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Enable MPI ensemble testing for gmxapi.
2020-05-26
M
.
Eri
c
I
rrgang
E
n
a
b
le MPI e
n
semble
tes
t
ing for gmxapi
.
commit
|
commitdiff
|
tree
2020-05-26
M
.
Eric Irrgang
N
o
rmali
z
e
g
m
xapi related rele
a
se-2
0
20 job logic
.
commit
|
commitdiff
|
tree
2020-05-20
M
.
Er
i
c Irrgang
Make sure im
a
ges have /usr/bin/py
t
hon
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Ir
r
gang
Update dock
e
r
im
a
ge bui
l
d scripts for mast
e
r bran
c
h
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
Make sure
C
I
script can ca
l
l /bin
/
e
nv python`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrga
n
g
Minor cle
a
n
up to buildall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgan
g
All
o
w llvm option a
l
r
e
ady used in
b
uildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
ang
Reduce c
o
nsole l
o
g output from sample_restraint te
s
ts
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrgang
Refi
n
e usa
g
e
o
f *job:tags*
parameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
U
p
d
ate header sort
i
ng
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irrgang
Require C++17 s
t
andard a
n
d
ST
L
f
e
a
t
ures
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eri
c
Irrgang
Apply more granular CTest
time-out
poli
c
y
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric
Irrgan
g
Resolve static analyzer wa
r
nings from google
tes
t
s
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Er
i
c
Ir
r
gang
Avoid tempo
r
ary
string
s
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric
I
rr
g
an
g
Note CUDA builds in job na
m
es
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
E
r
ic Ir
r
gang
Update bundle
d
pybi
n
d
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrga
n
g
Only set GMX_PYTHON_PACKAGE=O
N
wher
e
needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric Irrgang
Use
C
M
ake 3
.
12
+
facilities for detect
i
ng
P
y
t
hon
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
Eri
c
Irrgang
Ch
a
nge
default CMake versio
n
t
o
3
.
13
.
0 for C
I
i
mage
s
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Ir
r
g
a
ng
R
equire CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Irrga
n
g
Fix invalid g
i
tlab-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-04-09
M
.
Eric Ir
r
gang
Al
l
ow useful
CI
t
o
r
un in for
k
s
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Ir
r
gang
Ex
p
licitly set UTF-
8
encoding f
o
r gmxapi
C
L
I interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
E
r
ic Irrg
a
ng
Prep
a
re Python environme
n
t
s f
o
r GitLab CI pi
p
e
l
ine
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric
I
rrgang
Improve gmx
a
pi Python p
a
ckage dependenc
y
resolutio
n
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrgang
Pr
u
ne
change-manageme
n
t
.
rst and up
d
a
t
e links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Eric Irrgang
Modernize
s
o
m
e
Pyth
o
n subp
r
ocess
c
a
lls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
E
ric
I
r
rg
a
ng
Avoid
acc
i
d
en
t
ally i
n
itia
l
iz
i
ng pyen
v
i
n
CI
i
mag
e
s
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Prepa
r
e Python environments fo
r
GitLab CI pip
e
line
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eri
c
Irrgang
U
pd
a
te script
s
for a
l
l of the re
q
u
ested pr
e
-co
m
mit
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
E
r
ic
I
rrgang
Require Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrga
n
g
C
ompartmentalize
hpccm
b
u
i
ld stages
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Er
i
c Irrgang
Be fr
i
endlie
r
w
.
r
.
t
.
l
i
nkchecker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Er
i
c Irrga
n
g
Mock h
p
ccm
i
mport so infrastructure
d
ocs bui
l
d ea
s
ily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic
I
rrgang
Extr
a
c
t logic
f
or when CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irr
g
ang
Nor
m
ali
z
e
s
ome
m
ore
job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
S
im
p
lify
archive
.
g
itlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irr
g
ang
R
emove redund
a
n
t
j
obs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
Fix duplicate variables paramete
r
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Add requi
r
ed Infrast
r
u
c
ture for Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Norma
l
ize naming for gromacs bui
l
d/testin
g
jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
ang
Re
m
ove some unneces
s
ary indirect
i
on in job definitio
n
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Co
n
sol
i
date
.
u
se-cla
n
gX CI jo
b
mix
-
in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
C
onsol
i
date
.
use-gc
c
X CI job mi
x
-
i
n
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ri
c
Irrgan
g
Adopt
CI
job na
m
ing guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Norma
l
ize
G
i
t
Lab-CI *cache* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irr
g
ang
Merge environ
m
ent
support into g
l
obal
.
gitlab
-
ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Move
.
b
u
ild-template
.
yml
definitions
closer to poi
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
Merg
e
*-test-te
m
plate
.
yml in
t
o
t
esting-matrix
.
g
i
tlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Merg
e
.
test-runn
e
r-templat
e
.
yml into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merg
e
.
te
s
t-script-template
.
yml into testing-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irrg
a
ng
M
erge
.
regressiontest-template
.
yml int
o
archive config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
Irrgang
Consol
i
date docume
n
tation
t
emplates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rg
a
n
g
Reorganize release templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Er
i
c
I
rrgang
R
emove
c
on
f
usi
n
g
and d
u
pl
i
cated variables
assignment
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Er
i
c Irrgang
C
onsolidate global mi
x
-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip] Re
m
ove indi
r
ecti
o
n for defau
l
t tags para
m
e
t
er
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
r
ic Irrg
a
ng
[ci skip] Re
o
rganize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic
I
rrgan
g
Document CI variable and remove unused template
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eri
c
Irrgang
Disable sphinx
.
e
x
t
.
viewcode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Er
i
c
I
rrg
a
ng
Add stub Variables document
a
tion to
G
i
t
Lab CI
doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric
I
rr
g
ang
Re
m
ove duplicated YAML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgan
g
Ad
d
doc
u
ment for contai
n
erization
infr
a
structure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
A
lphabetize
l
ist for readab
i
l
i
t
y
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
ric Irrgang
Re
f
ormat arg
u
ments for re
a
dability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Define an
argparse
p
arent pa
r
ser for container ima
g
e
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
B
uild M
P
I in Dockerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
M
e
rge conf
.
py and conf
-
vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eri
c
Irrgang
Distin
g
u
ish Docker images for d
i
fferent re
l
ease
r
e
q
uirements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
ric
I
r
rgang
F
ree up Doc
k
er image tag namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
Irrgang
Remove duplica
t
ed GitLab-CI jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
ic Ir
r
gang
Reformat
.
gitlab-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrg
a
ng
Cons
o
lidate logic f
o
r
w
h
e
ther
t
o
use Mo
d
u
la
r
S
i
mulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Man
a
ge the list of image tags in Docker build
scr
i
pt
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eri
c
Irrgang
M
a
n
age the list of image tags in
D
o
cker build script
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrgang
Re
s
o
lve a Python linti
n
g error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
r
ic Irrgan
g
Fix broken Python erro
r
che
c
k
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric Irrgang
R
e
move cruft and resolve de
p
recat
i
o
n warni
n
gs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix docstring bugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrg
a
n
g
Fix sph
i
nx-b
u
ild option typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric
Ir
r
gang
Let comm
a
ndline_operati
o
n
accep
t
stdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c
Irrgan
g
Make gmx
a
pi
.
v
er
s
io
n
.
has_f
e
ature warn
i
ng
m
ore useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irrgang
Use su
b
process
.
run instead of sub
p
rocess
.
check
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric
I
r
r
gang
Improve gmxapi
.
operation error handling
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
rgan
g
C
l
arify annotat
i
on a
b
out GitLab C
I
Docker image
s
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Er
i
c Irrgang
Simplify
G
itL
a
b CI Dockerfiles
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric I
r
rgang
E
stablish stu
b
s f
o
r
documenting GitLab
configurat
i
o
n
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric Irr
g
a
ng
Reformat
.
git
l
ab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Use enum for
g
mxapi
.
tes
t
support fixtur
e
options
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Further consoli
d
ate
g
mxapi
.
t
e
sts
u
pport
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
U
pdate
g
mxapi Python pac
k
age v
e
rsion a
n
d
versioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric
Irrgang
R
emove
stra
y
"to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
E
ric Ir
r
gang
Remove t
r
ans
i
t
i
onal
links
f
or o
n
line
g
mxapi
Pyt
h
on
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
A
d
d Flak
e
8 linting to gmxapi tes
t
s
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrgang
Use `todo`
S
p
h
inx directi
v
e m
o
re
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
E
r
i
c Irr
g
ang
Add tra
c
king for
a document
e
d
a
c
t
i
o
n
item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Er
i
c Irrgang
Link so
m
e "to do"s in the dev man
u
al
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrg
a
ng
Make
gm
x
api
.
testsupport usable as a
p
yt
e
st plugin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irr
g
a
n
g
Resolve CM
a
ke ambiguities fo
r
gmxapi Py
t
hon pac
k
age
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
E
r
ic
I
rrgang
Up
d
a
te int
e
rsphinx
c
onfigurat
i
on
.
commit
|
commitdiff
|
tree
next