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cmake: install pbc.h for GMX_INSTALL_LEGACY_API
2020-01-09
M
.
Eric Irrgang
U
s
e e
n
um for gmxapi
.
testsu
p
por
t
fixt
u
re
o
p
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric
Irrgang
Fur
t
her co
n
s
o
lidate
g
mxapi
.
testsupp
o
rt
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Update gmxapi Python package ve
r
sion
and v
e
rsioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Er
i
c Irrgang
Remove stray
"to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric I
r
rgang
Rem
o
ve t
r
a
n
s
i
tional
l
inks
f
o
r online gmxapi P
y
thon
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
E
r
ic Irrgang
A
dd
Fla
k
e8 linting to gmxapi
t
ests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrg
a
ng
Use
`
t
o
d
o` Sphinx directive more
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Er
i
c Ir
r
ga
n
g
Add t
r
a
c
king fo
r
a documented actio
n
item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eri
c
Irrgang
Link so
m
e
"to do"s in
t
he dev
manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrg
a
ng
Make gmxapi
.
t
e
stsupport usable as
a pytes
t
plugin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irrgang
Resolve
C
M
ake
ambiguities fo
r
gmxap
i
Pyt
h
on packa
g
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric Irrgang
Update intersphi
n
x
configuration
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eri
c
Irrg
a
ng
Le
t
GMX_DEVELOP
E
R
_BUILD trigger a "to do" list in
t
he
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Set Sphi
n
x
d
efau
l
t role
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric I
r
rgang
Fix external web lin
k
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Enable Sp
h
inx todo dir
e
c
tiv
e
for GMX_DEVELO
P
E
R_BUIL
D
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric
I
rrgang
Clean up Sph
i
nx interpreted tex
t
i
n the defa
u
lt role
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eri
c
Irrg
a
n
g
Ad
d
issu
e
trac
k
ing for de
p
recat
i
o
n
s
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eri
c
Irrgang
Upd
a
te refer
e
nce
to unc
r
us
t
ify an
d
clan
g
-format
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
Eric Irrgang
B
e more
s
pecific wit
h
c
la
n
g-
f
ormat
s
uggestions
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
E
ric Irrgang
gmxapi landing page update
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Er
i
c Irrg
a
ng
gmxapi
do
c
umentat
i
o
n readabi
l
i
t
y improvements
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gmxapi docume
n
t
a
ti
o
n formatting improveme
n
t
s
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
E
r
i
c Irrgang
Finali
z
e gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
Irrgang
Add not
e
s
on MPI with gmxapi Py
t
hon package
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric Irrga
n
g
gmxapi Python packa
g
e us
a
ge prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
Improve pytest f
i
xtures for directory man
a
g
e
m
e
nt
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgan
g
Add gmxapi_exten
s
i
o
n
t
e
sts to 'tests' targ
e
t
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eri
c
Irr
g
ang
R
e
mov
e
stub content from gmxapi
docs
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric I
r
r
g
ang
Remove e
x
traneous
f
ile
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgan
g
Add tra
n
s
i
tional l
i
nks for onli
n
e gmx
a
pi Python p
a
c
k
age
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
I
rrgang
Improve g
m
x
api
Do
c
kerfiles
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrga
n
g
A
c
h
i
eve gm
x
ap
i
fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Er
i
c
Irrgang
U
p
dates to
gmxapi FR15 accepta
n
c
e
te
s
t
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Ir
r
gang
Update notes and
t
ests regard
i
ng gmxapi a
c
ceptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
r
ic Irrgang
Achieve gmxapi f
r
15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irr
g
ang
Update
s
t
o gmxapi FR1
5
accept
a
n
c
e
t
e
st
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Update notes and tests regarding gmxapi acc
e
ptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Irrgang
F
i
x bug int
r
od
u
c
ed
b
y
c
l
ang-format
r
eformat
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Ir
r
gang
Fix bug introduced
b
y clang
-
f
o
r
m
at reformat
.
commit
|
commitdiff
|
tree
2019-11-05
M
.
Eric Irrgang
Update goo
g
l
et
e
st lo
c
ation in CO
P
YIN
G
.
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
U
p
date
g
mxapi
Pyth
o
n
doc
u
men
t
a
tion i
n
structions
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrgang
U
p
d
ate Sphinx
link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrgang
Fix typos
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
E
ric Irrgang
Fix documentati
o
n typo
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric Irrgang
Normal
i
ze
s
ampl
e
_restraint tar
g
et names
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Ir
r
g
a
ng
Allow val
i
dation
o
f the g
e
ne
r
ated CMake
toolcha
i
n
f
i
le
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
ric Irrg
a
ng
Improve uniformi
t
y of OS X CMake configuration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eri
c
Irrgang
Restore
C
Make
c
onvenience
t
argets for
s
amp
l
e_restra
i
nt
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
ic Irrgang
Dedupl
i
cate gmx
a
pi docum
e
n
tation
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Disable i
t
s tests w
h
en samp
l
e_restra
i
nt is n
o
t the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Decrease the m
a
ximum allowed Python version for
g
m
xapi
.
commit
|
commitdiff
|
tree
2019-10-28
M
.
E
ric Irrgang
Upd
a
t
e bundled pybind
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Irrg
a
ng
F
ix CMake me
s
sage typo
.
commit
|
commitdiff
|
tree
2019-10-25
M
.
Eric Irrg
a
ng
Imp
r
o
ve gmxapi mdru
n
test
.
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric Irrgang
Supp
r
e
ss some output when sampl
e
_
restraint is buil
t
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric
Irrgang
Add
t
rajec
t
o
r
y
output
t
o mdr
u
n
oper
a
t
ion
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrga
n
g
Minor tid
y
in
g
to mdrun
.
py
commit
|
commitdiff
|
tree
2019-10-16
M
.
E
r
ic Irrgang
M
i
n
or clean-u
p
to
gmxapi package
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
E
ric Irr
g
ang
Up
d
at
e
gmxap
i
.
version module
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Irrg
a
ng
Fix logic error in
S
taticSourceManager in
t
i
a
lizat
i
o
n
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Irrgang
Add no
t
e
about libpython re
q
uirement to gmxapi in
s
tal
l
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric
I
rrgang
Add generic
chec
k
for g
m
xapi
supp
o
r
t
library to Python
.
.
.
commit
|
commitdiff
|
tree
2019-10-14
M
.
Eric Irrgang
F
i
x
logic error in gm
x
api
.
version
.
api_is_at_
l
east
(
)
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Eric Irr
g
a
ng
Upd
a
t
e
sa
m
ple_restraint documentati
o
n e
n
tr
y
point
s
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Eric Irrgang
Tes
t
float and
int gmxapi parameter updates
.
commit
|
commitdiff
|
tree
2019-10-13
M
.
Eric Irrgang
Usability upda
t
es for gmxapi/docs
Dock
e
r
im
a
ge
.
commit
|
commitdiff
|
tree
2019-10-12
M
.
Eric Irrgan
g
I
mprove
p
arameter typing for gmxa
p
i simula
t
io
n
p
a
rameter
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
M
.
Eric
I
rrgang
Updat
e
handli
n
g of
CMake policy 68
.
.
commit
|
commitdiff
|
tree
2019-10-07
M
.
Eric Irrgang
Upda
t
e
rpath comments i
n
s
r
c/api/cpp
commit
|
commitdiff
|
tree
2019-10-03
M
.
Eric Irrgan
g
Build
gmxapi documentation in
m
ain
G
ROMACS doc
u
mentation
.
commit
|
commitdiff
|
tree
2019-09-16
M
.
E
ric Irrgang
A
d
d gmxa
p
i r
e
lease notes
.
commit
|
commitdiff
|
tree
2019-09-15
M
.
Eric Irrgang
Import gmxapi docs
t
o m
a
i
n
GROMACS
d
ocs dir
e
c
t
ory
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
N
orma
l
i
ze usage of G
M
XTOOLCHAINDIR in
g
mxapi
setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrg
a
ng
Do not us
e
gromacs-toolchain in darwin
g
m
xapi builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
E
r
i
c Irr
g
a
n
g
Update gm
x
api setup
.
py
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irr
g
a
ng
Use GROM
A
CS
C
Mak
e
to
o
l
c
hai
n
f
ile for
g
mxapi Python
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Er
i
c Irrgang
Add gmxapi
.
modify_input ope
r
a
t
ion
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrg
a
ng
Provide a gmxapi
.
read_tpr
operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Irrga
n
g
Update gmxap
i
.
s
imulation
.
context det
a
ils
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
ric Irrg
a
ng
A
l
l
o
w gmx
a
pi
.
mdr
u
n to pro
p
erly dispatch
s
i
mulatio
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
i
c
I
r
r
g
a
ng
Upd
a
te g
m
xapi
Python package infrast
r
ucture f
o
r
n
ew
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irrgang
Norm
a
lize some testing
resources for the Pytho
n
packages
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric
Irrgang
Fix
parameter key lo
o
k-up in g
m
xapi TPR reader
.
commit
|
commitdiff
|
tree
2019-09-10
M
.
Eric I
r
rg
a
ng
Make gmx
c
li
p
ytes
t
fixtu
r
e
m
or
e
r
o
bus
t
.
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eric Irrgang
P
y
thon wrappin
g
code
for gmxapi mdrun bindings
.
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irr
g
ang
Import base code for Py
t
hon-driven simul
a
tio
n
fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric Irrgang
A
d
d sample_restraint Pyth
o
n tests to `check`
targe
t
.
commit
|
commitdiff
|
tree
2019-08-27
M
.
Eric Irrgang
Remove unused forward
d
ecl
a
rations
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Ir
r
ga
n
g
Re
a
rran
g
e exposu
r
e
of gmxapic
o
mpat
s
imulation
i
nput
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
M
o
ve gm
x
apic
o
mpat TPR tools to
l
ibgm
x
api
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
R
educe art
i
ficial header dependencies in res
t
raint
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
M
.
Eric Irrgang
C++ code and
P
ython bindings for TPR parameter
read
.
.
.
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eric Irrgang
Enable GM
X
API by
d
efault
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
Eric Irrgang
Cle
a
n up gmxa
p
i
docume
n
tation build
.
commit
|
commitdiff
|
tree
2019-08-19
M
.
E
r
ic
I
rrgang
Add
subgraph a
n
d
w
hile_l
o
op
operations
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
F
i
x
l
o
g
i
c error
i
n
python_pac
k
aging/src/CMakeList
s
.
txt
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrgang
Minor optimiz
a
ti
o
n to `pip i
n
stal
l
`
in gmxapi CI build
.
commit
|
commitdiff
|
tree
2019-08-14
M
.
Eric Irrga
n
g
Add initi
a
l
.
clang-fo
r
mat f
i
l
e
.
commit
|
commitdiff
|
tree
2019-08-13
M
.
Eric Irrgang
Impr
o
ve s
a
mpl
e
_restraint
proje
c
t integration
.
commit
|
commitdiff
|
tree
next