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nomad-lab
nomad-FAIR
Commits
9a46c6eb
Commit
9a46c6eb
authored
Aug 26, 2019
by
Markus Scheidgen
Browse files
Merge branch 'v0.5.3' into 'master'
v0.5.3 See merge request
!56
parents
e6bbf192
ccb3a4fa
Pipeline
#54362
passed with stage
in 23 seconds
Changes
10
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2
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README.md
View file @
9a46c6eb
...
...
@@ -76,6 +76,7 @@ Open [http://localhost:8888/html/setup.html](http://localhost:8888/html/setup.ht
your browser.
## Change log
Omitted versions are plain bugfix releases with only minor changes and fixes.
### v0.5.2
-
allows to download large files over longer time period
...
...
crystal
@
7863212e
Compare
a824f0f7
...
7863212e
Subproject commit
a824f0f72303bb8e39c8ae7ee710210edc287331
Subproject commit
7863212e4bde3443fae8fbb57caf3b0d95fb28f3
nomad/cli/admin/uploads.py
View file @
9a46c6eb
...
...
@@ -77,16 +77,47 @@ def query_uploads(ctx, uploads):
@
uploads
.
command
(
help
=
'List selected uploads'
)
@
click
.
argument
(
'UPLOADS'
,
nargs
=-
1
)
@
click
.
option
(
'-c'
,
'--calculations'
,
is_flag
=
True
,
help
=
'Show details about calculations.'
)
@
click
.
option
(
'--ids'
,
is_flag
=
True
,
help
=
'Only show a list of ids.'
)
@
click
.
option
(
'--json'
,
is_flag
=
True
,
help
=
'Output a JSON array of ids.'
)
@
click
.
pass_context
def
ls
(
ctx
,
uploads
):
def
ls
(
ctx
,
uploads
,
calculations
,
ids
,
json
):
_
,
uploads
=
query_uploads
(
ctx
,
uploads
)
def
row
(
upload
):
row
=
[
upload
.
upload_id
,
upload
.
name
,
upload
.
user_id
,
upload
.
process_status
,
upload
.
tasks_status
,
upload
.
published
]
if
calculations
:
row
+=
[
upload
.
total_calcs
,
upload
.
failed_calcs
,
upload
.
total_calcs
-
upload
.
processed_calcs
]
return
row
headers
=
[
'id'
,
'name'
,
'user'
,
'process'
,
'tasks'
,
'published'
]
if
calculations
:
headers
+=
[
'calcs'
,
'failed'
,
'processing'
]
if
ids
:
for
upload
in
uploads
:
print
(
upload
.
upload_id
)
return
if
json
:
print
(
'[%s]'
%
','
.
join
([
'"%s"'
%
upload
.
upload_id
for
upload
in
uploads
]))
return
print
(
'%d uploads selected, showing no more than first 10'
%
uploads
.
count
())
print
(
tabulate
(
[
[
upload
.
upload_id
,
upload
.
name
,
upload
.
user_id
,
upload
.
process_status
,
upload
.
published
]
for
upload
in
uploads
[:
10
]],
headers
=
[
'id'
,
'name'
,
'user'
,
'status'
,
'published'
]))
[
row
(
upload
)
for
upload
in
uploads
[:
10
]],
headers
=
headers
))
@
uploads
.
command
(
help
=
'Change the owner of the upload and all its calcs.'
)
...
...
nomad/cli/client/statistics.py
View file @
9a46c6eb
...
...
@@ -200,7 +200,7 @@ def bar_plot(client, retrieve, metric1, metric2=None, title=None):
@
client
.
command
(
help
=
'Generate various matplotlib charts'
)
@
click
.
option
(
'--errors'
,
is_flag
=
True
,
help
=
'Two charts with relative and absolute parser/normalizer errors per code.'
)
@
click
.
option
(
'--x-axis'
,
type
=
str
,
help
=
'Aggregation used for x-axis, values are "code" and "time".'
)
@
click
.
option
(
'--y-axis'
,
multiple
=
True
,
type
=
str
,
help
=
'Metrics used for y-axis, values are "entries", "energies", "users".'
)
@
click
.
option
(
'--y-axis'
,
multiple
=
True
,
type
=
str
,
help
=
'Metrics used for y-axis, values are "entries", "energies",
"calculations",
"users".'
)
@
click
.
option
(
'--cumulate'
,
is_flag
=
True
,
help
=
'Cumulate over x-axis.'
)
@
click
.
option
(
'--title'
,
type
=
str
,
help
=
'Override chart title with given value.'
)
@
click
.
option
(
'--total'
,
is_flag
=
True
,
help
=
'Provide total sums of key metrics.'
)
...
...
@@ -258,6 +258,11 @@ def statistics(errors, title, x_axis, y_axis, cumulate, total):
'total_energies'
,
label
=
'total energy calculations'
,
cumulate
=
cumulate
,
power
=
0.25
if
not
cumulate
else
1
,
multiplier
=
1e-6
,
format
=
'{x:,.1f}M'
),
'calculations'
:
Metric
(
'calculations'
,
label
=
'single configuration calculations'
,
cumulate
=
cumulate
,
power
=
0.25
if
not
cumulate
else
1
,
multiplier
=
1e-6
,
format
=
'{x:,.1f}M'
)
}
...
...
@@ -279,5 +284,5 @@ def statistics(errors, title, x_axis, y_axis, cumulate, total):
bar_plot
(
client
,
x_axis
,
*
y_axis
,
title
=
title
)
if
total
:
data
=
client
.
repo
.
search
(
per_page
=
1
,
owner
=
'admin'
,
metrics
=
[
'total_energies'
,
'users'
,
'datasets'
]).
response
().
result
data
=
client
.
repo
.
search
(
per_page
=
1
,
owner
=
'admin'
,
metrics
=
[
'total_energies'
,
'calculations'
,
'users'
,
'datasets'
]).
response
().
result
print
(
data
.
quantities
[
'total'
])
nomad/cli/parse.py
View file @
9a46c6eb
...
...
@@ -30,7 +30,7 @@ def parse(
else
:
parser_name
=
parser
.
__class__
.
__name__
assert
parser
is
not
None
,
'there is no
t
parser matching %s'
%
mainfile
assert
parser
is
not
None
,
'there is no parser matching %s'
%
mainfile
logger
=
logger
.
bind
(
parser
=
parser
.
name
)
# type: ignore
logger
.
info
(
'identified parser'
)
...
...
nomad/config.py
View file @
9a46c6eb
...
...
@@ -193,7 +193,7 @@ client = NomadConfig(
url
=
'http://localhost:8000/fairdi/nomad/latest/api'
)
version
=
'0.5.
2
'
version
=
'0.5.
3
'
commit
=
gitinfo
.
commit
release
=
'devel'
domain
=
'DFT'
...
...
nomad/parsing/__init__.py
View file @
9a46c6eb
...
...
@@ -263,13 +263,10 @@ parsers = [
LegacyParser
(
name
=
'parsers/gaussian'
,
code_name
=
'Gaussian'
,
parser_class_name
=
'gaussianparser.GaussianParser'
,
# This previous file matching string was too far down the line.
# r'\s*Cite this work as:'
# r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,'
# r'\s\*\*\*\*\*\*\*\*\*\*\*\**'
# r'\s*Gaussian\s*([0-9]+):\s*([A-Za-z0-9-.]+)\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)'
# r'\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)')
mainfile_contents_re
=
r
'Gaussian, Inc'
),
mainfile_contents_re
=
(
r
'\s*Cite this work as:'
r
'\s*Gaussian [0-9]+, Revision [A-Za-z0-9\.]*,'
)
),
LegacyParser
(
name
=
'parsers/quantumespresso'
,
code_name
=
'Quantum Espresso'
,
parser_class_name
=
'quantumespressoparser.QuantumEspressoParserPWSCF'
,
...
...
ops/deployments/nomad.reprocess.values.yaml
View file @
9a46c6eb
...
...
@@ -6,6 +6,7 @@ proxy:
api
:
disableReset
:
true
adminPasswordSecret
:
'
nomad-production-repository-password'
gui
:
debug
:
true
...
...
ops/helm/nomad/Chart.yaml
View file @
9a46c6eb
apiVersion
:
v1
appVersion
:
"
0.5.
2
"
appVersion
:
"
0.5.
3
"
description
:
A Helm chart for Kubernetes that only runs nomad services and uses externally hosted databases.
name
:
nomad
version
:
0.5.
2
version
:
0.5.
3
setup.py
View file @
9a46c6eb
...
...
@@ -12,7 +12,7 @@ reqs = [str(ir.req) for ir in install_reqs if 'sphinxcontrib.httpdomain' not in
setup
(
name
=
'nomad'
,
version
=
'0.5.
2
'
,
version
=
'0.5.
3
'
,
description
=
'The nomad@FAIRDI infrastructure python package'
,
py_modules
=
[
'nomad'
],
install_requires
=
reqs
,
...
...
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