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Use CenterOfMassPulling
2020-06-26
M
.
E
r
i
c
I
rrg
a
ng
Use Cen
t
erOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
r
g
a
n
g
U
s
e ReplicaExchang
e
membe
r
inst
e
a
d
of build() argumen
t
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
n
g
U
se
S
imulatorModules pa
r
ameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
Use
I
nteracti
v
e
M
D SimulatorBuilder
paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use Legac
y
Input
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use C
o
nstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
M
o
ve
Profiling parameter out of si
m
ulatorbuil
d
e
r
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
r
g
a
ng
U
se Simulator
E
nv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remainin
g
Simula
t
orBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Interf
a
ce fo
r
re
m
aining Simulat
o
rBuil
d
e
r
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
SimulatorBui
l
der
.
add
(
) for StopHandl
e
rBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
I
m
ple
m
e
nt Simul
a
t
o
rBuilder
.
buil
d
()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Ref
o
rma
t
pairs
.
c
p
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric
I
r
rgang
Use Gromacs::g
m
x
t
a
r
g
et to
h
int gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
Rem
o
ve workaround for gcc bug 5826
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgang
Improve p
y
test output
h
a
n
dli
n
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric I
r
r
g
a
n
g
Compa
r
t
m
entalize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
I
rrgang
Improve usage of Pyt
h
on logging module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric I
r
rgan
g
Remove unused
(
and broken) image from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrga
n
g
Docker i
m
age b
u
ilds:
simplify doxygen version handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
ic Irrga
n
g
Docker im
a
ge builds:
move
d
o
x
ygen hand
l
ing to
a sepa
r
ate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
Irrgang
E
xtend MP
I
e
n
s
emble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic Irrgan
g
Enable MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric
Irrgang
Make su
r
e im
a
g
es h
a
ve /usr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
rrg
a
ng
Update doc
k
er image
bui
l
d scripts for master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Ir
r
gang
Make sure
CI
sc
r
ipt can call /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Ir
r
g
an
g
Mino
r
clean
u
p to b
u
ildall
.
s
h
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgan
g
Allo
w
ll
v
m
o
p
t
ion alrea
d
y us
e
d in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrg
a
ng
U
p
date header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric
Irrga
n
g
Require C++17
s
tandard and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric
I
rrgang
A
pply more granular
CTes
t
time-out policy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric
I
rrgang
No
t
e
CUD
A
builds in
j
ob
n
ames
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irr
g
ang
O
n
ly
set GMX_
P
YTHON_PACKAGE
=
ON where needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Irrgang
Cha
n
ge default C
M
ake v
e
rsio
n
to 3
.
1
3
.
0 for CI ima
g
es
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgan
g
Require CMake >=
3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
r
i
c Ir
r
ga
n
g
Explicitly set UT
F
-
8
encodi
n
g
f
or
g
mxap
i
CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric I
r
rgan
g
Avo
i
d accidental
l
y
ini
t
ializing pyenv i
n
CI im
a
ges
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Er
i
c Irrgang
Mock
hpccm imp
o
rt so infrastructure docs build easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Ex
t
ract logic
for when CI jobs
e
xe
c
ute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
I
r
r
gang
Normalize some more
j
ob names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Irrgang
Si
m
pl
i
fy
a
rchive
.
gitlab-
c
i
.
ym
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove redundant jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Fix dupl
i
cate
va
r
iables paramete
r
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Add r
e
quired Infrastruct
u
re for Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Norma
l
ize naming
f
or
g
romacs build/tes
t
ing jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c Irrgang
Remove so
m
e
u
nnecessary indir
e
c
tion in j
o
b def
i
n
itions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rrgang
C
o
n
sol
i
date
.
use-clang
X
CI job
m
ix-
i
n
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Consoli
d
ate
.
use-
g
ccX
C
I
j
ob mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
Adopt CI job naming gui
d
elines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
I
r
r
gan
g
Normali
z
e G
i
tLab-
C
I *
c
ache* param
e
ter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrg
a
ng
Me
r
ge environm
e
nt support into gl
o
bal
.
gitla
b
-c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rg
a
ng
M
ove
.
build-templa
t
e
.
yml
def
i
niti
o
ns closer to point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgan
g
Merge
*-test
-
template
.
yml
i
nto test
i
ng-matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
gang
M
erg
e
.
te
s
t-runne
r
-
t
emplate
.
y
m
l into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic
Irr
g
ang
M
e
rge
.
test-script-te
m
plat
e
.
yml into testing-m
a
t
r
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Merge
.
regressiontes
t
-t
e
mplate
.
yml i
n
to a
r
chive config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Ir
r
gang
Consolidate do
c
umentation tem
p
late
s
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Reorgan
i
ze release templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
I
r
r
gang
Remove confusi
n
g and dupli
c
ated variables a
s
si
g
nmen
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrg
a
ng
Cons
o
lidate global mi
x
-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
r
ic
I
rrg
a
ng
[
ci skip]
Remove indirection
f
or default tags parame
t
er
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
I
rr
g
ang
[ci skip] Reorga
n
ize
.
g
i
tlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Document CI variable and remove unused
t
emplate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eri
c
Irr
g
ang
Disable sph
i
n
x
.
e
x
t
.
viewcode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Er
i
c Irrgang
Add stub Varia
b
l
es doc
u
men
t
atio
n
t
o
GitLab CI
doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Er
i
c Irrg
a
n
g
Remove duplicated YAML ke
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irr
g
an
g
Ad
d
d
ocument for containeri
z
ation infrastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Alp
h
abetize list
for read
a
b
i
lity
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
Irr
g
ang
Re
f
ormat argume
n
ts for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
D
e
fin
e
an argparse pa
r
ent parser for container image
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic I
r
rgang
Build M
P
I in Dockerf
i
l
e
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Me
r
ge conf
.
py and conf-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Er
i
c
I
r
rgang
Distinguish Docker images for different rele
a
se requ
i
rements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irr
g
ang
Free up Docker image t
a
g
n
a
me
s
pace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
ic I
r
rg
a
ng
R
e
move du
p
lic
a
t
e
d Gi
t
Lab
-
CI job
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Ir
r
g
ang
Reformat
.
g
i
tlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
I
rrgang
Consol
i
date logic for whether to u
s
e
ModularSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric
Ir
r
g
ang
Mana
g
e t
h
e
l
ist of image tags in
D
ocker b
u
ild script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eri
c
I
r
r
g
ang
Manage the list of
ima
g
e
tags in Docker bu
i
ld script
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric I
r
rgang
Resolve a Python l
i
ntin
g
error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrgan
g
Fix broken Python
e
rror check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
E
r
ic Irrgang
Remove
cruft and resolve depreca
t
ion
w
arnings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix
docstring bug
s
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric
Irrgang
F
i
x
s
phinx-build
o
ption t
y
po
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eri
c
Irrgang
Let commandlin
e
_operati
o
n accept s
t
din
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Make gmxapi
.
versio
n
.
h
as_fea
t
ure
warni
n
g
mo
r
e useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
r
gang
Use subprocess
.
r
u
n
ins
t
ead
o
f subpro
c
ess
.
c
heck
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c Irrgang
Improve
g
mxa
p
i
.
o
p
e
r
ation
e
rror
handling
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Ir
r
gang
C
la
r
ify annotation about GitLab
C
I
Docke
r
i
mages
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric
I
rrg
a
n
g
Simplify GitLab CI
D
ockerfil
e
s
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Irrgang
E
stablish stubs for
doc
u
menting
Git
L
a
b
configuration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric Irr
g
ang
Refo
r
m
a
t
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric
Irrg
a
ng
Use enum for gmxapi
.
testsupport fix
t
ur
e
opti
o
n
s
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
E
ric Irrgang
Fu
r
th
e
r consolidate gmxapi
.
test
s
uppor
t
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irr
g
ang
Update gmxapi Pyt
h
on package
versi
o
n and
v
ersioni
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric
Irr
g
ang
Remove s
t
ray "
t
o d
o
"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgang
Re
m
ov
e
transitional l
i
n
ks for onl
i
ne gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
Add Flake8 linting to gmxapi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
Use `todo` Sphin
x
directive more
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eri
c
Irrgang
Add tracking for a docume
n
te
d
actio
n
i
tem
.
commit
|
commitdiff
|
tree
next