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Fix warnings with clang 9
2020-04-15
M
.
Eric Irrgang
Change defaul
t
CMa
k
e version
t
o 3
.
13
.
0
for
CI imag
e
s
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric
Irrgang
Requir
e
CMake >=3
.
13
.
commit
|
commitdiff
|
tree
2020-04-14
M
.
Eric Ir
r
ga
n
g
Fix invalid gitlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-04-09
M
.
Eric Irr
g
ang
Allow useful CI
to run i
n
forks
commit
|
commitdiff
|
tree
2020-04-08
M
.
Eric Irrg
a
ng
Explicitly s
e
t UTF-8 encoding for gmx
a
pi CLI interaction
.
commit
|
commitdiff
|
tree
2020-04-07
M
.
E
r
ic Irrga
n
g
Prepare Python environme
n
ts
f
or GitLab CI
p
ipeline
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
E
r
ic Irrgan
g
Improve gmxapi Python packa
g
e de
p
endency resolu
t
ion
.
commit
|
commitdiff
|
tree
2020-04-03
M
.
Eric Irrgang
Prune chan
g
e-manage
m
en
t
.
rst and
u
pda
t
e links
.
commit
|
commitdiff
|
tree
2020-04-02
M
.
E
r
ic Irrgang
Mode
r
ni
z
e
so
m
e Python subprocess
calls
.
commit
|
commitdiff
|
tree
2020-04-01
M
.
Eric Irrg
a
ng
Av
o
id
a
ccident
a
lly initial
i
zing
pyenv in
CI i
m
ages
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Irrgang
Prepare Python envir
o
nments for G
i
tLab
C
I
pipeline
.
commit
|
commitdiff
|
tree
2020-03-31
M
.
Eric Ir
r
gan
g
U
pdate scripts f
o
r all of
t
he requested pre-co
m
mit
.
.
.
commit
|
commitdiff
|
tree
2020-03-30
M
.
Eric Irrga
n
g
R
e
quire Python 3
.
6
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric I
r
rgang
C
o
m
p
a
rtmentaliz
e
hpcc
m
build
s
tages
.
commit
|
commitdiff
|
tree
2020-03-27
M
.
Eric Ir
r
gang
B
e fri
e
ndlier w
.
r
.
t
.
linkchecker
.
commit
|
commitdiff
|
tree
2020-03-25
M
.
Eric Irrg
a
ng
Mock hpcc
m
import so infr
a
s
tructure docs build
easily
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irr
g
ang
Extract logic fo
r
when
C
I jobs execute
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
Normalize s
o
me more job names
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrgang
Simpli
f
y
archi
v
e
.
g
i
tlab-ci
.
y
m
l
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
r
i
c
Irrgang
Remove redund
a
nt
j
obs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
E
ric Irrg
a
ng
Fix
duplicate variables par
a
meter
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Er
i
c
Irrg
a
ng
Add
required Infrastructure for Gitlab merges
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Ir
r
gang
N
ormalize
n
a
m
ing for grom
a
c
s buil
d
/
testing jobs
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric Irrg
a
ng
Rem
o
ve some
u
nnece
s
s
ary indirection in j
o
b
def
i
n
i
tions
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
rg
a
ng
Consolidate
.
use
-
clangX CI
j
ob m
i
x
-in
.
commit
|
commitdiff
|
tree
2020-03-23
M
.
Eric I
r
r
gang
C
o
nsolid
a
te
.
use-
g
ccX CI job mix-i
n
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Adopt
CI job
n
aming guidel
i
n
es
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrgang
Normalize GitLab-CI *c
a
che* parameter
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
ric Irrgang
Merge
e
nvi
r
onment support into global
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-22
M
.
E
r
ic
Irrgang
Move
.
build
-
templ
a
t
e
.
yml defini
t
i
ons clos
e
r
to point
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
I
r
rgang
Merge *-test
-
tem
p
late
.
yml int
o
testin
g
-matrix
.
git
l
ab
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric Irrga
n
g
Merge
.
t
e
st-run
n
e
r
-templa
t
e
.
yml into te
s
ting-
m
atrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eri
c
Irrgang
Merge
.
test-
s
cript-t
e
m
plate
.
yml into test
i
ng-matrix
.
.
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
r
r
gang
Merg
e
.
r
egressiontes
t
-template
.
yml into
a
rc
h
ive co
n
fig
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric
I
rrgang
Consolida
t
e
documentation templates
.
commit
|
commitdiff
|
tree
2020-03-22
M
.
Eric I
r
rgang
Re
o
r
ganize release templates
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
Remo
v
e confus
i
ng
a
n
d duplic
a
ted
variables a
s
signment
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
Consolidat
e
g
lo
b
al mix-i
n
s
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
E
r
i
c
Irrgang
[ci ski
p
] Rem
o
ve indirec
t
io
n
for d
e
fault tags pa
r
ameter
.
commit
|
commitdiff
|
tree
2020-03-19
M
.
Eric Irrgang
[ci ski
p
]
Reorganize
.
gitlab-ci
.
yml
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
ic Irrgang
Document CI variable
a
nd rem
o
ve unused temp
l
ate
.
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
r
i
c
I
r
rgang
Disable
s
p
h
inx
.
ext
.
viewco
d
e
commit
|
commitdiff
|
tree
2020-03-18
M
.
E
ric Irrgang
Add stub
V
a
riables documentation to
G
itLab
C
I doc
.
commit
|
commitdiff
|
tree
2020-03-17
M
.
Eric Irrgang
Remov
e
duplicated
Y
AML key
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric
I
rrgang
A
d
d d
o
cu
m
ent for containerization infrastructure
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Irr
g
an
g
Alpha
b
e
t
ize
lis
t
fo
r
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Eric Ir
r
gan
g
R
e
forma
t
arguments for
readability
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
Er
i
c Irrgang
Defin
e
a
n
argparse parent par
s
er f
o
r co
n
tainer im
a
ge
.
.
.
commit
|
commitdiff
|
tree
2020-03-16
M
.
E
ric
I
rr
g
ang
Bui
l
d MPI
i
n Dockerfile
.
commit
|
commitdiff
|
tree
2020-03-15
M
.
Eric Irrgang
Me
r
ge c
o
nf
.
p
y and
c
onf-v
a
rs
.
py
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
ric Irr
g
an
g
Fre
e
up Dock
e
r im
a
g
e
tag nam
e
sp
a
c
e
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric
Irrgang
Re
m
ove
d
upli
c
a
t
ed GitLab-CI jobs
.
commit
|
commitdiff
|
tree
2020-03-09
M
.
Eric Irrgan
g
Ref
o
rmat
.
gitlab-ci
.
y
ml
commit
|
commitdiff
|
tree
2020-03-09
M
.
E
r
ic Irrg
a
ng
Consolid
a
te logic for whether
to u
s
e
M
odularSimulator
.
commit
|
commitdiff
|
tree
2020-03-07
M
.
Eric Irrgang
Manage th
e
list of imag
e
tags in Docker build scrip
t
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
E
ric Irrga
n
g
Resolve a Pyt
h
on l
i
nt
i
ng
error
.
commit
|
commitdiff
|
tree
2020-02-27
M
.
Eric I
r
rgang
Fix broken Pyt
h
on erro
r
check
.
commit
|
commitdiff
|
tree
2020-02-25
M
.
E
ric Irrgang
R
e
m
o
ve cruft and
resolve d
e
pre
c
ation warnings
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irrgang
F
ix docstrin
g
bugs
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
ric Irrgang
Fix sphinx-build option typo
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eri
c
I
rrgang
Let
c
ommandline_
o
pera
t
ion accept stdin
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
E
r
ic Irrgang
Make gmxapi
.
v
ersi
o
n
.
has_feat
u
re wa
r
ning
m
ore useful
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c Irrgang
U
se subprocess
.
r
un instead of subproce
s
s
.
c
h
e
ck
commit
|
commitdiff
|
tree
2020-02-24
M
.
Eric Ir
r
gang
Improv
e
gmx
a
p
i
.
o
p
eration er
r
or h
a
ndling
.
commit
|
commitdiff
|
tree
2020-02-24
M
.
Er
i
c
Irrgang
Clarify annot
a
tion
ab
o
u
t
GitLab C
I
Docker
i
m
a
g
es
.
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric I
r
rgang
Simplify GitLab CI Dockerfi
l
e
s
.
commit
|
commitdiff
|
tree
2020-02-17
M
.
Eric Irrgang
Establ
i
sh stu
b
s for documenting GitLab
co
n
figur
a
tion
.
commit
|
commitdiff
|
tree
2020-02-15
M
.
Eric Irrgang
Reforma
t
.
gitlab
-
ci
.
yml
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric I
r
rgang
U
s
e enum
for gmxapi
.
t
estsupport fixture options
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eri
c
Irrg
a
ng
Further conso
l
idate gm
x
api
.
testsupport
.
commit
|
commitdiff
|
tree
2020-01-09
M
.
Eric Irrgang
U
pdate gmxa
p
i Python package versi
o
n
and versioning
.
.
.
commit
|
commitdiff
|
tree
2020-01-07
M
.
Eric Irrga
n
g
Remove stray "to do"
.
commit
|
commitdiff
|
tree
2020-01-03
M
.
Eri
c
Irrgang
Remove tran
s
ition
a
l
links for online gmxapi Pyth
o
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Eric Irrg
a
ng
A
d
d Flake8 linting
t
o gmxapi tests
.
commit
|
commitdiff
|
tree
2020-01-02
M
.
Er
i
c Irrgang
Use `tod
o
` S
p
h
i
n
x di
r
ective more
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
E
r
ic Irrga
n
g
Add tracking for a documented action item
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irrgang
Link
s
ome "to d
o
"s in the dev manual
.
commit
|
commitdiff
|
tree
2019-12-30
M
.
Eric Irr
g
a
ng
Mak
e
gmxapi
.
tests
u
pp
o
rt
u
sab
l
e as a pytest
p
l
u
gin
.
commit
|
commitdiff
|
tree
2019-12-28
M
.
E
r
i
c Irrgang
R
e
s
o
lve
C
Make a
m
biguities for gmxapi
P
ython package
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
M
.
Eric
I
rrgan
g
Update inter
s
phinx configu
r
ation
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
L
e
t GMX_DE
V
ELOPE
R
_BUILD trigger a "to do"
li
s
t i
n
the
.
.
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Set Sphinx de
f
ault role
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Fix e
x
ter
n
a
l
web
link
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
Eric Irrgang
Enable
Sp
h
i
nx tod
o
d
i
rec
t
i
v
e for GMX_DEVELOPER_BUILD
.
commit
|
commitdiff
|
tree
2019-12-26
M
.
E
r
ic
Irrgang
Cl
e
an up Sphinx
interp
r
eted text in
t
he de
f
ault ro
l
e
.
commit
|
commitdiff
|
tree
2019-12-19
M
.
Eric Irrgang
Add issue tracking for deprec
a
t
i
o
n
s
.
commit
|
commitdiff
|
tree
2019-12-18
M
.
Eric Irrga
n
g
U
p
da
t
e ref
e
rence to uncr
u
stif
y
and
clang-for
m
at
.
commit
|
commitdiff
|
tree
2019-12-17
M
.
Eric Irrgang
Be more specific with
c
l
a
ng-format suggestions
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric
I
rrg
a
ng
gm
x
ap
i
landi
n
g page update
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Ir
r
gang
g
mxapi d
o
cumentati
o
n
readability im
p
rovement
s
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gmxapi
d
ocumentation fo
r
m
a
tting improvement
s
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Er
i
c Irrgang
Finalize gmxa
p
i 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
I
r
rgang
A
d
d no
t
es
o
n MPI wi
t
h gmxapi Python packag
e
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrga
n
g
gmxap
i
P
y
t
ho
n
package us
a
ge pr
o
se
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
I
mprove py
t
est fixtures
f
or directory ma
n
ag
e
ment
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
E
r
ic
Irrgang
Add gmxapi_extensio
n
t
e
sts to 'tests
'
t
a
rget
.
commit
|
commitdiff
|
tree
2019-11-20
M
.
Eric
Irrgang
Remove
stub
c
ontent from gmxapi docs
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
ric Irrgan
g
Re
m
ove
extraneous file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Ir
r
gang
Add
transitional links for online
gmxapi
P
ython
packag
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
i
c Ir
r
gang
Improve gmxapi Do
c
ker
f
ile
s
.
commit
|
commitdiff
|
tree
next