From 41441c6aae67c62dfdc605cca73bc92c66a00d90 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 26 Feb 2025 14:32:02 +0000
Subject: [PATCH] changed to using submodule

---
 .gitmodules                   |  3 +++
 Jenkinsfile                   | 44 ++++++++++-------------------------
 auto-updated-bioconda-recipes |  1 +
 environment.yml               |  3 ++-
 4 files changed, 18 insertions(+), 33 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 auto-updated-bioconda-recipes

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..4141163
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "auto-updated-bioconda-recipes"]
+	path = auto-updated-bioconda-recipes
+	url = https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git
diff --git a/Jenkinsfile b/Jenkinsfile
index e4fe815..d84a2bf 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -11,7 +11,6 @@ pipeline {
             parallel {
                 stage("recipes repo") {
                     steps {
-                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
                         dir('auto-updated-bioconda-recipes') {
                             sh 'git checkout update-autobigs-engine'
                         }
@@ -33,46 +32,27 @@ pipeline {
         }
         stage("build") {
             steps {
-                dir('auto-updated-bioconda-recipes') {
-                    sh 'conda build recipes/autobigs-engine --output-folder ./conda-bld'
-                }
+                sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
             }
         }
-        stage('publish') {
-            parallel {
-                stage("archive") {
+        stage("publish to bioconda") {
+            stages {
+                stage('lint') {
                     steps {
-                        archiveArtifacts artifacts: './conda-bld/**/*.conda', followSymlinks: false
-                    }
-                }
-                stage("bioconda") {
-                    stages {
-                        stage('lint') {
-                            steps {
-                                dir('auto-updated-bioconda-recipes') {
-                                    sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
-                                }
-                            }
-                        }
-                        stage('commit') {
-                            environment {
-                                TOKEN = credentials('github.com')
-                            }
-                            steps {
-                                dir('auto-updated-bioconda-recipes') {
-                                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
-                                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
-                                }
-                            }
+                        dir('auto-updated-bioconda-recipes') {
+                            sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
                         }
                     }
                 }
-                stage('git.reslate.systems') {
+                stage('commit') {
                     environment {
-                        AUTH = credentials('git.reslate.systems')
+                        TOKEN = credentials('github.com')
                     }
                     steps {
-                        sh 'curl --user AUTH_USR:AUTH_PSW --upload-file ./conda-bld/**/*.conda https://git.reslate.systems/api/packages/${AUTH_USR}/conda/package-1.0.conda'
+                        dir('auto-updated-bioconda-recipes') {
+                            sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
+                            sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
+                        }
                     }
                 }
             }
diff --git a/auto-updated-bioconda-recipes b/auto-updated-bioconda-recipes
new file mode 160000
index 0000000..8bdf7d8
--- /dev/null
+++ b/auto-updated-bioconda-recipes
@@ -0,0 +1 @@
+Subproject commit 8bdf7d8e65ec383ff3de875814a0b67abeba6ad7
diff --git a/environment.yml b/environment.yml
index 8449835..db5ba9b 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,4 +8,5 @@ dependencies:
   - git
   - bioconda-utils
   - python=3.10.*
-  - curl
\ No newline at end of file
+  - curl
+  - conda-verify
\ No newline at end of file