Merge remote-tracking branch 'upstream/main' into ben-main

.github/workflows/check-reproducibility-inconsistent-results.yml

@@ -0,0 +1,46 @@
+name: Reproducibility Check Inconsistent Results
+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/utils/build_inconsistent_merges.py
+        head -n 151 results/combined/result.csv > temp.csv && mv temp.csv results/combined/result.csv
+        make CSV_RESULTS=results/combined/inconsistent_results.csv check-merges-reproducibility
+      env:
+          GITHUB_TOKEN: ${{ secrets.TOKEN_GITHUB }}

.github/workflows/check-style.yml

@@ -8,7 +8,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: psf/black@stable
     - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
         args: ['--maxkb=20000']
@@ -44,12 +44,9 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
     -   id: text-unicode-replacement-char
--   repo: https://github.com/psf/black
-    rev: 23.11.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
     hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/pylint
-    rev: v3.0.1
-    hooks:
-    -   id: pylint
-        args: ['--disable=R0801,E0401,W0718,W0719,W1510,C0103,W0621']
+    -   id: ruff
+        args: [ --fix ]
+    -   id: ruff-format

Makefile

@@ -23,12 +23,12 @@ showvars:
 	@echo "PYTHON_FILES=${PYTHON_FILES}"
 
 python-style:
-	black ${PYTHON_FILES}
-	pylint -f parseable --disable=W,invalid-name,c-extension-no-member,duplicate-code ${PYTHON_FILES}
+	ruff format ${PYTHON_FILES}
+	ruff check ${PYTHON_FILES} --fix
 
 check-python-style:
-	black ${PYTHON_FILES} --check
-	pylint -f parseable --disable=W,invalid-name --disable=W,duplicate-code ${PYTHON_FILES}
+	ruff format ${PYTHON_FILES} --check
+	ruff check ${PYTHON_FILES}
 
 # This target deletes files that are not committed to version control.
 clean:

README.md

@@ -1,32 +1,32 @@
 # Evaluation of VCS merging algorithms
 
 ![small-test](https://github.com/benedikt-schesch/AST-Merging-Evaluation/actions/workflows/small-test.yml/badge.svg)
-
 ![check-style](https://github.com/benedikt-schesch/AST-Merging-Evaluation/actions/workflows/check-style.yml/badge.svg)
+![check-reproducibility](https://github.com/benedikt-schesch/AST-Merging-Evaluation/actions/workflows/check-reproducibility.yml/badge.svg)
 
 ## Requirements
 
 ### Python
 
-To install all the python requirements create a conda environment:
+To install all the Python requirements, create a conda or mamba environment:
 
-With mamba (faster https://github.com/mamba-org/mamba):
+With conda:
 
 ```bash
-mamba env create -f environment.yml
-mamba activate AST
+conda env create -f environment.yml
+conda activate AST
 ```
 
-With conda:
+With mamba (faster https://github.com/mamba-org/mamba):
 
 ```bash
-conda env create -f environment.yml
-conda activate AST
+mamba env create -f environment.yml
+mamba activate AST
 ```
 
 ### Maven
 
-Make sure you use maven version 3.9.*.
+You must use Maven version 3.9.*.
 
 ### Ubuntu
 
@@ -50,7 +50,7 @@ brew install gh
 
 ### Java
 
-Make sure you install Java 8, 11 and 17. You need to set the `JAVA8_HOME`, `JAVA11_HOME` and `JAVA17_HOME` environment variables to the respective Java installations.
+You must install Java 8, 11 and 17. You must set the `JAVA8_HOME`, `JAVA11_HOME` and `JAVA17_HOME` environment variables to the respective Java installations.
 
 ---
 
@@ -211,10 +211,10 @@ To run style checking run `make style`.
 
 * 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.
+
+* 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

@@ -25,12 +25,11 @@ dependencies:
       - matplotlib==3.8.4
       - numpy==1.26.4
       - pandas==2.2.2
-      - pylint==3.1.0
+      - ruff==0.4.4
       - GitPython==3.1.43
       - prettytable==3.10.0
       - seaborn==0.13.2
       - rich==13.7.1
-      - black==24.4.2
       - psutil==5.9.8
       - termplotlib==0.3.9
       - loguru==0.7.2

results/combined/defs.tex

@@ -19,8 +19,8 @@
 \def\combinedSporkOverOrtIncorrect{487\xspace}
 \def\combinedMainBranchMerges{3557\xspace}
 \def\combinedMainBranchMergesPercent{59\xspace}
-\def\combinedOtherBranceshMerges{2483\xspace}
-\def\combinedOtherBranchesMergesPercent{41\xspace}
+\def\combinedOtherBranchMerges{2483\xspace}
+\def\combinedOtherBranchMergesPercent{41\xspace}
 \def\combinedReposJava{42092\xspace}
 
 % Timeout

results/combined/merges_tested/abel533/echarts.csv

@@ -1,2 +1,2 @@
 idx,branch_name,merge,left,right,notes,test merge,diff contains java file,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,sampled for testing,gitmerge_ort,gitmerge_ort_merge_fingerprint,gitmerge_ort_ignorespace,gitmerge_ort_ignorespace_merge_fingerprint,gitmerge_recursive_histogram,gitmerge_recursive_histogram_merge_fingerprint,gitmerge_recursive_ignorespace,gitmerge_recursive_ignorespace_merge_fingerprint,gitmerge_recursive_minimal,gitmerge_recursive_minimal_merge_fingerprint,gitmerge_recursive_myers,gitmerge_recursive_myers_merge_fingerprint,gitmerge_recursive_patience,gitmerge_recursive_patience_merge_fingerprint,gitmerge_resolve,gitmerge_resolve_merge_fingerprint,gitmerge_ort_adjacent,gitmerge_ort_adjacent_merge_fingerprint,gitmerge_ort_imports,gitmerge_ort_imports_merge_fingerprint,gitmerge_ort_imports_ignorespace,gitmerge_ort_imports_ignorespace_merge_fingerprint,git_hires_merge,git_hires_merge_merge_fingerprint,spork,spork_merge_fingerprint,intellimerge,intellimerge_merge_fingerprint
-9,refs/heads/master,c6ad45b63a9ee7e20b45c4176695a72efa31606a,69757fc487bf247b74339de637cb48ed296e5a67,721cb6fa847595de1b4b58fb80ec6079d15d9a95,,True,True,05376667afdba29e22c97c992edaa40bf1866e03660bb315bdf828004927fae8,Tests_passed,0dd38c0c7dc253f9adc1ed53fbf0e6b43aca5ad15576b740bffdc47c97a43a47,Tests_passed,True,True,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,29326553a8028f23a6604f8ec4736c8e60bfedd7ee241f8f43a324a7a0cdd8e6,Merge_failed,d248842099ea25d2e20f49e617634a46ab4024dfb985523d95bccb6c5ec7b2bb,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,9c57575dab347e2e37bbf92c19a55a137bd5648fe61399131d68744e0801e3b6,Merge_failed,6a56b2c32156b5a3b892638ab2e7654f00fdb4c08c5b25fab88caf1c1db3bc09,Merge_failed,d248842099ea25d2e20f49e617634a46ab4024dfb985523d95bccb6c5ec7b2bb
+9,refs/heads/master,c6ad45b63a9ee7e20b45c4176695a72efa31606a,69757fc487bf247b74339de637cb48ed296e5a67,721cb6fa847595de1b4b58fb80ec6079d15d9a95,,True,True,05376667afdba29e22c97c992edaa40bf1866e03660bb315bdf828004927fae8,Tests_passed,0dd38c0c7dc253f9adc1ed53fbf0e6b43aca5ad15576b740bffdc47c97a43a47,Tests_passed,True,True,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,4702ab428931635d20d30f4091e3cce5d36aa4be418344382a53d6c16bb92692,Merge_failed,29326553a8028f23a6604f8ec4736c8e60bfedd7ee241f8f43a324a7a0cdd8e6,Merge_failed,d248842099ea25d2e20f49e617634a46ab4024dfb985523d95bccb6c5ec7b2bb,Merge_failed,f86893cf92b7b9f6bf70f2fd43463f0fb1119e4e2a2f0130001f6f2f823b4e75,Merge_failed,f86893cf92b7b9f6bf70f2fd43463f0fb1119e4e2a2f0130001f6f2f823b4e75,Merge_failed,9c57575dab347e2e37bbf92c19a55a137bd5648fe61399131d68744e0801e3b6,Merge_failed,6a56b2c32156b5a3b892638ab2e7654f00fdb4c08c5b25fab88caf1c1db3bc09,Merge_failed,d248842099ea25d2e20f49e617634a46ab4024dfb985523d95bccb6c5ec7b2bb

results/combined/merges_tested/acciente/oacc-core.csv

@@ -1,2 +1,2 @@
 idx,branch_name,merge,left,right,notes,test merge,diff contains java file,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,sampled for testing,gitmerge_ort,gitmerge_ort_merge_fingerprint,gitmerge_ort_ignorespace,gitmerge_ort_ignorespace_merge_fingerprint,gitmerge_recursive_histogram,gitmerge_recursive_histogram_merge_fingerprint,gitmerge_recursive_ignorespace,gitmerge_recursive_ignorespace_merge_fingerprint,gitmerge_recursive_minimal,gitmerge_recursive_minimal_merge_fingerprint,gitmerge_recursive_myers,gitmerge_recursive_myers_merge_fingerprint,gitmerge_recursive_patience,gitmerge_recursive_patience_merge_fingerprint,gitmerge_resolve,gitmerge_resolve_merge_fingerprint,gitmerge_ort_adjacent,gitmerge_ort_adjacent_merge_fingerprint,gitmerge_ort_imports,gitmerge_ort_imports_merge_fingerprint,gitmerge_ort_imports_ignorespace,gitmerge_ort_imports_ignorespace_merge_fingerprint,git_hires_merge,git_hires_merge_merge_fingerprint,spork,spork_merge_fingerprint,intellimerge,intellimerge_merge_fingerprint
-4,refs/heads/master,0ca7e4ea4fd000ca5a3b51bb5e2e2fc27f6217f2,57e7150a72573f547092a0054317ffab8219bc45,c32cb07eda7eae130ce52a9cada989e58a1fbfa3,,True,True,9648b81286e53d474cb0ca01597f0a94b155d0dd8b1bd322a8921c3ec40b15c2,Tests_passed,5137eaf1d40f9a64f41e55dfd63637b140570923d93196f215cb3b23151b0dea,Tests_passed,True,True,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,0ad53a1530f8a34063dbd30466d149f7910e477ea05235886981b3b336b9fda5,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Tests_passed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Tests_passed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,30edee8e81f9b0c03e7f51cbed04aa41ef8d692ce6cc6fe40aa9fe8042254ca2,Tests_passed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b
+4,refs/heads/master,0ca7e4ea4fd000ca5a3b51bb5e2e2fc27f6217f2,57e7150a72573f547092a0054317ffab8219bc45,c32cb07eda7eae130ce52a9cada989e58a1fbfa3,,True,True,9648b81286e53d474cb0ca01597f0a94b155d0dd8b1bd322a8921c3ec40b15c2,Tests_passed,5137eaf1d40f9a64f41e55dfd63637b140570923d93196f215cb3b23151b0dea,Tests_passed,True,True,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,0ad53a1530f8a34063dbd30466d149f7910e477ea05235886981b3b336b9fda5,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,8b0ba4e09c1fd34c6832eaf52a028c2ca4eec9b3486235de3d536a94cf7b21ff,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b,Merge_failed,30edee8e81f9b0c03e7f51cbed04aa41ef8d692ce6cc6fe40aa9fe8042254ca2,Merge_failed,44fab8c3a10bf70f3ccfa6e82abed9f89cba67e6824e36f9ad31258cd92af87b