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Use CenterOfMassPulling
2020-06-26
M
.
Eri
c
Irrgan
g
U
s
e
CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Repl
i
ca
E
xchange mem
b
er instead of build() arg
u
ment
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Us
e
Si
m
ulatorModu
l
es paramete
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Ir
r
gang
Use Interactiv
e
MD Simulat
o
rBuilder
p
a
ra
m
et
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Ir
r
gan
g
Use Legac
y
Input
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use Constra
i
ntsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Move Pr
o
fi
l
in
g
para
m
eter out of simulatorbuild
e
r
.
b
u
ild(
)
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
I
rrga
n
g
Use
S
imulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remaining
S
imul
a
torBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Interface f
o
r remai
n
ing SimulatorBuilder
.
add() meth
o
ds
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Simul
a
t
orBui
l
der
.
add() for
S
topHandlerB
u
ilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Implemen
t
SimulatorBui
l
der
.
bui
l
d()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Er
i
c
I
rr
g
ang
Reformat pair
s
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric Irrgang
U
s
e Gromacs::gmx target to hi
n
t gmxa
p
i
tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Er
i
c Irrgang
Remove w
o
rkaround
f
or
g
cc bug 58
2
65
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Er
i
c Irrgang
Improve pytest output
h
andling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Ir
r
gang
C
o
mp
a
rtmentalize
job rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric
I
rrgan
g
Imp
r
ove usa
g
e of Pyth
o
n
l
ogging
module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric
Irrgang
H
andle arbitrar
y
doxygen
v
ersion
s
i
n
Docker i
m
age build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric I
r
rgang
Remove unu
s
e
d
(
and bro
k
e
n) image
f
rom Docker
ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image builds:
simplify doxygen version han
d
ling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image b
u
ilds: move d
o
xyge
n
handling to a separat
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
E
xtend MPI ensemble t
e
sting
f
o
r gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic
I
rrg
a
ng
Enable MPI
e
nse
m
ble testing
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irr
g
a
n
g
Norm
a
l
ize gmxapi related
release-20
2
0 jo
b
l
og
i
c
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
E
r
i
c Irrgang
Make sure ima
g
es h
a
ve /usr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
r
r
g
ang
Up
d
ate docker image b
u
ild scripts for
m
a
ster branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make s
u
re CI
script can call /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
i
c
Irrg
a
n
g
Minor
c
lean up to
b
u
i
ldall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgan
g
All
o
w llvm
option alr
e
a
dy used in buildall
.
sh
script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgang
R
e
duce c
o
nso
l
e l
o
g o
u
tput from s
a
mple_r
e
s
traint tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Ir
r
gang
R
efin
e
usage of *job:tags* pa
r
ameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgan
g
Update
h
eader sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irr
g
a
n
g
Require C++
1
7 standard and ST
L
f
e
atur
e
s
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
A
p
pl
y
more
g
ranula
r
CT
e
st time-out policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Er
i
c Ir
r
gang
R
e
solve sta
t
ic analyzer war
n
ings
from google tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irrgang
Avoid tempo
r
ary
s
trings
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irr
g
ang
Note CUDA builds in job nam
e
s
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgan
g
Update bundl
e
d
pyb
i
nd
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
Only se
t
GMX_PYTH
O
N_PA
C
K
A
G
E=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
E
r
i
c Irr
g
ang
Use
C
Make
3
.
12+ facil
i
ties for de
t
ect
i
ng
Python
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
E
ric Ir
r
gang
C
h
ange default CMake
v
e
rsi
o
n t
o
3
.
13
.
0 for CI
im
a
ges
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrg
a
ng
Require
CMake
>
=
3
.
1
3
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
ric Irr
g
ang
Fix inval
i
d
g
i
tlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-04-09
M
.
E
r
ic
I
r
r
g
ang
Allow
u
se
f
ul
C
I t
o
r
u
n in forks
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
ric Ir
r
g
a
ng
Explicitly
set UTF-8 encoding for gmxapi CL
I
interact
i
on
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric
Irrgang
Prepare Python en
v
ironments f
o
r GitLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric I
r
rgang
I
m
p
r
o
v
e gmxapi Python
p
ackage
d
epe
n
den
c
y
re
s
olution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
ic
I
rrgang
Prune
change-management
.
rst and update link
s
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric Irrgang
M
o
de
r
nize some
Python
subprocess calls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Er
i
c Irr
g
ang
Avoid accidentally i
n
itia
l
izing pyenv in CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Prepare Python
environments f
o
r GitL
a
b CI pipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eri
c
Irrgang
Update scripts for al
l
of the requeste
d
pr
e
-commit
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrgang
Re
q
uire Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrgang
C
ompartmentalize
h
p
ccm build s
t
ages
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric
I
rr
g
ang
Be friendl
i
er w
.
r
.
t
.
linkchecker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrga
n
g
Mock hpccm impor
t
so i
n
frastructur
e
docs build easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Ir
r
gang
Extract logic
for w
h
en CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrgang
Nor
m
al
i
ze som
e
mo
r
e job
n
ames
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrg
a
ng
Simplify archive
.
gitlab
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
Rem
o
v
e redund
a
nt
jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrgang
F
ix duplicate variabl
e
s parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Add
required Inf
r
astructure for
Git
l
ab
merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irr
g
a
ng
N
orm
a
lize nam
i
ng fo
r
groma
c
s build/testing job
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove some u
n
neces
s
ary indirection in job definitio
n
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Consolidate
.
u
s
e-clangX CI
job mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
ang
Consolida
t
e
.
u
s
e-gccX CI job mix-i
n
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
rrgan
g
Adopt CI job
naming guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
N
ormalize
GitLab-CI *cache*
parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Irrgang
Merge environment suppo
r
t
into
g
lobal
.
gitla
b
-
ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgan
g
Move
.
bui
l
d-template
.
y
m
l defi
n
itions closer to point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
rrgang
Merge
*-test
-
t
emplate
.
yml into
testing-
m
a
t
rix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
a
ng
Merge
.
test-run
n
er-template
.
yml into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irr
g
ang
Me
r
ge
.
test-s
c
r
ipt
-
template
.
yml
i
nto testing-mat
r
ix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
r
e
gressiont
e
s
t-template
.
yml into archive c
o
nfig
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
r
rgang
C
onsol
i
date documentation temp
l
a
t
es
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
Reorganize release template
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
Re
m
ove
con
f
using and duplica
t
e
d v
a
riables assig
n
m
en
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irr
g
a
ng
Consolidate
g
lobal
m
ix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrga
n
g
[c
i
skip] Remove indi
r
e
c
tion f
o
r
defau
l
t
tags pa
r
ameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrg
a
ng
[ci skip] Re
o
r
ganize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
Irrgan
g
Document CI variab
l
e
and remo
v
e
u
nuse
d
templat
e
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
Irr
g
a
ng
Disable sphinx
.
ext
.
view
c
ode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
A
d
d stub Vari
a
bles doc
u
men
t
ation
t
o GitLab CI
d
oc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric
Irrgang
Remov
e
duplicated YAM
L
ke
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
Irrgang
Add document for c
o
ntainerization infras
t
ructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c
I
rrgang
Al
p
h
a
b
etize list
for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Reforma
t
arg
u
ments for
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrga
n
g
D
e
fi
n
e
an argparse pa
r
ent p
a
r
se
r
for con
t
ai
n
er
i
mage
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Bui
l
d
MPI in D
o
ckerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
E
r
ic
I
rrgang
Merge conf
.
py a
n
d conf-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric Irrgang
Distinguish Docke
r
images
for
d
i
f
f
e
rent rele
a
se requ
i
remen
t
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
Ir
r
gang
Fr
e
e
up Docker image tag
namesp
a
ce
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Remo
v
e du
p
lica
t
ed GitLab-CI jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Refor
m
a
t
.
gitl
a
b-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irr
g
ang
C
onsol
i
dat
e
l
og
i
c for whether to u
s
e Modul
a
rSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irr
g
a
n
g
Mana
g
e the list
o
f image tags in Docker build script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Manage the
lis
t
of ima
g
e tags in Doc
k
er bu
i
ld sc
r
ipt
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric
Irrgang
Resolve a Pyth
o
n linting error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrgang
Fix broken Python er
r
or check
.
commit
|
commitdiff
|
tree
next