diff --git a/docs/examples.rst b/docs/examples.rst
index 91aa8adc9c570f5a310637078fdc2718ff2c4683..e8b4b74e6000c81f08dc118ddf7b9e96475c8627 100644
--- a/docs/examples.rst
+++ b/docs/examples.rst
@@ -1,12 +1,10 @@
Examples
========
-Work in progress.
.. toctree::
- :maxdepth: 4
+ :maxdepth: 0
:glob:
- :caption: Examples:
- examples/*
+ ../examples/*
diff --git a/docs/snippets/1.ex_CI_build_docker_container.md b/docs/snippets/1.ex_CI_build_docker_container.md
deleted file mode 100644
index a7f3adc586720bb8a05068ad03868cf04bbb5b9b..0000000000000000000000000000000000000000
--- a/docs/snippets/1.ex_CI_build_docker_container.md
+++ /dev/null
@@ -1,31 +0,0 @@
-# Build a Docker container during the CI process
-
- - Builds a Docker container during the CI process.
- - Uploads the container to the GitLab container registry.
-
-**NOTE**. You should provide the Docker recipe (`Dockerfile`) and add it to a `Docker` directory in the root directory
-of your project.
-
-```yaml
-stages:
- - build_container
-
-
-build_docker:
- stage: build_container
- image: docker:19.03.12
- services:
- - docker:19.03.12-dind
- before_script:
- - cat /etc/os-release # "Alpine Linux v3.12"
- - apk add git
- - export LAST_RELEASE=`git ls-remote --tags --refs --sort="v:refname" $CI_PROJECT_URL.git | tail -n1 | sed 's/.*\///'`
- - echo $LAST_RELEASE
- script:
- - cd Docker # You should have added before your Dockerfile in this dir
- - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- - docker build -t $CI_REGISTRY_IMAGE:$LAST_RELEASE .
- - docker push $CI_REGISTRY_IMAGE:$LAST_RELEASE
- only:
- - tags
-```
\ No newline at end of file
diff --git a/docs/snippets/2.ex_CI_build_singularity_image.md b/docs/snippets/2.ex_CI_build_singularity_image.md
deleted file mode 100644
index 1fbb7299b9ff63171f40434a3f101353cd10d85c..0000000000000000000000000000000000000000
--- a/docs/snippets/2.ex_CI_build_singularity_image.md
+++ /dev/null
@@ -1,40 +0,0 @@
-# Build a Singularity image during the CI process
-
-This example is based on [this project](https://gitlab.com/singularityhub/gitlab-ci) (https://zenodo.org/record/3834833).
-To be able to include the following code snippet into your `.gitlab-ci.yml` file, you should check the License
-compatibility of your project and the origin one (an example can be found [here](
-https://gitlab.in2p3.fr/escape2020/wp3/template_project_escape/-/tree/master/.singularityci)).
-
-
-This code snippet
-
- - Builds a Singularity image during the CI process.
- - Makes available the created artifact (the image) to be used in the next CI stages.
-
-**PLEASE NOTE**
- - You should provide the Singularity recipe (`Singularity`) and add it to a `Singularity` directory in the
-root directory of your project.
- - The image will be built using **Singularity v2.6**.
-
-
-```yaml
-stages:
- - build_container
-
-build_singularity:
- stage: build_container
- image: singularityware/singularity:gitlab-2.6
- script:
- - export IMAGE_NAME=$CI_PROJECT_NAME # Choose the name of the image
- - singularity build $IMAGE_NAME.simg Singularity/Singularity
-
- - mkdir -p build && cp Singularity/*.simg build
- - mkdir -p build && cp Singularity/Singularity* build
- artifacts:
- paths:
- - build/Singularity.simg
- - build/Singularity
- only:
- - tags
-
-```
\ No newline at end of file
diff --git a/docs/snippets/3.ex_CI_upload_new_deposit.md b/docs/snippets/3.ex_CI_upload_new_deposit.md
deleted file mode 100644
index 76396e18bdab8496ed4592316289a62353cd436c..0000000000000000000000000000000000000000
--- a/docs/snippets/3.ex_CI_upload_new_deposit.md
+++ /dev/null
@@ -1,54 +0,0 @@
-# Upload a new entry to the OSSR
-
- - Uses the GitLab CI to upload the current project to the ESCAPE-OSSR (The ESCAPE2020 Zenodo community).
- - Note that the CI will be only triggered with the creation of a new release.
- - The `codemeta.json` file - compulsory if you want to run this code - will be also added to the Zenodo entry as
- a separate file.
- - The `eossr-check-connection-zenodo` stage will create a fist dummy upload (that will be always erased), to check
- that the released code will be successfully uploaded.
-
-
-### Upload to Zenodo
-```yaml
-stages:
- - deploy
-
-deploy_zenodo:
- stage: deploy
- image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:v0.1
- before_script:
- - eossr-check-connection-zenodo --token $ZENODO_TOKEN --sandbox False -p $CI_PROJECT_DIR
- script:
- - mkdir -p build
- - parse_last_release_git.sh $CI_PROJECT_NAME $CI_PROJECT_URL
- - if [[ -f ./codemeta.json ]]; then cp ./codemeta.json ./build; fi
- - ls ./build
-
- - eossr-upload-new-deposit -t $ZENODO_TOKEN -s False -i ./build -id $ZENODO_PROJECT_ID
- only:
- - tags
-
-```
-
-
-### Upload to Sandbox Zenodo
-```yaml
-stages:
- - deploy
-
-deploy_zenodo:
- stage: deploy
- image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:v0.1
- before_script:
- - eossr-check-connection-zenodo --token $SANDBOX_ZENODO_TOKEN --sandbox True -p $CI_PROJECT_DIR
- script:
- - mkdir -p build
- - parse_last_release_git.sh $CI_PROJECT_NAME $CI_PROJECT_URL
- - if [[ -f ./codemeta.json ]]; then cp ./codemeta.json ./build; fi
- - ls ./build
-
- - eossr-upload-new-deposit -t $SANDBOX_ZENODO_TOKEN -s True -i ./build -id $ZENODO_PROJECT_ID
- only:
- - tags
-
-```
diff --git a/docs/snippets/4.ex_CI_upload_new_version_deposit.md b/docs/snippets/4.ex_CI_upload_new_version_deposit.md
deleted file mode 100644
index 961cdc8261610d14bfd4adb5bc69a6df69abeaf1..0000000000000000000000000000000000000000
--- a/docs/snippets/4.ex_CI_upload_new_version_deposit.md
+++ /dev/null
@@ -1,69 +0,0 @@
-# Upload a new version of an existing entry to the OSSR
-
- - Uses the GitLab CI to upload a **new version** of the current project to the ESCAPE-OSSR (The ESCAPE2020 Zenodo
- community).
- - Note that the CI will be only triggered with the creation of a new release.
- - The `codemeta.json` file - compulsory if you want to run this code - will be also added to the Zenodo entry as
- a separate file.
- - The `eossr-check-connection-zenodo` stage will create a fist dummy upload (that will be always erased), to check
- that the released code will be successfully uploaded.
-
-**NOTE**.
-You should have saved the `deposit_id` of your project as a GitLab environment variable before the CI runs this stage.
-
-To do so:
-1. Go to https://zenodo.org/deposit,
-2. Click onto your just uploaded project,
-3. From your browser search bar, **just** copy the number (your `deposit id`) that it is included in the https direction.
- - ex: `https://zenodo.org/record/3884963` --> just copy `3884963`.
-4. Save it as a new environment variable in your GitLab project.
- * Go to your GitLab project.
- * Click on `Settings` --> `CI/CD` --> `Variables` --> `Add variable`
- * `KEY`=`$ZENODO_PROJECT_ID` and fill the value with the deposit id.
- * For Sandbox Zenodo use `KEY` = `SANDBOX_ZENODO_PROJECT_ID`
-
-
-### Upload to Zenodo
-```yaml
-stages:
- - deploy
-
-deploy_zenodo:
- stage: deploy
- image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:v0.1
- before_script:
- - eossr-check-connection-zenodo --token $ZENODO_TOKEN --sandbox False -p $CI_PROJECT_DIR
- script:
- - mkdir -p build
- - parse_last_release_git.sh $CI_PROJECT_NAME $CI_PROJECT_URL
- - if [[ -f ./codemeta.json ]]; then cp ./codemeta.json ./build; fi
- - ls ./build
-
- - eossr-upload-new-version-deposit -t $ZENODO_TOKEN -s False -i ./build -id $ZENODO_PROJECT_ID
- only:
- - tags
-
-```
-
-
-### Upload to Sandbox Zenodo
-```yaml
-stages:
- - deploy
-
-deploy_zenodo:
- stage: deploy
- image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:v0.1
- before_script:
- - eossr-check-connection-zenodo --token $SANDBOX_ZENODO_TOKEN --sandbox True -p $CI_PROJECT_DIR
- script:
- - mkdir -p build
- - parse_last_release_git.sh $CI_PROJECT_NAME $CI_PROJECT_URL
- - if [[ -f ./codemeta.json ]]; then cp ./codemeta.json ./build; fi
- - ls ./build
-
- - eossr-upload-new-version-deposit -t $SANDBOX_ZENODO_TOKEN -s True -i ./build -id $SANDBOX_ZENODO_PROJECT_ID
- only:
- - tags
-
-```
diff --git a/docs/snippets/5.ex_CI_build_image_and_upload_OSSR.md b/docs/snippets/5.ex_CI_build_image_and_upload_OSSR.md
deleted file mode 100644
index e392a029d94f635a56fd620d0a0b2c3f7c456ad4..0000000000000000000000000000000000000000
--- a/docs/snippets/5.ex_CI_build_image_and_upload_OSSR.md
+++ /dev/null
@@ -1,80 +0,0 @@
-# Build a Singularity image, a Docker container and upload your project and images to the OSSR
-
-This code snippet will:
-
- - Builds a Docker container during the CI process.
- - Builds a Singularity image during the CI process.
- - Makes available the created artifacts (both images) to be used in the next CI stages.
- - Uploads the next released version of the current project, together with both images, to the ESCAPE-OSSR
- (The ESCAPE2020 Zenodo community).
-
-Have a look before to the examples in this same directory.
-
-```yaml
-stages:
- - build_container
- - deploy
-
-build_singularity_image:
- stage: build
- image: singularityware/singularity:gitlab-2.6
- script:
- # You should have added before your Singularity recipe in a Singularity dir
- - singularity build $IMAGE_NAME.simg Singularity/Singularity
-
- - mkdir -p build && cp Singularity/*.simg build
- - mkdir -p build && cp Singularity/Singularity* build
- artifacts:
- paths:
- - build/Singularity.simg
- - build/Singularity
- only:
- - tags
-
-build_docker_image:
- stage: build
- image: docker:19.03.12
- services:
- - docker:19.03.12-dind
- before_script:
- - cat /etc/os-release # "Alpine Linux v3.12"
- - apk add git
- - export LAST_RELEASE=`git ls-remote --tags --refs --sort="v:refname" $CI_PROJECT_URL.git | tail -n1 | sed 's/.*\///'`
- - echo $LAST_RELEASE
- script:
- - cd Docker
- - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- - docker build -t $CI_REGISTRY_IMAGE:$LAST_RELEASE .
- - docker push $CI_REGISTRY_IMAGE:$LAST_RELEASE
-
- # Save docker image into a file to be uploaded in next stage
- - docker save -o Docker_image_ESCAPE_template_project_$LAST_RELEASE.tar $CI_REGISTRY_IMAGE:$LAST_RELEASE
- - cd .. && mkdir -p build && cp Docker/*.tar build
- - ls build
- artifacts:
- paths:
- - build/Docker_image_ESCAPE_template_project_*.tar
- only:
- - tags
-
-
-deploy_zenodo:
- stage: deploy
- image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:v0.1
- # The `dependencies` key (and field) is added to this stage ONLY because we have created
- # in previous stages some artifacts
- dependencies:
- - build_singularity_image
- - build_docker_image
- before_script:
- - test_connection_zenodo --token $ZENODO_TOKEN --sandbox False -p $CI_PROJECT_DIR
- script:
- - mkdir -p build
- - parse_last_release_git.sh $CI_PROJECT_NAME $CI_PROJECT_URL
- - if [[ -f ./codemeta.json ]]; then cp ./codemeta.json ./build; fi
- - ls ./build
-
- - upload_new_version_deposit -t $ZENODO_TOKEN -s False -i ./build -id $ZENODO_PROJECT_ID
- only:
- - tags
-```