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Wrong logic was used
2020-09-18
M
.
E
ric Irrgang
Improve naming and doc
s
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric
Irr
g
a
n
g
Document a Mdru
n
ner::Build
e
rImplementat
i
on m
e
m
ber
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric
I
rrgang
Re
m
o
v
e outdated
wo
r
karound
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
r
ic Irr
g
ang
C
r
e
ate and use S
i
mu
l
ationInput
m
o
d
ule
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric
Irrgang
Ref
i
ne
t
h
e CM
a
keLists
.
txt for
M
PI gmxapi tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eri
c
Irrgang
Ex
p
licitly include STL h
e
aders
u
sed
i
n
t
est
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
Re
p
lace fi
l
e
name-
b
a
s
e
d
initi
a
l
i
zation functi
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
ri
c
Irrgang
C
l
arify t_inputrec
allocat
i
on
l
ogic in
runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irrg
a
ng
Use
a
heap
o
bject for inputrec i
n
gmx::M
d
runner:
:
mdrun
n
e
r()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irr
g
a
n
g
Accep
t
Python v
e
rsions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Re
m
ov
e
conditional for CMake < 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
E
r
ic Ir
r
gan
g
Al
l
ow mo
r
e granularity for public int
e
rfaces
in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
P
r
e
v
e
nt
fail
e
d commandline_operation f
r
om publi
s
hing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Ir
r
gang
Minor additions to gmxa
p
i install
.
rs
t
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Use importlib
_
r
e
sources in Py
t
h
on 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c
Irrgang
Normalize d
o
cker
i
ma
g
e
n
ames
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
r
ic
I
rrg
a
ng
Fix s
o
me minor typesetting iss
u
es
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrga
n
g
Imp
r
ove inst
a
l
l docs lin
k
s
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
Irr
g
ang
Move sourc
e
s for libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irrgan
g
Remove disabled te
s
t for su
p
erseded feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore a gener
a
ted
f
ile
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
E
ric
I
rrgang
Use GMXAPI CMake option guard for gmxapi targ
e
t d
e
claration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric
Irrgang
B
egin
moving insta
l
led interface to `ap
i
/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
F
i
x
libgromacs CMake
t
arget install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Er
i
c Irrga
n
g
F
i
x libgroma
c
s CMake t
a
rget install
s
yntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric
Irrgang
C
lean up simulatorbui
l
der
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric I
r
rgan
g
Ad
d
miss
i
ng ABI he
a
der
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Ir
r
gan
g
Im
p
lement S
i
mul
a
to
r
B
uilder
.
add() for
BoxDeformat
i
onHandl
e
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Use T
o
pologyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrga
n
g
Use Ion
S
wap
p
ing parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Use Cen
t
e
r
O
fMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
U
se
ReplicaExcha
n
ge member instead o
f
build() argu
m
ent
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Irrga
n
g
U
se Sim
u
latorMod
u
l
es parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use
InteractiveMD
SimulatorBu
i
ld
e
r parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
Lega
c
yInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Use Constraints
P
aram
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
M
o
ve Profilin
g
parameter out
of s
i
mulatorbuilder
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
rgang
Use Si
m
u
latorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Implement remaining
SimulatorBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic I
r
rgang
Interface f
o
r re
m
aining
S
imulatorBuilder
.
add() methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Simul
a
torB
u
ilder
.
add() f
o
r StopHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
rgang
Implem
e
n
t
SimulatorBuil
d
er
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Ir
r
gan
g
R
eformat pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Gromacs::gm
x
targ
e
t to hin
t
gmxapi tes
t
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Er
i
c Irrgang
Remove workaround for gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrg
a
ng
Impr
o
v
e
pyte
s
t
o
u
tput
h
and
l
ing
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Com
p
artmentali
z
e
j
ob rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eri
c
Irr
g
ang
Impr
o
ve
u
sage
o
f Python
l
ogging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Er
i
c I
r
rgang
H
a
ndle
a
rbi
t
ra
r
y
doxygen ver
s
ions
i
n Docker image build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Ir
r
gang
Remove unused (and br
o
ken) image from Docker ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Er
i
c
Irrgang
D
ocker image builds: si
m
plify dox
y
g
e
n vers
i
on
handling
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
D
o
cker image builds: move doxygen handling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgan
g
E
xtend MPI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
Enable
MPI ensemble testing for
gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
i
c Irrg
a
ng
Normalize
gmxapi related r
e
lease-2020
j
ob
l
ogic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrga
n
g
Redu
c
e
c
o
n
sole log output fro
m
sample
_
restrai
n
t tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable
M
PI ensemble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
r
ic
I
rrgang
Normalize gmxapi r
e
lated release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric I
r
rgang
Make sur
e
imag
e
s have /usr/bin
/
p
y
tho
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
r
ic Irrgang
Update docker i
m
a
ge build
script
s
for master
b
ra
n
ch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrg
a
ng
Make sure
C
I
s
cri
p
t
c
an
c
all /
b
in/e
n
v python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Minor clean up
to buildal
l
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
rgang
Allow llv
m
option already used in buildall
.
sh
script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrg
a
ng
Reduce console log output from s
a
m
p
le_restr
a
int tests
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eri
c
Irrg
a
ng
R
e
fine usage
o
f
*
j
ob:ta
g
s* parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Updat
e
header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Req
u
ire C++17
s
tandard and STL features
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Apply more
g
r
anular CTest time-out po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
ric Irrgang
Resolv
e
static an
a
lyzer
w
arnings fro
m
g
oogle t
e
sts
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
r
ic Ir
r
gang
Avoid temporary strings
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrgang
N
o
te CUDA builds i
n
j
o
b
names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
U
p
d
ate bundled pybind
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric
I
rrga
n
g
Only s
e
t
G
MX
_
PYTHON
_
P
A
CKAGE
=
ON where
needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Er
i
c Irrgan
g
Use CMake 3
.
12+ facilities
f
o
r detecting
P
ython
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric
I
rrgang
Ch
a
nge
d
e
fau
l
t CMake ver
s
io
n
t
o
3
.
13
.
0 for CI imag
e
s
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
r
ic Irrgang
R
equire
C
Ma
k
e >
=
3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrgang
Fix invalid gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-04-09
M
.
Eric Irrgan
g
All
o
w
useful CI to run in f
o
r
ks
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
r
ic Irrgang
E
x
plicitly set UTF-8 en
c
o
d
i
ng for gmxapi CLI i
n
teracti
o
n
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
Eric Irrgang
Prep
a
re Pyt
h
on environments fo
r
GitLab CI p
i
pel
i
ne
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric
Irrga
n
g
Improve gmxapi Python packag
e
depen
d
ency re
s
o
l
ut
i
o
n
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irr
g
ang
Prune
change-management
.
rst a
n
d
update l
i
nks
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric
Irrgang
Modernize some Python
s
ubprocess
call
s
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric
Irrgang
A
void acci
d
e
ntally initi
a
lizin
g
p
yenv i
n
CI images
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Pr
e
pa
r
e Py
t
hon environments for GitLab
C
I
pipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric I
r
r
g
ang
Update scripts for all of the requested
p
re-com
m
i
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric
Irrg
a
n
g
Requir
e
Python
3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irr
g
ang
Com
p
artm
e
nta
l
ize hp
c
cm bu
i
ld sta
g
es
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrg
a
n
g
Be frien
d
lier w
.
r
.
t
.
lin
k
checker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrg
a
ng
Moc
k
hpc
c
m
import
so infrastruc
t
ure docs build e
a
sily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgang
Extrac
t
logic
for when CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
No
r
m
a
l
i
ze
s
ome
m
ore
job nam
e
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
S
i
mplify archi
v
e
.
gitlab-ci
.
ym
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Remove redundant jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Fix duplicate variables parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrgang
Add required Infra
s
truct
u
re for Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
r
r
gang
N
o
rmalize naming for gromac
s
build/test
i
n
g jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgang
Remove some
u
n
necessary indi
r
ection in job definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgang
Consolidate
.
use-
c
langX CI
j
ob mix-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgan
g
Conso
l
i
d
ate
.
u
se-
g
ccX CI j
o
b mi
x
-in
.
commit
|
commitdiff
|
tree
next