New Paper Fixes Changes

added files from extend_dataset

src/python/bulk_diff3_analysis.py

@@ -0,0 +1,181 @@
+"""Runs a merge and uses diff3 to compare it to the base and final branch of a given repo.
+See readme for details on shell scripts to run these methods.
+"""
+
+import sys
+import argparse
+import subprocess
+import re
+import os
+import shutil
+import tempfile
+import pandas as pd
+from repo import clone_repo_to_path
+from merge_tester import MERGE_STATE
+
+# pylint: disable-msg=too-many-locals
+
+
+def diff3_analysis(merge_tool: str, results_index: int, repo_output_dir):
+    """
+    Analyzes merge conflicts using the diff3 tool and opens the results in the default text viewer.
+
+    Args:
+        merge_tool (str): The merge tool to be used.
+        results_index (int): The index of the repository in the results DataFrame.
+        repo_output_dir (path): The path of where we want to store the results from the analysis
+
+    Returns:
+        None
+    """
+
+    # Deletes base, programmer_merge, and merge_attempt folders in repos dir
+    # We do this to prevent errors if cloning the same repo into the folder twice
+    shutil.rmtree("./repos", ignore_errors=True)
+
+    # Retrieve left and right branch from hash in repo
+    df = pd.read_csv("../../results_greatest_hits/result.csv")
+    repo_name = df.iloc[results_index]["repository"]
+
+    script = "../scripts/merge_tools/" + merge_tool + ".sh"
+    repo = clone_repo_to_path(
+        repo_name, "./repos/merge_attempt"
+    )  # Return a Git-Python repo object
+    repo.remote().fetch()
+    left_sha = df.iloc[results_index]["left"]
+    repo.git.checkout(left_sha, force=True)
+    print("Checking out left" + left_sha)
+    repo.submodule_update()
+    repo.git.checkout("-b", "TEMP_LEFT_BRANCH", force=True)
+    repo.git.checkout(df.iloc[results_index]["right"], force=True)
+    print("Checking out right" + df.iloc[results_index]["right"])
+    repo.submodule_update()
+    repo.git.checkout("-b", "TEMP_RIGHT_BRANCH", force=True)
+
+    base_sha = subprocess.run(
+        [
+            "git",
+            "merge-base",
+            "TEMP_LEFT_BRANCH",
+            "TEMP_RIGHT_BRANCH",
+        ],
+        cwd="./repos/merge_attempt/" + repo_name,
+        stdout=subprocess.PIPE,
+        text=True,
+    )
+    print("Found base sha" + base_sha.stdout)
+
+    repo2 = clone_repo_to_path(
+        repo_name, "./repos/base"
+    )  # Return a Git-Python repo object
+    repo2.remote().fetch()
+    base_sha = base_sha.stdout.strip()
+    repo2.git.checkout(base_sha, force=True)
+    repo2.submodule_update()
+
+    result = subprocess.run(
+        [
+            script,
+            repo.git.rev_parse("--show-toplevel"),
+            "TEMP_LEFT_BRANCH",
+            "TEMP_RIGHT_BRANCH",
+        ],
+        stdout=subprocess.PIPE,
+        text=True,
+    )
+
+    conflict_file_matches = re.findall(
+        r"CONFLICT \(.+\): Merge conflict in (.+)", result.stdout
+    )
+
+    print(result.stdout)
+
+    repo3 = clone_repo_to_path(
+        repo_name, "./repos/programmer_merge"
+    )  # Return a Git-Python repo object
+    repo3.git.checkout(df.iloc[results_index]["merge"], force=True)
+    repo3.submodule_update()
+
+    for conflict_file_match in conflict_file_matches:
+        conflicting_file = str(conflict_file_match)
+        conflict_path = os.path.join(repo_name, conflicting_file)
+        conflict_path_merge_attempt = os.path.join(
+            "./repos/merge_attempt", conflict_path
+        )
+
+        conflict_path_base = os.path.join("./repos/base", conflict_path)
+        conflict_path_programmer_merge = os.path.join(
+            "./repos/programmer_merge", conflict_path
+        )
+
+        diff_results = subprocess.run(
+            [
+                "diff3",
+                conflict_path_base,
+                conflict_path_merge_attempt,
+                conflict_path_programmer_merge,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+        )
+
+        # Check that diff3 didn't run into missing files in the base
+        error_message = "No such file or directory"
+        if error_message in diff_results.stderr:
+            # Since the conflict file was added in both parents we can't diff the base.
+            diff_results = subprocess.run(
+                [
+                    "diff",
+                    conflict_path_merge_attempt,
+                    conflict_path_programmer_merge,
+                ],
+                stdout=subprocess.PIPE,
+                text=True,
+            )
+
+        # Generate a filename for the diff result, including the new subdirectory
+        diff_filename = os.path.join(
+            repo_output_dir, f"diff_{os.path.basename(conflicting_file)}.txt"
+        )
+
+        # Write the diff results to the file
+        with open(diff_filename, "w") as diff_file:
+            diff_file.write(diff_results.stdout)
+
+        # Optionally, print or log the path of the diff file
+        print(f"Diff results saved to {diff_filename}")
+
+
+def main(merge_tool: str, results_index: int, repo_output_dir: str):
+    """
+    Entry point for the script when run from the command line.
+    """
+    # Convert results_index to int here if using argparse
+    diff3_analysis(merge_tool, results_index, repo_output_dir)
+
+
+if __name__ == "__main__":
+    # Use argparse to parse command line arguments
+    parser = argparse.ArgumentParser(
+        description="Analyze merge conflicts using the diff3 tool."
+    )
+    parser.add_argument("merge_tool", type=str, help="The merge tool to be used.")
+    parser.add_argument(
+        "results_index",
+        type=int,
+        help="The index of the repository in the results DataFrame.",
+    )
+    parser.add_argument(
+        "repo_output_dir",
+        type=str,
+        help="The path of where we want to store the results from the analysis.",
+    )
+
+    args = parser.parse_args()
+
+    # Ensure the output directory exists
+    os.makedirs(args.repo_output_dir, exist_ok=True)
+
+    # Call main function with parsed arguments
+    main(args.merge_tool, args.results_index, args.repo_output_dir)

src/python/diff3_analysis.py

@@ -0,0 +1,181 @@
+"""Runs a merge and uses diff3 to compare it to the base and final branch of a given repo.
+See readme for details on shell scripts to run these methods.
+"""
+
+import sys
+import argparse
+import subprocess
+import re
+import os
+import shutil
+import tempfile
+import pandas as pd
+from repo import clone_repo_to_path
+from merge_tester import MERGE_STATE
+
+# pylint: disable-msg=too-many-locals
+
+
+def diff3_analysis(merge_tool: str, results_index: int, repo_output_dir):
+    """
+    Analyzes merge conflicts using the diff3 tool and opens the results in the default text viewer.
+
+    Args:
+        merge_tool (str): The merge tool to be used.
+        results_index (int): The index of the repository in the results DataFrame.
+        repo_output_dir (path): The path of where we want to store the results from the analysis
+
+    Returns:
+        None
+    """
+
+    # Deletes base, programmer_merge, and merge_attempt folders in repos dir
+    # We do this to prevent errors if cloning the same repo into the folder twice
+    shutil.rmtree("./repos", ignore_errors=True)
+
+    # Retrieve left and right branch from hash in repo
+    df = pd.read_csv("../../results_greatest_hits/result.csv")
+    repo_name = df.iloc[results_index]["repository"]
+
+    script = "../scripts/merge_tools/" + merge_tool + ".sh"
+    repo = clone_repo_to_path(
+        repo_name, "./repos/merge_attempt"
+    )  # Return a Git-Python repo object
+    repo.remote().fetch()
+    left_sha = df.iloc[results_index]["left"]
+    repo.git.checkout(left_sha, force=True)
+    print("Checking out left" + left_sha)
+    repo.submodule_update()
+    repo.git.checkout("-b", "TEMP_LEFT_BRANCH", force=True)
+    repo.git.checkout(df.iloc[results_index]["right"], force=True)
+    print("Checking out right" + df.iloc[results_index]["right"])
+    repo.submodule_update()
+    repo.git.checkout("-b", "TEMP_RIGHT_BRANCH", force=True)
+
+    base_sha = subprocess.run(
+        [
+            "git",
+            "merge-base",
+            "TEMP_LEFT_BRANCH",
+            "TEMP_RIGHT_BRANCH",
+        ],
+        cwd="./repos/merge_attempt/" + repo_name,
+        stdout=subprocess.PIPE,
+        text=True,
+    )
+    print("Found base sha" + base_sha.stdout)
+
+    repo2 = clone_repo_to_path(
+        repo_name, "./repos/base"
+    )  # Return a Git-Python repo object
+    repo2.remote().fetch()
+    base_sha = base_sha.stdout.strip()
+    repo2.git.checkout(base_sha, force=True)
+    repo2.submodule_update()
+
+    result = subprocess.run(
+        [
+            script,
+            repo.git.rev_parse("--show-toplevel"),
+            "TEMP_LEFT_BRANCH",
+            "TEMP_RIGHT_BRANCH",
+        ],
+        stdout=subprocess.PIPE,
+        text=True,
+    )
+
+    conflict_file_matches = re.findall(
+        r"CONFLICT \(.+\): Merge conflict in (.+)", result.stdout
+    )
+
+    print(result.stdout)
+
+    repo3 = clone_repo_to_path(
+        repo_name, "./repos/programmer_merge"
+    )  # Return a Git-Python repo object
+    repo3.git.checkout(df.iloc[results_index]["merge"], force=True)
+    repo3.submodule_update()
+
+    for conflict_file_match in conflict_file_matches:
+        conflicting_file = str(conflict_file_match)
+        conflict_path = os.path.join(repo_name, conflicting_file)
+        conflict_path_merge_attempt = os.path.join(
+            "./repos/merge_attempt", conflict_path
+        )
+
+        conflict_path_base = os.path.join("./repos/base", conflict_path)
+        conflict_path_programmer_merge = os.path.join(
+            "./repos/programmer_merge", conflict_path
+        )
+
+        diff_results = subprocess.run(
+            [
+                "diff3",
+                conflict_path_base,
+                conflict_path_merge_attempt,
+                conflict_path_programmer_merge,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+        )
+
+        # Check that diff3 didn't run into missing files in the base
+        error_message = "No such file or directory"
+        if error_message in diff_results.stderr:
+            # Since the conflict file was added in both parents we can't diff the base.
+            diff_results = subprocess.run(
+                [
+                    "diff",
+                    conflict_path_merge_attempt,
+                    conflict_path_programmer_merge,
+                ],
+                stdout=subprocess.PIPE,
+                text=True,
+            )
+
+        # Generate a filename for the diff result, including the new subdirectory
+        diff_filename = os.path.join(
+            repo_output_dir, f"diff_{os.path.basename(conflicting_file)}.txt"
+        )
+
+        # Write the diff results to the file
+        with open(diff_filename, "w") as diff_file:
+            diff_file.write(diff_results.stdout)
+
+        # Optionally, print or log the path of the diff file
+        print(f"Diff results saved to {diff_filename}")
+
+
+def main(merge_tool: str, results_index: int, repo_output_dir: str):
+    """
+    Entry point for the script when run from the command line.
+    """
+    # Convert results_index to int here if using argparse
+    diff3_analysis(merge_tool, results_index, repo_output_dir)
+
+
+if __name__ == "__main__":
+    # Use argparse to parse command line arguments
+    parser = argparse.ArgumentParser(
+        description="Analyze merge conflicts using the diff3 tool."
+    )
+    parser.add_argument("merge_tool", type=str, help="The merge tool to be used.")
+    parser.add_argument(
+        "results_index",
+        type=int,
+        help="The index of the repository in the results DataFrame.",
+    )
+    parser.add_argument(
+        "repo_output_dir",
+        type=str,
+        help="The path of where we want to store the results from the analysis.",
+    )
+
+    args = parser.parse_args()
+
+    # Ensure the output directory exists
+    os.makedirs(args.repo_output_dir, exist_ok=True)
+
+    # Call main function with parsed arguments
+    main(args.merge_tool, args.results_index, args.repo_output_dir)