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Update instructions in containers.rst
2020-12-04
M
.
E
r
ic Irrgang
Add CI j
o
bs for gmxapi 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric Irrgang
U
pdat
e
r
ules for release-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
ric
I
rrgang
Se
p
arate job scri
p
t fil
e
s for gmxapi package versi
o
ns
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
Eric Irrgang
Imp
r
ove gmxa
p
i C++ tes
t
c
overage f
o
r f
a
i
l
ed mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
E
r
i
c
Irrgang
One argument per line for long function si
g
natures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Irrg
a
n
g
Look for t
h
e variou
s
possib
l
e nam
e
s of the gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Er
i
c I
r
rgang
C
r
e
ate C
M
ake targ
e
ts
f
o
r each of the modules
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric I
r
r
g
ang
Replace gmxapi `erroroutput` with `stderr
`
and `
s
tdout`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric Ir
r
g
ang
Separat
e
the
testutils m
o
d
u
le
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
E
r
ic Irrgang
gmxapi version
i
ng updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric
I
r
r
gan
g
Be
more ex
p
licit
about build-tree
-
only dependencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eri
c
Irrgan
g
Provide a catch-all target for librar
y
modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Er
i
c Irrgang
Provide common library hea
d
e
rs t
h
rou
g
h ne
w
CMake target
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
E
r
ic Irrgang
H
e
lp clients find dependen
c
ies of imported CMa
k
e targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric Irrgang
E
s
tabl
i
sh `ap
i
/
`
as
t
he
h
ome f
o
r ins
t
all
e
d
h
eaders
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgang
R
e
move an unnecessa
r
y transiti
v
e dependency of imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
rga
n
g
U
se the correct CI script for sa
m
pl
e
_restra
i
nt jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
ric Irrgang
Normalize Find
M
PI
h
i
nts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irr
g
a
n
g
Cla
r
ify behavior of LegacyMdrun
O
ption
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
r
g
an
g
Update i
m
age n
a
me
s
in job definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
E
r
ic
I
rrgang
Tell
gmxapi to look for M
P
I
,
w
hen appropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Er
i
c Irrgang
Update
D
ocker image b
u
ild scripts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgang
Use updated C
I
p
i
peline rules for
P
y
thon package tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
E
ric
Irrg
a
ng
U
p
date gmxapi version detai
l
s
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
E
r
ic
I
r
r
g
a
n
g
Clarify the G
M
X_BUILD_MD
R
UN_
O
N
L
Y full testing instruc
t
ions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
E
ric Ir
r
g
a
n
g
Improve g
m
xPythonDiscovery
.
c
ma
k
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irr
g
ang
Do
n
't override user
p
rovided CMAKE_OSX_DEPL
O
YMENT_TARGET
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Er
i
c Irrgang
Handl
e
g
mxap
i
tmpi par
a
met
e
r
s bett
e
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
ric Irrgang
L
e
t
gmxa
p
i
in
s
ta
l
lation record the GROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
E
ric Irrgang
Use updated imag
e
s for Py
t
h
o
n
C
I
jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
E
ric Ir
r
ga
n
g
Restrict gmxapi
pytest tests to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irrga
n
g
Sp
e
cify
O
MP_NUM_
T
HRE
A
DS for P
y
hon CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irr
g
ang
Clar
i
fications f
o
r Res
o
urceAssi
g
nm
e
nt interf
a
ce
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
Irrgang
Supp
o
rt
Re
s
ourceAssig
n
ment interfac
e
for tMPI li
b
r
ary
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
A
l
low
M
PI-ena
b
l
ed clients to p
r
o
vide
t
he li
b
r
a
ry communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
Use M
p
iC
o
nt
e
xt
M
anager to provide M
P
I comm
u
nic
a
tor
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
rrgang
Relocat
e
MpiContextManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
rga
n
g
Inte
r
fac
e
updates allowing
clien
t
to prov
i
de MPI
co
m
municator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irrgang
Impr
o
ve naming
a
nd
d
o
c
s
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric Irr
g
a
n
g
D
ocument
a
Mdrunner::Bu
i
lde
r
I
mp
l
ementation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric
Irrgang
R
emo
v
e
o
utdated worka
r
ound
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Ir
r
g
ang
Create and use
Simulati
o
nI
n
put modu
l
e
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Refine the C
M
ake
L
is
t
s
.
t
x
t for
M
P
I
gmxapi te
s
ts
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrgang
Exp
l
icitl
y
include STL headers used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
E
r
ic Irrgang
Replace fi
l
ena
m
e-based in
i
tializ
a
tion functi
o
ns
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c
Ir
r
gan
g
Clarify
t
_inp
u
trec allocation logic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eri
c
I
r
rga
n
g
Use a heap obj
e
ct for
i
nputre
c
in gmx
:
:
Mdrunner::mdrunner()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eri
c
Irrgan
g
Accept Python versions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c Irrgang
R
emo
v
e conditional for CMake <
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
E
r
ic I
r
rgang
Allow more
g
ra
n
ula
r
ity for publ
i
c interfaces in bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eri
c
I
r
rgang
P
re
v
en
t
failed com
m
andline
_
oper
a
tio
n
from publishing
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
E
ric Irrga
n
g
Mino
r
a
dd
i
tions
t
o gmxapi
i
nstal
l
.
rs
t
commit
|
commitdiff
|
tree
2020-08-03
M
.
Er
i
c Irrg
a
ng
Use impo
r
tli
b
_resources
i
n Py
t
h
o
n
3
.
6 i
m
age
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Normalize docker image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrga
n
g
Fix
some mi
n
or typese
t
t
i
ng iss
u
es
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
Irrgan
g
Improve inst
a
l
l
docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eri
c
Irrga
n
g
Move sources for li
b
g
m
xap
i
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgan
g
R
emove dis
a
b
l
ed
t
est fo
r
su
p
erseded
feature
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Er
i
c Irrgang
Ig
n
ore a generated file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irr
g
a
n
g
Use GMXA
P
I CMa
k
e o
p
tion guard for gmxapi target dec
l
a
ration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irr
g
a
n
g
Begin movin
g
installed inter
f
ace to `
a
pi/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric
I
r
r
ga
n
g
Fix
libgrom
a
cs CMake target install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
ric Irr
g
a
n
g
F
ix
l
ibgrom
a
c
s
CMa
k
e targ
e
t inst
a
ll s
y
ntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
E
r
ic
I
rrgang
Clean up simulatorbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrg
a
ng
Add
m
i
s
sing ABI head
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Implement Sim
u
l
atorBui
l
d
e
r
.
add() for BoxDeformation
H
a
ndle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Ir
r
gang
Use Topol
o
g
yData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Ir
r
g
ang
Use Io
n
Swa
p
ping par
a
meter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
Use
C
enterO
f
MassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use ReplicaExchange me
m
ber instead of buil
d
()
a
rgument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric
Irrgang
Use Simulato
r
Modules paramet
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use Int
e
ra
c
t
i
v
e
MD SimulatorBu
i
lde
r
parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use
LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use ConstraintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Move Profil
i
ng param
e
ter out of
s
imulator
b
uilder
.
bu
i
ld()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
g
a
n
g
Use Simulat
o
r
E
nv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
I
mple
m
e
n
t rema
i
ning SimulatorBuilder
.
a
d
d(
)
methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Interface for re
m
aini
n
g SimulatorBuilder
.
add
(
)
me
t
hod
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
ng
S
i
mu
l
atorBuilder
.
add() for Sto
p
HandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
I
m
p
lement Sim
u
lator
B
uilder
.
build()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Refor
m
a
t pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use
G
romacs::gmx t
a
rget
to hint gmxapi te
s
t
s
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irrgan
g
Remove wo
r
karound for g
c
c bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric
I
r
rgang
I
m
p
r
o
ve pytest output han
d
l
i
ng
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric I
r
rgang
Co
m
p
artm
e
n
t
a
l
i
ze job rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Er
i
c Irrga
n
g
I
mprove usage of
Python logging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Ir
r
gang
Handle arbitrary doxyg
e
n
versions
i
n Dock
e
r
image
b
uild
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irrga
n
g
R
e
move un
u
s
e
d
(
and
b
roke
n
) image fr
o
m Docker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
r
i
c
I
rrgang
Docker image builds: simplify
d
o
x
ygen
v
er
s
io
n
handlin
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eri
c
Irrga
n
g
Docker image
b
uilds: move doxyg
e
n handling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
E
r
ic Irrgang
Extend MPI ense
m
ble test
i
ng for gmxap
i
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric
I
rrga
n
g
Enable
M
PI ensemble testing
f
or gmx
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrg
a
ng
Normali
z
e gmxapi r
e
l
a
ted release
-
2
0
20
job
logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric I
r
rgang
Reduce c
o
nsole lo
g
outp
u
t
f
rom sample_restraint tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
E
ric Irrgang
Enable MPI ensemble testin
g
for gm
x
api
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric
Irrgang
Normalize gmxapi related r
e
lease-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric I
r
rgang
Make
s
u
re image
s
ha
v
e
/
us
r
/bin/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgan
g
Upd
a
te
d
o
c
k
e
r image
b
uild scri
p
t
s for master bra
n
ch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make sure CI scri
p
t
c
a
n call /b
i
n/en
v
python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrgang
Minor clean u
p
t
o
buildall
.
sh
commit
|
commitdiff
|
tree
next