Return pr url

proteobench/github/gh.py

@@ -4,6 +4,8 @@
 import pandas as pd
 from git import Repo
 
+from github import Github
+
 
 def clone_repo_anon(
     clone_dir="K:/pb/",
@@ -37,20 +39,50 @@ def clone_repo(
 
 def pr_github(
     clone_dir="K:/pb/",
-    token="",
-    remote_git="github.com/Proteobot/Results_Module2_quant_DDA.git",
+    token="YOUR_GITHUB_TOKEN",
+    remote_git="Proteobot/Results_Module2_quant_DDA",
     username="Proteobot",
     branch_name="test",
     commit_message="New commit",
+    repo_name="Proteobot/Results_Module2_quant_DDA",
 ):
-    remote = f"https://{username}:{token}@{remote_git}"
-    repo = Repo(clone_dir)
+    # Construct the remote URL with the token
+    remote_url = f"https://{username}:{token}@{remote_git}"
 
-    repo.git.pull()
+    # Clone the repository if it doesn't exist
+    try:
+        repo = Repo(clone_dir)
+    except:
+        repo = Repo.clone_from(remote_url, clone_dir)
 
-    current = repo.create_head(branch_name)
-    current.checkout()
+    # Fetch the latest changes from the remote
+    origin = repo.remote(name="origin")
+    origin.fetch()
 
+    # Create and checkout the new branch
+    current_branch = repo.create_head(branch_name)
+    current_branch.checkout()
+
+    # Stage all changes, commit, and push to the new branch
     repo.git.add(A=True)
-    repo.git.commit(m=commit_message)
-    repo.git.push("--set-upstream", "origin", current)
+    repo.index.commit(commit_message)
+    repo.git.push("--set-upstream", "origin", current_branch)
+
+    # Create a pull request using PyGithub
+    g = Github(token)
+    repo = g.get_repo(repo_name)
+    base = repo.get_branch("master")
+    head = f"{username}:{branch_name}"
+    title = commit_message
+    body = "Pull request body"
+
+    pr = repo.create_pull(
+        title=title,
+        body=body,
+        base=base.name,
+        head=head,
+    )
+
+    pr_number = pr.number
+    print(pr_number)
+    return pr_number

proteobench/modules/dda_quant/module.py

@@ -332,7 +332,7 @@ def clone_pr(
         f.close()
         commit_message = f"Added new run with id {branch_name} \n user comments: {submission_comments}"
 
-        pr_github(
+        pr_id = pr_github(
             clone_dir=t_dir,
             token=token,
             remote_git=remote_git,
@@ -341,6 +341,8 @@ def clone_pr(
             commit_message=commit_message,
         )
 
+        return "https://" + remote_git.replace(".git", "") + "/pull/" + str(pr_id)
+
     def write_json_local_development(self, temporary_datapoints):
         t_dir = TemporaryDirectory().name
         os.mkdir(t_dir)

pyproject.toml

@@ -20,7 +20,8 @@ dependencies = [
   "matplotlib",
   "importlib-metadata; python_version < '3.8'",
   "toml",
-  "psm_utils",
+  "PyGithub",
+  "GitPython",
 ]
 dynamic = ["version", "description"]
 keywords = ['proteomics', 'peptides', 'retention time', 'mass spectrometry']

webinterface/pages/DDA_Quant.py

@@ -308,7 +308,7 @@ def generate_results(
                 st.session_state[SUBMIT] = True
                 user_comments = self.user_input["comments_for_submission"]
                 if not LOCAL_DEVELOPMENT:
-                    Module().clone_pr(
+                    pr_url = Module().clone_pr(
                         st.session_state[ALL_DATAPOINTS],
                         st.secrets["gh"]["token"],
                         username="Proteobot",
@@ -339,6 +339,8 @@ def generate_results(
             if st.session_state[SUBMIT]:
                 # status_placeholder.success(":heavy_check_mark: Successfully uploaded data!")
                 st.subheader("SUCCESS")
+                st.write(f"Follow your submission approval here: [{pr_url}]({pr_url})")
+
                 st.session_state[SUBMIT] = False
                 rain(emoji="🎈", font_size=54, falling_speed=5, animation_length=1)