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Update instructions in containers.rst
2020-05-14
M
.
Eric Irrgang
Allow llvm
option already used in bui
l
dall
.
sh script
.
commit
|
commitdiff
|
tree
2020-05-14
M
.
Eric Irr
g
a
n
g
Reduce consol
e
log
output fr
o
m sample
_
r
e
s
tr
a
int tes
t
s
.
commit
|
commitdiff
|
tree
2020-05-12
M
.
Eric Irrgang
Refine us
a
ge o
f
*
j
ob:tags*
p
arameter
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
Er
i
c Irr
g
ang
Update header sorting
.
commit
|
commitdiff
|
tree
2020-04-30
M
.
E
r
ic
I
rrg
a
ng
Requir
e
C++17 standard an
d
STL featu
r
es
.
commit
|
commitdiff
|
tree
2020-04-29
M
.
Eri
c
Irrg
a
ng
Ap
p
ly more granula
r
CTest time-out policy
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
E
ric Irrgang
Resolve st
a
tic ana
l
yzer warnings f
r
om
g
oogle tests
.
commit
|
commitdiff
|
tree
2020-04-27
M
.
Eric Irr
g
ang
Avoid temporar
y
strings
.
commit
|
commitdiff
|
tree
2020-04-25
M
.
Eric Irrgang
Note CUD
A
builds in job names
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Eric
I
rrgang
Upda
t
e bundled pybi
n
d
.
commit
|
commitdiff
|
tree
2020-04-24
M
.
Er
i
c
Irrgang
O
nl
y
se
t
G
MX_PYTHON
_
PACKAGE=ON where needed
.
commit
|
commitdiff
|
tree
2020-04-23
M
.
Eric Irrgang
Use CMake 3
.
1
2
+
facilities
f
or d
e
tecti
n
g Python
.
commit
|
commitdiff
|
tree
2020-04-15
M
.
E
r
i
c
I
r
rgang
C
han
g
e default CMake versio
n
to
3
.
13
.
0 for
CI images
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
E
r
ic Ir
r
ga
n
g
Require CMake
>
=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Ir
r
gang
Fix
i
n
valid gi
t
la
b
-
ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-04-09
M
.
Eric Irrgang
Allow
u
seful CI to run in
f
orks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Er
i
c Ir
r
gan
g
Explicitly set UTF-8 encoding for gmxa
p
i CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
E
ric Irrgang
Prepare Python environme
n
t
s
for GitLab
C
I pipeline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric
Irrgang
I
mpro
v
e
gm
x
a
p
i
P
y
thon pa
c
kage
d
ependency r
e
solution
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrgang
Prune
cha
n
g
e-management
.
rst and upd
a
te li
n
ks
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
Er
i
c Irr
g
ang
Modernize some Pyth
o
n subp
r
oces
s
calls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
E
r
i
c
Irrgang
Avoi
d
accidentally initializing
pyenv in C
I
im
a
ges
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgan
g
Prepare Python envi
r
onments for GitLab CI pipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Update sc
r
ip
t
s
for all of the requeste
d
p
r
e-commi
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrgang
Require Pyth
o
n
3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Irrgang
C
o
mpartment
a
liz
e
hp
c
cm
b
uild stages
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
E
r
i
c
Irrgang
Be friendl
i
er
w
.
r
.
t
.
l
i
nkcheck
e
r
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrgang
Mock hpccm import so
i
nfra
s
tructure
docs bui
l
d
eas
i
ly
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Extract logic f
o
r
w
hen CI jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrga
n
g
N
o
rmalize som
e
m
o
re job
n
ames
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irr
g
a
n
g
S
i
mplify a
r
ch
i
ve
.
gitlab-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric
Irrgang
R
e
move
redundant jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c Irrgang
F
i
x dup
l
icate variables par
a
m
eter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Add required
I
nfrastructure
f
or Gi
t
l
ab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Normalize naming
f
o
r
gr
o
macs build/test
i
ng jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Ir
r
g
a
ng
Remove some un
n
ecessar
y
i
n
d
ir
e
ct
i
on in job
definitions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c Ir
r
gang
Consolida
t
e
.
us
e
-clangX CI j
o
b mi
x
-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
ic Irr
g
ang
C
onsolidate
.
us
e
-gcc
X
CI
j
ob mix-in
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Adopt CI job naming guidelines
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irrgang
Nor
m
a
lize
G
i
tLab-CI *cache*
p
ara
m
eter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
Merge environment support in
t
o g
l
o
bal
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c I
r
r
g
a
n
g
Move
.
build-template
.
yml
definitions closer to poi
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
I
rrg
a
ng
Merge *-test-template
.
yml into testing
-
matrix
.
gitlab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merge
.
t
est-runner-temp
l
ate
.
yml into
t
esting-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
M
e
rge
.
tes
t
-
s
c
r
ipt-temp
l
ate
.
y
m
l into testin
g
-
m
a
trix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Merg
e
.
regressio
n
te
s
t-
t
em
p
l
a
te
.
yml i
n
to
a
rchiv
e
config
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Er
i
c Irr
g
ang
C
onso
l
i
d
ate documentation tem
p
lates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irr
g
ang
Reorganize release template
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
Remove confusin
g
and dupl
i
cated vari
a
ble
s
assignme
n
t
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrg
a
ng
C
o
nsolidate global mix-ins
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric
I
rrgang
[
c
i s
k
i
p] Remove indirection for def
a
ult t
a
gs paramete
r
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci skip
]
Reo
r
g
a
nize
.
gitl
a
b
-ci
.
ym
l
commit
|
commitdiff
|
tree
2020-03-18
M
.
Eric Irrgang
D
o
cument
C
I variable and re
m
ove unused t
e
mplate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic Irrgang
Dis
a
ble sphi
n
x
.
ext
.
viewcode
commit
|
commitdiff
|
tree
2020-03-18
M
.
Er
i
c Irrgang
Add stub Variables documentation to GitLab
CI doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric Irrgang
Remove duplicated YA
M
L key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
ric Irrgang
Add
doc
u
ment
for
containerization in
f
rastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric I
r
rgang
Alphabet
i
ze list for reada
b
ility
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Reformat arguments fo
r
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
Define an argparse parent
p
a
rser for container
image
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irrgang
B
u
ild MPI in Dockerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Er
i
c Irrg
a
ng
Merg
e
conf
.
py a
n
d conf-vars
.
py
.
commit
|
commitdiff
|
tree
2020-03-10
M
.
Eric
I
rrg
a
n
g
Dis
t
ing
u
ish Docker images for di
f
fe
r
ent release requ
i
rements
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Er
i
c
Irrgang
Free
up Docke
r
imag
e
tag nam
e
space
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
I
rrgang
R
e
move duplicated GitLab-
C
I jo
b
s
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrga
n
g
Reformat
.
gitl
a
b
-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
I
rrgang
Conso
l
i
d
at
e
l
o
g
ic f
o
r wh
e
ther to use Modula
r
S
i
mulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eri
c
I
r
rg
a
ng
Manag
e
the list of image tags in Docker
bu
i
ld
script
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Er
i
c I
r
r
g
ang
M
a
na
g
e the list of image
tags in Docker b
u
ild script
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric Ir
r
gang
Res
o
lv
e
a Python lin
t
ing error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Er
i
c
I
rrg
a
ng
Fix
brok
e
n Pytho
n
err
o
r
c
heck
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
Eric
I
rrgang
Remove cruft and res
o
lve de
p
recat
i
on war
n
ings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irr
g
ang
Fix do
c
s
t
ri
n
g bugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
i
c I
r
rgang
Fi
x
sph
i
nx-build opti
o
n
typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eri
c
Irrgang
Let co
m
mandline
_
op
e
r
ation accept st
d
i
n
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrga
n
g
Make gmxapi
.
version
.
has_featur
e
w
arnin
g
more
useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irr
g
ang
Use subpro
c
ess
.
ru
n
instead of
s
ubprocess
.
c
h
eck
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c
I
r
rgang
Im
p
rove gmxapi
.
operation erro
r
handlin
g
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Irrgan
g
Clarify a
n
n
otation about GitLab CI Docker images
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
E
ric
I
rrga
n
g
Simp
l
i
fy GitLa
b
CI Docke
r
fi
l
es
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric
Irrgang
Est
a
blish stub
s
f
o
r
d
o
cument
i
ng GitLab configuration
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric Ir
r
gang
R
e
format
.
gitla
b
-c
i
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
Use enum fo
r
gmxap
i
.
tes
t
suppo
r
t fixture o
p
tions
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric I
r
rgang
Further
consolidat
e
gmxapi
.
testsupport
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrg
a
n
g
Upda
t
e gmxapi Python packag
e
ver
s
ion and ve
r
s
ioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric Irrga
n
g
Remove stray "to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eric
I
rrgan
g
Remove
t
ransitiona
l
lin
k
s for
online gmxapi Python
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Er
i
c
I
rrgang
Add
Flake8 linting to g
m
xapi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Ir
r
gang
Use
`todo` Sphinx directive mor
e
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Add
t
racking for a documented acti
o
n item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric
I
rrga
n
g
Lin
k
s
o
me "to do"s in the
dev manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric
Irrgang
Make gm
x
a
p
i
.
tes
t
support usab
l
e a
s
a pytest plu
g
in
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irrgan
g
Res
o
lve C
M
ake ambiguities
f
or g
m
xapi Python package
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric Irrgang
Updat
e
intersphin
x
configuration
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
ic Irrgang
L
et GMX_DEVELOPER
_
BUI
L
D trigger a "to do" list in the
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irr
g
ang
Set
Sphinx def
a
ult rol
e
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Fix exter
n
al web link
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Er
i
c Irrgang
Enable Sphinx todo
d
ir
e
ct
i
ve for GM
X
_DEVELO
P
E
R_BUILD
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric
I
r
rgang
Clean up Sphinx interp
r
e
t
e
d
text in t
h
e defa
u
lt
role
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric Irrg
a
ng
Add issue track
i
ng for de
p
recations
.
commit
|
commitdiff
|
tree
next