diff --git a/.coveragerc b/.coveragerc
index f62066140176e4a83729b618191ab3758d6626b0..4139d8ddaff56643bf0bc6a21c9495ea49ee9e49 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,5 +1,4 @@
[run]
-parallel = true
omit =
nomad/cli/admin/migrate.py
nomad/cli/admin/springer.py
@@ -10,4 +9,4 @@ omit =
nomad/metainfo/benchmarks.py
nomad/metainfo/generate.py
nomad/metainfo/pylint_plugin.py
- nomad/mkdocs.py
+ nomad/mkdocs.py
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3a9b5e5bdb4bcdbb4121623e7fb7e1b347eaeed4..e9884e4aa307161f3de4bb1e5c706470c1022128 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -57,52 +57,35 @@ update changelog:
rules:
- if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/
-.build_image:
- image:
- name: gcr.io/kaniko-project/executor:debug
- entrypoint: [""]
- before_script:
- - echo "{\"auths\":{\"${CI_REGISTRY}\":{\"auth\":\"$(printf "%s:%s" "${CI_REGISTRY_USER}" "${CI_REGISTRY_PASSWORD}" | base64 | tr -d '\n')\"},\"$CI_DEPENDENCY_PROXY_SERVER\":{\"auth\":\"$(printf "%s:%s" ${CI_DEPENDENCY_PROXY_USER} "${CI_DEPENDENCY_PROXY_PASSWORD}" | base64 | tr -d '\n')\"}}}" > /kaniko/.docker/config.json
- script:
- - /kaniko/executor
- --context "."
- --dockerfile "Dockerfile"
- --target "${TARGET}"
- --destination "${DESTINATION}"
- --cache-repo "${CI_REGISTRY_IMAGE}/cache"
- --cache=true
- --skip-unused-stages
- --build-arg SETUPTOOLS_SCM_PRETEND_VERSION
-
-build gui:
+build:
stage: build
- extends: .build_image
variables:
GIT_SUBMODULE_STRATEGY: recursive
GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- GIT_SUBMODULE_PATHS: gui/*
- TARGET: dev_node
- DESTINATION: "${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG}"
-
-# kaniko image doesn't contain pip, so we have to save the scm_pretend_version in an earlier job and reuse it later
-update_scm_pretend_version:
- stage: build
- script:
+ DOCKER_BUILDKIT: 1
+ before_script:
+ - docker --version
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
- pip install --upgrade setuptools_scm
- - echo "SETUPTOOLS_SCM_PRETEND_VERSION=$(python -m setuptools_scm)" >> build.env
+ - export SETUPTOOLS_SCM_PRETEND_VERSION=$(python -m setuptools_scm)
+ - echo "SETUPTOOLS_SCM_PRETEND_VERSION=$SETUPTOOLS_SCM_PRETEND_VERSION"
+ script:
+ - docker build --build-arg SETUPTOOLS_SCM_PRETEND_VERSION -t ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} .
+ - docker build --build-arg SETUPTOOLS_SCM_PRETEND_VERSION --target dev_node -t ${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG} .
+ - docker build --build-arg SETUPTOOLS_SCM_PRETEND_VERSION --target dev_python -t ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG} .
+ - docker push ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker push ${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG}
+ - docker push ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ after_script:
+ - docker run --rm ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG} bash -c 'cat dist/`ls dist`' > nomad-lab.tar.gz
+ - docker run --rm ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG} cat tests/data/parsers/vasp/vasp.xml > vasp.xml
artifacts:
- reports:
- dotenv: build.env
-
-build python:
- stage: build
- extends: .build_image
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- GIT_SUBMODULE_PATHS: gui/*
- TARGET: dev_python
- DESTINATION: "${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}"
+ paths:
+ - nomad-lab.tar.gz
+ - vasp.xml
+ expire_in: 1 hour
+ rules:
+ - when: on_success
build helm chart:
stage: build
@@ -114,28 +97,13 @@ build helm chart:
- when: manual
allow_failure: true
-check helm chart:
- stage: test
- image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
- script:
- - uv pip install -e "."
- - scripts/check_helm_chart.sh
- after_script:
- - >
- if [ $CI_JOB_STATUS == 'failed' ]; then
- echo 'Make sure that the helm chart values.yaml has been updated and committed by running'
- echo './scripts/update_hem_chart.sh'
- fi
- rules:
- - if: $CI_COMMIT_TAG
- when: never
- - when: on_success
-
python linting:
stage: test
image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
variables:
- GIT_SUBMODULE_STRATEGY: none
+ GIT_STRATEGY: none
+ before_script:
+ - cd /app
script:
- ruff check nomad tests
- ruff format nomad tests --check
@@ -150,17 +118,31 @@ python linting:
when: always
reports:
codequality: gl-code-quality-report.json
+
expire_in: never
+gui linting:
+ stage: test
+ image: ${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG}
+ variables:
+ GIT_STRATEGY: none
+ before_script:
+ - cd /app/gui
+ script:
+ - yarn run lint
+ rules:
+ - if: $CI_COMMIT_TAG
+ when: never
+ - when: on_success
+
check python dependencies:
stage: test
image: python:3.9
variables:
GIT_SUBMODULE_STRATEGY: recursive
GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- GIT_SUBMODULE_PATHS: dependencies/*
before_script:
- - pip install --upgrade uv
+ - pip install --upgrade pip-tools
script:
- scripts/check_python_dependencies.sh
rules:
@@ -169,9 +151,47 @@ check python dependencies:
- when: manual
allow_failure: true
-.base_test:
+check helm chart:
+ stage: test
+ image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ script:
+ - scripts/check_helm_chart.sh
+ after_script:
+ - >
+ if [ $CI_JOB_STATUS == 'failed' ]; then
+ echo 'Make sure that the helm chart values.yaml has been updated and committed by running'
+ echo './scripts/update_hem_chart.sh'
+ fi
+ rules:
+ - if: $CI_COMMIT_TAG
+ when: never
+ - when: on_success
+
+check gui artifacts:
+ stage: test
image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ variables:
+ GIT_STRATEGY: none
+ before_script:
+ - cd /app
+ script:
+ # Install default plugins. TODO: This can be removed once we have a proper
+ - scripts/install_default_plugins.sh
+ - scripts/check_gui_artifacts.sh
+ after_script:
+ - >
+ if [ $CI_JOB_STATUS == 'failed' ]; then
+ echo 'Make sure that the right GUI artifacts have been regenerated and committed by running'
+ echo './scripts/generate_gui_artifacts.sh'
+ fi
+ rules:
+ - if: $CI_COMMIT_TAG
+ when: never
+ - when: on_success
+
+python tests:
stage: test
+ image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
services:
- name: rabbitmq:3.11.5
alias: rabbitmq
@@ -184,10 +204,7 @@ check python dependencies:
- name: mongo:5.0.6
alias: mongo
variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- GIT_SUBMODULE_PATHS: dependencies/*
+ GIT_STRATEGY: none
RABBITMQ_ERLANG_COOKIE: SWQOKODSQALRPCLNMEQG
RABBITMQ_DEFAULT_USER: rabbitmq
RABBITMQ_DEFAULT_PASS: rabbitmq
@@ -198,50 +215,13 @@ check python dependencies:
NOMAD_KEYCLOAK_PASSWORD: ${CI_KEYCLOAK_ADMIN_PASSWORD}
NOMAD_NORMALIZE_SPRINGER_DB_PATH: /nomad/fairdi/db/data/springer.msg
before_script:
+ - cd /app
- scripts/check_elastic.sh
- - uv pip install -e ".[dev]"
-
-generate pytest timings:
- extends: .base_test
script:
- - python -m pytest --store-durations
- artifacts:
- expire_in: 1 days
- when: on_success
- paths:
- - .test_durations
-
- rules:
- - if: $CI_COMMIT_TAG
- when: never
- - when: manual
- allow_failure: true
-
-python tests:
- parallel: 3
- extends: .base_test
- script:
- - python -m pytest --cov=nomad --cov-report term --cov-config=.coveragerc -sv tests --splits $CI_NODE_TOTAL --group=$CI_NODE_INDEX
+ - python -m pytest --cov=nomad --cov-report term --cov-report xml:coverage.xml --cov-config=.coveragerc -sv tests
after_script:
- - cp .coverage .coverage_${CI_NODE_INDEX}
- artifacts:
- expire_in: 1 days
- when: on_success
- paths:
- - .coverage_${CI_NODE_INDEX}
- rules:
- - if: $CI_COMMIT_TAG
- when: never
- - when: on_success
-
-python coverage report:
- stage: test
- image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
- needs: ["python tests"]
- script:
- - coverage combine .coverage_*
- - coverage report
- - coverage xml
+ - cd /app
+ - cp coverage.xml $CI_PROJECT_DIR
coverage: /(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/
artifacts:
when: always
@@ -254,19 +234,17 @@ python coverage report:
when: never
- when: on_success
-gui linting:
+install tests:
stage: test
- image: ${CI_REGISTRY_IMAGE}/dev_node:${DOCKER_TAG}
- variables:
- GIT_STRATEGY: none
- before_script:
- - cd /app/gui
+ image: python:3.9
script:
- - yarn run lint
- rules:
- - if: $CI_COMMIT_TAG
- when: never
- - when: on_success
+ - pip install --upgrade pip
+ - pip install nomad-lab.tar.gz
+ - python -c 'import nomad.cli'
+ - python -c 'from nomad.client import ArchiveQuery'
+ - python -m nomad.cli parse vasp.xml
+ - pip install git+https://github.com/nomad-coe/nomad-parser-example.git
+ - python -m exampleparser tests/data/examples/example.out
gui tests:
stage: test
@@ -300,215 +278,141 @@ gui tests:
when: never
- when: on_success
-check gui artifacts:
- stage: test
- image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- GIT_SUBMODULE_PATHS: dependencies/*
- script:
- - uv pip install ".[dev,parsing,infrastructure]"
- - uv pip install -r default_plugins.txt # remove this after moving to distro
- - scripts/check_gui_artifacts.sh
- after_script:
- - >
- if [ $CI_JOB_STATUS == 'failed' ]; then
- echo 'Make sure that the right GUI artifacts have been regenerated and committed by running'
- echo './scripts/generate_gui_artifacts.sh'
- fi
- rules:
- - if: $CI_COMMIT_TAG
- when: never
- - when: on_success
-
-build python package:
- stage: test
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- extends: .build_image
- script:
- - /kaniko/executor
- --context "."
- --dockerfile "Dockerfile"
- --target "package_python"
- --destination "${CI_REGISTRY_IMAGE}/package_python:${DOCKER_TAG}"
- --skip-unused-stages
- --cache-repo "${CI_REGISTRY_IMAGE}/cache"
- --cache=true
- --build-arg SETUPTOOLS_SCM_PRETEND_VERSION
- - mkdir -p $CI_PROJECT_DIR/dist
- - cp -r /app/dist/* $CI_PROJECT_DIR/dist
- - cp /app/tests/data/parsers/vasp/vasp.xml $CI_PROJECT_DIR/
- artifacts:
- expire_in: 1 days
- when: on_success
- paths:
- - dist/
- - vasp.xml
-
-install tests:
- stage: test
- image: python:3.9
- needs: ["build python package"]
- variables:
- UV_SYSTEM_PYTHON: true
- before_script:
- - pip install --upgrade pip
- - pip install uv
- script:
- - ls dist/
- - pip install dist/nomad-*.tar.gz
- - python -c 'import nomad.cli'
- - python -c 'from nomad.client import ArchiveQuery'
- - python -m nomad.cli parse vasp.xml
- - uv pip install git+https://github.com/nomad-coe/nomad-parser-example.git@9312f1e
- - python -m exampleparser tests/data/examples/example.out
-
-.deploy image: &deploy_image
+deploy prod:
stage: deploy
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair/ci-runner:latest
+ environment:
+ name: staging
+ deployment_tier: production
+ url: https://nomad-lab.eu/prod/v1
before_script:
- mkdir ~/.kube/
- echo ${CI_K8S_CLOUD_CONFIG} | base64 -d > ~/.kube/config
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
script:
- - echo ${TARGET_ENV}
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:prod
+ - docker push ${CI_REGISTRY_IMAGE}:prod
- helm dependency update ops/kubernetes/nomad
- - helm upgrade nomad-prod-${TARGET_ENV} ops/kubernetes/nomad
+ - helm upgrade nomad-prod ops/kubernetes/nomad
--install
- --namespace nomad-prod-${TARGET_ENV}
+ --namespace nomad-prod
--values ops/kubernetes/values.yaml
- --values plugins-values.yaml
- --values ops/kubernetes/nomad-prod-${TARGET_ENV}.yaml
- --set nomad.image.tag=${TARGET_ENV}
+ --values ops/kubernetes/nomad-prod.yaml
+ --set nomad.image.tag=prod
--set roll=true
--timeout=15m
--wait
-
-.test_deployment: &test_deployment
- stage: deploy
- image:
- name: ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
- entrypoint: [""]
- script:
- - CLIENT_URL="https://nomad-lab.eu/prod/v1/${TARGET_ENV}/api"
- - echo ${CLIENT_URL}
- - nomad client -n $CLIENT_URL -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
-
-deploy test:
- stage: deploy
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- TARGET: final
- DESTINATION: ${CI_REGISTRY_IMAGE}/test
- TARGET_ENV: test
- extends: .build_image
- before_script:
- - echo "TARGET_ENV=test" >> build.env
- - echo "name=test" >> build.env
- - echo "deployment_tier=production" >> build.env
- - echo "url=https://nomad-lab.eu/prod/v1/test" >> build.env
- artifacts:
- reports:
- dotenv: build.env
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod -e NOMAD_KEYCLOAK_SERVER_URL=https://nomad-lab.eu/fairdi/keycloak/auth/ ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ nomad client -n https://nomad-lab.eu/prod/v1/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
rules:
- when: manual
allow_failure: true
-deploy test image:
+deploy prod staging:
stage: deploy
- needs: ["deploy test"]
- <<: *deploy_image
-
-test test deployment:
- stage: deploy
- needs: ["deploy test", "deploy test image"]
- <<: *test_deployment
-
-deploy staging:
- stage: deploy
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- TARGET: final
- DESTINATION: ${CI_REGISTRY_IMAGE}/staging
- TARGET_ENV: staging
- extends: .build_image
+ environment:
+ name: staging
+ deployment_tier: production
+ url: https://nomad-lab.eu/prod/v1/staging
before_script:
- - echo "TARGET_ENV=staging" >> build.env
- - echo "name=staging" >> build.env
- - echo "deployment_tier=production" >> build.env
- - echo "url=https://nomad-lab.eu/prod/v1/staging" >> build.env
- artifacts:
- reports:
- dotenv: build.env
+ - mkdir ~/.kube/
+ - echo ${CI_K8S_CLOUD_CONFIG} | base64 -d > ~/.kube/config
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ script:
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:staging
+ - docker push ${CI_REGISTRY_IMAGE}:staging
+ - helm dependency update ops/kubernetes/nomad
+ - helm upgrade nomad-prod-staging ops/kubernetes/nomad
+ --install
+ --namespace nomad-prod-staging
+ --values ops/kubernetes/values.yaml
+ --values ops/kubernetes/nomad-prod-staging.yaml
+ --set nomad.image.tag=staging
+ --set roll=true
+ --timeout=15m
+ --wait
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod -e NOMAD_KEYCLOAK_SERVER_URL=https://nomad-lab.eu/fairdi/keycloak/auth/ ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ nomad client -n https://nomad-lab.eu/prod/v1/staging/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
rules:
- when: manual
allow_failure: true
-deploy staging image:
- stage: deploy
- needs: ["deploy staging"]
- <<: *deploy_image
-
-test staging deployment:
- stage: deploy
- needs: ["deploy staging", "deploy staging image"]
- <<: *test_deployment
-
-deploy develop:
+deploy prod develop:
stage: deploy
- variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- TARGET: final
- DESTINATION: ${CI_REGISTRY_IMAGE}/develop
- TARGET_ENV: develop
- extends: .build_image
+ environment:
+ name: develop
+ deployment_tier: production
+ url: https://nomad-lab.eu/prod/v1/develop
before_script:
- - echo "TARGET_ENV=develop" >> build.env
- - echo "name=develop" >> build.env
- - echo "deployment_tier=production" >> build.env
- - echo "url=https://nomad-lab.eu/prod/v1/develop" >> build.env
- artifacts:
- reports:
- dotenv: build.env
+ - mkdir ~/.kube/
+ - echo ${CI_K8S_CLOUD_CONFIG} | base64 -d > ~/.kube/config
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ script:
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:develop
+ - docker push ${CI_REGISTRY_IMAGE}:develop
+ - helm dependency update ops/kubernetes/nomad
+ - helm upgrade nomad-prod-develop ops/kubernetes/nomad
+ --install
+ --namespace nomad-prod-develop
+ --values ops/kubernetes/values.yaml
+ --values ops/kubernetes/nomad-prod-develop.yaml
+ --set nomad.image.tag=develop
+ --set roll=true
+ --timeout=15m
+ --wait
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod -e NOMAD_KEYCLOAK_SERVER_URL=https://nomad-lab.eu/fairdi/keycloak/auth/ ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ nomad client -n https://nomad-lab.eu/prod/v1/develop/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
rules:
- if: $CI_COMMIT_BRANCH == "develop" && $NIGHTLY
- when: manual
allow_failure: true
-deploy develop image:
- stage: deploy
- needs: ["deploy develop"]
- <<: *deploy_image
-
-test develop deployment:
+deploy prod test:
stage: deploy
- needs: ["deploy develop", "deploy develop image"]
- <<: *test_deployment
+ environment:
+ name: test
+ deployment_tier: production
+ url: https://nomad-lab.eu/prod/v1/test
+ before_script:
+ - mkdir ~/.kube/
+ - echo ${CI_K8S_CLOUD_CONFIG} | base64 -d > ~/.kube/config
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ script:
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:test
+ - docker push ${CI_REGISTRY_IMAGE}:test
+ - helm dependency update ops/kubernetes/nomad
+ - helm upgrade nomad-prod-test ops/kubernetes/nomad
+ --install
+ --namespace nomad-prod-test
+ --values ops/kubernetes/values.yaml
+ --values ops/kubernetes/nomad-prod-test.yaml
+ --set nomad.image.tag=test
+ --set roll=true
+ --timeout=15m
+ --wait
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ - docker run -t -e NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod -e NOMAD_KEYCLOAK_SERVER_URL=https://nomad-lab.eu/fairdi/keycloak/auth/ ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ nomad client -n https://nomad-lab.eu/prod/v1/test/api -u test -w $CI_NOMAD_TEST_PASSWORD integrationtests --skip-publish --skip-doi
+ rules:
+ - when: manual
+ allow_failure: true
release latest image:
stage: release
variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- TARGET: final
- DESTINATION: ${CI_REGISTRY_IMAGE}/latest
- extends: .build_image
+ GIT_STRATEGY: none
+ before_script:
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ script:
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:latest
+ - docker push ${CI_REGISTRY_IMAGE}:latest
rules:
- when: manual
allow_failure: true
@@ -516,22 +420,29 @@ release latest image:
release stable image:
stage: release
variables:
- GIT_SUBMODULE_STRATEGY: recursive
- GIT_SUBMODULE_DEPTH: 1
- GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
- SETUPTOOLS_SCM_PRETEND_VERSION: "${SETUPTOOLS_SCM_PRETEND_VERSION}"
- TARGET: final
- DESTINATION: ${CI_REGISTRY_IMAGE}/stable
- extends: .build_image
+ GIT_STRATEGY: none
+ before_script:
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ - docker pull ${CI_REGISTRY_IMAGE}:${DOCKER_TAG}
+ script:
+ - docker tag ${CI_REGISTRY_IMAGE}:${DOCKER_TAG} ${CI_REGISTRY_IMAGE}:stable
+ - docker push ${CI_REGISTRY_IMAGE}:stable
rules:
- - when: manual
+ - if: $CI_COMMIT_TAG
+ when: manual
allow_failure: true
+ - when: never
python package:
stage: release
variables:
GIT_STRATEGY: none
- script: twine upload -u gitlab-ci-token -p ${CI_JOB_TOKEN} --repository-url https://gitlab.mpcdf.mpg.de/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/nomad-lab-*.tar.gz
+ before_script:
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ - docker pull ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ script:
+ - docker run --rm ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ twine upload -u gitlab-ci-token -p ${CI_JOB_TOKEN} --repository-url https://gitlab.mpcdf.mpg.de/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/nomad-lab-*.tar.gz
rules:
- when: manual
allow_failure: true
@@ -540,7 +451,12 @@ pypi package:
stage: release
variables:
GIT_STRATEGY: none
- script: twine upload -u $CI_TWINE_USER -p $CI_TWINE_PASSWORD dist/nomad-lab-*.tar.gz
+ before_script:
+ - echo "${CI_REGISTRY_PASSWORD}" | docker login ${CI_REGISTRY} --username ${CI_REGISTRY_USER} --password-stdin
+ - docker pull ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ script:
+ - docker run --rm ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ twine upload -u $CI_TWINE_USER -p $CI_TWINE_PASSWORD dist/nomad-lab-*.tar.gz
rules:
- if: $CI_COMMIT_TAG
when: manual
diff --git a/.test_durations b/.test_durations
deleted file mode 100644
index 0b89dddddbba6d91dbc101993a961d26a380e4a5..0000000000000000000000000000000000000000
--- a/.test_durations
+++ /dev/null
@@ -1,3465 +0,0 @@
-{
- "tests/app/test_app.py::test_alive": 0.011212967336177826,
- "tests/app/test_app.py::test_docs": 0.012479428201913834,
- "tests/app/test_app.py::test_gui[artifacts.js]": 0.03583385795354843,
- "tests/app/test_app.py::test_gui[env.js]": 0.03884676843881607,
- "tests/app/test_dcat.py::test_get_catalog[None-2020-01-07]": 0.061986833810806274,
- "tests/app/test_dcat.py::test_get_catalog[None-None]": 0.0664084292948246,
- "tests/app/test_dcat.py::test_get_catalog[test-id-3-2020-01-07]": 0.050207220017910004,
- "tests/app/test_dcat.py::test_get_dataset": 0.040334347635507584,
- "tests/app/test_dcat.py::test_mapping": 0.8411957286298275,
- "tests/app/test_h5grove.py::test_h5grove[file-in-published]": 1.3705982379615307,
- "tests/app/test_h5grove.py::test_h5grove[file-in-staging]": 1.341416109353304,
- "tests/app/test_h5grove.py::test_h5grove[file-not-found]": 1.3571092300117016,
- "tests/app/test_h5grove.py::test_h5grove[invalid-credentials]": 1.3744616694748402,
- "tests/app/test_h5grove.py::test_h5grove[no-credentials]": 1.3771197497844696,
- "tests/app/test_optimade.py::test_base_info_endpoint": 1.1135990098118782,
- "tests/app/test_optimade.py::test_entry_info_endpoint": 0.07494392618536949,
- "tests/app/test_optimade.py::test_get_entry": 2.08111409842968,
- "tests/app/test_optimade.py::test_links_endpoint": 0.022978022694587708,
- "tests/app/test_optimade.py::test_list_endpoint": 0.09581926092505455,
- "tests/app/test_optimade.py::test_list_endpoint_pagination[1-1-1]": 0.11123903468251228,
- "tests/app/test_optimade.py::test_list_endpoint_pagination[3-2-2]": 0.07605012133717537,
- "tests/app/test_optimade.py::test_list_endpoint_pagination[5-0-4]": 0.0938260518014431,
- "tests/app/test_optimade.py::test_list_endpoint_response_fields": 0.06650922447443008,
- "tests/app/test_optimade.py::test_list_endpoint_sort[-nelements--1]": 0.09037810936570168,
- "tests/app/test_optimade.py::test_list_endpoint_sort[nelements-1]": 0.09631828963756561,
- "tests/app/test_optimade.py::test_nmd_properties": 0.06024051457643509,
- "tests/app/test_optimade.py::test_nmd_properties_include_all": 0.16311729699373245,
- "tests/app/test_optimade.py::test_nmd_properties_info": 0.07863131165504456,
- "tests/app/test_optimade.py::test_no_optimade": 0.5482258535921574,
- "tests/app/test_optimade.py::test_optimade_parser[(nelements > 1 OR nperiodic_dimensions = 1) AND nelements = 2-3]": 0.020151104778051376,
- "tests/app/test_optimade.py::test_optimade_parser[1 < nelements-4]": 0.015108875930309296,
- "tests/app/test_optimade.py::test_optimade_parser[2 != nelements-1]": 0.012575354427099228,
- "tests/app/test_optimade.py::test_optimade_parser[3 <= nelements-1]": 0.011757824569940567,
- "tests/app/test_optimade.py::test_optimade_parser[LENGTH nelements = 1--1]": 0.0022171437740325928,
- "tests/app/test_optimade.py::test_optimade_parser[NOT chemical_formula_anonymous STARTS WITH \"A\"-0]": 0.01105402410030365,
- "tests/app/test_optimade.py::test_optimade_parser[NOT chemical_formula_descriptive ENDS WITH \"1\"-4]": 0.0164925716817379,
- "tests/app/test_optimade.py::test_optimade_parser[NOT nelements = 2 AND elements HAS ANY \"H\", \"O\", \"C\"-1]": 0.016982953995466232,
- "tests/app/test_optimade.py::test_optimade_parser[NOT nelements = 3 AND NOT elements HAS ONLY \"H\", \"O\"-0]": 0.014347709715366364,
- "tests/app/test_optimade.py::test_optimade_parser[NOT nperiodic_dimensions = 1-3]": 0.012879438698291779,
- "tests/app/test_optimade.py::test_optimade_parser[_nmd_results_material_chemical_formula_reduced = \"H20\"-0]": 0.00764002650976181,
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- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_hill CONTAINS \"1\"-0]": 0.010410808026790619,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_hill STARTS WITH \"H\" AND chemical_formula_hill ENDS WITH \"O\"-3]": 0.019101034849882126,
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- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced CONTAINS \"H\"-4]": 0.015521109104156494,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced CONTAINS \"H2\"-3]": 0.019976362586021423,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced ENDS \"C\"-0]": 0.00957471877336502,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced ENDS WITH \"O\"-4]": 0.01575193926692009,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced STARTS \"H2\"-2]": 0.012405261397361755,
- "tests/app/test_optimade.py::test_optimade_parser[chemical_formula_reduced STARTS WITH \"H2\"-2]": 0.013396859169006348,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS \"H\"-4]": 0.01698615401983261,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ALL \"H\", \"C\"-1]": 0.013185422867536545,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ALL \"H\", \"O\" AND nelements = 2-3]": 0.017147336155176163,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ALL \"H\", \"O\"-4]": 0.01743578538298607,
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- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ONLY \"C\"-0]": 0.009763222187757492,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ONLY \"H\", \"O\"-3]": 0.014467757195234299,
- "tests/app/test_optimade.py::test_optimade_parser[elements HAS ONY \"H\", \"O\"--1]": 0.0025656409561634064,
- "tests/app/test_optimade.py::test_optimade_parser[elements IS KNOWN-4]": 0.015902433544397354,
- "tests/app/test_optimade.py::test_optimade_parser[elements IS UNKNOWN-0]": 0.009243074804544449,
- "tests/app/test_optimade.py::test_optimade_parser[elements LENGTH 2-3]": 0.01319650188088417,
- "tests/app/test_optimade.py::test_optimade_parser[elements LENGTH = 2-3]": 0.014780953526496887,
- "tests/app/test_optimade.py::test_optimade_parser[elements LENGTH = 3-1]": 0.011679742485284805,
- "tests/app/test_optimade.py::test_optimade_parser[elements:elements_ratios HAS \"H\":>0.66-2]": 0.017886795103549957,
- "tests/app/test_optimade.py::test_optimade_parser[elements:elements_ratios HAS ALL \"O\":>0.33,\"O\":<0.34-2]": 0.019430287182331085,
- "tests/app/test_optimade.py::test_optimade_parser[elements:elements_ratios HAS ALL \"O\":>0.33-3]": 0.017680559307336807,
- "tests/app/test_optimade.py::test_optimade_parser[last_modified >= \"2009-02-01T20:07:00Z\"-0]": 0.016285385936498642,
- "tests/app/test_optimade.py::test_optimade_parser[nelements != 2-1]": 0.01821324974298477,
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- "tests/app/v1/routers/test_auth.py::test_get_signature_token": 0.010533485561609268,
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- "tests/test_files.py::TestStagingUploadFiles::test_rawfile_size[rr]": 0.007674355059862137,
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- "tests/test_mkdocs.py::test_field_type_info[literal-not-shown-int]": 0.0015775784850120544,
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- "tests/test_mkdocs.py::test_field_type_info[union]": 0.0019465386867523193,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[admin-none]": 0.3544670268893242,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[admin-user0]": 0.015492096543312073,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[admin-user1]": 0.003690004348754883,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[all-none]": 0.011606462299823761,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[all-user1]": 0.017497189342975616,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[all-user2]": 0.48451458290219307,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[public-none]": 0.009007424116134644,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[public-user1]": 0.010114341974258423,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[public-user2]": 0.009270206093788147,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[shared-none]": 0.001834716647863388,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[shared-user1]": 0.023205485194921494,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[shared]": 0.013662297278642654,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[staging-none]": 0.0018424615263938904,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[staging-user1]": 0.013597741723060608,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[staging-user2]": 0.014522731304168701,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[user-none]": 0.0018607601523399353,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[user-user1]": 0.013458240777254105,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[user-user2]": 0.00992390513420105,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[visible-none]": 0.01117248460650444,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[visible-user1]": 0.018895570188760757,
- "tests/test_search.py::TestsWithGroups::test_search_query_groups[visible-user2]": 0.016106605529785156,
- "tests/test_search.py::test_index": 0.2637154199182987,
- "tests/test_search.py::test_indices": 0.08442328870296478,
- "tests/test_search.py::test_mapping_compatibility": 0.016689836978912354,
- "tests/test_search.py::test_pagination_dynamic[python-default]": 0.6995438151061535,
- "tests/test_search.py::test_pagination_dynamic[python-sort-float-single-asc]": 0.7255277596414089,
- "tests/test_search.py::test_pagination_dynamic[python-sort-float-single-desc]": 0.7603009305894375,
- "tests/test_search.py::test_pagination_dynamic[python-sort-int-single-asc]": 0.7352528870105743,
- "tests/test_search.py::test_pagination_dynamic[python-sort-int-single-desc]": 0.7192558646202087,
- "tests/test_search.py::test_pagination_dynamic[python-sort-string-single-asc]": 0.7315422929823399,
- "tests/test_search.py::test_pagination_dynamic[python-sort-string-single-desc]": 0.7322619818150997,
- "tests/test_search.py::test_pagination_dynamic[yaml-default]": 0.7629043869674206,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-float-single-asc]": 0.7711977176368237,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-float-single-desc]": 0.7786140963435173,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-int-single-asc]": 0.7503675259649754,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-int-single-desc]": 0.758877981454134,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-string-single-asc]": 0.7928727716207504,
- "tests/test_search.py::test_pagination_dynamic[yaml-sort-string-single-desc]": 0.7850771583616734,
- "tests/test_search.py::test_quantity_values": 0.29444752261042595,
- "tests/test_search.py::test_search_hits_dynamic[python-nested-repeating-section]": 0.7451089434325695,
- "tests/test_search.py::test_search_hits_dynamic[python-nested-section]": 0.7704052999615669,
- "tests/test_search.py::test_search_hits_dynamic[python-root-section]": 0.7632381208240986,
- "tests/test_search.py::test_search_hits_dynamic[yaml-nested-repeating-section]": 0.7911391369998455,
- "tests/test_search.py::test_search_hits_dynamic[yaml-nested-section]": 0.7899585328996181,
- "tests/test_search.py::test_search_hits_dynamic[yaml-root-section]": 0.7561509720981121,
- "tests/test_search.py::test_search_quantities[bool]": 0.2557779848575592,
- "tests/test_search.py::test_search_quantities[datetime]": 0.2608446329832077,
- "tests/test_search.py::test_search_quantities[empty]": 0.30221526324748993,
- "tests/test_search.py::test_search_quantities[float]": 0.29853536933660507,
- "tests/test_search.py::test_search_quantities[int]": 0.3019488491117954,
- "tests/test_search.py::test_search_quantities[keyword-as-text]": 0.2918712943792343,
- "tests/test_search.py::test_search_quantities[simple-negative]": 0.27925313264131546,
- "tests/test_search.py::test_search_quantities[simple-positive]": 0.3221767023205757,
- "tests/test_search.py::test_search_quantities[uses-nested]": 0.2950446158647537,
- "tests/test_search.py::test_search_query[all]": 0.22426453232765198,
- "tests/test_search.py::test_search_query[and]": 0.43697455897927284,
- "tests/test_search.py::test_search_query[any]": 0.23943428322672844,
- "tests/test_search.py::test_search_query[empty]": 0.18317941948771477,
- "tests/test_search.py::test_search_query[gt]": 0.24158230051398277,
- "tests/test_search.py::test_search_query[gte]": 0.23908747732639313,
- "tests/test_search.py::test_search_query[lt]": 0.2663024105131626,
- "tests/test_search.py::test_search_query[lte]": 0.23649261519312859,
- "tests/test_search.py::test_search_query[match]": 0.2422659955918789,
- "tests/test_search.py::test_search_query[match_all]": 0.2478555627167225,
- "tests/test_search.py::test_search_query[none]": 0.2596292793750763,
- "tests/test_search.py::test_search_query[not]": 0.23170699179172516,
- "tests/test_search.py::test_search_query[or]": 0.23717041686177254,
- "tests/test_search.py::test_search_query_dynamic_required[python-exclude-both]": 0.7283140495419502,
- "tests/test_search.py::test_search_query_dynamic_required[python-exclude-dynamic]": 0.7623861096799374,
- "tests/test_search.py::test_search_query_dynamic_required[python-exclude-searchable-quantities-subset]": 0.7575289309024811,
- "tests/test_search.py::test_search_query_dynamic_required[python-exclude-searchable-quantities]": 0.7538994215428829,
- "tests/test_search.py::test_search_query_dynamic_required[python-include-both]": 0.7076013460755348,
- "tests/test_search.py::test_search_query_dynamic_required[python-include-dynamic-multiple]": 0.7805941812694073,
- "tests/test_search.py::test_search_query_dynamic_required[python-include-dynamic]": 0.7403209768235683,
- "tests/test_search.py::test_search_query_dynamic_required[python-include-nothing]": 0.7498195208609104,
- "tests/test_search.py::test_search_query_dynamic_required[python-include-searchable-quantities]": 0.7425358593463898,
- "tests/test_search.py::test_search_query_dynamic_required[python-no-required]": 0.773296907544136,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-exclude-both]": 0.7470451556146145,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-exclude-dynamic]": 0.7449392527341843,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-exclude-searchable-quantities-subset]": 0.7147984802722931,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-exclude-searchable-quantities]": 0.747620552778244,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-include-both]": 0.73673140630126,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-include-dynamic-multiple]": 0.7441352605819702,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-include-dynamic]": 0.7547043934464455,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-include-nothing]": 0.7254207767546177,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-include-searchable-quantities]": 0.7406651340425014,
- "tests/test_search.py::test_search_query_dynamic_required[yaml-no-required]": 0.7154770158231258,
- "tests/test_search.py::test_search_query_nexus[nexus float]": 0.4760790280997753,
- "tests/test_search.py::test_search_query_nexus[nexus str]": 0.23898140713572502,
- "tests/test_search.py::test_text_search[also match for partial word]": 0.21723156422376633,
- "tests/test_search.py::test_text_search[case insensitive]": 0.250173594802618,
- "tests/test_search.py::test_text_search[exact match]": 0.21050594002008438,
- "tests/test_search.py::test_text_search[no match]": 0.22737690806388855,
- "tests/test_search.py::test_text_search[single word match]": 0.2158343568444252,
- "tests/test_search.py::test_update_by_query": 0.3265136443078518,
- "tests/test_test.py::test_nowarn": 0.002306804060935974,
- "tests/test_utils.py::TestDictDataFrameConverter::test_dataframe_to_dict[dict]": 0.002256326377391815,
- "tests/test_utils.py::TestDictDataFrameConverter::test_dataframe_to_dict[list-dict]": 0.002339780330657959,
- "tests/test_utils.py::TestDictDataFrameConverter::test_dict_to_dataframe[dict]": 0.008776873350143433,
- "tests/test_utils.py::TestDictDataFrameConverter::test_dict_to_dataframe[dict_with_keys_to_filter]": 0.005249973386526108,
- "tests/test_utils.py::TestDictDataFrameConverter::test_dict_to_dataframe[list-dict]": 0.004319533705711365,
- "tests/test_utils.py::TestDictDataFrameConverter::test_invalid_input_type[123]": 0.0013580955564975739,
- "tests/test_utils.py::TestDictDataFrameConverter::test_invalid_input_type[None]": 0.001119866967201233,
- "tests/test_utils.py::TestDictDataFrameConverter::test_invalid_input_type[invalid_input]": 0.0015463270246982574,
- "tests/test_utils.py::test_class_logger": 0.00224912166595459,
- "tests/test_utils.py::test_common_prefix": 0.0011287704110145569,
- "tests/test_utils.py::test_decode_handle_id": 0.001295521855354309,
- "tests/test_utils.py::test_deep_get[empty-dict]": 0.0012867972254753113,
- "tests/test_utils.py::test_deep_get[empty-list]": 0.0013268813490867615,
- "tests/test_utils.py::test_deep_get[missing-index]": 0.0013818852603435516,
- "tests/test_utils.py::test_deep_get[missing-key-1]": 0.0012761391699314117,
- "tests/test_utils.py::test_deep_get[missing-key-2]": 0.0012916959822177887,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict-dict]": 0.0011591129004955292,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict-list-dict-list]": 0.0015559643507003784,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict-list-dict]": 0.0011921897530555725,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict-list-no-list-flattening]": 0.001156877726316452,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict-list]": 0.0011633113026618958,
- "tests/test_utils.py::test_dict_flatten_rebuild[dict]": 0.0012250468134880066,
- "tests/test_utils.py::test_dict_flatten_rebuild[empty]": 0.0011898651719093323,
- "tests/test_utils.py::test_extract_section": 0.0023477599024772644,
- "tests/test_utils.py::test_logging": 0.002394065260887146,
- "tests/test_utils.py::test_sanitize_logevent": 0.004339691251516342,
- "tests/test_utils.py::test_sleep_timer": 0.7053144164383411,
- "tests/test_utils.py::test_timer": 0.10272178426384926,
- "tests/test_utils.py::test_uuid": 0.0012068375945091248
-}
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 553961f93c56061177cc8d2fd42f3b29ce5501cc..3c9eb29171fef04fee9ef8862112bfd80a196576 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -14,49 +14,19 @@
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
-# syntax=docker/dockerfile:1
-
-# Comments are provided throughout this file to help you get started.
-# If you need more help, visit the Dockerfile reference guide at
-# https://docs.docker.com/engine/reference/builder/
-
-FROM node:16.15 AS base_node
-FROM python:3.9-slim AS base_python
-# Keeps Python from buffering stdout and stderr to avoid situations where
-# the application crashes without emitting any logs due to buffering.
-ENV PYTHONUNBUFFERED 1
-ENV PYTHONPATH "${PYTHONPATH}:/backend/"
-ENV UV_SYSTEM_PYTHON=1
-
-FROM base_python AS dev_python
-
-# Prevents Python from writing pyc files.
-ENV PYTHONDONTWRITEBYTECODE=1
+#
-ENV RUNTIME docker
+# This dockerfile describes an image that can be used to run the
+# - nomad processing worker
+# - nomad app (incl serving the gui)
-WORKDIR /app
-
-RUN apt-get update \
- && apt-get install --yes --quiet --no-install-recommends \
- libgomp1 \
- libmagic1 \
- file \
- gcc \
- build-essential \
- curl \
- zip \
- unzip \
- git \
- && rm -rf /var/lib/apt/lists/*
+# The dockerfile is multistaged to use a fat, more convinient build image and
+# copy only necessities to a slim final image
-# Install UV
-RUN pip install uv
-# Python environment
-COPY requirements-dev.txt .
+FROM node:16.15 AS base_node
+FROM python:3.9-slim AS base_python
-RUN uv pip install -r requirements-dev.txt
# ================================================================================
# Built the GUI in the gui build image
@@ -83,14 +53,42 @@ COPY tests/states/archives/dft.json /app/tests/states/archives/dft.json
COPY gui .
RUN echo "REACT_APP_BACKEND_URL=/fairdi/nomad/latest" > .env
-FROM dev_node as build_node
-
RUN yarn run build
-FROM dev_python as package_python
+
+# ================================================================================
+# Build all python stuff in a python build image
+# ================================================================================
+
+FROM base_python AS dev_python
+
+# Linux applications and libraries
+RUN apt-get update \
+ && apt-get install --yes --quiet --no-install-recommends \
+ libgomp1 \
+ libmagic-dev \
+ curl \
+ gcc \
+ build-essential \
+ make \
+ cmake \
+ swig \
+ libnetcdf-dev \
+ zip \
+ vim \
+ git \
+ && rm -rf /var/lib/apt/lists/*
WORKDIR /app
+ENV PIP_NO_CACHE_DIR=1
+
+# Python environment
+COPY requirements-dev.txt .
+
+RUN pip install build \
+ && pip install --progress-bar off --prefer-binary -r requirements-dev.txt
+
COPY dependencies ./dependencies
COPY docs ./docs
COPY examples ./examples
@@ -113,16 +111,6 @@ COPY .coveragerc \
# Files requiered for artifact generation/testing
COPY ops/docker-compose ./ops/docker-compose
-# Build documentation with static version
-RUN SETUPTOOLS_SCM_PRETEND_VERSION='0.0' uv pip install ".[parsing,infrastructure,dev]"
-
-RUN ./scripts/generate_docs_artifacts.sh \
- && mkdocs build \
- && mkdir -p nomad/app/static/docs \
- && cp -r site/* nomad/app/static/docs
-
-RUN RUN_DOCS_TEST=1 python -m pytest tests/app/test_app.py
-
COPY gui/tests/nomad.yaml ./gui/tests/nomad.yaml
COPY gui/tests/env.js ./gui/tests/env.js
COPY gui/tests/artifacts.js ./gui/tests/artifacts.js
@@ -131,21 +119,35 @@ COPY gui/tests/artifacts.js ./gui/tests/artifacts.js
RUN ./scripts/generate_example_uploads.sh
# Copy the built gui code
-COPY --from=build_node /app/gui/build nomad/app/static/gui
+COPY --from=dev_node /app/gui/build nomad/app/static/gui
# Set up the version as a build argument (default: '0.0')
ARG SETUPTOOLS_SCM_PRETEND_VERSION='0.0'
-# Re-install project with correct version
-RUN uv pip install ".[parsing,infrastructure,dev]"
+# Build documentation
+
+RUN pip install ".[parsing,infrastructure,dev]"
+
+# Install default plugins. TODO: This can be removed once we have a proper
+# distribution project.
+RUN ./scripts/install_default_plugins.sh
+
+RUN ./scripts/generate_docs_artifacts.sh \
+ && mkdocs build \
+ && mkdir -p nomad/app/static/docs \
+ && cp -r site/* nomad/app/static/docs
# Build the python source distribution package
RUN python -m build --sdist
+# (Re)install the full packages docs included
+RUN pip install dist/nomad-lab-*.tar.gz
+
# ================================================================================
# We use slim for the final image
# ================================================================================
+
FROM base_python AS builder
RUN apt-get update \
@@ -171,13 +173,13 @@ COPY requirements.txt .
RUN pip install --progress-bar off --prefer-binary -r requirements.txt
# install
-COPY --from=package_python /app/dist/nomad-lab-*.tar.gz .
+COPY --from=dev_python /app/dist/nomad-lab-*.tar.gz .
RUN pip install nomad-lab-*.tar.gz
# Install default plugins. TODO: This can be removed once we have a proper
# distribution project.
-COPY default_plugins.txt .
-RUN pip install -r default_plugins.txt
+COPY scripts/install_default_plugins.sh ./scripts/install_default_plugins.sh
+RUN ./scripts/install_default_plugins.sh
# Reduce the size of the packages
RUN find /usr/local/lib/python3.9/ -type d -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + \
@@ -207,19 +209,18 @@ RUN apt-get update \
WORKDIR /app
-RUN useradd -u 1000 nomad
-
# transfer installed packages from the build stage
COPY --chown=nomad:1000 scripts/run.sh .
COPY --chown=nomad:1000 scripts/run-worker.sh .
COPY --chown=nomad:1000 nomad/jupyterhub_config.py ./nomad/jupyterhub_config.py
-COPY --chown=nomad:1000 examples/data/uploads /app/examples/data/uploads
+COPY --chown=nomad:1000 --from=dev_python /app/examples/data/uploads /app/examples/data/uploads
COPY --chown=nomad:1000 --from=builder /usr/local/lib/python3.9/site-packages /usr/local/lib/python3.9/site-packages
COPY --chown=nomad:1000 --from=builder /usr/local/share/jupyterhub /usr/local/share/jupyterhub
COPY --chown=nomad:1000 --from=builder /usr/local/bin/nomad /usr/local/bin/nomad
-RUN mkdir -p /app/.volumes/fs \
+RUN useradd -ms /bin/bash nomad \
+ && mkdir -p /app/.volumes/fs \
&& chown -R nomad:1000 /app \
&& chown -R nomad:1000 /usr/local/lib/python3.9/site-packages/nomad
diff --git a/default_plugins.txt b/default_plugins.txt
deleted file mode 100644
index 9217115a2b7291bf88970eb1968202e2ff5d6c4a..0000000000000000000000000000000000000000
--- a/default_plugins.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-git+https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database.git@f394d21abafeb659729af0c94e5f90949fce01c1
-git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@795a53f35ffa52604cf7971c16cc3d4f9ce80f2f
-git+https://github.com/FAIRmat-NFDI/nomad-aitoolkit.git@70e6261c746e579ad0f177a965d16134efb50c35
-nomad-simulations==0.0.1
-
diff --git a/pyproject.toml b/pyproject.toml
index 3feaa2d5c768b7894593b4154dec5297ffce6575..3ddb534dfb5be68ecb2b6688c46667c7079c37e4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -131,7 +131,6 @@ dev = [
'pytest-timeout>=1.4.2',
'pytest-xdist>=1.30.0',
'pytest>= 5.3.0, <8',
- 'pytest-split',
'python-gitlab==2.10.1',
'rope==0.21.0',
'ruamel.yaml',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 8dd1e510d41f0616f4819b8f83941e169200fa66..0e8b50b44c047c8898064fcd3dc5bd180c07880f 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -276,10 +276,9 @@ pyopenssl==24.1.0 # via certipy, -r requirements.txt
pyparsing==3.1.2 # via matplotlib, rdflib, -r requirements.txt
pyproject-hooks==1.1.0 # via build
pyrsistent==0.20.0 # via jsonschema, -r requirements.txt
-pytest==7.4.4 # via pytest-asyncio, pytest-cov, pytest-split, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
+pytest==7.4.4 # via pytest-asyncio, pytest-cov, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
pytest-asyncio==0.23.7 # via nomad-lab (pyproject.toml)
pytest-cov==5.0.0 # via nomad-lab (pyproject.toml)
-pytest-split==0.8.2 # via nomad-lab (pyproject.toml)
pytest-timeout==2.3.1 # via nomad-lab (pyproject.toml)
pytest-xdist==3.6.1 # via nomad-lab (pyproject.toml)
python-box==6.1.0 # via rosettasciio, -r requirements.txt
diff --git a/scripts/install_default_plugins.sh b/scripts/install_default_plugins.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1b406e778af9ed85818bcf0424d65821d5df6f3d
--- /dev/null
+++ b/scripts/install_default_plugins.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+pip install git+https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database.git@f394d21abafeb659729af0c94e5f90949fce01c1
+pip install git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@795a53f35ffa52604cf7971c16cc3d4f9ce80f2f
+pip install git+https://github.com/FAIRmat-NFDI/nomad-aitoolkit.git@70e6261c746e579ad0f177a965d16134efb50c35
+pip install nomad-simulations==0.0.1
diff --git a/scripts/setup_dev_env.sh b/scripts/setup_dev_env.sh
index ce9e644a5432bf215840450e539b501e0f8a2a4b..58898a3607e2a201274b9c37dbbabad339d96a35 100755
--- a/scripts/setup_dev_env.sh
+++ b/scripts/setup_dev_env.sh
@@ -21,7 +21,7 @@ pip install -e ".[infrastructure,parsing,dev]"
# Install "default" plugins. TODO: This can be removed once we have proper
# distributions projects.
-pip install -r default_plugins.txt
+sh scripts/install_default_plugins.sh
# Build documentation
sh scripts/generate_docs_artifacts.sh
diff --git a/tests/app/test_app.py b/tests/app/test_app.py
index 12a36607c0894240027972d8c5fabd4664d73e00..b7caf70d71d0c80a8763d8737a3ecd9395aedcd1 100644
--- a/tests/app/test_app.py
+++ b/tests/app/test_app.py
@@ -17,7 +17,6 @@
#
import pytest
-import os
from nomad.config import config
@@ -27,7 +26,6 @@ def test_alive(client):
assert rv.status_code == 200
-@pytest.mark.skipif(os.getenv('RUN_DOCS_TEST') != '1', reason='Only run in build stage')
def test_docs(client):
rv = client.get('/docs/index.html')
assert rv.status_code == 200