Merge ../AST-Merging-Evaluation-branch-master into ben-main

.gitconfig

@@ -0,0 +1,3 @@
+[user]
+        email = [email protected]
+        name = Example Example

.github/workflows/check-reproducibility.yml

@@ -0,0 +1,46 @@
+name: Reproducibility Check
+on: [push, pull_request]
+jobs:
+  test:
+    strategy:
+      matrix:
+        maven: [ '3.9.2' ]
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/setup-java@v4
+      with:
+        distribution: 'zulu'
+        java-version: 17.0.7
+    - run: echo "JAVA17_HOME=$JAVA_HOME" >> $GITHUB_ENV
+    - run: java -version
+    - uses: actions/checkout@v4
+      with:
+        submodules: 'true'
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Setup miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: 3.12
+        auto-update-conda: true
+        mamba-version: "*"
+        channels: conda-forge,defaults
+        activate-environment: AST
+        environment-file: environment.yml
+    - name: Clean caches & workspace
+      run: make clean
+    - run: echo "LOGURU_COLORIZE=NO" >> $GITHUB_ENV
+    - name: Build
+      run: cd src/scripts/merge_tools/merging && ./gradlew -q shadowJar
+    - name: make check-merges-reproducibility
+      run: |
+        python3 src/python/replay_merge.py --merges_csv results/combined/result.csv -delete_workdir --idx 38-192
+        head -n 151 results/combined/result.csv > temp.csv && mv temp.csv results/combined/result.csv
+        make check-merges-reproducibility
+      env:
+          GITHUB_TOKEN: ${{ secrets.TOKEN_GITHUB }}

.github/workflows/check-style.yml

@@ -9,15 +9,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: psf/black@stable
-    - name: Set up Python 3.8
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.12'
     - name: Setup miniconda
-      uses: conda-incubator/setup-miniconda@v3.0.3
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: 3.8
+        python-version: 3.12
         auto-update-conda: true
+        mamba-version: "*"
         channels: conda-forge,defaults
         activate-environment: AST
         environment-file: environment.yml

.github/workflows/push-plots-to-paper.yml

@@ -0,0 +1,38 @@
+name: Update Overleaf with Plots
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  update-overleaf:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: GuillaumeFalourd/[email protected]
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Git Config and Credentials
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub CI/CD Bot"
+
+      - name: Create directory for Overleaf Repository
+        run: mkdir -p ../AST-Merging-Evaluation-Paper
+
+      - name: Clone Overleaf Repository
+        env:
+          OVERLEAF_GIT_REPO: ${{ secrets.OVERLEAF_GIT_REPO }}
+        run: |
+          git clone ${OVERLEAF_GIT_REPO} ../AST-Merging-Evaluation-Paper
+
+      - name: Run make command to copy plots
+        run: make copy-paper
+
+      - name: Commit and Push to Overleaf
+        run: |
+          cd ../AST-Merging-Evaluation-Paper
+          git add .
+          git diff --staged --exit-code || (git commit -m "Automated plot updates by GitHub CI/CD Bot" && git push origin master)

.github/workflows/small-test.yml

@@ -1,62 +1,65 @@
-name: Run Small test
+name: Small test
 on: [push, pull_request]
 jobs:
   test:
     strategy:
       matrix:
-        maven: [ '3.9.2']
+        maven: [ '3.9.2' ]
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/setup-java@v3
+    - uses: actions/setup-java@v4
       with:
         distribution: 'zulu'
         java-version: 8
     - run: echo "JAVA8_HOME=$JAVA_HOME" >> $GITHUB_ENV
     - run: java -version
-    - uses: actions/setup-java@v3
+    - uses: actions/setup-java@v4
       with:
         distribution: 'zulu'
         java-version: 11
     - run: echo "JAVA11_HOME=$JAVA_HOME" >> $GITHUB_ENV
     - run: java -version
-    - uses: actions/setup-java@v3
+    - uses: actions/setup-java@v4
       with:
         distribution: 'zulu'
         java-version: 17
     - run: echo "JAVA17_HOME=$JAVA_HOME" >> $GITHUB_ENV
-    - run: echo "${GITHUB_WORKSPACE}/src/scripts/merge_tools" >> $GITHUB_PATH
     - run: java -version
     - uses: actions/checkout@v4
-    - name: Set up Python 3.8
+      with:
+        submodules: 'true'
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.12'
     - name: Setup miniconda
-      uses: conda-incubator/setup-miniconda@v3.0.3
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: 3.8
+        python-version: 3.12
         auto-update-conda: true
+        mamba-version: "*"
         channels: conda-forge,defaults
         activate-environment: AST
         environment-file: environment.yml
     - name: Install PdfLaTeX
       run: sudo apt update && sudo apt install texlive-latex-extra -y
     - name: Install maven
-      uses: s4u/setup-maven-action@v1.8.0
+      uses: s4u/setup-maven-action@v1.12.0
       with:
         java-version: 17
         maven-version: ${{ matrix.maven }}
     - name: Clean caches & workspace
       run: make clean
-    - name: Build Java programs
-      run: ./gradlew build
+    - name: Install killall
+      run: sudo apt update && sudo apt install psmisc -y
+    - run: echo "LOGURU_COLORIZE=NO" >> $GITHUB_ENV
     - name: Run small test
       run: |
-        git config --global user.email "[email protected]"
-        git config --global user.name "Example Example"
+        git config --global merge.customMerge.name "Always incorrect custom merge driver"
+        git config --global merge.customMerge.driver 'fake-merge-driver %O %A %B %L %P'
         make small-test
       env:
           GITHUB_TOKEN: ${{ secrets.TOKEN_GITHUB }}

.gitignore

@@ -16,6 +16,7 @@ cache*.tar
 cache.tar
 output.txt
 replay_logs/
+my.secrets
 
 output/
 merge_repo/

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "src/scripts/merge_tools/merging"]
+	path = src/scripts/merge_tools/merging
+	url = https://github.com/plume-lib/merging.git
+	ignore = dirty

Makefile

@@ -6,6 +6,13 @@ SH_SCRIPTS   = $(shell grep --exclude-dir=build --exclude-dir=repos --exclude-di
 BASH_SCRIPTS = $(shell grep --exclude-dir=build --exclude-dir=repos --exclude-dir=cache -r -l '^\#! \?\(/bin/\|/usr/bin/env \)bash' * | grep -v /.git/ | grep -v '~$$' | grep -v '\.tar$$' | grep -v gradlew)
 PYTHON_FILES = $(shell find .  -name '*.py' ! -path './repos/*' -not -path "./.workdir/*" -not -path "./cache*/*" | grep -v '/__pycache__/' | grep -v '/.git/' | grep -v gradlew)
 
+CSV_RESULTS_COMBINED = results/combined/result.csv
+CSV_RESULTS_GREATEST_HITS = results/greatest_hits/result.csv
+CSV_RESULTS_REAPER = results/reaper/result.csv
+CSV_RESULTS = $(CSV_RESULTS_COMBINED)
+
+NUM_PROCESSES = 0
+
 shell-script-style:
 	shellcheck -e SC2153 -x -P SCRIPTDIR --format=gcc ${SH_SCRIPTS} ${BASH_SCRIPTS}
 	checkbashisms ${SH_SCRIPTS}
@@ -25,7 +32,7 @@ check-python-style:
 
 # This target deletes files that are not committed to version control.
 clean:
-	rm -rf .workdir
+	${MAKE} clean-workdir
 	rm -rf repos
 	rm -rf scratch
 	rm -rf results/small
@@ -38,6 +45,7 @@ clean-cache:
 # This target deletes files in the test cache.
 clean-test-cache:
 	rm -rf cache-small
+	rm -f cache-small.tar
 
 # This target deletes files that are committed to version control.
 clean-stored-hashes:
@@ -90,25 +98,43 @@ small-test:
 	./run_small.sh --include_trivial_merges --no_timing
 	${MAKE} small-test-diff
 
+small-test-without-cleaning:
+	${MAKE} clean-test-cache
+	./run_small.sh --include_trivial_merges --no_timing
+	${MAKE} small-test-diff
+
 update-figures:
 	./run_combined.sh -op
 	./run_greatest_hits.sh -op
 	./run_reaper.sh -op
 
 run-all:
+	${MAKE} clean-workdir
+	${MAKE} small-test-without-cleaning
 	./run_combined.sh
 	./run_greatest_hits.sh
 	./run_reaper.sh
 
+
 small-test-diff:
 	python3 test/check_equal_csv.py --actual_folder results/small/ --goal_folder test/small-goal-files/
 	@echo
 
 gradle-assemble:
 	./gradlew -q assemble -g ../.gradle/
 
+clean-workdir:
+	if [ -d .workdir ]; then chmod -R u+w .workdir; fi
+	rm -rf .workdir
+
 clean-local:
-	rm -rf repos .workdir
+	${MAKE} clean-workdir
+	rm -rf repos
+
+check-merges-reproducibility:
+	@echo "Running replay_merge for each idx in parallel using GNU Parallel..."
+	@set -e; \
+	tail -n +2 $(CSV_RESULTS) | awk -F, '{print $$1}' | parallel --halt now,fail=1 -j 50% python3 src/python/replay_merge.py --merges_csv $(CSV_RESULTS) -skip_build -delete_workdir --idx {}
 
 protect-repos:
 	find repos -mindepth 1 -type d -exec chmod a-w {} +

README.md

@@ -210,3 +210,11 @@ To run style checking run `make style`.
 * results/small/ -> Contains all the results for the small analysis.
 
 * jars/ -> Location for the IntelliMerge and Spork jars.
+
+
+## Comparing merge algorithms
+
+To investigate differences between two mergers:
+ * edit file `src/python/select_from_results.py` to reflect the differences you are interested in.
+ * run `src/python/select_from_results.py` to create a .csv database containing only the differences.
+ * run `src/python/replay_merge.py --merges_csv CSV_FILE --idx INDEX` (maybe add `-test`) for the index of the merge you are interested in.

environment.yml

@@ -19,19 +19,18 @@ dependencies:
   - wheel
   - xz
   - zlib
-  - python=3.8
+  - python=3.12
   - pip:
-      - fasteners==0.18
-      - matplotlib==3.6.3
-      - numpy==1.23.5
-      - pandas==2.0.2
-      - pylint==2.17.5
-      - GitPython==3.1.31
-      - prettytable==3.8.0
-      - seaborn==0.12.2
+      - fasteners==0.19
+      - matplotlib==3.8.4
+      - numpy==1.26.4
+      - pandas==2.2.2
+      - pylint==3.1.0
+      - GitPython==3.1.43
+      - prettytable==3.10.0
+      - seaborn==0.13.2
       - rich==13.7.1
-      - black==23.3.0
-      - psutil==5.9.5
+      - black==24.4.2
+      - psutil==5.9.8
       - termplotlib==0.3.9
-      - timeout-decorator==0.5.0
       - loguru==0.7.2

gitmerge_ort_imports.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env sh
+
+# usage: ./gitmerge_ort_imports.sh <clone_dir> <branch-1> <branch-2>
+
+clone_dir=$1
+branch1=$2
+branch2=$3
+
+export JAVA_HOME="$JAVA17_HOME"
+
+cd "$clone_dir" || exit 1
+
+git checkout "$branch1" --force
+
+attributes_file=".git/info/attributes"
+echo "*.java merge=merge-java" >> "$attributes_file"
+git config --local merge.merge-java.name "Merge Java files"
+git config --local merge.merge-java.driver 'java-merge-driver.sh "%A" "%O" "%B"'
+
+git merge --no-edit "$branch2"
+retVal=$?
+
+# report conflicts
+if [ "$retVal" -ne 0 ]; then
+    echo "Conflict"
+fi
+
+exit "$retVal"

results/combined/all_repos_head_test_results.csv

@@ -12263,7 +12263,7 @@ idx,repository,head hash,head tree fingerprint,head test result
 13017,guuuo/dubai,209abb098265c4ef19711d68617e16b7350f6a18,3092a210e730e4aa3236a71eb018ab3d5841d906851b4c0ad1e90dcb98339ff9,Tests_passed
 13018,soarcn/coco-accessory,4abba9f09c4055ead412c86bd25e4404565dd5d4,d97031b0d82b873ff02eea9e8194b5244d61f89514624705cd931ee25d049f86,Tests_failed
 13019,hoverruan/sae-spring-template,8e81017cc6b6e32ff8dbe15a34bcb8f9bf5aaa84,1cfd1d9c42e5fb43d658194421a3154882d1ef8b1f11ea1d02d49fb63f60b978,Tests_passed
-13020,sonarcommunity/sonar-web,aee1b2c066bad507918b662973c602a728ef9491,ebf71ae6f83b183f55f268ddc48c16ecd0904dca02873b3543cb6348d1dde5fc,Tests_passed
+13020,sonarcommunity/sonar-web,aee1b2c066bad507918b662973c602a728ef9491,f7934ed60c94334bfca1398c09f6580d902a1732ee362810a37410b1196579c7,Tests_passed
 13021,slimroms/apktool,c1ab20ee4b03364d5120d7e71cf02dba346bfcd5,34128662c0608d553f6829488e38d8a822b2eee9df6da4770b507cb6bbc6aff1,Tests_failed
 13022,ahiraz/pushnotificationdemo,2714e0c135608914dca0a3b07f2364eb580ee4ba,d55b62dc5e771438d67fbab71b624de7c573cf7a5918470ec3e40474a969cb0b,Tests_failed
 13023,melin/dubbo-rpc-swift,32673ba8cf1c733a6b6672f345382e95809e73fb,44c8dbed2417e90c89907fe654cdc7d060e331fdf0426c491e1b70ae772e4b91,Tests_passed
@@ -15965,7 +15965,7 @@ idx,repository,head hash,head tree fingerprint,head test result
 16925,chrislongo/download-hls,243722ecf156881c8cf42d6eb9fe8459bb6f5c55,89a624c18459772025110f492c3d5f631877d17ca27122c431d518d8c671b24c,Tests_passed
 16926,carbonfive/hellod,01423b6118177dcc7a44388543775369780da6e7,4deb0d911c36a7b75bf44cfc893b96734450bb0fc29a3cb5972a08b7f93d41cc,Tests_failed
 16927,shipilev/java-object-layout,d4b41c8a8bcb897aee3ae3ca91410738c4a2ef3d,a6e0064545d231464c0a688cf1a06a4987460ad5e6a211d65c445565723a75d7,Tests_failed
-16928,deegree/deegree3,3088ebfab9e27898aa80577d27a9ca8b51ce5fbc,8e5119315831dda2ce955a960abb450132de37d9df0a7ed3305eb5b03063e952,Tests_passed
+16928,deegree/deegree3,3088ebfab9e27898aa80577d27a9ca8b51ce5fbc,f28128951414277a486e5a3fc556b6d9677e76e6515bc5479fd060c6d6e0a4d6,Tests_failed
 16929,sethm/symon,ecd4bbbd9a448f4f546eef9648149700b93c91ec,a1d3eeda91c9902d4a63a9d16ae5ad2317dc3e3dd418f8e764345aa1e9e38601,Tests_passed
 16930,yannis666/coherence-jsr-107,b6d95fe625ad6369f7733be82092ecb4affe0102,b51a16742cb3ea0ce04992157aa2e6f6deeedfb1ccd84bbe84c367526cd20a82,Tests_failed
 16931,geonode/geoserver-geonode-ext,c553cbf6d702e82f1febb8911b280fa7e1307c5a,d56d71dd8f0d4007db31c8d5960a14f68137809146773ebc49c16b0f9731ddb1,Tests_failed