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One argument per line for long function signatures.
2020-12-02
M
.
Er
i
c
Irrgang
One argum
e
nt per
l
ine for long fu
n
ction signa
t
u
r
e
s
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Ir
r
g
a
ng
Look fo
r
the various
p
o
s
s
i
ble
n
a
mes of the gromacs
.
.
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
E
r
i
c
Irrgang
gm
x
ap
i
versioning updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
E
r
ic Irrgang
Be
m
ore exp
l
icit a
b
o
u
t
bui
l
d-tree-only dependenci
e
s
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric
Irrg
a
ng
Help clients f
i
n
d
dep
e
nden
c
ies o
f
importe
d
CM
a
ke
t
argets
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgang
Remove an unnecessary trans
i
t
i
ve dependency of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrgang
Normali
z
e FindMPI h
i
nts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
r
i
c
I
r
r
gang
Clari
f
y
behavior o
f
LegacyMdrun
O
p
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
E
ric Ir
r
gan
g
Tell gm
x
api to look for
M
PI, when appropriate
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgan
g
U
s
e up
d
ated C
I
pipeli
n
e rules for Python pa
c
kage t
e
sts
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric I
r
rgan
g
Update g
m
xapi version
d
e
tai
l
s
.
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric
I
rrg
a
ng
D
on't over
r
ide user
p
r
ovided CMAKE_OSX_DEP
L
O
YME
N
T_TA
R
GET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irr
g
ang
Handle gmxapi
t
mpi
p
a
r
ame
t
ers bet
t
er
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
r
i
c Irrgang
Le
t
gm
x
api
i
n
stallation
r
ecord the G
R
OMACS li
b
ra
r
y
.
.
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Ir
r
gang
Restrict
g
mxap
i
py
t
est tests to `-nt
2
`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eri
c
I
rrga
n
g
Specif
y
OMP_N
U
M
_THREADS
for Pyhon CI scri
p
ts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgan
g
Clarifica
t
ions for ResourceA
s
signment interface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
ng
Support ResourceAssignment i
n
terface fo
r
tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
a
ng
Al
l
ow MPI-enable
d
clie
n
ts to
p
r
o
vide the li
b
ra
r
y communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrg
a
ng
Use Mpi
C
ontextMan
a
g
e
r to provide MPI communica
t
or
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
Re
l
ocat
e
M
p
iContex
t
Manager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
I
nte
r
f
a
ce updates allowing c
l
ient to
provide MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrg
a
ng
Improve
n
a
ming and d
o
cs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irr
g
ang
Document
a Mdrunn
e
r::
B
uil
d
erImple
m
enta
t
i
on memb
e
r
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrg
a
ng
R
emove outdate
d
workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eri
c
Irrgan
g
Refine the CMakeLists
.
t
xt
f
or MPI
gmxapi t
e
sts
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Irr
g
ang
C
l
arif
y
t_in
p
u
t
r
e
c
alloc
a
tion log
i
c in r
u
nner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Acc
e
p
t P
y
th
o
n vers
i
ons hi
g
her than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
R
emove conditional for CM
a
ke <
3
.
1
2
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irr
g
ang
Allo
w
more granularity for
public interfaces i
n
build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Prevent faile
d
c
o
mma
n
dline
_
operat
i
on from pub
l
ishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrga
n
g
Minor additions to gmxapi insta
l
l
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c I
r
rgang
Use importli
b
_resources in Python
3
.
6 ima
g
es
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Normalize d
o
c
ker imag
e
n
a
m
e
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric I
r
rg
a
n
g
F
ix some minor
t
ype
s
etting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c Irrgang
Imp
r
o
v
e install
d
o
c
s links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
M
o
ve
s
o
urces
fo
r
libgmxa
p
i
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic
Irrgang
Remove disabled test for supers
e
d
e
d
f
eature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ignore a generated file
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
ang
Begin mo
v
ing insta
l
l
ed int
e
rf
a
ce to
`ap
i
/`
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
r
ic Irr
g
ang
Fix libgromacs CM
a
ke t
a
rg
e
t in
s
tall syntax
.
commit
|
commitdiff
|
tree
2020-06-27
M
.
E
ric
I
rr
g
ang
Add
miss
i
ng ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Im
p
l
emen
t
SimulatorBuil
d
er
.
a
d
d
() fo
r
BoxDe
f
or
m
ationHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgan
g
Use TopologyDa
t
a
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use
IonSwapp
i
ng parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
r
rgang
Us
e
CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Ir
r
gang
Use ReplicaEx
c
hange member
i
nstead of b
u
ild() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgan
g
Use S
i
mul
a
torM
o
dul
e
s pa
r
ameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
Use Inte
r
a
c
tiveMD Simu
l
atorBuild
e
r
parame
t
er
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrg
a
ng
Use
L
egacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrg
a
n
g
Use Constrain
t
sParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irr
g
a
n
g
Move
Pr
o
fi
l
ing parameter
o
u
t
of
simulatorbui
l
de
r
.
bu
i
ld()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Use SimulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Imple
m
e
nt rem
a
ining
S
imulatorBuilder
.
add() me
t
hods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Inter
f
ace fo
r
remaining Simul
a
torBuilder
.
add() meth
o
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
S
i
m
ulator
B
uilder
.
a
d
d
(
)
for St
o
p
H
a
ndler
B
uilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
I
m
p
lement Sim
u
lato
r
B
uilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic
I
rrgang
Reformat pairs
.
cp
p
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic Irrgang
Use
G
r
oma
c
s:
:
gmx target
t
o hint gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgang
R
emove workaround
f
or gcc bug 58
2
65
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgan
g
Improve
p
ytest output hand
l
in
g
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric I
r
rgang
C
ompartmentali
z
e job rul
e
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Improve
u
sage of Pytho
n
lo
g
gi
n
g module
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric I
r
rgang
Remove unused (and b
r
oken) i
m
age from Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Er
i
c
I
rrg
a
ng
Docker
ima
g
e buil
d
s: simplify doxyg
e
n v
e
rsion ha
n
dli
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image builds: move
d
oxygen
hand
l
ing to
a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic I
r
rg
a
ng
Extend MPI
e
ns
e
mble te
s
ting for
g
m
x
api
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
Irrga
n
g
E
na
b
le MPI e
n
sembl
e
testing for gmxa
p
i
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgang
Enable MPI
ens
e
mble
testing for g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric Irrgang
Nor
m
alize
gmxapi re
l
a
t
ed release-
2
020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Ir
r
gang
M
a
ke s
u
re images
h
ave /usr/bin/pyth
o
n
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irr
g
ang
Update docker image build scripts
for mast
e
r
branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eri
c
Irrg
a
ng
M
a
ke sure CI
s
cript can cal
l
/
b
in/env p
y
th
o
n
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrga
n
g
M
i
n
o
r
clean u
p
to build
a
ll
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
E
ric Irrgang
Allow llvm op
t
ion a
l
rea
d
y used in
b
uild
a
l
l
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Updat
e
hea
d
er sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric I
r
rgang
R
equire
C
++17
stand
a
r
d
and ST
L
f
eatures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgang
Ap
p
ly more gr
a
nular CTes
t
t
ime-o
u
t polic
y
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric I
r
rg
a
n
g
Note CUDA build
s
in j
o
b names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eri
c
Irrga
n
g
O
n
ly set
GMX_P
Y
THON_
P
ACK
A
GE=ON wher
e
n
e
e
ded
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eric Ir
r
gang
Change default
C
Make
ver
s
ion
to 3
.
13
.
0
fo
r
CI
im
a
ges
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irr
g
ang
Require CMake >=3
.
1
3
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Irrga
n
g
E
x
plic
i
t
l
y set UTF
-
8 en
c
odin
g
for gmxapi CLI interactio
n
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric
Irrgang
A
v
o
id accidentally
i
ni
t
i
a
l
iz
i
ng
pyenv in CI imag
e
s
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrgang
Mock hpccm
i
mport
so infrastructure docs
b
u
ild
easi
l
y
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Irrgang
Extrac
t
logic for when CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Normalize some mor
e
j
ob
na
m
e
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrgan
g
S
i
mplify archive
.
git
l
a
b-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
Remo
v
e re
d
undan
t
j
o
bs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrgang
Fix duplicate
v
ari
a
bl
e
s p
a
r
ameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irr
g
ang
Add required Infrastr
u
ctu
r
e
f
o
r
G
i
tl
a
b merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irr
g
ang
Normal
i
z
e
na
m
ing for gromacs build/te
s
tin
g
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgang
Re
m
ove some u
n
neces
s
a
ry indirecti
o
n in job definit
i
ons
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
ga
n
g
Consolida
t
e
.
use-clangX CI job m
i
x-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
Co
n
solidate
.
use-gccX CI job
mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
g
a
n
g
Ado
p
t
CI j
o
b naming guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
rrgang
Normalize GitLab-CI *cache* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Me
r
ge environm
e
n
t
s
up
p
ort into global
.
git
l
ab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Move
.
build-templat
e
.
yml d
e
f
i
nitio
n
s closer t
o
point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
n
g
M
e
rge
*-tes
t
-t
e
mplate
.
yml into testing-matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
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