Commit 873efcae authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Merge branch 'v0.10.0' into 'master'

Merge v0.10.0 into master for release

Closes #475, #484, #497, #492, #498, and #500

See merge request !283
parents 5636e115 015742db
Pipeline #95934 passed with stage
in 2 minutes and 28 seconds
......@@ -5,6 +5,7 @@
.python-version
.ipynb_checkpoints/
.python-version
.coverage_html/
__pycache__
.mypy_cache
*.pyc
......@@ -12,7 +13,8 @@ __pycache__
/data/
.volumes/
.pytest_cache/
.coverage
.coverage*
htmlcov
try.http
project/
test_*/
......@@ -23,8 +25,8 @@ target/
.vscode/
vscode/
nomad.yaml
./gunicorn.log.conf
./gunicorn.conf
gunicorn.log.conf
gunicorn.conf
build/
dist/
setup.json
......@@ -33,4 +35,5 @@ gui/src/metainfo.json
gui/src/searchQuantities.json
examples/workdir/
gunicorn.log.conf
nomad/gitinfo.py
\ No newline at end of file
nomad/gitinfo.py
*/node_modules/
......@@ -164,9 +164,9 @@ deploy dev:
script:
- RELEASE_NAME=`echo ${CI_COMMIT_REF_NAME} | sed -e 's/[^A-Za-z0-9\-]/-/g'`
- helm dependency update ops/helm/nomad
- helm upgrade --namespace nomad --install $RELEASE_NAME ops/helm/nomad -f ops/helm/nomad/deployments/dev-values.yaml --set proxy.external.path=/dev/nomad/$RELEASE_NAME,image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
- helm upgrade --namespace nomad --install $RELEASE_NAME ops/helm/nomad -f ops/helm/nomad/deployments/dev-values.yaml --set proxy.external.path=/dev/rae/$RELEASE_NAME,image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
- docker pull $TEST_IMAGE
- docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod $TEST_IMAGE python -m nomad.cli client -n https://nomad-lab.eu/dev/nomad/$RELEASE_NAME/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
- docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod $TEST_IMAGE python -m nomad.cli client -n https://nomad-lab.eu/dev/rae/$RELEASE_NAME/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
except:
- /^dev-.*$/
when: manual
......@@ -178,13 +178,27 @@ deploy prod beta:
- echo ${CI_K8S_PROD_CONFIG} | base64 -d > ${KUBECONFIG}
script:
- helm dependency update ops/helm/nomad
- helm upgrade --install nomad-prod-test ops/helm/nomad -f ops/helm/nomad/deployments/prod-beta-values.yaml --set image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
- helm upgrade --install nomad-beta ops/helm/nomad -f ops/helm/nomad/deployments/prod-beta-values.yaml --set image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
- docker pull $TEST_IMAGE
- docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod $TEST_IMAGE python -m nomad.cli client -n https://nomad-lab.eu/prod/rae/beta/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
except:
- /^dev-.*$/
when: manual
deploy prod test:
stage: release
before_script:
- mkdir -p /etc/deploy
- echo ${CI_K8S_PROD_CONFIG} | base64 -d > ${KUBECONFIG}
script:
- helm dependency update ops/helm/nomad
- helm upgrade --install nomad-test ops/helm/nomad -f ops/helm/nomad/deployments/prod-test-values.yaml --set image.tag=$CI_COMMIT_REF_NAME,roll=true --wait
- docker pull $TEST_IMAGE
- docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod $TEST_IMAGE python -m nomad.cli client -n https://nomad-lab.eu/prod/rae/test/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
except:
- /^dev-.*$/
when: manual
release latest image:
stage: release
script:
......
......@@ -4,191 +4,208 @@
branch = nomad-fair
[submodule "dependencies/parsers/vasp"]
path = dependencies/parsers/vasp
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-vasp.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-vasp.git
branch = master
[submodule "dependencies/parsers/exciting"]
path = dependencies/parsers/exciting
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting-fairdi.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-exciting.git
branch = master
[submodule "dependencies/parsers/fhi-aims"]
path = dependencies/parsers/fhi-aims
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fhi-aims.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-fhi-aims.git
branch = master
[submodule "dependencies/parsers/cp2k"]
path = dependencies/parsers/cp2k
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-cp2k.git
branch = master
[submodule "dependencies/parsers/crystal"]
path = dependencies/parsers/crystal
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-crystal.git
branch = master
[submodule "dependencies/parsers/cpmd"]
path = dependencies/parsers/cpmd
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cpmd.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-cpmd.git
branch = master
[submodule "dependencies/parsers/nwchem"]
path = dependencies/parsers/nwchem
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-nwchem.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-nwchem.git
branch = master
[submodule "dependencies/parsers/bigdft"]
path = dependencies/parsers/bigdft
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-big-dft.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-bigdft.git
branch = master
[submodule "dependencies/parsers/wien2k"]
path = dependencies/parsers/wien2k
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-wien2k.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-wien2k.git
branch = master
[submodule "dependencies/parsers/band"]
path = dependencies/parsers/band
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-band.git
url = https://github.com/nomad-coe/nomad-parser-band.git
branch = master
[submodule "dependencies/parsers/gaussian"]
path = dependencies/parsers/gaussian
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gaussian.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-gaussian.git
branch = master
[submodule "dependencies/parsers/quantum-espresso"]
path = dependencies/parsers/quantum-espresso
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-quantum-espresso.git
branch = nomad-fair
[submodule "dependencies/parsers/abinit"]
path = dependencies/parsers/abinit
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-abinit.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-abinit.git
branch = master
[submodule "dependencies/parsers/orca"]
path = dependencies/parsers/orca
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-orca.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-orca.git
branch = master
[submodule "dependencies/parsers/castep"]
path = dependencies/parsers/castep
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-castep.git
branch = master
[submodule "dependencies/parsers/dl-poly"]
path = dependencies/parsers/dl-poly
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dl-poly.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-dl-poly.git
branch = master
[submodule "dependencies/parsers/lib-atoms"]
path = dependencies/parsers/lib-atoms
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lib-atoms.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-lib-atoms.git
branch = master
[submodule "dependencies/parsers/octopus"]
path = dependencies/parsers/octopus
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-octopus.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-octopus.git
branch = master
[submodule "dependencies/parsers/phonopy"]
path = dependencies/parsers/phonopy
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-phonopy.git
branch = nomad-fair
[submodule "dependencies/parsers/gpaw"]
path = dependencies/parsers/gpaw
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gpaw.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-gpaw.git
branch = master
[submodule "dependencies/parsers/atk"]
path = dependencies/parsers/atk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-atk.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-atk.git
branch = master
[submodule "dependencies/parsers/gulp"]
path = dependencies/parsers/gulp
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gulp.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-gulp.git
branch = master
[submodule "dependencies/parsers/siesta"]
path = dependencies/parsers/siesta
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-siesta.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-siesta.git
branch = master
[submodule "dependencies/parsers/elk"]
path = dependencies/parsers/elk
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elk.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-elk.git
branch = master
[submodule "dependencies/parsers/elastic"]
path = dependencies/parsers/elastic
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elastic.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-elastic.git
branch = master
[submodule "dependencies/parsers/gamess"]
path = dependencies/parsers/gamess
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gamess.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-gamess.git
branch = master
[submodule "dependencies/parsers/turbomole"]
path = dependencies/parsers/turbomole
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-turbomole.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-turbomole.git
branch = master
[submodule "dependencies/parsers/skeleton"]
path = dependencies/parsers/skeleton
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-skeleton.git
branch = nomad-fair
[submodule "dependencies/parsers/mpes"]
path = dependencies/parsers/mpes
url = https://gitlab.mpcdf.mpg.de/rpx/parser-mpes.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-mpes.git
branch = master
[submodule "dependencies/parsers/aptfim"]
path = dependencies/parsers/aptfim
url = https://gitlab.mpcdf.mpg.de/mkuehbac/parser-aptfim.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-aptfim.git
branch = master
[submodule "dependencies/parsers/dmol3"]
path = dependencies/parsers/dmol3
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dmol3.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-dmol3.git
branch = master
[submodule "dependencies/parsers/fleur"]
path = dependencies/parsers/fleur
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fleur.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-fleur.git
branch = master
[submodule "dependencies/parsers/molcas"]
path = dependencies/parsers/molcas
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-molcas.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-molcas.git
branch = master
[submodule "dependencies/parsers/qbox"]
path = dependencies/parsers/qbox
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-qbox.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-qbox.git
branch = master
[submodule "dependencies/parsers/onetep"]
path = dependencies/parsers/onetep
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-onetep.git
branch = nomad-fair
url = https://github.com/nomad-coe/nomad-parser-onetep.git
branch = master
[submodule "dependencies/optimade-python-tools"]
path = dependencies/optimade-python-tools
url = https://github.com/markus1978/optimade-python-tools.git
[submodule "dependencies/parsers/namd"]
path = dependencies/parsers/namd
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-namd.git
url = https://github.com/nomad-coe/nomad-parser-namd.git
branch = master
[submodule "dependencies/parsers/charmm"]
path = dependencies/parsers/charmm
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-charmm.git
url = https://github.com/nomad-coe/nomad-parser-charmm.git
branch = master
[submodule "dependencies/parsers/dftbplus"]
path = dependencies/parsers/dftbplus
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dftb-plus.git
url = https://github.com/nomad-coe/nomad-parser-dftbplus.git
branch = master
[submodule "dependencies/parsers/asap"]
path = dependencies/parsers/asap
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-asap.git
url = https://github.com/nomad-coe/nomad-parser-asap.git
branch = master
[submodule "dependencies/parsers/fplo"]
path = dependencies/parsers/fplo
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fplo.git
url = https://github.com/nomad-coe/nomad-parser-fplo.git
branch = master
[submodule "dependencies/parsers/mopac"]
path = dependencies/parsers/mopac
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mopac.git
url = https://github.com/nomad-coe/nomad-parser-mopac.git
branch = master
[submodule "dependencies/parsers/amber"]
path = dependencies/parsers/amber
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-amber.git
url = https://github.com/nomad-coe/nomad-parser-amber.git
branch = master
[submodule "dependencies/parsers/gromacs"]
path = dependencies/parsers/gromacs
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromacs.git
url = https://github.com/nomad-coe/nomad-parser-gromacs.git
branch = master
[submodule "dependencies/parsers/gromos"]
path = dependencies/parsers/gromos
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromos.git
url = https://github.com/nomad-coe/nomad-parser-gromos.git
branch = master
[submodule "dependencies/parsers/lammps"]
path = dependencies/parsers/lammps
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps.git
url = https://github.com/nomad-coe/nomad-parser-lammps.git
branch = master
[submodule "dependencies/parsers/openkim"]
path = dependencies/parsers/openkim
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-openkim.git
url = https://github.com/nomad-coe/nomad-parser-openkim.git
branch = master
[submodule "dependencies/parsers/tinker"]
path = dependencies/parsers/tinker
url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-tinker.git
url = https://github.com/nomad-coe/nomad-parser-tinker.git
branch = master
[submodule "dependencies/encyclopedia-gui"]
path = dependencies/encyclopedia-gui
url = https://gitlab.mpcdf.mpg.de/nomad-lab/encyclopedia-gui.git
[submodule "dependencies/materia"]
path = dependencies/materia
url = https://github.com/nomad-coe/materia
[submodule "dependencies/nomad-dos-fingerprints"]
path = dependencies/nomad-dos-fingerprints
url = https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-dos-fingerprints.git
[submodule "dependencies/parsers/eelsdb"]
path = dependencies/parsers/eelsdb
url = https://gitlab.mpcdf.mpg.de/nomad-lab/eelsdb.git
url = https://github.com/nomad-coe/nomad-parser-eelsdb.git
branch = master
[submodule "dependencies/parsers/example"]
path = dependencies/parsers/example
url = https://github.com/nomad-coe/nomad-parser-example.git
......@@ -3,7 +3,7 @@
# A comma-separated list of package or module names from where C extensions may
# be loaded. Extensions are loading into the active Python interpreter and may
# run arbitrary code.
extension-pkg-whitelist=
extension-pkg-whitelist=pydantic
# Add files or directories to the blacklist. They should be base names, not
# paths.
......@@ -666,7 +666,7 @@ ignore-on-opaque-inference=yes
# List of class names for which member attributes should not be checked (useful
# for classes with dynamically set attributes). This supports the use of
# qualified names.
ignored-classes=optparse.Values,thread._local,_thread._local
ignored-classes=optparse.Values,thread._local,_thread._local,SearchResponse
# List of module names for which member attributes should not be checked
# (useful for modules/projects where namespaces are manipulated during runtime
......
......@@ -87,6 +87,7 @@ WORKDIR /app
ENV PATH /app/node_modules/.bin:$PATH
COPY gui/package.json /app/package.json
COPY gui/yarn.lock /app/yarn.lock
COPY dependencies/materia /dependencies/materia
RUN yarn
COPY gui /app
COPY --from=build /install/gui/src/metainfo.json /app/src/metainfo.json
......@@ -123,12 +124,12 @@ COPY --from=build /install/docs/.build /app/docs/.build
COPY --from=build /usr/local/bin/nomad /usr/bin/nomad
# copy the gui
RUN mkdir -p /app/gui
COPY --from=gui_build /app/build /app/nomad/app/static/gui
COPY --from=gui_build /app/build /app/nomad/app/flask/static/gui
# copy the encyclopedia gui production code
COPY --from=gui_build /encyclopedia /app/nomad/app/static/encyclopedia
COPY --from=gui_build /encyclopedia /app/nomad/app/flask/static/encyclopedia
# remove the developer config on the gui, will be generated by run.sh from nomad.yaml
RUN rm -f /app/nomad/app/static/gui/env.js
RUN rm -f /app/nomad/app/static/encyclopedia/conf.js
RUN rm -f /app/nomad/app/flask/static/gui/env.js
RUN rm -f /app/nomad/app/flask/static/encyclopedia/conf.js
# build the python package dist
RUN python setup.py compile
RUN python setup.py sdist
......
recursive-include dependencies/optimade-python-tools *.txt *.g *.py *.ini
recursive-include dependencies/optimade-python-tools *.txt *.g *.py *.ini *.json
recursive-include nomad *.json *.j2 *.md *.yaml
include nomad/units/*.txt
include README.md
......
......@@ -46,6 +46,12 @@ contributing, and API reference.
Omitted versions are plain bugfix releases with only minor changes and fixes.
### v0.10.0
- The entries page shows visualizations for key properties of the underlying data
- A new more consistent API (/api/v1) alongside the old API (/api)
- OPTIMADE implementation based on optimade-python-tools
- Re-written parsers for VASP, FHI-aims, exciting, ABINIT, and Crystal
### v0.9.9
- A rdf-API that provides dcat datasets and catalog for NOMAD entries.
- Support to directly publish upon upload via API.
......
......@@ -83,8 +83,8 @@ pip install nomad-lab
Clone the parser project and install it in development mode:
```
git clone $parserGitUrl$ parser-$codeName$
pip install -e parser-$codeName$
git clone $parserGitUrl$ nomad-parser-$codeName$
pip install -e nomad-parser-$codeName$
```
Running the parser now, will use the parser's Python code from the clone project.
......
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