.dockerignore

@@ -3,4 +3,4 @@
 **/.gitmodules
 **/.dockerignore
 
-.gitlab-ci
\ No newline at end of file
+.gitlab-ci.yml
\ No newline at end of file

.gitignore

-.vscode/
-.idea/
-.ipython/
-.keras/
-.local/
-
-.DS_Store
 
+# https://github.com/github/gitignore/blob/main/Python.gitignore
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -29,6 +23,7 @@ parts/
 sdist/
 var/
 wheels/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
@@ -47,14 +42,17 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
+*.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -64,6 +62,7 @@ coverage.xml
 *.log
 local_settings.py
 db.sqlite3
+db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -76,16 +75,49 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# IPython
+profile_default/
+ipython_config.py
+
 # pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
 .python-version
 
-# celery beat schedule file
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
 celerybeat-schedule
+celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
@@ -111,3 +143,252 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+
+# https://github.com/github/gitignore/blob/main/Node.gitignore
+
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+.pnpm-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional stylelint cache
+.stylelintcache
+
+# Microbundle cache
+.rpt2_cache/
+.rts2_cache_cjs/
+.rts2_cache_es/
+.rts2_cache_umd/
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variable files
+.env
+.env.development.local
+.env.test.local
+.env.production.local
+.env.local
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+.parcel-cache
+
+# Next.js build output
+.next
+out
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and not Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# vuepress v2.x temp and cache directory
+.temp
+.cache
+
+# Docusaurus cache and generated files
+.docusaurus
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# TernJS port file
+.tern-port
+
+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
+
+# yarn v2
+.yarn/cache
+.yarn/unplugged
+.yarn/build-state.yml
+.yarn/install-state.gz
+.pnp.*
+
+
+# https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore/
+
+.vscode/*
+!.vscode/settings.json
+# !.vscode/tasks.json
+# !.vscode/launch.json
+# !.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+
+# https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+
+# https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
+
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+
+# https://github.com/github/gitignore/blob/main/Global/Linux.gitignore
+
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+
+# Analitics
+deployments
+.keras/

.gitlab-ci.yml

-# default installed image for docker executor is: python:3.6
-# using an image that can do git, docker, docker-compose
-# https://docs.gitlab.com/ee/ci/docker/using_docker_build.html
-image: docker:dind
+image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair/ci-runner
 
-variables:
-  GIT_SUBMODULE_STRATEGY: recursive
-  APP_REGISTRY: gitlab-registry.mpcdf.mpg.de/nomad-lab/aitoolkit-app
-  DEVELOP_REGISTRY: gitlab-registry.mpcdf.mpg.de/nomad-lab/aitoolkit-develop
+# variables:
+#   IMAGE_NAME: ${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_SLUG}
 
 stages:
   - build
   - deploy
-
+  - release
 
 build to develop:
   stage: build
+  variables:
+    GIT_SUBMODULE_STRATEGY: recursive
+    GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
   before_script:
     - echo "Building the single user notebook image"
     - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
     - docker info
   script:
-    # Using cache to speed up the build process
-    - docker pull ${CI_REGISTRY_IMAGE}:develop || true
-    - docker build --cache-from ${CI_REGISTRY_IMAGE}:develop --tag ${CI_REGISTRY_IMAGE}:develop${CI_COMMIT_SHORT_SHA} --tag ${CI_REGISTRY_IMAGE}:develop --tag ${DEVELOP_REGISTRY}:develop${CI_COMMIT_SHORT_SHA} --tag ${DEVELOP_REGISTRY}:develop .
-    - docker push ${CI_REGISTRY_IMAGE}:develop${CI_COMMIT_SHORT_SHA}
-    - docker push ${CI_REGISTRY_IMAGE}:develop
-    - docker login -u ai_toolkit -p ${AI_TOOLKIT_TOKEN} ${DEVELOP_REGISTRY}
-    - docker push ${DEVELOP_REGISTRY}:develop${CI_COMMIT_SHORT_SHA}
-    - docker push ${DEVELOP_REGISTRY}:develop
-    
-  rules:
-    # Execute jobs when a new commit is pushed to develop branch
-    - if: $CI_COMMIT_BRANCH == "develop"  
-
-
-build to staging:
-  stage: build
-  before_script:
-    - echo "Building the single user notebook image"
-    - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
-    - docker info
-  script:
-    # Using cache to speed up the build process --cache-from ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME} 
-    - docker pull ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME} || true
-    - docker build --tag ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}${CI_COMMIT_SHORT_SHA} --tag ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME} .
-    - docker push ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}${CI_COMMIT_SHORT_SHA}
-    - docker push ${CI_REGISTRY_IMAGE}:${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}
+    - docker build -t ${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_SLUG} .
+    - docker push ${CI_REGISTRY_IMAGE}:${CI_COMMIT_REF_SLUG}
   rules:
     # Execute jobs when a new commit is pushed to master branch
-    - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "master"
+    - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "develop"
 
+# build to staging:
+#   stage: build
+#   variables:
+#     GIT_SUBMODULE_STRATEGY: recursive
+#     GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
+#   before_script:
+#     - echo "Building the single user notebook image"
+#     - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
+#   script:
+#     - docker build -t ${STAGING_IMAGE} .
+#     - docker push ${STAGING_IMAGE}
+#   rules:
+#     # Execute jobs when a new commit is pushed to develop branch
+#     - if: $CI_COMMIT_BRANCH == "develop"
 
-build to production:
-  stage: build
-  before_script:
-    - echo "Building the single user notebook image"
-    - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
-    - docker info
-  script:
-    # Using cache to speed up the build process
-    - docker pull ${CI_REGISTRY_IMAGE}:latest || true
-    - docker build --cache-from ${CI_REGISTRY_IMAGE}:latest --build-arg CACHEBUST=$(date +%s) --tag ${CI_REGISTRY_IMAGE}:production${CI_COMMIT_SHORT_SHA} --tag ${CI_REGISTRY_IMAGE}:latest .
-    - docker push ${CI_REGISTRY_IMAGE}:production${CI_COMMIT_SHORT_SHA}
-    - docker push ${CI_REGISTRY_IMAGE}:latest
-  rules:
-    # Execute jobs when a new commit is pushed to master branch
-    - if: $CI_COMMIT_BRANCH == 'master'
+# build to production:
+#   stage: build
+#   variables:
+#     GIT_SUBMODULE_STRATEGY: recursive
+#     GIT_SUBMODULE_UPDATE_FLAGS: --jobs 4
+#   before_script:
+#     - echo "Building the single user notebook image"
+#     - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER $CI_REGISTRY --password-stdin
+#   script:
+#     - docker build -t ${STAGING_IMAGE} .
+#     - docker push ${STAGING_IMAGE}
+#   rules:
+#     # Execute jobs when a new commit is pushed to master branch
+#     - if: $CI_COMMIT_BRANCH == 'master'
 
 deploy to develop:
-  image: python:3.6
   stage: deploy
-  variables:
-    GIT_SUBMODULE_STRATEGY: none
-  script:
-    - ./.gitlab-ci/update_tag_develop.sh
-    - ./.gitlab-ci/update_tag_app_develop.sh
-    - ./.gitlab-ci/update_metainfo_gui_develop.sh
   environment:
-    name: develop
-    url: https://analytics-toolkit.nomad-coe.eu/develop
-  rules:
-    # Execute jobs when a new commit is pushed to develop branch
-    - if: $CI_COMMIT_BRANCH == "develop"  
-
-deploy to staging:
-  image: python:3.6
-  stage: deploy
+    name: dev/$CI_COMMIT_REF_NAME
+    deployment_tier: development
+    url: https://analytics-toolkit.nomad-coe.eu/dev/${CI_ENVIRONMENT_SLUG}
+    auto_stop_in: 7 days
+    on_stop: stop deploy dev
   variables:
-    GIT_SUBMODULE_STRATEGY: none
+    NAMESPACE: analytics-develop
+  before_script:
+    - mkdir ~/.kube/
+    - echo ${CI_KUBE_CONFIG} | base64 -d > ~/.kube/config
+    - helm repo add jupyterhub https://jupyterhub.github.io/helm-chart
+    - helm repo update
+    - helm version
   script:
-    - ./.gitlab-ci/update_tag_staging.sh
-  environment:
-    name: staging
-    url: https://nomad-lab.eu/dev/analytics/staging
+    - helm upgrade ${CI_ENVIRONMENT_SLUG} jupyterhub/jupyterhub
+      --install
+      --namespace ${NAMESPACE}
+      --version=1.2.0
+      --timeout=40m0s
+      --cleanup-on-fail
+      --values deployments/dev-values.yaml
+      --set hub.baseUrl=/dev/${CI_ENVIRONMENT_SLUG}
+      --set fullnameOverride=${CI_ENVIRONMENT_SLUG}
+      --set singleuser.podNameTemplate="${CI_ENVIRONMENT_SLUG}-{username}"
+      --set hub.config.GenericOAuthenticator.oauth_callback_url=https://analytics-toolkit.nomad-coe.eu/dev/${CI_ENVIRONMENT_SLUG}/hub/oauth_callback
+      --set singleuser.image.name=${CI_REGISTRY_IMAGE}
+      --set singleuser.image.tag=${CI_COMMIT_REF_SLUG}
+      --set roll=true
+      --wait
   rules:
     # Execute jobs when a new commit is pushed to master branch
-    - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "master"
+    - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "develop"
 
-
-deploy to production:
-  image: python:3.6
+stop deploy dev:
   stage: deploy
-  script:
-    - ./.gitlab-ci/update_tag_production.sh
   environment:
-    name: production
-    url: https://nomad-lab.eu/prod/analytics/hub
-  rules:
-    # Execute jobs when a new commit is pushed to master branch
-    - if: $CI_COMMIT_BRANCH == 'master'
+    name: dev/$CI_COMMIT_REF_NAME
+    action: stop
+  before_script:
+    - mkdir ~/.kube/
+    - echo ${CI_K8S_CONFIG} | base64 -d > ~/.kube/config
+  script:
+    - helm uninstall ${CI_ENVIRONMENT_SLUG} --namespace analytics
+  when: manual
+  needs: ["build to develop"]
+
+# deploy to staging:
+#   stage: deploy
+#   environment:
+#     name: staging
+#     url: https://nomad-lab.eu/dev/analytics/staging
+#   script:
+#     - ./.gitlab-ci/update_tag_staging.sh
+#   rules:
+#     # Execute jobs when a new commit is pushed to master branch
+#     - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "develop"
+
+# deploy to production:
+#   stage: deploy
+#   environment:
+#     name: production
+#     url: https://nomad-lab.eu/prod/analytics/hub
+#   script:
+#     - ./.gitlab-ci/update_tag_production.sh
+#   rules:
+#     # Execute jobs when a new commit is pushed to master branch
+#     - if: $CI_COMMIT_BRANCH == 'develop'

.gitlab-ci/update_metainfo_gui_develop.sh

-# !/bin/bash
-
-# Based on: https://docs.gitlab.com/ee/ci/ssh_keys/README.html
-
-# Install ssh-agent if not already installed, it is required by Docker.
-# (change apt-get to yum if you use an RPM-based image)
-# - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-# Run ssh-agent (inside the build environment)
-eval $(ssh-agent -s)
-
-# Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
-# We're using tr to fix line endings which makes ed25519 keys work
-# without extra base64 encoding.
-# https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
-echo "$SSH_PRIVATE_KEY_APP" | tr -d '\r' | ssh-add -
-
-# Create the SSH directory and give it the right permissions
-mkdir -p ~/.ssh
-chmod 700 ~/.ssh
-
-# Use ssh-keyscan to scan the keys of your private server.
-ssh-keyscan gitlab.mpcdf.mpg.de >> ~/.ssh/known_hosts
-chmod 644 ~/.ssh/known_hosts
-
-# Set the user name and email.
-git config --global user.name $GITLAB_USER_NAME
-git config --global user.email $GITLAB_USER_EMAIL
-
-
-# Clone the private repositories
-git clone -b develop --recurse git@gitlab.mpcdf.mpg.de:nomad-lab/analytics.git /tmp/analytics
-git clone -b develop git@gitlab.mpcdf.mpg.de:nomad-lab/aitoolkit-gui.git /tmp/aitoolkit-gui
-
-# Create new metainfo based on develop version
-cd /tmp/analytics
-python generate_tutorials_json.py > toolkitMetadata.json
-
-# Copy new metainfo if files are different
-cd /tmp
-if ! cmp analytics/toolkitMetadata.json aitoolkit-gui/src/toolkitMetadata.json~ >/dev/null 2>&1
-then
-    echo 'Update GUI with new metadata'
-    cp analytics/toolkitMetadata.json aitoolkit-gui/src/toolkitMetadata.json
-    cd /tmp/aitoolkit-gui
-    git add src/toolkitMetadata.json
-    git commit -m "CI: Update metainfo in the GUI"
-    git push
-fi
-
-rm -rf /tmp

.gitlab-ci/update_tag_app_develop.sh

-# !/bin/bash
-
-# Based on: https://docs.gitlab.com/ee/ci/ssh_keys/README.html
-
-# Install ssh-agent if not already installed, it is required by Docker.
-# (change apt-get to yum if you use an RPM-based image)
-# - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-# Run ssh-agent (inside the build environment)
-eval $(ssh-agent -s)
-
-# Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
-# We're using tr to fix line endings which makes ed25519 keys work
-# without extra base64 encoding.
-# https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
-echo "$SSH_PRIVATE_KEY_APP" | tr -d '\r' | ssh-add -
-
-# Create the SSH directory and give it the right permissions
-mkdir -p ~/.ssh
-chmod 700 ~/.ssh
-
-# Use ssh-keyscan to scan the keys of your private server.
-ssh-keyscan gitlab.mpcdf.mpg.de >> ~/.ssh/known_hosts
-chmod 644 ~/.ssh/known_hosts
-
-# Set the user name and email.
-git config --global user.name $GITLAB_USER_NAME
-git config --global user.email $GITLAB_USER_EMAIL
-
-
-# Clone the private repository
-git clone git@gitlab.mpcdf.mpg.de:nomad-lab/aitoolkit-develop.git /tmp/aitoolkit-develop
-cd /tmp/aitoolkit-develop
-
-# Update the tag of the docker image
-sed  -i "s/aitoolkit-develop:develop.*/aitoolkit-develop:develop$CI_COMMIT_SHORT_SHA/1" docker-compose.yml
-
-# Finally, commit and push the changes
-git add docker-compose.yml
-git commit -m "CI: Update the Analytics image ($CI_COMMIT_SHORT_SHA)"
-git push
-
-rm -rf /tmp/aitoolkit-app

.gitlab-ci/update_tag_develop.sh

-# !/bin/bash
-
-# Based on: https://docs.gitlab.com/ee/ci/ssh_keys/README.html
-
-# Install ssh-agent if not already installed, it is required by Docker.
-# (change apt-get to yum if you use an RPM-based image)
-# - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-# Run ssh-agent (inside the build environment)
-eval $(ssh-agent -s)
-
-# Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
-# We're using tr to fix line endings which makes ed25519 keys work
-# without extra base64 encoding.
-# https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
-echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
-
-# Create the SSH directory and give it the right permissions
-mkdir -p ~/.ssh
-chmod 700 ~/.ssh
-
-# Use ssh-keyscan to scan the keys of your private server.
-ssh-keyscan gitlab.mpcdf.mpg.de >> ~/.ssh/known_hosts
-chmod 644 ~/.ssh/known_hosts
-
-# Set the user name and email.
-git config --global user.name $GITLAB_USER_NAME
-git config --global user.email $GITLAB_USER_EMAIL
-echo $GITLAB_USER_NAME
-echo $GITLAB_USER_EMAIL
-
-
-# Clone the private repository
-git clone git@gitlab.mpcdf.mpg.de:nomad-lab/analytics-deployment.git /tmp/analytics-deployment
-cd /tmp/analytics-deployment
-
-# Update the tag of the docker image 
-sed  -i "s/^    tag\:.*/    tag\: develop$CI_COMMIT_SHORT_SHA/g" deployments/hub/develop.yaml
-
-# Finally, commit and push the changes
-git add deployments/hub/develop.yaml
-git commit -m "CI: Update the hub image for develop ($CI_PIPELINE_URL)"
-git push
-
-rm -rf /tmp/analytics-deployment

.gitlab-ci/update_tag_production.sh

-  # !/bin/bash
-
-# Based on: https://docs.gitlab.com/ee/ci/ssh_keys/README.html
-
-# Install ssh-agent if not already installed, it is required by Docker.
-# (change apt-get to yum if you use an RPM-based image)
-# - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-# Run ssh-agent (inside the build environment)
-eval $(ssh-agent -s)
-
-# Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
-# We're using tr to fix line endings which makes ed25519 keys work
-# without extra base64 encoding.
-# https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
-echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
-
-# Create the SSH directory and give it the right permissions
-mkdir -p ~/.ssh
-chmod 700 ~/.ssh
-
-# Use ssh-keyscan to scan the keys of your private server.
-ssh-keyscan gitlab.mpcdf.mpg.de >> ~/.ssh/known_hosts
-chmod 644 ~/.ssh/known_hosts
-
-# Set the user name and email.
-git config --global user.name $GITLAB_USER_NAME
-git config --global user.email $GITLAB_USER_EMAIL
-
-
-# Clone the private repository
-git clone git@gitlab.mpcdf.mpg.de:nomad-lab/analytics-deployment.git /tmp/analytics-deployment
-
-cd /tmp/analytics-deployment
-
-# Update the tag of the docker image
-
-sed  -i "s/^    tag\:.*/    tag\: production$CI_COMMIT_SHORT_SHA/g" deployments/hub/config.yaml
-sed  -i "s/^    tag\:.*/    tag\: production$CI_COMMIT_SHORT_SHA/g" deployments/hub/public.yaml
-
-# Finally, commit and push the changes
-git add deployments/hub/config.yaml
-git add deployments/hub/public.yaml
-git commit -m "CI: Update the hub image for production ($CI_PIPELINE_URL)"
-git push
-
-rm -rf /tmp/analytics-deployment

.gitlab-ci/update_tag_staging.sh

-# !/bin/bash
-
-# Based on: https://docs.gitlab.com/ee/ci/ssh_keys/README.html
-
-# Install ssh-agent if not already installed, it is required by Docker.
-# (change apt-get to yum if you use an RPM-based image)
-# - 'which ssh-agent || ( apt-get update -y && apt-get install openssh-client -y )'
-# Run ssh-agent (inside the build environment)
-eval $(ssh-agent -s)
-
-# Add the SSH key stored in SSH_PRIVATE_KEY variable to the agent store
-# We're using tr to fix line endings which makes ed25519 keys work
-# without extra base64 encoding.
-# https://gitlab.com/gitlab-examples/ssh-private-key/issues/1#note_48526556
-echo "$SSH_PRIVATE_KEY" | tr -d '\r' | ssh-add -
-
-# Create the SSH directory and give it the right permissions
-mkdir -p ~/.ssh
-chmod 700 ~/.ssh
-
-# Use ssh-keyscan to scan the keys of your private server.
-ssh-keyscan gitlab.mpcdf.mpg.de >> ~/.ssh/known_hosts
-chmod 644 ~/.ssh/known_hosts
-
-# Set the user name and email.
-git config --global user.name $GITLAB_USER_NAME
-git config --global user.email $GITLAB_USER_EMAIL
-
-
-# Clone the private repository
-git clone git@gitlab.mpcdf.mpg.de:nomad-lab/analytics-deployment.git /tmp/analytics-deployment
-cd /tmp/analytics-deployment
-
-# Update the tag of the docker image
-sed  -i "s/^    tag\:.*/    tag\: $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME$CI_COMMIT_SHORT_SHA/g" deployments/hub/staging.yaml
-
-# Finally, commit and push the changes
-git add deployments/hub/staging.yaml
-git commit -m "CI: Update the hub image for staging ($CI_PIPELINE_URL)"
-git push
-
-rm -rf /tmp/analytics-deployment

.gitmodules

+[submodule "3rdparty/atomic-features-package"]
+	path = 3rdparty/atomic-features-package
+	url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
+[submodule "3rdparty/cmlkit"]
+	path = 3rdparty/cmlkit
+	url = https://gitlab.mpcdf.mpg.de/nomad-lab/cmlkit.git
+[submodule "3rdparty/keras-vis"]
+	path = 3rdparty/keras-vis
+	url = https://github.com/raghakot/keras-vis.git
+[submodule "3rdparty/qmmlpack"]
+	path = 3rdparty/qmmlpack
+	url = https://gitlab.com/qmml/qmmlpack.git
+[submodule "3rdparty/quip"]
+	path = 3rdparty/quip
+	url = git@github.com:libAtoms/QUIP.git
+[submodule "3rdparty/sissopp"]
+	path = 3rdparty/sissopp
+	url = https://gitlab.com/sissopp_developers/sissopp.git
 [submodule "tutorials/analytics-compressed-sensing"]
 	path = tutorials/analytics-compressed-sensing
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-compressed-sensing.git
@@ -22,9 +40,6 @@
 [submodule "tutorials/analytics-cmlkit"]
 	path = tutorials/analytics-cmlkit
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-cmlkit.git
-[submodule "3rdparty/qmmlpack"]
-	path = 3rdparty/qmmlpack
-	url = https://gitlab.com/qmml/qmmlpack.git
 [submodule "tutorials/analytics-descriptor-role"]
 	path = tutorials/analytics-descriptor-role
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-descriptor-role.git
@@ -52,27 +67,12 @@
 [submodule "tutorials/analytics-domain-of-applicability"]
 	path = tutorials/analytics-domain-of-applicability
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-domain-of-applicability.git
-[submodule "tutorials/analytics-query-nomad-archive"]
-	path = tutorials/analytics-query-nomad-archive
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-query-nomad-archive.git
-[submodule "tutorials/analytics-cmlkit"]
-	path = tutorials/analytics-cmlkit
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-cmlkit.git
-[submodule "3rdparty/qmmlpack"]
-	path = 3rdparty/qmmlpack
-	url = https://gitlab.com/qmml/qmmlpack.git
 [submodule "tutorials/analytics-tetradymite-PRM2020"]
 	path = tutorials/analytics-tetradymite-PRM2020
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-tetradymite-PRM2020.ipynb.git
 [submodule "tutorials/analytics-clustering-tutorial"]
 	path = tutorials/analytics-clustering-tutorial
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-clustering-tutorial.git
-[submodule "3rdparty/atomic-features-package"]
-	path = 3rdparty/atomic-features-package
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
-[submodule "3rdparty/keras-vis"]
-	path = 3rdparty/keras-vis
-	url = https://github.com/raghakot/keras-vis.git
 [submodule "tutorials/analytics-arise"]
 	path = tutorials/analytics-arise
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-arise.git
@@ -82,12 +82,6 @@
 [submodule "tutorials/analytics-atomic-features"]
 	path = tutorials/analytics-atomic-features
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-atomic-features.git
-[submodule "3rdparty/atomic-features-package"]
-	path = 3rdparty/atomic-features-package
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/atomic-features-package.git
-[submodule "3rdparty/cpp_sisso"]
-	path = 3rdparty/cpp_sisso
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/cpp_sisso.git
 [submodule "tutorials/analytics-sgd-alloys-oxygen-reduction-evolution"]
 	path = tutorials/analytics-sgd-alloys-oxygen-reduction-evolution
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-sgd-alloys-oxygen-reduction-evolution.git
@@ -109,12 +103,12 @@
 [submodule "tutorials/analytics-dos-similarity-search"]
 	path = tutorials/analytics-dos-similarity-search
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-dos-similarity-search.git
-[submodule "3rdparty/cmlkit"]
-	path = 3rdparty/cmlkit
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/cmlkit.git
 [submodule "tutorials/analytics-dimensionality-reduction"]
 	path = tutorials/analytics-dimensionality-reduction
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-dimensionality-reduction.git
 [submodule "tutorials/analytics-kappa-screening-sisso"]
 	path = tutorials/analytics-kappa-screening-sisso
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-kappa-screening-sisso.git
+[submodule "3rdparty/nomad-FAIR"]
+	path = 3rdparty/nomad-FAIR
+	url = git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-FAIR.git

atomic-features-package @ 7dda7a91

-Subproject commit 3f3ef10534d3a296cd465699241926a69d36e1f6
+Subproject commit 7dda7a911e99b87c4470f01d619664e39f56dd9c

cmlkit @ 3ce44fd3

-Subproject commit ccdde6e67dc441c3d84e2f95c607e5018000f4cb
+Subproject commit 3ce44fd3933c17d567fbf783fa784b2b6c98ba7c

cpp_sisso @ 7cf0dc12

-Subproject commit 7cf0dc12bae7481aaed1bb5660416dcb05bc6c44

3rdparty/gap/.gitignore

-*~

3rdparty/gap/LICENSE.md

-### GAP suite — Non-commercial License Agreement
-
-*Last updated: 19th April 2017*
-
-The GAP suite of programs, comprising the GAP-filler and GAP packages
-(together “the Software”), written by Dr Gabor Csanyi and Dr Albert
-Bartok-Partay of the University of Cambridge (the “Authors”) for
-describing the chemical environments of atoms and molecules and
-predicting potential energy surfaces, is copyrighted by the University
-of Cambridge and the Authors. Users at non-commercial institutions may
-obtain a copy for Non-commercial Purposes. "Non-commercial Purposes" 
-means use of the Software and/or any **Software-derived data (including
-interatomic potentials)** for academic research or other not-for-profit
-or scholarly purposes which are undertaken at an educational, 
-non-profit, charitable or governmental institution that does not
-involve the production or manufacture of products for sale or the 
-performance of services for a fee or other non-monetary value.
-
-For commercial use of either or both the Software or any
-Software-derived data, please contact Cambridge Enterprise Limited at
-<enquiries@enterprise.cam.ac.uk>.
-
-1.  This is a legal agreement between you (“USER”), and the Authors. By
-    accepting, receiving, and using this Software, you are agreeing to
-    be bound by the terms of this Agreement.
-2.  The Authors hereby grant to the USER a non-exclusive,
-    non-transferable personal licence to use the Software.
-3.  The licence granted under this Agreement shall only entitle the USER
-    to use the Software for Non-commercial Purposes. The use of the
-    Software, or any code which is a modification of, enhancement to,
-    derived from or based upon the Software, or Software-derived data,
-    either directly or indirectly for any commercial purpose whatsoever
-    is expressly forbidden. The USER may not sublicense, distribute or
-    copy (except for archival purposes) the Software or enhancements
-    thereto.
-4.  If any academic paper or publication by the USER includes any set of
-    interatomic potentials or other Software-derived data then the USER
-    must timeously publish their full GAP model and source data (i.e.
-    the underlying quantum mechanical data which were used as input to
-    the GAP-filler). Any publication of any GAP models, interatomic
-    potentials or other Software-derived data must specifically state
-    that such data is provided for non-commercial use only.
-5.  If any academic paper or publication by the USER is based wholly or
-    partially, directly or indirectly on the Software or any results
-    derived from the Software then that paper or publication must cite:
-    -   A. P. Bartok et al. *Physical Review Letters* **104**
-        136403 (2010)
-    -   A. P. Bartok et al. *Physical Review B* **87** 184115 (2013)
-    -   That this Software is available for non-commercial use from
-        `www.libatoms.org`
-6.  The Software is the subject of copyright. Unauthorised copying of
-    the Software is expressly forbidden. The University of Cambridge and
-    the Authors retain all the rights in and title to the Software.
-7.  The Software is provided "AS IS" and except as expressly provided in
-    this Agreement no warranty, condition, undertaking or term, express
-    or implied, statutory or otherwise, as to the condition,
-    performance, satisfactory quality or fitness for purpose of the
-    Software is given or assumed by the Authors or the University of
-    Cambridge, and all such warranties, conditions, undertakings and
-    terms are hereby excluded.
-8.  The limitations and exclusions in this Agreement shall not apply in
-    respect of claims for personal injury or death caused by negligence
-    or in respect of fraud or fraudulent misrepresentation.
-9.  EXCEPT AS PROVIDED BY CLAUSE 8, neither the AUTHORS nor the
-    University OF CAMBRIDGE or its employees or students shall be liable
-    for any damages or expenses of whatsoever nature and howsoever
-    arising (including without limitation in contract, tort, negligence
-    or for breach of statutory duty or misrepresentation) in connection
-    with any right or licence granted or use of the Software or
-    otherwise in connection with this Licence or any relationships
-    established by it. Without prejudice to the generality of the
-    foregoing, in the event that the AUTHORS, the University OF
-    CAMBRIDGE, its employees or students should be found liable, then
-    their aggregate liability for direct damages shall be limited to
-    £100; and none of them shall be liable for any indirect, incidental,
-    consequential or special damages including without limitation loss
-    of profits, revenue, or business opportunity, loss of goodwill, data
-    loss, business disruption or computer failure.
-10. The USER shall indemnify the Authors, the University of Cambridge,
-    its employees and students in full against each and every claim made
-    against any of them by any third party (including without limitation
-    in contract, tort, negligence or for breach of statutory duty or
-    misrepresentation) arising out of or in connection with the USER's
-    use of the Software.
-11. The Authors accept no obligation to provide maintenance nor do they
-    guarantee the expected functionality of the Software or of any part
-    of the Software.
-12. This Agreement is effective until terminated. This Agreement will
-    terminate automatically on notice from the Authors if the USER fails
-    to comply with any provision of this Agreement. Upon termination the
-    USER shall immediately destroy all copies of the Software.
-13. This Agreement and any matters relating to it shall be governed and
-    construed in accordance with the laws of England and Wales and
-    Authors and the USER hereby irrevocably submit to the exclusive
-    jurisdiction of the English Courts.
-

3rdparty/gap/Makefile

-# HND XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-# HND X
-# HND X   libAtoms+QUIP: atomistic simulation library
-# HND X
-# HND X   Portions of this code were written by
-# HND X     Albert Bartok-Partay, Silvia Cereda, Gabor Csanyi, James Kermode,
-# HND X     Ivan Solt, Wojciech Szlachta, Csilla Varnai, Steven Winfield.
-# HND X
-# HND X   Copyright 2006-2010.
-# HND X
-# HND X   Not for distribution
-# HND X
-# HND X   Portions of this code were written by Noam Bernstein as part of
-# HND X   his employment for the U.S. Government, and are not subject
-# HND X   to copyright in the USA.
-# HND X
-# HND X   When using this software, please cite the following reference:
-# HND X
-# HND X   http://www.libatoms.org
-# HND X
-# HND X  Additional contributions by
-# HND X    Alessio Comisso, Chiara Gattinoni, and Gianpietro Moras
-# HND X
-# HND XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-
-
-
-ifeq (${QUIP_ARCH},)
-  include Makefile.arch
-else
-  include Makefile.${QUIP_ARCH}
-endif
-include Makefile.inc
-include Makefile.rules
-
-GAP1_F95_FILES = make_permutations_v2 descriptors gp_predict descriptors_wrapper clustering 
-GAP1_F95_SOURCES = ${addsuffix .f95, ${GAP1_F95_FILES}}
-GAP1_F95_OBJS = ${addsuffix .o, ${GAP1_F95_FILES}}
-
-GAP2_F95_FILES = gp_fit gap_fit_module 
-GAP2_F95_SOURCES = ${addsuffix .f95, ${GAP2_F95_FILES}}
-GAP2_F95_OBJS = ${addsuffix .o, ${GAP2_F95_FILES}}
-
-default: ${GAP_LIBFILE}
-
-
-
-ifeq (${USE_MAKEDEP},1)
-GAP1_F95_FPP_FILES = ${addsuffix .fpp, ${GAP1_F95_FILES}}
-GAP2_F95_FPP_FILES = ${addsuffix .fpp, ${GAP2_F95_FILES}}
-GAP1.depend: ${GAP1_F95_FPP_FILES}
-	${SCRIPT_PATH}/${MAKEDEP} ${MAKEDEP_ARGS} -- ${addprefix ../../src/GAP/,${GAP1_F95_SOURCES}} > GAP1.depend
-GAP2.depend: ${GAP2_F95_FPP_FILES} ${GAP1_F95_FPP_FILES}
-	${SCRIPT_PATH}/${MAKEDEP} ${MAKEDEP_ARGS} -- ${addprefix ../../src/GAP/,${GAP2_F95_SOURCES}} > GAP2.depend
-
--include GAP1.depend
--include GAP2.depend
-endif
-
-
-PROGRAMS = gap_fit 
-
-LIBS = -L. -lquiputils -lquip_core -lgap -latoms
-ifeq (${HAVE_THIRDPARTY},1)
-  LIBS += -lthirdparty
-endif
-LIBFILES = libatoms.a ${GAP_LIBFILE} libquip_core.a libquiputils.a
-
-.PHONY : clean allclean depend doc install
-
-Programs: ${PROGRAMS} 
-	cp ${QUIP_ROOT}/src/GAP/teach_sparse .
-
-${PROGRAMS}: % : ${LIBFILES} ${GAP2_F95_OBJS} ${GAPFIT_LIBFILE}  %.o
-	$(LINKER) $(LINKFLAGS) -o $@ ${F90OPTS} $@.o ${GAPFIT_LIBFILE} ${LIBS} ${LINKOPTS}
-
-
-
-${GAP_LIBFILE}: ${GAP1_F95_OBJS}
-ifneq (${LIBTOOL},)
-	${LIBTOOL} -o ${GAP_LIBFILE} ${GAP1_F95_OBJS}
-else
-	${AR} ${AR_ADD} ${GAP_LIBFILE} $?
-endif
-
-${GAPFIT_LIBFILE}: ${GAP2_F95_OBJS}
-ifneq (${LIBTOOL},)
-	${LIBTOOL} -o ${GAPFIT_LIBFILE} ${GAP2_F95_OBJS}
-else
-	${AR} ${AR_ADD} ${GAPFIT_LIBFILE} $?
-endif
-
-
-
-
-install:
-	@if [ ! -d ${QUIP_INSTALLDIR} ]; then \
-	  echo "make install: QUIP_INSTALLDIR '${QUIP_INSTALLDIR}' doesn't exist or isn't a directory"; \
-	  exit 1; \
-	else	\
-	  for f in ${PROGRAMS} ; do \
-	    echo "Copying $$f to ${QUIP_INSTALLDIR}/$${f}${QUIP_MPI_SUFFIX}" ; \
-	    cp $$f ${QUIP_INSTALLDIR}/$${f}${QUIP_MPI_SUFFIX} ; \
-	  done ;\
-	  cp ${QUIP_ROOT}/src/GAP/teach_sparse ${QUIP_INSTALLDIR}; \
-	fi
-
-
-clean:
-	rm -f *.o *.mod *.mod.save ${GAP_LIBFILE} ${GAPFIT_LIBFILE} ${PROGRAMS} GAP1.depend GAP2.depend
-
-

3rdparty/gap/doc/Makefile

-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = gap
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

3rdparty/gap/doc/conf.py

-# -*- coding: utf-8 -*-
-# HQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-# HQ X
-# HQ X   quippy: Python interface to QUIP atomistic simulation library
-# HQ X
-# HQ X   Copyright James Kermode 2010
-# HQ X
-# HQ X   These portions of the source code are released under the GNU General
-# HQ X   Public License, version 2, http://www.gnu.org/copyleft/gpl.html
-# HQ X
-# HQ X   If you would like to license the source code under different terms,
-# HQ X   please contact James Kermode, james.kermode@gmail.com
-# HQ X
-# HQ X   When using this software, please cite the following reference:
-# HQ X
-# HQ X   http://www.jrkermode.co.uk/quippy
-# HQ X
-# HQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
-
-#
-# quippy documentation build configuration file, created by
-# sphinx-quickstart on Wed Sep  2 14:17:01 2009.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import glob
-import os
-import sys
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-
-sys.path.insert(1, os.path.abspath('..'))
-sys.path.insert(1, os.path.abspath('.'))
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-needs_sphinx = '1.4'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
-    'nbsphinx',
-    'modcontents',
-    'numpydoc']
-
-# This list was generated by grep as a workaround to
-# https://github.com/sphinx-doc/sphinx/issues/2485
-autosummary_generate = [
-    'gap_fit.rst',
-]
-
-nbsphinx_allow_errors = True
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = ['.rst', '.ipynb']
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'gap'
-copyright = u'20010-2019, Gabor Csanyi'
-author= u'Gabor Csanyi'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-import os
-version=os.popen('cat ../GIT_VERSON 2> /dev/null|| '
-                 'git describe --always --tags --dirty=+ 2> /dev/null || '
-                 'echo ').read().strip()
-# The full version, including alpha/beta/rc tags.
-release = version
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# A list of ignored prefixes for module index sorting.
-modindex_common_prefix = ['quippy.']
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-html_theme_options = {
-}
-
-html_logo = 'hybrid.png'
-html_favicon = 'favicon.ico'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Fix for RTD tables
-html_context = {
-    'css_files': [
-        '_static/theme_overrides.css',
-    ],
-}
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'gapdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'gap.tex', u'GAP Documentation',
-     u'Gabor Csanyi', 'manual'),
-]
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'gap', u'GAP Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'gap', u'GAP Documentation',
-     author, 'gap', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-
-intersphinx_mapping = {'python': ('https://docs.python.org/2.7', None),
-                       'ase': ('https://wiki.fysik.dtu.dk/ase/', None),
-                       'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-                       'matplotlib': ('https://matplotlib.org/', None)}
-
-###
-### sphinx-quickstart output ends here
-###
-
-from quippy.oo_fortran import FortranDerivedType, FortranDerivedTypes
-
-import re
-
-# classnames = [v.__name__ for v in FortranDerivedTypes.values()]
-# classname_re = re.compile('(^|\s+)((``)?)('+'|'.join([v.__name__ for v in FortranDerivedTypes.values()])+r')\2(?=[\s\W]+)')
-# method_or_attr_re = re.compile('(^|\s+)((``)?)('+'|'.join([v.__name__+'\.([a-zA-Z][a-zA-Z0-9_]*)' for v in FortranDerivedTypes.values()])+r')\2(?=[\s\W]+)')
-
-# doc_subs = [(classname_re, r'\1:class:`~.\4`'),
-#             (method_or_attr_re, r'\1:meth:`.\4`')]
-
-global_options = None
-
-def process_docstring(app, what, name, obj, options, lines):
-    global global_options
-    global_options = options
-        
-def process_signature(app, what, name, obj, options, signature, return_annotation):
-    return (signature, return_annotation)
-
-def maybe_skip_member(app, what, name, obj, skip, options):
-    if hasattr(FortranDerivedType, name) and options.inherited_members:
-        return True
-    return skip
-
-from docutils import nodes, utils
-from docutils.parsers.rst.roles import set_classes
-
-def get_github_url(view, path):
-    return 'https://github.com/{project}/{view}/{branch}/{path}'.format(
-        project='libAtoms/GAP',
-        view=view,
-        branch='public',
-        path=path)
-
-def github_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
-    if text[-1] == '>':
-        i = text.index('<')
-        name = text[:i - 1]
-        text = text[i + 1:-1]
-    else:
-        name = text
-    ref = get_github_url('blob', name)
-    set_classes(options)
-    node = nodes.reference(rawtext, name, refuri=ref, **options)
-    return [node], []
-
-def mol_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
-    n = []
-    t = ''
-    while text:
-        if text[0] == '_':
-            n.append(nodes.Text(t))
-            t = ''
-            n.append(nodes.subscript(text=text[1]))
-            text = text[2:]
-        else:
-            t += text[0]
-            text = text[1:]
-    n.append(nodes.Text(t))
-    return n, []
-
-def setup(app):
-    app.connect('autodoc-process-docstring', process_docstring)
-    app.connect('autodoc-process-signature', process_signature)
-    app.connect('autodoc-skip-member', maybe_skip_member)
-
-    app.add_role('git', github_role)
-    app.add_role('mol', mol_role)
-
-
-autodoc_member_order = 'groupwise'
-#autoclass_content = 'both'
-
-def add_line(self, line, source, *lineno):
-    """Append one line of generated reST to the output."""
-    sys.stdout.write(self.indent + line + '\n')
-    self.directive.result.append(self.indent + line, source, *lineno)
-
-# Uncomment two lines below to debug autodoc rst output
-
-#import sphinx.ext.autodoc
-#sphinx.ext.autodoc.Documenter.add_line = add_line
-
-# Monkey patch numpydoc to exclude methods and attributes inherited
-# from base classes, and to include attributes wrapped by Python
-# properties
-
-numpydoc_show_class_members = True
-
-import inspect
-import pydoc
-import numpydoc
-import numpydoc.docscrape
-
-@property
-def methods(self):
-    if self._cls is None:
-        return []
-    do_inherited = False
-    if global_options is not None and hasattr(global_options, 'inherited_members'):
-        do_inherited = global_options.inherited_members
-
-    return [name for name,func in inspect.getmembers(self._cls)
-            if not name.startswith('_') and callable(func) and
-            (do_inherited or not any(hasattr(base, name) for base in self._cls.__bases__)) and
-            pydoc.getdoc(getattr(self._cls, name))]
-
-@property
-def properties(self):
-    if self._cls is None:
-        return []
-    do_inherited = False
-    if global_options is not None and hasattr(global_options, 'inherited_members'):        
-        do_inherited = global_options.inherited_members
-    return [name for name,func in inspect.getmembers(self._cls) if not name.startswith('_') and
-            (do_inherited or not any(hasattr(base, name) for base in self._cls.__bases__)) and
-            (func is None or isinstance(getattr(self._cls, name), property)) and
-            pydoc.getdoc(getattr(self._cls, name))]
-
-numpydoc.docscrape.ClassDoc.methods = methods
-numpydoc.docscrape.ClassDoc.properties = properties
-
-# generate .rst versions of any .ipynb notebooks under Examples/
-# Superseded by nbsphinx extension
-# for notebook in glob.glob(os.path.join('Examples/*.ipynb')):
-    # cmd = 'jupyter nbconvert --to rst {0}'.format(notebook)
-    # print cmd
-    # os.system(cmd)
-