Merge branch 'main' into revert_plumelib_2

Makefile

@@ -166,8 +166,7 @@ check-merges-reproducibility:
 		echo "Running replay_merge for idx $$idx"; \
 		src/python/replay_merge.py --testing --merges_csv $(CSV_RESULTS) -skip_build -delete_workdir --idx $$idx || FAILED_IDXES="$$FAILED_IDXES $$idx"; \
 	done; \
-	echo "$$FAILED_IDXES"; \
-	test -z "$$FAILED_IDXES"
+	test -z "$$FAILED_IDXES" || { echo "Failed indexes = $$FAILED_IDXES"; false; }
 
 protect-repos:
 	find repos -mindepth 1 -type d -exec chmod a-w {} +

README.md

@@ -113,6 +113,14 @@ If `make small-test` fails in a branch that you wish to merge into the main
 branch, run `make small-test` in the main branch (which should succeed) and also
 in your branch, and investigate the differences.
 
+#### Updating the goal files
+
+If you make a change to the mergers that changes merge results, you need to
+update the goal files or else reproducibility checks will fail.
+Copy certain files from `results/small/` to `test/small-goal-files/`.
+
+To update the reproducibility tests, run `make run-all`.
+
 ### Load the stored cache
 
 To decompress the cache run `make decompress-cache`. This is done automatically in `run_combined.sh` if `cache/` does not exist.
@@ -238,6 +246,8 @@ To investigate differences between two mergers:
 * Set `DELETE_WORKDIRS` to `false` in `src/python/variables.py`.
 * run `src/python/replay_merge.py --idx INDEX` (maybe add `-test`) for the index of the merge you are interested in.
 
+If the merge is in the small test, you may need to add `--merges_csv ./test/small-goal-files/result.csv`.
+
 ## Overwriting results manually
 
 In some cases it might be worth to overwrite the computed results. To do that you should modify the `results/manual_override.csv` file. In that file for the merge you want to overwrite a result of you should include at least the information `repository,merge,left,right` and a new column for the result you want to overwrite. You can overwrite anything you want but if there is a column you don't want to overwrite either do not include that column or leave the entry blanck i.e. `,,`. See the file for an example.

run.sh

@@ -129,7 +129,7 @@ fi
   cd ./src/scripts/merge_tools/merging
   export JAVA_HOME=$JAVA17_HOME
   export PATH="$JAVA_HOME/bin:$PATH"
-  ./gradlew shadowJar
+  ./gradlew -q nativeCompile
 )
 
 echo "Machine ID: $machine_id"

src/python/replay_merge.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """Replay merges and their test results.
-The output appears in the .workdirs/ directory.
+The output appears in the `.workdirs`/ directory.
+Logs appear in the `replay_logs/merges/` directory.
 Command-line arguments are listed just after the line:
   if __name__ == "__main__":
 
@@ -268,11 +269,11 @@ def merge_replay(
                     stderr=subprocess.PIPE,
                 )
                 if len(process.stderr.decode("utf-8")) == 0:
-                    conflict_files = process.stdout.decode("utf-8")
-                    is_conflict = len(conflict_files) > 0
+                    git_conflict_files = process.stdout.decode("utf-8")
+                    is_conflict = len(git_conflict_files) > 0
                     assert (
                         is_conflict == (merge_result == MERGE_STATE.Merge_failed)
-                    ), f"merge_replay: tool{merge_tool} merge_result {merge_result} does not match conflict_files {conflict_files} at path {repo.local_repo_path}"
+                    ), f"merge_replay: tool merge result is inconsistent with `git diff --diff-filter=U`: tool={merge_tool} merge_result={merge_result} git_conflict_files={git_conflict_files} path={repo.local_repo_path}"
 
             result_df.loc[
                 merge_tool.name,
@@ -308,10 +309,11 @@ def merge_replay(
                     store_artifacts(result_df)
                 if delete_workdir:
                     delete_workdirs(result_df)
-                print("=====================================\n")
+                print("fingerprints differ; details follow.")
+                print(f"=================== start of {log_path}:")
                 with open(log_path, "r", encoding="utf-8") as f:
                     print(f.read())
-                print("=====================================\n")
+                print(f"=================== end of {log_path}.")
                 raise Exception(
                     f"fingerprints differ: after merge of {workdir} with {merge_tool}, found"
                     + f" {merge_fingerprint} but expected "

src/python/repo.py

@@ -152,11 +152,20 @@ def stdout_and_stderr(
     source: Union[subprocess.TimeoutExpired, subprocess.CompletedProcess],
 ) -> str:
     """Produces the standard output and standard error of a timedout process."""
-    explanation = "Run Command: " + " ".join(command) + "\nTimed out"
+    explanation = "Here is the output from: " + " ".join(command)
     if source.stdout:
-        explanation += "\nstdout:\n" + source.stdout.decode("utf-8", "replace")
+        explanation += (
+            "\nstdout:\n"
+            + source.stdout.decode("utf-8", "replace")
+            + "\nEnd of stdout."
+        )
     if source.stderr:
-        explanation += "\nstderr:\n" + source.stderr.decode("utf-8", "replace")
+        explanation += (
+            "\nstderr:\n"
+            + source.stderr.decode("utf-8", "replace")
+            + "\nEnd of stderr."
+        )
+    explanation += "\nEnd of output from: " + " ".join(command)
     return explanation
 
 
@@ -549,13 +558,18 @@ def merge(
             str(timeout),
             f"src/scripts/merge_tools/{tool.name}.sh {self.local_repo_path.resolve()} {LEFT_BRANCH_NAME} {RIGHT_BRANCH_NAME}",
         ]
+        logger.debug(
+            f"merge: Merging {self.repo_slug} {left_commit} {right_commit} with {tool.name}"
+        )
         p = subprocess.run(
             command,
             capture_output=True,
             check=False,
         )
+        std_streams = stdout_and_stderr(command, p)
+        logger.debug(std_streams)
         if p.returncode == 124:  # Timeout
-            explanation = explanation + "\n" + stdout_and_stderr(command, p)
+            explanation = explanation + "\n" + std_streams
             if use_cache:
                 cache_entry["merge status"] = MERGE_STATE.Merge_timedout.name
                 cache_entry["explanation"] = explanation
@@ -574,7 +588,7 @@ def merge(
                 -1,
             )
         run_time = time.time() - start_time
-        explanation = explanation + "\n" + stdout_and_stderr(command, p)
+        explanation = explanation + "\n" + std_streams
         merge_status = (
             MERGE_STATE.Merge_success if p.returncode == 0 else MERGE_STATE.Merge_failed
         )

src/scripts/merge_tools/adjacent.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./adjacent.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/adjacent_ignorespace.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./adjacent_ignorespace.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/adjacent_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./adjacent.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/git_hires_merge.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./git_hires_merge.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 set -o nounset
 
@@ -13,8 +13,10 @@ clone_dir=$1
 branch1=$2
 branch2=$3
 
+SCRIPTDIR="$(cd "$(dirname "$0")" && pwd -P)"
+
 # Print the current PATH
-echo "PATH: $PATH"
+echo "$0 PATH: $PATH"
 
 cd "$clone_dir" || { echo "$0: cannot cd to $clone_dir from $(pwd)"; exit 2; }
 
@@ -25,7 +27,7 @@ attributes_file=".git/info/attributes"
 echo "* merge=git-hires-merge" >> "$attributes_file"
 
 git config --local merge.git-hires-merge.name "An interactive merge driver for resolving conflicts on individual or adjacent lines"
-git config --local merge.git-hires-merge.driver "git-hires-merge %O %A %B %L %P"
+git config --local merge.git-hires-merge.driver "${SCRIPTDIR}/git-hires-merge %O %A %B %L %P"
 git config --local merge.git-hires-merge.recursive "binary"
 git config --local merge.conflictstyle diff3
 

src/scripts/merge_tools/git_hires_merge_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./git_hires_merge_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge.sh

@@ -19,19 +19,35 @@ branch1=$2
 branch2=$3
 git_strategy=$4
 
+VERBOSE=
+## Enable for debugging
+# VERBOSE=YES
+
+
 ## Perform merge
 
 cd "$clone_dir" || { echo "$0: cannot cd to $clone_dir"; exit 2; }
 
+if [ -n "$VERBOSE" ] ; then
+  echo "$0: about to run: git checkout $branch1 in $(pwd)"
+fi
 git checkout "$branch1" --force
+if [ -n "$VERBOSE" ] ; then
+  echo "$0: ran: git checkout $branch1 in $(pwd)"
+fi
 git config --local merge.conflictstyle diff3
 git config --local mergetool.prompt false
 
-echo "Running: git merge --no-edit $git_strategy $branch2"
+echo "$0: about to run: git merge --no-edit $git_strategy $branch2 in $(pwd)"
+
 # shellcheck disable=SC2086
 git merge --no-edit $git_strategy "$branch2"
 retVal=$?
 
+if [ -n "$VERBOSE" ] ; then
+  echo "$0: ran: git merge --no-edit $git_strategy $branch2 in $(pwd)"
+fi
+
 # report conflicts
 if [ $retVal -ne 0 ]; then
     echo "gitmerge.sh: Conflict after running: git merge --no-edit $git_strategy $branch2"

src/scripts/merge_tools/gitmerge_ort.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_ort.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_ort_ignorespace.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_ort_ignorespace.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_histogram.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_histogram.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_histogram_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_histogram_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_ignorespace.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_ignorespace.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_DIR="$(dirname "$0")"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_ignorespace_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_ignorespace_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_minimal.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_minimal.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_minimal_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_minimal_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_myers.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_myers.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_myers_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_myers_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_patience.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_patience.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_recursive_patience_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_recursive_patience_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_resolve.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# usage: ./gitmerge_resolve.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/gitmerge_resolve_plus.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./gitmerge_resolve_plus.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/imports.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./imports.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/imports_ignorespace.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./imports_ignorespace.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 
 MERGE_SCRIPTS_DIR="$(cd "$(dirname "$0")" && pwd -P)"
 clone_dir=$1

src/scripts/merge_tools/intellimerge.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-# usage: ./intellimerge.sh <clone_dir> <branch-1> <branch-2>
+# usage: <scriptname> <clone_dir> <branch-1> <branch-2>
 # <clone_dir> must contain a clone of a repository.
 # Merges branch2 into branch1, in <clone_dir>.
 # Return code is 0 for merge success, 1 for merge failure, 2 for script failure.
@@ -44,13 +44,13 @@ git checkout "$branch1" --force
 git merge --no-edit "$branch2"
 
 # List conflicitng files
-conflict_files=$(git diff --name-only --diff-filter=U)
+git_conflict_files=$(git diff --name-only --diff-filter=U)
 
 # Initialize a flag to track conflict resolution
 conflicts_resolved=true
 
 # Iterate through conflicting files
-for file in $conflict_files; do
+for file in $git_conflict_files; do
     # Check if the conflicting file exists in the temp_out_dir
     if [ ! -f "$temp_out_dir$file" ]; then
         echo "Conflict not resolved for file: $file"
@@ -62,7 +62,7 @@ done
 if [ "$conflicts_resolved" = false ]; then
     echo "Conflict detected. Aborting the merge. Please resolve the conflicts."
     echo "All conflicting files:"
-    echo "$conflict_files"
+    echo "$git_conflict_files"
     rm -rf $temp_out_dir $temp_intellimerge_dir
     exit 1
 fi