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Improve gmxapi C++ test coverage for failed mdrun.
2020-03-22
M
.
Eric Irrgang
Merge *
-
test-temp
l
a
te
.
y
m
l into testing-matr
i
x
.
git
l
ab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irrgang
Merge
.
test-runn
e
r
-templa
t
e
.
yml into test
i
n
g
-ma
t
rix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic Irrgang
Merg
e
.
test-scr
i
p
t
-template
.
yml into
t
esting-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irrgang
Merg
e
.
regressiontest-templ
a
te
.
yml int
o
archive config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Consoli
d
ate do
c
umentati
o
n templates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Reor
g
anize
r
eleas
e
templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
Irr
g
ang
Remove
confusing and dup
l
icated variables assi
g
nmen
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eri
c
Irrgang
Consolidate global mix
-
ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip]
Remove
i
n
d
irec
t
io
n
for default tags para
m
e
t
e
r
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgan
g
[ci
s
k
ip]
Reorgan
i
ze
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
i
c Irrgang
Document CI
v
aria
b
le
an
d
remove unus
e
d template
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
Disable
s
p
h
inx
.
ex
t
.
vie
w
c
o
de
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrg
a
ng
Add
s
tub Variables d
o
cumentation
to GitLab CI
d
oc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric I
r
rg
a
ng
Remove dupli
c
ated Y
A
ML
k
ey
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
I
rrgan
g
Add
d
ocu
m
en
t
f
o
r con
t
ainerization infrastructur
e
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric I
r
rg
a
n
g
Alphabetize list for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric I
r
rgang
Reformat
argumen
t
s fo
r
readabi
l
ity
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c
Irrgang
D
e
fine an argp
a
r
se parent parser for conta
i
ner
i
mage
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
Irr
g
ang
Buil
d
MPI in
D
oc
k
erfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Merge
c
onf
.
py an
d
c
o
nf-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric Irr
g
ang
Disti
n
guish
D
o
cker images for
differe
n
t re
l
ease requirements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Free up Docker
image tag namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
ric
I
r
r
gang
Remove duplicated Gi
t
Lab-CI
jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Er
i
c Irrgang
Refo
r
mat
.
gi
t
lab-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Er
i
c
I
rrgang
Consolidate l
o
gic for wheth
e
r to u
s
e M
o
dularSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Manage the list of image tags in
D
ocker build
script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Manage the l
i
st of image tags
in Docke
r
build scrip
t
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
r
ic Irrg
a
ng
Resolve a Pyth
o
n linting error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eri
c
Irrga
n
g
Fix
b
roken Py
t
hon error ch
e
ck
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric Irrg
a
n
g
Remove
c
r
uft and resolve deprecation warnings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix do
c
stri
n
g
b
ugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric
Irrgang
Fix sphinx-build op
t
ion typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c Ir
r
gang
L
e
t com
m
andl
i
ne_ope
r
at
i
on a
c
cept stdi
n
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irr
g
ang
Mak
e
gmxapi
.
vers
i
on
.
has_feature warning m
o
r
e useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgan
g
Use subproc
e
s
s
.
run in
s
tead of subpr
o
cess
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irrgang
Improve gmx
a
p
i
.
ope
r
ation error handli
n
g
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrga
n
g
Cl
a
ri
f
y annotat
i
on ab
o
ut GitLab CI Docker images
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Er
i
c Irr
g
ang
S
i
mplify GitLab CI D
o
ckerf
i
les
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Irrgang
Estab
l
i
sh stubs for d
o
cumenting
G
itLab
c
onf
i
guration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
E
r
ic Irrgang
R
eform
a
t
.
gitla
b
-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eri
c
Irrga
n
g
U
s
e
en
u
m for gmxapi
.
testsupport
fixture options
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric I
r
rgang
Fur
t
her
c
onsolidate gmxapi
.
t
e
stsupport
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Updat
e
g
m
xapi
P
ython
packag
e
version and versioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric Irrg
a
ng
R
emove stray "to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric Irrgang
Remove
transitional links fo
r
online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric I
r
rgan
g
Add Flake8 linting to gmx
a
pi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
Use `todo` Sphi
n
x dire
c
tive
more
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
E
ric Ir
r
gang
Add tr
a
cking f
o
r
a documented action
item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Link some
"
to do"s in the dev manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Make
g
mxapi
.
testsupport usa
b
le as a pytest plugin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irrgang
R
e
sol
v
e CMa
k
e ambiguit
i
es for gmx
a
pi Pyth
o
n package
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric Irrgang
Update inte
r
sphin
x
con
f
ig
u
ratio
n
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Le
t
GMX
_
DEVEL
O
PER_BU
I
LD tr
i
g
g
er a "t
o
do" list
i
n t
h
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric
I
rrgang
S
et Sphi
n
x
d
efau
l
t role
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
i
c
Irrgang
F
i
x external web link
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Enable
Sphinx todo direct
i
ve for GMX_DEV
E
LOPER
_
BUILD
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Er
i
c Irrgang
Clean u
p
Sphinx interpreted text in the def
a
ult
rol
e
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric I
r
rgang
A
dd issue tracking fo
r
deprecations
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eric Irrga
n
g
Update reference to uncrustify and c
l
ang-fo
r
m
a
t
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
Eric Irrgang
Be more s
p
ecific with clang-forma
t
suggestions
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gmxapi land
i
ng pa
g
e upd
a
t
e
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric
I
rr
g
ang
gmx
a
pi
d
ocumentation readabilit
y
improvemen
t
s
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Er
i
c I
r
rgang
gmxapi documen
t
ation
formatting improvem
e
n
t
s
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eri
c
Irrgang
Finalize gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irr
g
ang
Add
n
o
t
es on
M
PI with
gmxap
i
Python package
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
g
mxapi
P
ython p
a
ckag
e
usage
p
ros
e
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irr
g
an
g
Improve
pytest fixtu
r
es for
d
irectory management
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Er
i
c Irrgang
A
d
d gmxapi_exte
n
s
ion test
s
to 'tests' target
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
Er
i
c
Irrgang
Remov
e
s
tub content
from gmxap
i
d
o
c
s
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Remove ext
r
aneous file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
I
rrga
n
g
Add
t
ransitional links for online gmxapi Pytho
n
package
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
ic Irrgang
Improve gmx
a
pi Do
c
kerfiles
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Achieve gmxapi fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Ir
r
gang
Upda
t
es to gm
x
api FR15 ac
c
eptance
t
est
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
ric
I
rrgang
U
p
date no
t
es
a
nd tests regarding
g
mxapi
acce
p
tance
.
.
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric
Irrgang
Achieve gmxapi fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric
Irrga
n
g
U
p
d
ates to gm
x
api FR15 acceptance
test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric
I
rr
g
ang
Update notes and te
s
ts regarding gmxapi
acceptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
Er
i
c Irr
g
a
n
g
Fix bug intro
d
u
ced by clan
g
-format reformat
.
commit
|
commitdiff
|
tree
2019-11-08
M
.
E
r
ic I
r
r
g
a
n
g
Fi
x
bug i
n
tr
o
duced by clang-format reformat
.
commit
|
commitdiff
|
tree
2019-11-05
M
.
Eric Ir
r
gan
g
Upd
a
te
g
ooglete
s
t
l
ocation in
COPYING
.
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric
Irrgan
g
Update gmxapi Python document
a
tion instruct
i
ons
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eri
c
Irrgang
U
p
date Sphinx li
n
k
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric I
r
rgang
Fix
typ
o
s
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
E
ric I
r
rgang
Fix docu
m
e
n
t
ation typo
.
commit
|
commitdiff
|
tree
2019-11-01
M
.
E
r
ic Ir
r
g
ang
Normalize sa
m
pl
e
_restraint targ
e
t names
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric
Irr
g
ang
A
l
l
o
w validation of th
e
g
e
nerated
C
M
ake toolchain fi
l
e
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
ric Irrgang
Improve uni
f
ormity
o
f OS X CMake
c
onfigu
r
ati
o
n
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Re
s
tore CMake
c
onven
i
e
n
ce targets for
s
ample_restraint
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric
Ir
r
gang
Deduplicate g
m
x
ap
i
documentat
i
on
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrga
n
g
Disable
i
ts tests when s
a
mple
_
r
estraint is not the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
D
ecreas
e
the maximum all
o
wed Python version for gmxapi
.
commit
|
commitdiff
|
tree
2019-10-28
M
.
Eric Irrgang
Update bundled
pybi
n
d
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Ir
r
gan
g
Fix CMake me
s
sage typo
.
commit
|
commitdiff
|
tree
2019-10-25
M
.
Eric Irrgang
Improv
e
gmxapi md
r
un test
.
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric
I
r
rgang
Suppress some
o
u
t
pu
t
when sample_restra
i
nt i
s
built
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgang
Add trajector
y
outp
u
t
to mdrun operation
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrgang
Minor tidying to mdrun
.
py
commit
|
commitdiff
|
tree
2019-10-16
M
.
Er
i
c Irrg
a
ng
Mino
r
clean-u
p
to gmxapi package
.
commit
|
commitdiff
|
tree
2019-10-16
M
.
Eric Irrgang
U
p
d
ate g
m
xapi
.
version module
.
commit
|
commitdiff
|
tree
next