Re-merged separation process and finished initial Jenkins pipeline

Jenkinsfile

@@ -15,7 +15,7 @@ pipeline {
                         dir('bioconda-recipes') {
                             sh 'git pull'
                             sh 'git pull origin update-autobigs-engine'
-                            sh 'git pull origin update-autobigs-engine'
+                            sh 'git pull origin update-autobigs-cli'
                         }
                     }
                 }
@@ -44,8 +44,15 @@ pipeline {
             stage("overwrite") {
                 steps {
                     dir('bioconda-recipes') {
-                        sh 'checkout '
+                        sh 'git checkout -b update-autobigs-engine'
-                        sh 'cp autobigs-engine/* '
+                        sh 'cp -r ../autobigs-engine/* recipes/autobigs-engine/.'
+                        sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."'
+                        sh 'git push origin update-autobigs-engine'
+
+                        sh 'git checkout -b update-autobigs-cli'
+                        sh 'cp -r ../autobigs-engine/* recipes/autobigs-cli/.'
+                        sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."'
+                        sh 'git push origin update-autobigs-cli'
                     }
                 }
             }

scripts/adapt_names.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 import argparse
 from os import fdopen, path
 import os
@@ -6,8 +8,8 @@ import shutil
 from sys import argv
 import tempfile
 
-def main():
+def update_naming_scheme(recipe_path):
-    original_recipe = path.abspath(argv[1])
+    original_recipe = path.abspath(recipe_path)
     original_meta = path.join(original_recipe, "meta.yaml")    
     new_fd, new_file_path = tempfile.mkstemp()
     with fdopen(new_fd, "w") as new_file_handle:
@@ -27,4 +29,4 @@ def main():
                 new_recipe_name)
 
 if __name__ == "__main__":
-    main()
+    update_naming_scheme(argv[1])

scripts/package_latest_version.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+
+import sys
+import requests
+import json
+try:
+    from packaging.version import parse
+except ImportError:
+    from pip._vendor.packaging.version import parse
+
+
+URL_PATTERN = 'https://pypi.python.org/pypi/{package}/json'
+
+
+def get_version(package, url_pattern=URL_PATTERN):
+    """Return version of package on pypi.python.org using json."""
+    req = requests.get(url_pattern.format(package=package))
+    version = parse('0')
+    if req.status_code == requests.codes.ok:
+        j = json.loads(req.text.encode(req.encoding or "utf-8"))
+        releases = j.get('releases', [])
+        for release in releases:
+            ver = parse(release)
+            if not ver.is_prerelease:
+                version = max(version, ver)
+    return version
+
+
+if __name__ == '__main__':
+    print(get_version(sys.argv[1]), end="")