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Update rules for release-2021.
2020-12-04
M
.
E
ric
Irrgan
g
Updat
e
rul
e
s
f
or rel
e
as
e
-2021
.
commit
|
commitdiff
|
tree
2020-12-04
M
.
E
ric Irr
g
a
ng
Se
p
ar
a
te job sc
r
ipt
f
i
l
es for g
m
xapi package v
e
rsions
.
commit
|
commitdiff
|
tree
2020-12-03
M
.
E
r
i
c Irrg
a
ng
Impr
o
v
e gmxapi C++ test coverag
e
for failed mdrun
.
commit
|
commitdiff
|
tree
2020-12-02
M
.
Eric Irr
g
a
ng
O
n
e argument per line
f
or long
f
u
n
ction
s
i
gnatures
.
commit
|
commitdiff
|
tree
2020-11-23
M
.
E
ric Irrgang
Look
for t
h
e various p
o
ss
i
b
l
e
n
ames of t
h
e groma
c
s
.
.
.
commit
|
commitdiff
|
tree
2020-11-20
M
.
Er
i
c Irrgang
Create
C
M
a
ke targets for each of
t
h
e
mod
u
l
e
s
.
commit
|
commitdiff
|
tree
2020-11-18
M
.
Eric Irrgang
R
e
place g
m
xapi `erro
r
output` with `s
t
d
e
rr` and `std
o
ut`
commit
|
commitdiff
|
tree
2020-11-17
M
.
Eric
I
rrgan
g
Separate
the
testut
i
ls module
.
commit
|
commitdiff
|
tree
2020-11-16
M
.
E
ric Irrgang
gmxapi version
i
ng updates
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric Irrgang
Be more exp
l
icit about bui
l
d-tr
e
e-only
dependencies
.
commit
|
commitdiff
|
tree
2020-11-13
M
.
Eric I
r
rgang
Provid
e
a
catch-all tar
g
et for
l
i
brar
y
modules
.
commit
|
commitdiff
|
tree
2020-11-12
M
.
E
r
ic Ir
r
gang
Provide common library he
a
ders throu
g
h new
CMake target
.
commit
|
commitdiff
|
tree
2020-11-09
M
.
Er
i
c
I
rrgang
Help client
s
find depen
d
enc
i
e
s
o
f
imported CMa
k
e targets
.
commit
|
commitdiff
|
tree
2020-11-04
M
.
Eric Irrg
a
n
g
E
s
t
ablish `
a
pi/` as t
h
e
home fo
r
install
e
d headers
.
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eric Irrgang
Remove an unnecessary transit
i
ve dependency of
i
mported
.
.
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Irrg
a
n
g
Use th
e
corre
c
t C
I
script f
o
r sample_restraint jobs
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
E
r
ic I
r
rgang
Normalize FindMPI hints
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eri
c
Irrgang
Cl
a
r
i
fy
b
e
havior of L
e
gacyMdrun
O
p
t
ions
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric
I
r
rgang
Update image names in job definitions
.
commit
|
commitdiff
|
tree
2020-10-26
M
.
E
r
ic Irrgang
T
e
l
l
gmx
a
pi to look
f
or M
P
I, when appropriate
.
commit
|
commitdiff
|
tree
2020-10-23
M
.
E
r
ic Irrgang
U
p
date
Do
c
ker i
m
ag
e
build scri
p
ts
.
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Ir
r
ga
n
g
Use update
d
CI
p
ipeline rules fo
r
Py
t
hon package test
s
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric
Irr
g
ang
Upd
a
t
e gmxapi version details
.
commit
|
commitdiff
|
tree
2020-10-08
M
.
Eri
c
Irrgan
g
Clarify
t
he GMX_BUILD_MDRUN_ONLY
f
ull
t
esting
i
nstru
c
tions
.
commit
|
commitdiff
|
tree
2020-10-07
M
.
Er
i
c Irrga
n
g
Impr
o
ve gmxPy
t
h
onD
i
sc
o
v
e
r
y
.
cma
k
e
commit
|
commitdiff
|
tree
2020-10-05
M
.
Eric Irrgang
Don't ov
e
r
ride
u
ser provided CMA
K
E_OSX_DEPLOY
M
ENT
_
T
ARG
E
T
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
ric Irrgang
Handle gmxapi tmpi pa
r
amete
r
s bett
e
r
.
commit
|
commitdiff
|
tree
2020-10-02
M
.
E
r
ic
I
r
rgang
Le
t
gmxapi installati
o
n record
the GROMACS library
.
.
.
commit
|
commitdiff
|
tree
2020-10-01
M
.
Eric Ir
r
ga
n
g
U
se updated imag
e
s for Python CI jobs
.
commit
|
commitdiff
|
tree
2020-09-30
M
.
Er
i
c Irrgang
Restrict gmxapi pytest tests to `-nt 2`
commit
|
commitdiff
|
tree
2020-09-30
M
.
Eric I
r
rgang
S
p
ecify OM
P
_
N
UM_TH
R
EADS for Pyhon CI scripts
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
ric Irrgang
Clarification
s
f
o
r
R
eso
u
rceAssign
m
ent inte
r
f
a
ce
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrg
a
n
g
Support ResourceAssignment in
t
e
r
face for tMPI
l
i
brary
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric Irrgang
Allow MPI-enabled c
l
ie
n
ts t
o
provide the library
c
ommunic
a
tor
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric
I
r
rgang
Use
M
piC
o
ntextManager to provide
MPI commu
n
icator
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
E
r
ic Irrgan
g
R
e
locate
M
piContextManager
.
commit
|
commitdiff
|
tree
2020-09-29
M
.
Eric I
r
rgang
Inter
f
a
c
e updates
a
llowing client to provi
d
e
MPI communicator
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Eric I
r
r
g
ang
Improve naming and do
c
s
.
commit
|
commitdiff
|
tree
2020-09-18
M
.
Er
i
c Irrga
n
g
Doc
u
ment a Mdrunne
r
::BuilderImplementation mem
b
er
.
commit
|
commitdiff
|
tree
2020-09-15
M
.
Eric Irrgang
Remove outdated
w
orkar
o
und
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric Irrgang
Create and use Simulation
I
nput
modu
l
e
.
commit
|
commitdiff
|
tree
2020-09-14
M
.
Eric
I
rrgang
Refine the
CMa
k
eLists
.
txt for MPI gmxapi test
s
.
commit
|
commitdiff
|
tree
2020-09-09
M
.
Eri
c
Irrga
n
g
E
x
p
lici
t
ly include STL header
s
used in test
.
commit
|
commitdiff
|
tree
2020-09-07
M
.
Eric Irrgang
Replace
filenam
e
-based
ini
t
ialization functions
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
E
ric Irrgang
Clar
i
fy t
_
i
n
p
utrec allocation logic in runner
.
cpp
.
commit
|
commitdiff
|
tree
2020-08-27
M
.
Eric Ir
r
gang
Use a heap object for inp
u
trec in gmx::Mdrunner::mdru
n
ne
r
()
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irr
g
ang
Accept Python versions
h
igher than 3
.
8
.
commit
|
commitdiff
|
tree
2020-08-21
M
.
Eric Irrgang
Remov
e
conditional for CM
a
ke
< 3
.
12
.
commit
|
commitdiff
|
tree
2020-08-18
M
.
Eric Irr
g
ang
Allow more
g
ranu
l
a
rity fo
r
public interface
s
in build
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrg
a
ng
Preve
n
t fail
e
d commandline_oper
a
t
ion from publishi
n
g
.
.
.
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgang
Minor
additions to gmx
a
pi install
.
rst
commit
|
commitdiff
|
tree
2020-08-03
M
.
Eric Irrgan
g
Use impor
t
lib_resource
s
in Python 3
.
6 ima
g
e
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Er
i
c Irrga
n
g
N
o
rmal
i
ze do
c
k
er im
a
ge
n
ame
s
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eric Irrgang
Fix
some
minor typeset
t
ing issues
.
commit
|
commitdiff
|
tree
2020-07-31
M
.
Eri
c
Irrgang
Improv
e
install docs links
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
E
r
ic Irrga
n
g
Move sources for l
i
bg
m
x
api
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgan
g
R
emov
e
disabled test
for supe
r
seded fea
t
ure
.
commit
|
commitdiff
|
tree
2020-07-30
M
.
Eric Irrgang
Ig
n
ore a gene
r
a
t
ed file
.
commit
|
commitdiff
|
tree
2020-07-29
M
.
Eric Irrg
a
ng
U
se
GMXAPI C
M
a
ke option guard f
o
r gmxapi target d
e
claration
.
commit
|
commitdiff
|
tree
2020-07-15
M
.
Eric Irrgang
Begin
mov
i
n
g
installed inter
f
a
ce
t
o `api/`
commit
|
commitdiff
|
tree
2020-07-11
M
.
E
ri
c
Irrgang
Fix libgro
m
acs CMake target install syntax
.
commit
|
commitdiff
|
tree
2020-07-10
M
.
E
r
ic
Irrg
a
n
g
F
i
x libgrom
a
cs CMa
k
e target install syntax
.
commit
|
commitdiff
|
tree
2020-07-01
M
.
Eric I
r
rga
n
g
Clea
n
u
p
s
imulat
o
rbuilder
.
h
commit
|
commitdiff
|
tree
2020-06-27
M
.
Eric Irrgang
A
dd missing ABI
h
ead
e
r
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Imp
l
e
ment Si
m
ulatorBuilder
.
a
dd() for BoxDeform
a
tionHandle
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Us
e
To
p
o
logyData
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irr
g
ang
U
se I
o
nSwapping param
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use
CenterOfMa
s
sPul
l
i
ng
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
U
s
e ReplicaExch
a
nge memb
e
r instead of build() argument
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Us
e
SimulatorModul
e
s pa
r
am
e
ter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Use Interactiv
e
M
D
S
imulatorBuilder parameter
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
rrg
a
ng
Use LegacyIn
p
ut
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
ric Irrgang
Use
Con
s
traintsPar
a
m
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
E
r
ic Irrgang
Move
Profilin
g
paramete
r
out of
s
im
u
latorbuilde
r
.
build()
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
Irrga
n
g
Use
S
i
mulatorEnv
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric
Irrgang
Implemen
t
remaining Simul
a
t
o
r
Builder
.
a
dd() method
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Er
i
c Irrgang
Interfa
c
e f
o
r remainin
g
SimulatorBu
i
lder
.
a
dd() m
e
tho
d
s
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eri
c
I
rrgang
Si
m
ulatorB
u
ild
e
r
.
add(
)
for S
t
opHandlerBuilder
.
commit
|
commitdiff
|
tree
2020-06-26
M
.
Eric Irrgang
Impl
e
men
t
Si
m
u
l
a
t
orBuilder
.
b
u
ild()
commit
|
commitdiff
|
tree
2020-06-22
M
.
Eri
c
Irrgang
Reformat pairs
.
c
pp
commit
|
commitdiff
|
tree
2020-06-22
M
.
E
r
ic Irr
g
ang
U
s
e Grom
a
c
s
::gmx target to hint gmxa
p
i tests
.
commit
|
commitdiff
|
tree
2020-06-19
M
.
Eric Irr
g
ang
Rem
o
ve workaround for gcc bug 582
6
5
.
commit
|
commitdiff
|
tree
2020-06-16
M
.
Eri
c
Irrgan
g
Improve pytest ou
t
p
u
t handling
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric
I
r
r
ga
n
g
Compartme
n
talize job rule
s
.
commit
|
commitdiff
|
tree
2020-06-09
M
.
Eric Irrgang
Imp
r
o
v
e usage of P
y
thon logging module
.
commit
|
commitdiff
|
tree
2020-05-29
M
.
Eric Irrgang
Handle
arbi
t
rary doxyge
n
versions in Docke
r
imag
e
build
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
E
ric
Irrgang
Remo
v
e unuse
d
(
and broken
)
im
a
ge f
r
o
m Dock
e
r
i
m
age
.
.
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Docker image bu
i
lds: simplify doxygen
v
ersion hand
l
ing
.
commit
|
commitdiff
|
tree
2020-05-28
M
.
Eric Irrgang
Doc
k
er imag
e
builds: move doxygen handling to a separate
.
.
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric I
r
rgang
Extend MPI ense
m
ble te
s
ting for g
m
xapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
En
a
ble
MPI ense
m
ble testi
n
g
for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Er
i
c Ir
r
gang
N
o
rmal
i
ze
gmxapi relate
d
r
el
e
ase-2
0
20 job
l
o
g
ic
.
commit
|
commitdiff
|
tree
2020-05-25
M
.
Eric Irrgang
Redu
c
e console log o
u
tpu
t
from sample_restr
a
int tests
.
commit
|
commitdiff
|
tree
2020-05-24
M
.
Eric
I
r
rg
a
ng
E
n
a
bl
e
M
P
I
e
n
semble testing for gm
x
a
pi
.
commit
|
commitdiff
|
tree
2020-05-21
M
.
E
r
ic Irrgang
N
o
rmalize
g
m
x
api r
e
lated release-2020
job lo
g
ic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Eric Irrgang
Mak
e
su
r
e images have /usr/bin/p
y
t
h
on
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Update do
c
k
e
r image build scripts
for ma
s
ter branch
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
I
r
rgang
Make sure
CI scrip
t
can call /bin/env
pyth
o
n`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Er
i
c Irrgang
Min
o
r clean up to bui
l
dall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Al
l
ow llvm option alrea
d
y used
i
n
bu
i
ldall
.
sh scrip
t
.
commit
|
commitdiff
|
tree
next