From d27aaf8127fa052240f31dc32b7a066c21fbe08a Mon Sep 17 00:00:00 2001
From: Gensollen <nicolas.gensollen@gmail.com>
Date: Tue, 4 Jun 2024 10:27:19 +0200
Subject: [PATCH] [CI] Move build and deploy to GitHub Actions (#47)

---
 .github/workflows/build_and_deploy.yml | 45 +++++++++++++
 .jenkins/Jenkinsfile                   | 87 --------------------------
 Makefile                               |  9 +--
 3 files changed, 47 insertions(+), 94 deletions(-)
 create mode 100644 .github/workflows/build_and_deploy.yml
 delete mode 100644 .jenkins/Jenkinsfile

diff --git a/.github/workflows/build_and_deploy.yml b/.github/workflows/build_and_deploy.yml
new file mode 100644
index 0000000..b2d1e85
--- /dev/null
+++ b/.github/workflows/build_and_deploy.yml
@@ -0,0 +1,45 @@
+name: Build and Deloy Handbook
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+env:
+  POETRY_VERSION: '1.6.1'
+  PYTHON_VERSION: '3.10'
+
+jobs:
+  build-and-deploy:
+    runs-on:
+      - self-hosted
+      - Linux
+      - gpu
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+        with:
+          version: ${{ env.POETRY_VERSION }}
+          virtualenvs-create: false
+      - name: Build documentation
+        run: |
+          source ~/miniconda3/etc/profile.d/conda.sh
+          conda env update -n clinicadl_handbook -f environment.yml
+          conda activate clinicadl_handbook
+          make install
+          make build.notebooks
+          make build.book
+          sed -i 's+github/aramis-lab/clinicadl_handbook/blob/main/jupyter-book/notebooks+github/aramis-lab/clinicadl_handbook/blob/main/notebooks+g' ./jupyter-book/_build/html/notebooks/*.html
+      - name: Deploy documentation
+        run: |
+          ls jupyter-book/_build/html
+          scp -r jupyter-book/_build/html aramislab:/srv/local/clinicadl/tutoriel/2023/
+
diff --git a/.jenkins/Jenkinsfile b/.jenkins/Jenkinsfile
deleted file mode 100644
index 93f0098..0000000
--- a/.jenkins/Jenkinsfile
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/usr/bin/env groovy
-
-// Continuous Integration script to build mkdocs in Docker
-// Author: mauricio.diaz@inria.fr
-
-pipeline {
-  agent none
-    stages {
-      stage('Build the docs') {
-        agent {
-          dockerfile {
-              filename 'Dockerfile'
-              reuseNode true
-          }
-        }
-        environment {
-          CONDA_HOME = '/opt/conda'
-          PATH = "/opt/conda/bin:/opt/conda/condabin:$PATH"
-        }
-        steps {
-          echo 'My branch name is ${BRANCH_NAME}'
-          sh 'echo "My branch name is ${BRANCH_NAME}"'
-          sh 'echo "Agent name: ${NODE_NAME}"'
-          sh 'pwd'
-          sh '$MAMBA_EXE info'
-          sh 'printenv'
-          //sh '. /usr/local/bin/_activate_current_env.sh'
-          sh '''#!/bin/bash
-            source /usr/local/bin/_activate_current_env.sh
-            poetry about
-            poetry install
-            make build.notebooks
-            make build.book
-            sed -i 's+github/aramis-lab/clinicadl_handbook/blob/main/jupyter-book/notebooks+github/aramis-lab/clinicadl_handbook/blob/main/notebooks+g' ./jupyter-book/_build/html/notebooks/*.html
-          '''
-          stash(name: 'doc_html', includes: 'jupyter-book/_build/html/**')
-        }
-      }
-      stage('Deploy') {
-        parallel {
-          stage('Deploy site') {
-            agent { label 'gpu' }
-            when {
-                branch 'main'
-            }
-            steps {
-              echo 'Deploying in webserver...'
-              unstash(name: 'doc_html')
-              sshPublisher(
-                publishers: [
-                  sshPublisherDesc(
-                    configName: 'web',
-                    transfers: [
-                      sshTransfer(
-                        cleanRemote: false,
-                        excludes: '',
-                        execCommand: '',
-                        execTimeout: 120000,
-                        flatten: false,
-                        makeEmptyDirs: false,
-                        noDefaultExcludes: false,
-                        patternSeparator: '[, ]+',
-                        remoteDirectory: 'clinicadl/tutoriel/2023',
-                        remoteDirectorySDF: false,
-                        removePrefix: 'jupyter-book/_build',
-                        sourceFiles: 'jupyter-book/_build/html/**')
-                        ],
-                      usePromotionTimestamp: false,
-                      useWorkspaceInPromotion: false,
-                      verbose: false)
-                ]
-              )
-              echo 'Finish uploading artifacts'
-            }
-          }
-        }
-      }
-    }
-//    post {
-//      failure {
-//        mail to: 'clinicadl-ci@inria.fr',
-//          subject: "This build of the welcome guide has failed: ${currentBuild.fullDisplayName}",
-//          body: "Something is wrong with the build of the welcome guide ${env.BUILD_URL}"
-//      }
-//    }
-}
-
diff --git a/Makefile b/Makefile
index baed034..ac1ee4a 100644
--- a/Makefile
+++ b/Makefile
@@ -11,18 +11,13 @@ help: Makefile
 	@echo "Commands to use ClinicaDL Makefile:"
 	@sed -n 's/^##//p' $<
 
-## env             : Bootstrap an environment
-.PHONY: env
-env: env.dev
-
 ## env.conda       : Create a Conda environment
 .PHONY: env.conda
 env.conda:
 	@$(CONDA) env create -f environment.yml -p $(CONDA_ENV)
 
-## env.dev         : Install with Poetry
-.PHONY: env.dev
-env.dev:
+.PHONY: install
+install:
 	@$(POETRY) install
 
 ## build.notebooks : Build notebooks from source using jupytext