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Make sure CI script can call /bin/env python`
2020-05-14
M
.
E
ric Irrgang
Make sure C
I
script can call /bi
n
/env
p
yt
h
on
`
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric
Irrga
n
g
Minor
c
lean up to bu
i
ldall
.
sh
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irrgang
All
o
w llvm optio
n
alre
a
dy used in buildall
.
sh script
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric Irr
g
ang
Update heade
r
sort
i
ng
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Eric I
r
rgang
Req
u
ire C++17
s
tandard
a
nd
S
TL feat
u
res
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eric Irrgan
g
Apply more granular
C
Tes
t
time-out po
l
icy
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrg
a
n
g
Note CUDA builds in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric Irrgang
On
l
y
s
et GMX_PYTHO
N
_PACKAGE=ON whe
r
e needed
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
E
ric Irrgang
Change default CMake version to
3
.
13
.
0
f
or CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
r
i
c
I
rrgang
Require C
M
ake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-08
M
.
E
ri
c
Irrgang
E
xplic
i
tly set
U
TF-8 encod
i
n
g
fo
r
gmxapi CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Er
i
c Irrg
a
ng
A
v
oid a
c
cidentally initializing pyenv
i
n CI images
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
E
r
ic Irr
g
ang
Moc
k
hpccm import so i
n
frastructure docs bu
i
l
d
easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
rr
g
ang
Extract l
o
gic for when CI
jo
b
s
e
xecute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgan
g
Normalize some
more j
o
b names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rgang
S
implify archi
v
e
.
gitlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
R
emove
re
d
undant
j
obs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irr
g
a
n
g
Fix du
p
licate
vari
a
b
les parameter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c I
r
r
g
ang
Add require
d
Infra
s
tructure for Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eri
c
Irrga
n
g
Normalize na
m
i
n
g for gromacs
b
uild/te
s
ting jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
I
r
rgang
Remov
e
so
m
e unn
e
ce
s
sary indirec
t
io
n
in
j
ob
definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irrga
n
g
Consolidate
.
use-clangX CI job m
i
x-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
an
g
Consolidate
.
us
e
-gccX C
I
job mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Adopt C
I
j
ob nam
i
ng guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrg
a
ng
Normalize GitLab-CI *c
a
che* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
M
e
r
ge
e
nvironme
n
t support
i
n
to global
.
g
i
tlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Move
.
buil
d
-template
.
yml defini
t
ions
closer to po
i
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Ir
r
ga
n
g
M
e
rge *-te
s
t
-temp
l
ate
.
yml
i
n
t
o testing-matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Merge
.
test-run
n
er
-
t
emplate
.
y
m
l
int
o
testing
-
m
atrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
test-script-template
.
yml int
o
testing-matri
x
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Mer
g
e
.
regressionte
s
t-
t
e
m
plate
.
y
ml into archive conf
i
g
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Consolidate documen
t
at
i
on templates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
R
e
o
rganiz
e
rel
e
ase templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Er
i
c I
r
rgang
Remove con
f
using and
duplica
t
e
d variables a
s
s
i
gnment
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
r
ic Irrgang
Co
n
solida
t
e gl
o
bal mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric I
r
rgang
[ci skip]
R
emove indi
r
ection
f
or default tags parame
t
er
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip] R
e
organize
.
gi
t
lab-
c
i
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrga
n
g
Document CI variable and remove
u
nused temp
l
ate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric Irrgang
Disable sphin
x
.
ext
.
v
i
ewc
o
de
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgan
g
Add
s
tub V
a
riables documentation to G
i
tLab CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Er
i
c
Irrgan
g
Remove
d
upl
i
cat
e
d
Y
AML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Add
document for conta
i
ner
i
z
at
i
o
n
in
f
rastruc
t
ure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Alphabet
i
ze lis
t
for readab
i
lity
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
r
ic
Irrg
a
n
g
Reforma
t
argument
s
for readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c Irrgang
Define
a
n
a
r
g
parse parent pars
e
r for co
n
ta
i
ner image
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Build MPI in
Dockerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eri
c
Irrgang
Me
r
ge
c
o
nf
.
py and con
f
-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric
I
rrgang
D
istingu
i
sh Docke
r
images
f
or d
i
fferent
r
elease requi
r
ements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
Irrgan
g
Fr
e
e up Docker image
ta
g
namespace
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrga
n
g
Remo
v
e duplicated GitLab-CI j
o
b
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgang
Reformat
.
gitlab-
c
i
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eri
c
Irrgang
Consolidate l
o
gic fo
r
whe
t
her to use
ModularSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
E
r
ic Irrgang
Man
a
g
e the list of image tags in Docker
bui
l
d sc
r
ipt
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
M
ana
g
e the list of image
tag
s
in Docke
r
build scrip
t
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrga
n
g
Resol
v
e a Python linting error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Irrg
a
ng
Fi
x
broken Pyt
h
on erro
r
check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric Irrgang
R
e
move
c
ruft an
d
re
s
olve deprecation wa
r
nings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric
Irrgang
Fix d
o
cstring b
u
gs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgang
Fix sphinx
-
build option typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric I
r
rgang
Let
commandline_oper
a
tio
n
accept
s
tdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eri
c
Irrgan
g
Make gmxap
i
.
version
.
has_feature warning more
useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrg
a
ng
Use subprocess
.
run
i
nstead of subproce
s
s
.
c
h
eck
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irr
g
a
n
g
Improve gmxapi
.
operation e
r
ror han
d
l
i
ng
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irr
g
ang
Clarify anno
t
atio
n
about Git
L
ab
C
I Docker im
a
ges
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Er
i
c Irrgang
Simplif
y
GitLab CI Dockerfiles
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric
I
rrg
a
ng
Establish stubs for doc
u
menting GitL
a
b conf
i
guration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eri
c
Irrgang
R
e
f
ormat
.
gitlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Use e
n
u
m
for gmxapi
.
testsupport fix
t
ure opti
o
ns
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Further consolidate gmxapi
.
testsupport
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Upd
a
te gmxapi Py
t
hon p
a
c
k
age version and versioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
E
r
ic Irr
g
ang
R
e
m
o
ve stra
y
"to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
E
r
i
c
Irrgang
Remove t
r
ansitio
n
a
l links f
o
r
o
nline
g
mxapi P
y
thon
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eri
c
I
r
r
ga
n
g
Add Flake8 linting to gmxap
i
tes
t
s
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Ir
r
gang
Use `tod
o
`
Sphi
n
x directive mor
e
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Add tracking for
a docum
e
nted acti
o
n item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric
Irr
g
ang
Link some "to
d
o"s in
the dev manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
E
ric Irrgang
Make gmxapi
.
t
e
stsupport usab
l
e as
a pytest
p
lug
i
n
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Er
i
c Irrgang
R
esolve C
M
ake am
b
igui
t
ies f
o
r
gmx
a
pi Python package
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric Irrgang
Update intersphinx confi
g
uration
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eri
c
Irrgang
Let GMX_DEVE
L
O
P
ER_BUILD trigger a
"to do"
l
ist in
th
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
ic
Irrga
n
g
Set Sph
i
nx def
a
ult
r
ole
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric
I
r
rgang
Fix external web link
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
ric
I
rrg
a
ng
Enable Sphinx to
d
o
directive for GMX_DE
V
E
LOPE
R
_BU
I
L
D
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Clean up Sp
h
inx int
e
rpreted tex
t
in the default role
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric Irr
g
ang
Add issue track
i
ng fo
r
deprecations
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eric Irrg
a
ng
Upda
t
e reference to uncrustify an
d
clang-format
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
Eric Irrgang
Be m
o
r
e
s
pecific with clang-format sugges
t
io
n
s
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric
Irrgang
gmxapi landing page update
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrg
a
ng
gm
x
api documentation readability improvements
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Er
i
c Irrgang
gmxapi doc
u
mentation for
m
atting im
p
rovements
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric Irrga
n
g
F
inalize gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrga
n
g
Add notes on MPI wi
t
h gmxa
p
i Py
t
h
on pa
c
k
age
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgan
g
gmxapi Python p
a
ckage usage prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
Improve pytest
f
ixtur
e
s
f
or
di
r
ecto
r
y management
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgang
Add gmxapi_exte
n
si
o
n tests
to 'test
s
'
tar
g
e
t
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric Irr
g
a
ng
R
e
m
ov
e
s
t
ub content from gmxapi
d
ocs
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
i
c
Irrgang
Rem
o
ve extran
e
ous file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Add transitional l
i
nks
for
online
g
mxapi Python package
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric
I
rrgang
Improve gmxap
i
Do
c
kerfiles
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Achieve gmxapi fr15
.
commit
|
commitdiff
|
tree
next