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Use importlib_resources in Python 3.6 images.
2020-08-03
M
.
Eric Irrgan
g
Use
import
l
i
b
_resou
r
ces
i
n
Pyt
h
on 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic Ir
r
gang
Normaliz
e
docker ima
g
e names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
Fix
s
o
m
e
minor typeset
t
ing
i
s
s
ues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
i
c Irrgang
Improv
e
install d
o
cs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
Move so
u
rces
f
or
l
ibgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
R
e
move d
i
s
a
ble
d
test
for sup
e
rseded f
e
at
u
re
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irr
g
ang
Ignore a
ge
n
erated file
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrgang
Begin movin
g
inst
a
lled inte
r
face
t
o
`
a
pi/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
ric Irrgang
F
ix libgroma
c
s CMake targe
t
install sy
n
tax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eri
c
Irrgang
A
d
d
mi
s
sing ABI hea
d
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
I
m
pleme
n
t Simu
l
atorBuilder
.
add() for BoxDeforma
t
ionHan
d
le
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric
Irr
g
ang
U
se Topolo
g
yData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
i
c Irrgang
Use IonSwapping par
a
meter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use ReplicaExchange member i
n
stead of bu
i
ld()
argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Us
e
Simul
a
torModules parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
U
s
e Inter
a
ctiveMD
S
imulatorBuilder paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrg
a
ng
Use LegacyIn
p
ut
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irr
g
ang
Use Constraint
s
Param
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rg
a
ng
Move Profiling param
e
ter out of
s
i
mulator
b
uil
d
er
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Us
e
Sim
u
l
a
torEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Implement
r
emain
i
ng Simulator
B
uilder
.
a
d
d() me
t
hods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Int
e
rfac
e
for
r
emaining Simulat
o
r
B
u
i
l
der
.
add(
)
metho
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Simulato
r
B
u
ilder
.
ad
d
() f
o
r StopHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ri
c
Irrgan
g
Impleme
n
t SimulatorBuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric
I
rrg
a
n
g
Reformat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
ric Irrgang
Use Gromacs::gmx
t
arget to hint gmxapi test
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgan
g
Remove
workaround for g
c
c
bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrga
n
g
Improve pytest output handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
ric
Irrga
n
g
Co
m
par
t
me
n
talize job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
I
mprove usage of
Py
t
hon logging module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove un
u
s
ed (and broken
)
i
m
age from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
o
cke
r
image
builds: simplify doxygen ve
r
si
o
n handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
gang
D
o
cker
i
mage builds: move doxy
g
e
n
handl
i
ng to
a separ
a
te
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
Irr
g
ang
Exten
d
MPI
ensemble
testing for gmxap
i
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enabl
e
MPI en
s
emble testing f
o
r g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
E
ric Irrgang
M
ake sure i
m
ages have /
u
sr/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
i
c Irrgang
Upda
t
e docker image
b
ui
l
d
s
c
ripts for m
a
s
ter
bran
c
h
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make sure CI scr
i
pt
can call /bin/env python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Ir
r
gang
Minor clean
up to buildall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
A
l
low llvm
optio
n
already used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c
I
rrgang
Update
header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
R
e
qui
r
e C
+
+17 standard
a
nd STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Ir
r
gang
Apply more
gran
u
lar CT
e
st time-out po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric
I
r
rgang
Note CUDA builds
in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
r
ic
Irrgang
Only set GMX_PYTHON_PACKAG
E
=
ON where need
e
d
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric
Irrgang
Chang
e
default C
M
a
k
e
vers
i
o
n to 3
.
13
.
0 for CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
ric Irrgang
Require
C
Make >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
r
ic Irrgang
Exp
l
i
c
it
l
y set UTF-
8
encoding for
gmxapi CLI
intera
c
tion
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric
I
rrgang
A
v
oi
d
accid
e
nt
a
lly initializing
pyenv i
n
CI image
s
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrgang
Mock
h
pccm i
m
port so infra
s
tr
u
cture do
c
s build ea
s
ily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrgang
Extract log
i
c for wh
e
n
C
I
jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrg
a
ng
Normalize some more jo
b
names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric I
r
rga
n
g
S
i
mpl
i
f
y archive
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
R
e
m
o
ve redunda
n
t jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
ang
Fix duplicat
e
v
a
riables parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Irrgang
Add requir
e
d
Infrastructur
e
for Gitla
b
mer
g
es
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gan
g
Normalize n
a
m
i
ng for gro
m
acs
build/testi
n
g
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Remove som
e
unn
e
c
essary indirection in job
definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Consolidat
e
.
use-
c
langX CI job m
i
x
-
i
n
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Consolidate
.
use-gccX CI job mix-
i
n
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrgang
A
dopt
CI job n
a
ming guid
e
lines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c
I
rrgang
Normalize GitLab
-
CI *c
a
che
*
parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge en
v
ironment support
int
o
global
.
gitlab
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
i
c Irrgang
Move
.
build-tem
p
l
a
t
e
.
yml defin
i
ti
o
n
s closer t
o
point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge *-test-templat
e
.
yml into testing-matrix
.
gi
t
lab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
r
r
g
ang
Merge
.
test-
r
unner-templa
t
e
.
yml into
testi
n
g-
m
a
t
rix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irr
g
a
n
g
Merge
.
test
-
s
cript-
t
emplate
.
yml into
testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Merge
.
regres
s
iontest-tem
p
late
.
ym
l
into archiv
e
config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c
Irrg
a
ng
C
o
nsol
i
date
documen
t
a
t
ion temp
l
a
te
s
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgan
g
Reorganize
release
t
emplates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrg
a
n
g
Remo
v
e con
f
using a
n
d
duplicated va
r
iables assignmen
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
ri
c
I
rrg
a
n
g
Cons
o
l
i
date global mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci
s
kip] Remove in
d
irection for defau
l
t tags parameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Er
i
c Irrgang
[ci skip]
R
eorganize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric
I
rrgang
Document CI v
a
ri
a
b
le and rem
o
ve unused
temp
l
ate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Disable sphinx
.
ext
.
view
c
ode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
A
d
d stub Vari
a
bles
d
o
c
umentation t
o
GitLab CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
E
r
ic Irrga
n
g
Remove
d
uplicated YAML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
i
c
I
r
rgang
A
d
d document for containeri
z
ation
i
nfrastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c Irrgang
Alp
h
abetize list for reada
b
ility
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Reformat argument
s
for
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
i
c
Irrg
a
ng
Define
a
n
a
rg
p
arse paren
t
parse
r
for container ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrga
n
g
Build MPI in Dockerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Mer
g
e c
o
n
f
.
py and conf-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
E
r
ic I
r
rgang
Distinguish Doc
k
er images for dif
f
ere
n
t release requirements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
i
c Irrgang
Fre
e
u
p D
o
cker image t
a
g namesp
a
ce
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
I
rrgang
R
e
m
ove
du
p
l
i
cated GitLab-CI
jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Ir
r
gang
R
eformat
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
I
rrgan
g
Consolidate logic
for whether
to use Modu
l
ar
S
i
mulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irr
g
ang
Manage the li
s
t of image tags
in Docker bu
i
ld script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Man
a
ge t
h
e list of
image tags
i
n Docker b
u
i
l
d s
c
ript
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrga
n
g
R
esolve
a Python l
i
nting error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric
Irrgang
Fix broke
n
P
yth
o
n error check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric
I
r
rgang
Remove cruft and reso
l
ve deprecation warnin
g
s
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
rgang
Fi
x
doc
s
tring bugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix sphinx-build option typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irrgan
g
L
e
t
commandline_
o
pe
r
ation accept
s
tdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
r
g
ang
Make gmxapi
.
version
.
h
a
s_feature warning m
o
re useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irrga
n
g
Use subp
r
ocess
.
ru
n
instead of
s
ub
p
ro
c
ess
.
check
commit
|
commitdiff
|
tree
next