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Simplify GitLab CI Dockerfiles.
2020-02-21
M
.
Eric Irrga
n
g
S
i
mpl
i
fy
GitLab CI D
o
cker
f
i
l
es
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
E
r
ic Irrgang
Remove transitio
n
al links
for online
gm
x
api Python
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
E
ric Ir
r
gang
Resolv
e
CMak
e
ambi
g
uities for
gmx
a
pi Pyt
h
o
n
pa
c
kage
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
E
r
i
c Irrga
n
g
U
p
date i
n
t
e
r
s
phinx conf
i
g
uratio
n
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
ic
Irrgang
Set Sphinx default rol
e
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Ir
r
gang
Fix
extern
a
l
w
eb l
i
nk
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Clean
u
p S
p
hin
x
interpreted text in the default role
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric Irrgang
Add i
s
sue tracking for
d
epreca
t
ion
s
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eric I
r
rg
a
ng
Update referen
c
e to u
n
cr
u
stify and cla
n
g-format
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
E
ric Irrgang
Be more spe
c
ific with
c
lang-format sugg
e
st
i
ons
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
g
m
xa
p
i
l
a
nding page
u
p
date
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gm
x
a
pi docu
m
entation readabilit
y
improve
m
ents
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric I
r
rgang
gmx
a
p
i docume
n
tation formatti
n
g improvem
e
nts
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
E
ric Irrgang
Finalize gmxap
i
0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
r
ic Irrgan
g
Add
notes on MPI with
g
mxa
p
i Python packag
e
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
gmxapi Python
p
ackage usa
g
e
p
rose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Er
i
c Irrgang
Improve p
y
test fixtu
r
es for
direc
t
ory man
a
gement
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgang
Add gm
x
api_
e
xtension tes
t
s to 'tests'
t
arget
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
E
ric Irr
g
a
ng
Remove stub
content
f
rom gmxapi
d
ocs
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Er
i
c
Ir
r
ga
n
g
Remove extraneous file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrg
a
n
g
Add t
r
ans
i
tion
a
l l
i
nks for
o
nlin
e
g
mxapi Python packa
g
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irr
g
a
ng
Improve gm
x
api Dockerfiles
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irr
g
a
n
g
Achieve gmxapi
f
r
15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
U
p
d
a
tes to gmxapi FR15 ac
c
eptance test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Up
d
ate n
o
tes
a
n
d
tes
t
s regarding
gm
x
api
a
ccept
a
nce
.
.
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
E
ric
I
rrgang
Fix bug i
n
troduced by clang-format
r
eformat
.
commit
|
commitdiff
|
tree
2019-11-05
M
.
E
r
ic Irrgan
g
Update go
o
glete
s
t location
in
COPYING
.
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
Updat
e
gmxapi Py
t
hon docum
e
ntation i
n
structio
n
s
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric
I
rrgang
Update
S
phinx link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Er
i
c Irrgang
Fix t
y
pos
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
Er
i
c Irrgang
Fix
d
ocumentati
o
n typ
o
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric Irrgang
Normalize
sample_restr
a
int target
n
ames
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irr
g
ang
Allow
v
alidati
o
n
of the generated CMake tool
c
hain file
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
ic Ir
r
gan
g
I
mprove
uniformi
t
y
o
f OS X CM
a
ke configuration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irr
g
a
ng
Restore CMake convenien
c
e targets f
o
r sample_r
e
straint
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Deduplicate gmxapi documentation
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irr
g
a
ng
D
i
sabl
e
its
t
ests when sampl
e
_
restr
a
in
t
is
not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgan
g
Decrease th
e
maximum allowe
d
Python v
e
rsion
f
or gmxap
i
.
commit
|
commitdiff
|
tree
2019-10-28
M
.
Eric Irrgang
Update bun
d
l
e
d pybi
n
d
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Irrgang
Fix CMake messag
e
typo
.
commit
|
commitdiff
|
tree
2019-10-25
M
.
Eric Ir
r
gan
g
Improv
e
gmxapi mdrun t
e
st
.
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric Irrg
a
ng
S
u
ppress some output whe
n
sample_restraint is built
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric I
r
rgang
Add trajectory ou
t
put to mdr
u
n operatio
n
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrgan
g
Minor tid
y
ing t
o
mdrun
.
py
commit
|
commitdiff
|
tree
2019-10-16
M
.
Er
i
c Irrgan
g
Minor clean-up t
o
gmxa
p
i
p
a
c
k
a
g
e
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrgan
g
Updat
e
gmxa
p
i
.
version mod
u
le
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Irrgang
F
i
x logic error i
n
StaticSourc
e
Man
a
ge
r
intializatio
n
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Irrg
a
ng
Add
n
ote
a
b
o
u
t
libpython requirement
t
o gmxap
i
install
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Er
i
c
Ir
r
g
ang
Add
g
eneric chec
k
f
or gmxap
i
support library to Python
.
.
.
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irr
g
ang
Fix l
o
gic err
o
r i
n
gmxapi
.
v
e
r
s
ion
.
api_i
s
_at_le
a
st
(
)
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Er
i
c Irrga
n
g
Update sample_restraint documentatio
n
ent
r
y poin
t
s
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Er
i
c Irrgang
Test float and int gmxapi
parameter updates
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
E
ric
I
r
r
gang
Usab
i
lity upda
t
es for gm
x
a
p
i/docs
Dock
e
r
image
.
commit
|
commitdiff
|
tree
2019-10-12
M
.
E
r
ic
Irrga
n
g
Impr
o
ve p
a
rameter typi
n
g for gmxapi simula
t
ion parameter
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
M
.
Eric I
r
r
g
ang
Update handling of CMa
k
e policy 6
8
.
.
commit
|
commitdiff
|
tree
2019-10-07
M
.
Eric Irrgang
Update rpath commen
t
s in src/api/cp
p
commit
|
commitdiff
|
tree
2019-10-03
M
.
Eric Irrgang
Build gmxapi documentat
i
on
in main
G
ROMAC
S
docu
m
e
ntatio
n
.
commit
|
commitdiff
|
tree
2019-09-16
M
.
E
ric Irr
g
a
ng
Add gmxa
p
i release
n
otes
.
commit
|
commitdiff
|
tree
2019-09-15
M
.
E
ric Irrgang
Import gmxapi docs to
mai
n
GROMA
C
S docs directory
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
N
o
rmal
i
ze u
s
age of GMXT
O
O
L
C
H
A
INDIR in gmxapi setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
ri
c
I
rrgang
Do
not use
gro
m
acs-toolch
a
in i
n
darwin gmxapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
Upd
a
t
e g
m
xapi
setup
.
py
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Irrgang
Use GROMAC
S
CMake toolchain
f
ile for g
m
xapi P
y
th
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Add
g
mxapi
.
modify_input ope
r
at
i
on
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Provide a gmx
a
pi
.
read_tpr operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrg
a
ng
Update g
m
xap
i
.
simulati
o
n
.
c
o
nte
x
t det
a
i
l
s
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Allow gmxapi
.
mdru
n
to
p
r
operly dis
p
atch simula
t
ion
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irr
g
a
n
g
Upd
a
te gmxapi Python package infrastru
c
ture for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrg
a
ng
No
r
m
a
l
ize some
t
e
s
t
i
ng res
o
urces
f
or
t
he Python
p
a
c
ka
g
es
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric Irrgang
Fix pa
r
amet
e
r k
e
y l
o
ok-up in
gmxapi TP
R
r
eader
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric Irrg
a
ng
Make gmxcl
i
pytes
t
f
ixture more robust
.
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eri
c
Irrg
a
n
g
Python wrapping
code for gmxapi mdrun bindings
.
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irrgang
Import bas
e
c
o
de for Python-driven
sim
u
la
t
io
n
from
.
.
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric
I
rrg
a
n
g
Add
s
ampl
e
_re
s
t
r
a
i
nt Python tests to
`che
c
k` targe
t
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric Irrga
n
g
Remove un
u
sed fo
r
ward d
e
c
l
ar
a
tions
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
ric Irrgang
Rear
r
ange
expo
s
u
re of g
m
xapicompat simulation
i
nput
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
Move gmxapicompat TPR tools t
o
libgmxap
i
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
Reduce
artificial header dependencies in res
t
rai
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
M
.
Eric Irrgang
C++ co
d
e
a
n
d Python bindings for TPR para
m
eter read
.
.
.
commit
|
commitdiff
|
tree
2019-08-21
M
.
E
r
ic
I
rrgang
Enable GMXAPI by default
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
Eric Irr
g
a
n
g
Cle
a
n u
p
gmxapi do
c
ument
a
ti
o
n build
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
E
ric
Irrgang
Add subgraph and while_loop operations
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
E
r
ic Ir
r
ga
n
g
F
ix logic e
r
ror
i
n
pytho
n
_packaging/src/
C
MakeLists
.
txt
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irr
g
ang
M
i
nor o
p
timization
to `pip install
`
i
n
g
m
xapi
C
I build
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
A
dd initial
.
clang-format file
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric Irrgang
Improve sampl
e
_restr
a
int
project integration
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric Irr
g
a
ng
D
o
n't install
googletest
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eri
c
Irrgang
Map gmxapi C++ exceptio
n
s
to Pytho
n
exceptions
.
commit
|
commitdiff
|
tree
2019-08-12
M
.
E
r
ic Irrgang
Introd
u
ce Cont
e
xt
requirement
.
commit
|
commitdiff
|
tree
2019-08-12
M
.
Eric Ir
r
gang
Separate out som
e
abstract base classes
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Add gmx
a
pi_
p
ytest custom target to CMake `che
c
k` target
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrg
a
ng
Allow gmxapi P
y
th
o
n
packa
g
e
tests to be run
f
rom GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
E
r
ic Irrgang
Let base
G
ROMACS docker
i
mage be a li
t
tl
e
more useful
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric
Irrgang
Reenable g
t
est_main ta
r
get
.
commit
|
commitdiff
|
tree
2019-08-07
M
.
E
r
ic
I
rrgang
Use
g
mock and gtest targets from googletest-r
e
lease
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric
Irrgang
Separate out OperationDeta
i
ls
B
ase
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Er
i
c Irrg
a
ng
C
o
nvert test inf
r
as
t
ructure targets t
o
s
tatic
library
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eri
c
Irrg
a
ng
Resolve a compiler warnin
g
for the gmxapi Python
p
ackage
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric
Irrgang
A
d
d
l
ibgromacs d
e
p
endency to gpu_utilstest_cuda target
.
commit
|
commitdiff
|
tree
2019-08-05
M
.
Er
i
c
I
rrgang
S
e
parate out Operation
D
irector
.
commit
|
commitdiff
|
tree
next