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Update instructions in containers.rst
2020-12-04
M
.
Eri
c
Irrga
n
g
Add
CI jobs f
o
r
gmxapi 0
.
3
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eri
c
Irrgang
Updat
e
rules for rel
e
ase-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
Eric Irrgang
Separate job sc
r
ipt
files for gmxapi package versions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
E
r
ic Irrgang
I
m
p
ro
v
e gmxa
p
i C++ test coverag
e
for
f
a
iled mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irrgang
One argument per line for long function sig
n
atures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
Er
i
c
I
r
r
ga
n
g
Look for the various pos
s
ible names of
the gr
o
m
a
cs
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Eri
c
I
rrgang
Cre
a
te CMake
target
s
for each
o
f the modul
e
s
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Er
i
c Irrgang
Replace gmxapi `erro
r
o
u
tput` w
i
th `stderr` and `stdout
`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric
Irr
g
ang
Separat
e
the test
u
tils module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
Eric Irrga
n
g
g
m
x
api versioning upda
t
es
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric
I
rrgang
B
e more explici
t
about buil
d
-t
r
ee-onl
y
d
ep
e
ndencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrg
a
ng
P
rovide a catch-
a
ll t
a
r
get for library modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
Eric Irrgang
P
rovide commo
n
li
b
rary
head
e
rs th
r
ough new CMake target
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Eric Irrgang
Help
client
s
fin
d
dependencies of imp
o
rted CMake targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric Irr
g
ang
Establish `api/` as th
e
h
o
me f
o
r installed h
e
a
d
ers
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgang
Remove an
unnecessary transiti
v
e depe
n
dency of impo
r
ted
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c Irrgan
g
U
se the correct CI script for sample_restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric I
r
rg
a
ng
Norm
a
liz
e
Fi
n
dMPI
hi
n
ts
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
r
i
c
I
rrgang
Clar
i
fy
b
e
ha
v
i
o
r of
Legac
y
Mdrun
O
p
tions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
ric
Irrgang
U
p
date image na
m
e
s in job
definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
Er
i
c Irr
g
ang
Tell gmxapi to
l
ook fo
r
MPI
,
when
appropr
i
ate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
Eric I
r
r
g
an
g
Update
D
oc
k
e
r image build scrip
t
s
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrg
a
ng
Use updated CI pi
p
eline rules for
P
ython pa
c
k
a
ge tests
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgan
g
Update gmxap
i
versi
o
n d
e
tails
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
E
r
ic Irrgang
Clarify
t
he GMX_BUILD_MDRU
N
_ONLY
full test
i
ng i
n
st
r
uctions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Eric Irrgang
Impr
o
ve g
m
xPythonDiscove
r
y
.
cmake
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric I
r
rgang
Don't o
v
er
r
id
e
user provi
d
ed C
M
AKE_OSX_DEPLOYMENT_TARGE
T
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
ri
c
Irrga
n
g
Hand
l
e gmxapi tmpi p
a
ram
e
t
e
r
s bette
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric
I
rr
g
ang
Le
t
gm
x
a
p
i
in
s
tallation record the GROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
E
ric Irrgan
g
Use updated images
f
o
r
P
y
thon CI jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric Irr
g
ang
Res
t
rict gmx
a
pi pytest tests to `-nt
2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric
I
rrgang
S
p
ecify OMP_NUM_T
H
READS for Pyh
o
n
C
I
scri
p
ts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c
I
rrgang
Clar
i
fic
a
tions
for
R
e
s
ourceAssignme
n
t in
t
erface
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Ir
r
gang
Supp
o
r
t ResourceAssignment interface
f
o
r tMPI library
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
i
c
I
rrgang
Allo
w
MPI-enabled clie
n
ts to provide the
l
i
bra
r
y
c
ommunicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic I
r
rgang
Use MpiContextMana
g
er to pro
v
ide
M
PI communicator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Er
i
c
Irrgang
R
elocate
Mp
i
Con
t
extManage
r
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
r
ga
n
g
Interface updates allow
i
n
g
c
lient to
pro
v
ide MP
I
com
m
u
n
i
c
a
tor
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
E
ric Irrgang
Impr
o
v
e
naming and docs
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Er
i
c
Irrgang
Document a Mdr
u
nner::Build
e
rI
m
pleme
n
tation member
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Ir
r
gang
R
e
m
ove outdated workaround
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
E
ric Irrgan
g
Create and use SimulationInput mod
u
le
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric
Irrgang
Re
f
ine
t
h
e
CMa
k
e
Lists
.
txt fo
r
MPI gmxap
i
tests
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eric Irrgang
Explicitly includ
e
STL h
e
aders used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
E
r
i
c
I
rrgang
R
e
place filename-ba
s
ed initializa
t
ion functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
ric I
r
rgang
Clarify t_inputrec a
l
loc
a
tion logic in runn
e
r
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Er
i
c Irrgang
Us
e
a
heap ob
j
ect for inputrec
i
n
gmx::
M
drunner::mdrunn
e
r()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
E
r
ic Irrg
a
ng
Accept Python ve
r
sions higher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Er
i
c Irrg
a
ng
R
e
move
con
d
i
tion
a
l
f
or CMake
<
3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
E
r
ic
Ir
r
g
ang
Al
l
ow more granularity for public interfaces in bui
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrg
a
ng
Prevent failed comman
d
line_
o
perat
i
on fr
o
m publishi
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eri
c
Irrgang
Minor
a
dditions to gm
x
ap
i
install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
U
se import
l
ib_resources in Python 3
.
6 images
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Normalize
dock
e
r image names
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
E
ric Irrgang
Fix some minor typesetting issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric
I
rrgang
Imp
r
ove inst
a
ll
docs lin
k
s
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric
Irrgan
g
Move s
o
u
rces for libgmxapi
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
i
c
I
rrgang
Remove disabled t
e
st
f
or superseded
fe
a
ture
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ig
n
ore a generated
file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrga
n
g
Use
GMXAP
I
C
M
ake option
g
uard for gmxapi
t
a
r
get dec
l
aration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
E
ric Irr
g
ang
Begin moving
i
nstal
l
e
d
int
e
r
face to `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
Eric Irrgang
Fix
l
i
b
gromacs CM
a
k
e target i
n
stall
s
yntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
Er
i
c Irrga
n
g
Fix li
b
gromacs
C
Make t
a
rget i
n
stall
s
yntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric Irrga
n
g
Clean up simulatorbuilde
r
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric
I
r
r
g
a
n
g
Add m
i
s
s
i
n
g ABI header
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Impleme
n
t
S
imul
a
torBuilder
.
a
d
d() for Bo
x
D
e
formationHa
n
d
le
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Ir
r
gang
Use Topolo
g
yData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrgang
Use IonSw
a
p
ping
p
ara
m
e
te
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c
Ir
r
gang
Use
CenterOfMassPulling
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Replica
E
xchang
e
member instead of b
u
il
d
()
ar
g
u
m
ent
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrg
a
n
g
Use Sim
u
latorModules parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrga
n
g
Us
e
I
n
te
r
a
ct
i
veMD Sim
u
l
at
o
rBuilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
rrgang
Use LegacyInput
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Cons
t
raintsParam
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric I
r
rgang
Move Profi
l
ing parameter
out
o
f sim
u
l
atorbui
l
der
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Simulat
o
rEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irr
g
ang
Implement
r
emaining
S
imulatorBuilder
.
add
(
) method
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Inter
f
ace for remaining SimulatorBuilder
.
add
(
) methods
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Simu
l
atorBuilder
.
add() for StopHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
I
r
r
g
an
g
Implement Simula
t
or
B
uilder
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irr
g
a
ng
R
e
format pairs
.
cpp
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eric Irrgang
Use Groma
c
s::gmx target to h
i
nt gmxapi tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
E
r
i
c Irrgan
g
Remove worka
r
ound f
o
r gcc bug 58265
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eric Irrgang
Im
p
rove pytest
output
h
and
l
i
ng
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Compartmentaliz
e
job
rules
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
E
r
i
c
I
r
r
gang
Improve usage of Pytho
n
lo
g
gin
g
modul
e
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Irrgang
H
andle arbi
t
rary doxyge
n
v
e
rsions in Docker
i
mage bu
i
l
d
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Remove unused (and b
r
o
k
en) image fr
o
m D
o
cker image
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric Irrgang
Docker
image buil
d
s: si
m
plify doxyg
e
n version handli
n
g
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docke
r
image builds: mo
v
e doxygen h
a
n
dling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eri
c
I
rrg
a
ng
Exte
n
d MPI ense
m
ble testing for gmx
a
pi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
E
nable MP
I
ensem
b
l
e
testing for g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgan
g
Normalize gmxapi related relea
s
e-2020
j
ob logic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrgang
Reduce console l
o
g
out
p
ut
f
r
o
m sample_restraint tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric Irrgan
g
Enable MPI en
s
emble testing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
Eric
I
rrgang
Normalize
g
mxapi
r
e
l
ated release-2020 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Make
s
u
re image
s
ha
v
e /usr
/
b
in/python
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Ir
r
gang
U
p
dat
e
do
c
ker image build sc
r
ipts
f
o
r
master branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make su
r
e
C
I script can call /bin/env pytho
n
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric I
r
r
gang
M
i
nor
c
lean
up to buildall
.
s
h
commit
|
commitdiff
|
tree
next