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nomad-lab
nomad-FAIR
Commits
f522e4b6
Commit
f522e4b6
authored
Jul 16, 2020
by
Markus Scheidgen
Browse files
Merge branch 'v0.8.2' into 'master'
0.8.2 release See merge request
!134
parents
04f1385a
e02dd4cf
Pipeline
#78750
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in 10 minutes and 9 seconds
Changes
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.gitlab-ci.yml
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f522e4b6
...
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@@ -143,19 +143,20 @@ release:
-
docker pull $TEST_IMAGE
-
docker tag $TEST_IMAGE $LATEST_IMAGE
-
docker push $LATEST_IMAGE
except
:
-
/^dev-.*$/
when
:
manual
only
:
-
branches
release_version
:
stage
:
release
script
:
-
docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN gitlab-registry.mpcdf.mpg.de
-
docker pull $LATEST_IMAGE
-
docker tag $LATEST_IMAGE $CI_COMMIT_TAG
-
docker tag $LATEST_IMAGE $STABLE_IMAGE
-
docker pull $TEST_IMAGE
-
docker tag $TEST_IMAGE $LATEST_IMAGE
-
docker push $LATEST_IMAGE
-
docker tag $TEST_IMAGE $STABLE_IMAGE
-
docker push $STABLE_IMAGE
-
docker push $CI_COMMIT_TAG
only
:
-
tags
.gitmodules
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f522e4b6
[submodule "dependencies/nomad-meta-info"]
path = dependencies/nomad-meta-info
url = https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
branch = nomad-fair
[submodule "dependencies/python_common"]
path = dependencies/python_common
url = https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
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@@ -12,7 +8,7 @@
branch = nomad-fair
[submodule "dependencies/parsers/exciting"]
path = dependencies/parsers/exciting
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting.git
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting
-fairdi
.git
branch = nomad-fair
[submodule "dependencies/parsers/fhi-aims"]
path = dependencies/parsers/fhi-aims
...
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Dockerfile
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f522e4b6
...
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@@ -106,26 +106,23 @@ WORKDIR /app
# transfer installed packages from dependency stage
COPY
--from=build /usr/local/lib/python3.7/site-packages /usr/local/lib/python3.7/site-packages
RUN
echo
"copy 1"
# copy the meta-info, since it files are loaded via relative paths. TODO that should change.
COPY
--from=build /install/dependencies/nomad-meta-info /app/dependencies/nomad-meta-info
RUN
echo
"copy 2"
# copy the documentation, its files will be served by the API
COPY
--from=build /install/docs/.build /app/docs/.build
RUN
echo
"copy
3
"
RUN
echo
"copy
2
"
# copy the source distribution, its files will be served by the API
COPY
--from=build /install/dist /app/dist
RUN
echo
"copy
4
"
RUN
echo
"copy
3
"
# copy the nomad command
COPY
--from=build /usr/local/bin/nomad /usr/bin/nomad
RUN
echo
"copy
5
"
RUN
echo
"copy
4
"
# copy the gui
RUN
mkdir
-p
/app/gui
COPY
--from=gui_build /app/build /app/gui/build
RUN
echo
"copy
6
"
RUN
echo
"copy
5
"
# copy the encyclopedia gui production code
COPY
--from=gui_build /encyclopedia /app/dependencies/encyclopedia-gui/client
RUN
rm
-rf
/app/dependencies/encyclopedia-gui/client/src
RUN
echo
"copy
7
"
RUN
echo
"copy
6
"
RUN
mkdir
-p
/app/.volumes/fs
RUN
useradd
-ms
/bin/bash nomad
...
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README.md
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f522e4b6
...
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@@ -37,7 +37,7 @@ nomad parse --show-backend <your-file-to-parse>
### For NOMAD developer
Read the
[
docs
](
https://repository.nomad-coe.eu/app/docs
)
. The documentation is also part
Read the
[
docs
](
https://repository.nomad-coe.eu/app/docs
/index.html
)
. The documentation is also part
of the source code. It covers aspects like introduction, architecture, development setup/deployment,
contributing, and API reference.
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docs/api.rst
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API
(s) Documentation
API
Reference
====================
This is just a brief summary of all API endpoints of the NOMAD API. For a more compelling documention
...
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docs/api_tutorial.md
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...
@@ -69,10 +69,24 @@ identified an entry (given via a `upload_id`/`calc_id`, see the query output), a
you want to download it:
```
curl "http://repository.nomad-coe.eu/app/api/raw/calc/
f0KQE2aiSz2KRE47QtoZtw/6xe9fZ9xoxBYZOq5lTt8JMgPa3gX
/*" -o download.zip
curl "http://repository.nomad-coe.eu/app/api/raw/calc/
JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z
/*" -o download.zip
```
This basically requests all the files (
`*`
) that belong to this entry. If you have a query
With
`*`
you basically requests all the files under an entry or path..
If you need a specific file (that you already know) of that calculation:
```
curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/INFO.OUT"
```
You can also download a specific file from the upload (given a
`upload_id`
), if you know
the path of that file:
```
curl "http://repository.nomad-coe.eu/app/api/raw/JvdvikbhQp673R4ucwQgiA/exciting_basis_set_error_study/monomers_expanded_k8_rgkmax_080_PBE/72_Hf/INFO.OUT"
```
If you have a query
that is more selective, you can also download all results. Here all compounds that only
consist of Si, O, bulk material simulations of cubic systems (currently ~100 entries):
...
...
docs/archive.rst
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f522e4b6
.. _access-the-archive-label:
Acces
sing the Archive
=====================
U
sing the
NOMAD
Archive
=====================
==
Of course, you can access the NOMAD Archive directly via the NOMAD API (see the `API tutorial <api_tutorial.html>`_
and `API reference <api.html>`_). But, it is more effective and convenient to use NOMAD's Python client
...
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docs/client/install.rst
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...
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@@ -5,14 +5,16 @@ We release the NOMAD client library as a Python `distutils <https://docs.python.
You can download and install it the usual way using *pip* (or *conda*).
Install from pypi
.. code-block:: sh
pip install nomad-lab
Download and install latest release from nomad
.. code-block:: sh
curl https://repository.nomad-coe.eu/
v0.8
/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
curl https://repository.nomad-coe.eu/
app
/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
pip install ./nomad-lab.tar.gz
There are different layers of dependencies that you have to install, in order to use
...
...
docs/conf.py
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@@ -25,8 +25,8 @@ sys.path.insert(0, os.path.abspath('..'))
# -- Project information -----------------------------------------------------
project
=
'
nomad-FAIRDI
'
copyright
=
'201
8
, FAIRDI e.V.'
project
=
'
NOMAD Repository and Archive
'
copyright
=
'201
4-2020
, FAIRDI e.V.'
author
=
'FAIRDI e.V.'
# The short X.Y version
...
...
@@ -200,4 +200,4 @@ def setup(app):
# }, True)
# app.add_transform(AutoStructify)
extlinks
=
{
'api'
:
(
'https://repository.nomad-coe.eu/v0.8/api/%s'
,
'NOMAD API '
)}
\ No newline at end of file
extlinks
=
{
'api'
:
(
'https://repository.nomad-coe.eu/app/api/%s'
,
'NOMAD API '
)}
\ No newline at end of file
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