fix: add files to PR and switch reretry with tenacity

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "pygithub>=2.6.1",
     "pyyaml>=6.0.2",
     "requests>=2.32.4",
-    "reretry>=0.11.8",
+    "tenacity>=9.1.2",
     "toml>=0.10.2",
 ]
 

snakedeploy/prs.py

@@ -2,10 +2,9 @@
 import os
 import re
 from typing import Optional
-from reretry import retry
+from tenacity import retry, stop_after_attempt, wait_exponential
 from urllib3.util.retry import Retry
 
-import github
 from github import Github, GithubException
 
 from snakedeploy.exceptions import UserError
@@ -57,7 +56,7 @@ def __init__(
     def add_file(self, filepath, content, is_updated, msg):
         self.files.append(File(str(filepath), content, is_updated, msg))
 
-    @retry(tries=2, delay=60)
+    @retry(stop=stop_after_attempt(2), wait=wait_exponential(multiplier=2, min=60))
     def create(self):
         if not self.files:
             logger.info("No files to commit.")
@@ -83,7 +82,7 @@ def create(self):
                 try:
                     # try to get sha if file exists
                     sha = self.repo.get_contents(file.path, self.branch).sha
-                except github.GithubException.UnknownObjectException as e:
+                except GithubException.UnknownObjectException as e:
                     if e.status != 404:
                         raise e
             elif file.is_updated:

snakedeploy/snakemake_wrappers.py

@@ -188,6 +188,13 @@ def update_spec(matchobj):
 
             if create_prs:
                 assert pr is not None
+                pr.add_file(
+                    snakefile,
+                    snakefile_content,
+                    is_updated=True,
+                    msg=f"perf: update {snakefile}.",
+                )
+
                 pr.create()
 
         if create_prs and not per_snakefile_prs: