab
m
e
rg
e
s
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Irrgang
Normalize nam
i
ng for gromacs build/testing j
o
bs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove so
m
e unneces
s
ary i
n
dir
e
ction in
j
ob definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgang
Consolidate
.
use-clang
X
CI job mix-
i
n
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Conso
l
idate
.
use
-
g
c
cX
C
I
job mix-i
n
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Adopt
CI job naming g
u
ide
l
ines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Norma
l
ize G
i
tLab-C
I
*ca
c
he* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
Me
r
ge e
n
vironmen
t
support into global
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
M
ove
.
build-template
.
y
m
l definitions closer
t
o poin
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c
Ir
r
gang
Merge *-test-
t
emplate
.
yml into testing-matrix
.
git
l
ab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merg
e
.
t
est
-
r
u
nn
e
r-
t
emplate
.
ym
l
into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
Mer
g
e
.
te
s
t
-
s
cr
i
pt-t
e
mplate
.
yml into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
regr
e
s
s
io
n
test-template
.
yml
into archive c
o
nfig
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Irrgang
Consolidate docu
m
entation temp
l
ates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Reo
r
ganize release temp
l
at
e
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Ir
r
gang
R
e
m
o
ve co
n
fu
s
i
n
g and dupl
i
c
ate
d
variables assi
g
n
m
ent
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
ric
Irr
g
ang
Con
s
olidate global mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgan
g
[
c
i
skip]
Rem
o
ve indirection f
o
r de
f
ault tags para
m
eter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip] Re
o
rganize
.
g
i
tlab-ci
.
ym
l
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgan
g
Document CI
v
ariable and remove
u
nu
s
e
d
templat
e
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
I
rrgan
g
D
isab
l
e sph
i
n
x
.
ext
.
viewcod
e
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
I
rrgang
Add s
t
ub V
a
r
iable
s
documenta
t
ion
t
o GitLab CI
doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eri
c
I
rrgang
Remove
duplic
a
ted YAML k
e
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic Irrgan
g
Add document
f
or con
t
ainer
i
z
a
tion infr
a
s
t
ructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irr
g
ang
Alphabetize lis
t
for readabil
i
ty
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic Irrgang
Re
f
o
rma
t
a
rguments for readab
i
lity
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c
I
rrgang
Def
i
n
e
an
arg
p
ars
e
parent parser fo
r
container image
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c I
r
rg
a
ng
Build MPI i
n
Dock
e
rfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
E
r
i
c
Ir
r
g
a
n
g
Mer
g
e conf
.
py and conf-vars
.
p
y
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric I
r
rgang
Distinguish Docke
r
images for diffe
r
ent release req
u
iremen
t
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
ic
Irrgang
F
ree
u
p Do
c
ker image tag namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
Irrgan
g
R
e
move
duplicat
e
d GitLab-CI jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Reforma
t
.
gitlab
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
ic Irrgang
Co
n
solidate logic
f
o
r whether to use Modu
l
arSimula
t
or
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrga
n
g
Ma
n
age the
list of image tags i
n
D
o
cker b
u
ild scr
i
pt
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Er
i
c I
r
rgang
Manage the list of image tags in
Docker bu
i
ld sc
r
ipt
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
ric Ir
r
g
a
ng
R
e
s
o
l
ve a Python linting
error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrgang
Fix b
r
oken Py
t
hon
error chec
k
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric Irr
g
ang
Remove cruft and
r
es
o
lve depr
e
cation warni
n
gs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix docstring b
u
gs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fi
x
sphi
n
x-bu
i
ld opt
i
on
typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Let
c
omm
a
ndline_operation accept
st
d
in
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irrgang
M
a
ke gmxapi
.
version
.
has_
f
eature warning more use
f
ul
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Use s
u
bproces
s
.
r
un instead of su
b
process
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Im
p
rove gmxa
p
i
.
operation error handling
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c
Irrgan
g
Clarify
a
nnota
t
ion about
G
itLab CI Docker images
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eri
c
Irrgang
Simplify G
i
t
L
ab CI Dockerfiles
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Irrgang
Est
a
blish stubs for docum
e
nting
GitLab co
n
figurati
o
n
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
E
r
i
c Irrgang
Refor
m
at
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
E
ric Irrgang
Use e
n
u
m
for g
m
xapi
.
tes
t
su
p
port f
i
xture options
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Fur
t
her consolidate gmxap
i
.
testsup
p
o
r
t
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgan
g
Update
gmxapi Python packa
g
e
v
ersio
n
and versio
n
ing
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric Irrga
n
g
Remove
s
t
ray "to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgang
R
emove transitio
n
al
link
s
f
o
r onl
i
ne gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgan
g
A
d
d Flake8 linting
t
o gmxapi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric
Irrgang
Use `todo`
Sp
h
inx directive more
.
commit
|
commitdiff
|
tree
next