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Update reference to uncrustify and clang-format.
2019-12-18
M
.
Eric Irrgang
Update reference to
uncrustify an
d
clang-form
a
t
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
E
r
ic Irrgan
g
Be more specific with clang
-
format suggestions
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eri
c
Irrgang
g
mxap
i
l
a
n
d
ing page update
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric
Irrgang
gmxapi documentatio
n
readability improvem
e
nts
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gmxapi d
o
cumentation formatting im
p
rove
m
ents
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric Irrgang
Finalize gmxapi
0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric I
r
rgang
Add notes on MPI wi
t
h
g
m
xapi Pyt
h
on pa
c
kage
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric Irrgang
gmxa
p
i
P
y
thon package u
s
age prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
I
rrgan
g
Improve pytest fixtures for d
i
rectory management
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgang
A
dd gmxapi_e
x
tension te
s
ts to 'tests' target
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irrgang
Re
m
o
v
e stub
content from gmxapi doc
s
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
Irrgang
Remo
v
e extraneo
u
s file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
ic
Irrgan
g
Add transi
t
ional
links for onl
i
n
e
gm
x
api Pyt
h
on
p
ackage
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Improve gmxapi Dockerfiles
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eri
c
Irrgang
Achieve gmxapi fr
1
5
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Ir
r
g
an
g
Updates to gmxapi FR
1
5
a
ccept
a
nce test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
r
ic I
r
rgang
Up
d
a
t
e
notes an
d
t
e
st
s
rega
r
di
n
g gmxapi
ac
c
ept
a
nce
.
.
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eri
c
Irrgang
Fix bug
introd
u
ced by
clang
-
format
r
e
f
o
r
mat
.
commit
|
commitdiff
|
tree
2019-11-05
M
.
Eri
c
Irrgang
Up
d
ate googletest location
i
n COPY
I
NG
.
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
Update gmxapi Python documentation instr
u
ctions
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric I
r
rgang
U
pdate Sphinx l
i
nk
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Ir
r
g
a
ng
Fix typo
s
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric Irr
g
ang
F
ix documen
t
a
t
ion typo
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric Irrgang
Normalize
sample_restraint tar
g
et names
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrga
n
g
A
l
low validation of the g
e
ner
a
ted
C
Make toolchain
fil
e
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Improve uniformity of
OS X CMake c
o
nfigurati
o
n
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
ri
c
I
r
r
g
an
g
Resto
r
e CMake convenience ta
r
gets for sampl
e
_restr
a
int
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
ric
I
rrgang
Deduplicate
g
mxapi do
c
umentatio
n
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
E
r
ic Irrgang
D
i
sable its test
s
w
h
e
n sam
p
le_res
t
r
aint is not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrg
a
ng
Decrease t
h
e
m
aximum allo
w
e
d Py
t
hon
ve
r
sion for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-28
M
.
E
ric Irrgang
Update bundled pybind
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric
I
rrga
n
g
F
ix CMak
e
message typo
.
commit
|
commitdiff
|
tree
2019-10-25
M
.
E
r
ic I
r
r
g
ang
Impro
v
e gmxapi mdrun test
.
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric
Irrgang
Sup
p
ress some outp
u
t w
h
en sa
m
ple_restra
i
n
t
i
s built
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgang
Add
traject
o
ry output to m
d
r
u
n o
p
era
t
ion
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
E
ric I
r
rgang
M
i
nor t
i
dying to mdr
u
n
.
py
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrgang
M
i
n
or clea
n
-
u
p t
o
gmxapi package
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric I
r
rg
a
ng
Upd
a
te gmxapi
.
v
e
r
s
ion module
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Er
i
c Irr
g
ang
Fix
log
i
c error in
S
taticS
o
urceMan
a
ger intializatio
n
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric I
r
rgan
g
Add
note abou
t
libpy
t
hon
requirement t
o
gmxapi i
n
s
t
all
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
E
ric I
r
rgang
Add generic ch
e
ck for
gmxapi
support
library to Python
.
.
.
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrgang
Fix logic error in gmxapi
.
version
.
api_is_at_least()
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Eric Irrgang
U
pdate s
a
mple_restrai
n
t documentation entry points
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Eric Irrgang
Test fl
o
a
t
and int
g
mxapi para
m
eter upd
a
tes
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Er
i
c Irrgang
Usa
b
ility updates fo
r
gmxapi/docs Docke
r
image
.
commit
|
commitdiff
|
tree
2019-10-12
M
.
Eric Irrgang
Impr
o
ve paramete
r
t
y
pi
n
g for gmxapi simul
a
tio
n
parame
t
er
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
M
.
Er
i
c Irrga
n
g
Update handling of
C
Make polic
y
68
.
.
commit
|
commitdiff
|
tree
2019-10-07
M
.
E
ric Irrga
n
g
Update rp
a
th comments in src/
a
pi
/
cpp
commit
|
commitdiff
|
tree
2019-10-03
M
.
Eric I
r
rgang
Build gmxapi documenta
t
ion
i
n main GROMACS do
c
um
e
nt
a
tion
.
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric Irrgang
Add gmx
a
pi relea
s
e notes
.
commit
|
commitdiff
|
tree
2019-09-15
M
.
Eric
I
rr
g
ang
Import
gmx
a
pi docs
t
o
m
ain GROMACS doc
s
d
i
rectory
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
N
ormalize
u
sage of GMXTOOLCH
A
INDIR in gmx
a
pi setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Er
i
c Irrgang
D
o
not use
g
roma
c
s
-
toolchain
in
d
arwin gmxap
i
b
uilds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
Upd
a
te gm
x
api
s
etup
.
py
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ri
c
I
r
rgang
Us
e
GROMACS CMa
k
e
toolchai
n
file for gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ri
c
Ir
r
gan
g
Add gmxapi
.
modify_input
o
peration
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrgang
P
rovide a
g
mxapi
.
read_tpr op
e
ratio
n
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrgang
Update g
m
xa
p
i
.
s
i
m
ulation
.
context
de
t
ail
s
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
A
l
low gmxapi
.
m
drun
to
p
rop
e
rly
d
ispatch
s
imulati
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
U
pdate gmxapi Pyth
o
n package infrastructu
r
e for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Ir
r
gang
Normal
i
ze some
t
esting resources
f
or th
e
Pyt
h
on pac
k
a
ges
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric Irrgang
Fix parameter key look-up in gmxapi TPR reader
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric Ir
r
gang
Mak
e
gmxcli p
y
test
f
i
x
ture mo
r
e
r
o
bust
.
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eric
I
rrgang
Python wrapping code fo
r
gmxapi m
d
run
b
i
n
dings
.
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irrgang
I
m
p
ort
base code
f
o
r
P
ython
-
driven
s
imulati
o
n from
.
.
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric Irrgang
Add
s
a
mp
l
e_restraint
Py
t
hon tests
to
`c
h
eck` target
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric Irrgang
R
e
move unu
s
ed forw
a
rd declarati
o
ns
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric I
r
rgang
Rearrange exposure of gmxa
p
icompat simulation input
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
r
ic Irr
g
ang
Move
gmxapicompat
T
P
R
t
o
o
ls to libgm
x
api
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
r
ic
I
r
r
ga
n
g
Reduce arti
f
ic
i
al header
dependencies in restr
a
i
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
ric Irrga
n
g
C++ code and Py
t
hon b
i
ndings for TPR parameter
r
e
ad
.
.
.
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eric Irrg
a
ng
E
n
able GMX
A
PI by default
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
Eric Irrgang
Clean up gmx
a
p
i
d
o
cum
e
ntation build
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
Eric Irrgang
Add subg
r
aph and
wh
i
le_
l
oop
o
p
erations
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
Fix logic error in python_
p
ackaging/src/CMakeLists
.
txt
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
Minor optimization
t
o `pi
p
insta
l
l` in gm
x
api CI build
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
E
ric Ir
r
gang
Add
initial
.
clang-for
m
at
f
ile
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric Irrgang
Improve sample
_
restrain
t
pro
j
ect integ
r
ation
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric Irrgang
D
on
'
t install goo
g
letest
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric
Irrgang
Map g
m
xapi
C
++ e
x
ce
p
ti
o
ns
to Python exc
e
ptions
.
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Ir
r
gang
Introduce Context requirement
.
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Irrgang
Separa
t
e out some
a
bstr
a
ct base
c
l
asses
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Er
i
c Irrgang
Add gmxapi_pyte
s
t custom target to CMake
`
che
c
k`
target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrga
n
g
Al
l
ow gmxapi Python packa
g
e test
s
to be run fr
o
m GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
ric
I
rr
g
ang
Let bas
e
GROMACS docker
image be a lit
t
le mo
r
e
use
f
ul
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric I
r
rg
a
ng
Reenable gtest_main target
.
commit
|
commitdiff
|
tree
2019-08-07
M
.
Er
i
c Irrgang
Use gmock
and
gtest tar
g
e
t
s f
r
o
m
googletest-release
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
ric I
r
rga
n
g
S
e
p
a
rate out OperationDetail
s
Base
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
r
i
c
I
r
rgang
C
o
nvert test
i
nfrastructur
e
targets to
stat
i
c librar
y
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
r
i
c Irrgang
Resolve a com
p
ile
r
warn
i
ng for the gmxapi Python package
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irrgang
Add libgromacs depend
e
ncy
to gpu_utilstest
_
cu
d
a
t
a
r
get
.
commit
|
commitdiff
|
tree
2019-08-05
M
.
E
ric Irrga
n
g
S
eparate out Ope
r
ationDire
c
tor
.
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eri
c
Irrgang
Rearchi
t
ect gmx
a
p
i
.
operation
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eric
I
rr
g
ang
Reduce conf
l
icts wi
t
h
external googletest files
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
E
ric Irrgang
Remo
v
e o
n
e o
f
the exa
m
p
l
es from
sample_
r
estraint
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Begin new sample_restraint d
e
v
e
lopment
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric
I
r
r
g
ang
F
i
x gmx
a
pi noteboo
k
ima
g
e and sa
m
ple_restra
i
n
t docker
.
.
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrga
n
g
Clarify use
o
f Python venv in gmx
a
pi docker images
.
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrgang
Improve gmxapi docker t
e
stin
g
environ
m
ent
.
commit
|
commitdiff
|
tree
2019-07-23
M
.
Eric Irrgang
Improve doc
s
for gmxapi Python environment
p
reparation
.
commit
|
commitdiff
|
tree
next