From 6b8376c4709a953ac0c8663380d3cb6c0d992efc Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Fri, 21 Feb 2025 06:33:07 +0000
Subject: [PATCH] Added publishing to personal git repo

---
 Jenkinsfile     | 12 ++++++++----
 environment.yml | 12 ++++++++++++
 2 files changed, 20 insertions(+), 4 deletions(-)
 create mode 100644 environment.yml

diff --git a/Jenkinsfile b/Jenkinsfile
index a11d976..a5de9b3 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -2,14 +2,14 @@ pipeline {
     agent {
         kubernetes {
             cloud 'rsys-devel'
-            defaultContainer 'pip'
-            inheritFrom 'pip'
+            defaultContainer 'miniforge3'
+            inheritFrom 'miniforge'
         }
     }
     stages {
         stage("install") {
             steps {
-                sh 'python -m pip install -r requirements.txt'
+                sh 'conda env update -n base -f environment.yml'
             }
         }
         stage("unit tests") {
@@ -22,11 +22,14 @@ pipeline {
         stage("build") {
             steps {
                 sh "python -m build"
+                sh "grayskull pypi dist/*.tar.gz --maintainers 'Harrison Deng'"
+                sh "python scripts/patch_recipe.py"
+                sh 'conda build autobigs-cli -c bioconda --output-folder conda-bld --verify'
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl, conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish") {
@@ -42,6 +45,7 @@ pipeline {
                     }
                     steps {
                         sh script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh 'curl --user ${CREDS_USR}:${CREDS_PSW} --upload-file conda-bld/**/*.conda https://git.reslate.systems/api/packages/${CREDS_USR}/conda/$(basename conda-bld/**/*.conda)'
                     }
                 }
                 stage ("pypi.org") {
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..78fcfe0
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,12 @@
+name: base
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - pytest
+  - pytest-asyncio
+  - python-build
+  - conda-build
+  - twine==6.0.1
+  - setuptools_scm
+  
\ No newline at end of file