feat: stable sh outputs in the right folder

mutation-testing/packages-output/pox-locking/missed.txt

@@ -0,0 +1,30 @@
+pox-locking/src/pox_1.rs:128: replace handle_contract_call -> Result<(), ClarityError> with Ok(())
+pox-locking/src/pox_2.rs:217: replace pox_lock_extend_v2 -> Result<u128, LockingError> with Ok(1)
+pox-locking/src/pox_3.rs:72: replace pox_lock_extend_v3_not_tested -> Result<u128, LockingError> with Ok(0)
+pox-locking/src/events.rs:47: replace create_event_info_stack_or_delegate_code -> String with String::new()
+pox-locking/src/events.rs:351: replace synthesize_pox_2_or_3_event_info -> Result<Option<Value>, ClarityError> with Ok(None)
+pox-locking/src/events.rs:76: replace create_event_info_aggregation_code -> String with "xyzzy".into()
+pox-locking/src/pox_2.rs:248: replace pox_lock_v2 -> Result<(), LockingError> with Ok(())
+pox-locking/src/pox_2.rs:280: replace handle_stack_lockup_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_1.rs:90: replace pox_lock_v1 -> Result<(), LockingError> with Ok(())
+pox-locking/src/pox_3.rs:363: replace handle_contract_call -> Result<(), ClarityError> with Ok(())
+pox-locking/src/events.rs:103: replace create_event_info_data_code -> String with String::new()
+pox-locking/src/events.rs:103: replace create_event_info_data_code -> String with "xyzzy".into()
+pox-locking/src/pox_3.rs:236: replace handle_stack_lockup_extension_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_2.rs:409: replace handle_stack_lockup_increase_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_1.rs:69: replace is_read_only -> bool with false
+pox-locking/src/pox_3.rs:300: replace handle_stack_lockup_increase_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_1.rs:69: replace is_read_only -> bool with true
+pox-locking/src/pox_2.rs:33: replace is_read_only -> bool with true
+pox-locking/src/pox_3.rs:87: replace pox_lock_extend_v3 -> Result<u128, LockingError> with Ok(1)
+pox-locking/src/pox_3.rs:169: replace handle_stack_lockup_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_2.rs:33: replace is_read_only -> bool with false
+pox-locking/src/events.rs:76: replace create_event_info_aggregation_code -> String with String::new()
+pox-locking/src/lib.rs:65: replace handle_contract_call_special_cases -> Result<(), ClarityError> with Ok(())
+pox-locking/src/pox_2.rs:345: replace handle_stack_lockup_extension_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(None)
+pox-locking/src/pox_3.rs:42: replace pox_lock_v3 -> Result<(), LockingError> with Ok(())
+pox-locking/src/pox_3.rs:87: replace pox_lock_extend_v3 -> Result<u128, LockingError> with Ok(0)
+pox-locking/src/events.rs:47: replace create_event_info_stack_or_delegate_code -> String with "xyzzy".into()
+pox-locking/src/pox_2.rs:473: replace handle_contract_call -> Result<(), ClarityError> with Ok(())
+pox-locking/src/pox_2.rs:217: replace pox_lock_extend_v2 -> Result<u128, LockingError> with Ok(0)
+pox-locking/src/pox_3.rs:72: replace pox_lock_extend_v3_not_tested -> Result<u128, LockingError> with Ok(1)

mutation-testing/packages-output/pox-locking/unviable.txt

@@ -0,0 +1,22 @@
+pox-locking/src/events.rs:32: replace get_stacker -> Value with Default::default()
+pox-locking/src/events.rs:351: replace synthesize_pox_2_or_3_event_info -> Result<Option<Value>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_3.rs:236: replace handle_stack_lockup_extension_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:409: replace handle_stack_lockup_increase_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:127: replace parse_pox_increase -> std::result::Result<(PrincipalData, u128), i128> with Ok((Default::default(), 0))
+pox-locking/src/pox_1.rs:36: replace parse_pox_stacking_result_v1 -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 1, 1))
+pox-locking/src/pox_2.rs:127: replace parse_pox_increase -> std::result::Result<(PrincipalData, u128), i128> with Ok((Default::default(), 1))
+pox-locking/src/pox_2.rs:64: replace parse_pox_stacking_result -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 0, 0))
+pox-locking/src/pox_3.rs:123: replace pox_lock_increase_v3 -> Result<STXBalance, LockingError> with Ok(Default::default())
+pox-locking/src/pox_3.rs:169: replace handle_stack_lockup_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:164: replace pox_lock_increase_v2 -> Result<STXBalance, LockingError> with Ok(Default::default())
+pox-locking/src/pox_1.rs:36: replace parse_pox_stacking_result_v1 -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 1, 0))
+pox-locking/src/pox_1.rs:36: replace parse_pox_stacking_result_v1 -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 0, 1))
+pox-locking/src/pox_3.rs:300: replace handle_stack_lockup_increase_pox_v3 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:98: replace parse_pox_extend_result -> std::result::Result<(PrincipalData, u64), i128> with Ok((Default::default(), 0))
+pox-locking/src/pox_2.rs:64: replace parse_pox_stacking_result -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 0, 1))
+pox-locking/src/pox_2.rs:98: replace parse_pox_extend_result -> std::result::Result<(PrincipalData, u64), i128> with Ok((Default::default(), 1))
+pox-locking/src/pox_2.rs:280: replace handle_stack_lockup_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:64: replace parse_pox_stacking_result -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 1, 0))
+pox-locking/src/pox_1.rs:36: replace parse_pox_stacking_result_v1 -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 0, 0))
+pox-locking/src/pox_2.rs:345: replace handle_stack_lockup_extension_pox_v2 -> Result<Option<StacksTransactionEvent>, ClarityError> with Ok(Some(Default::default()))
+pox-locking/src/pox_2.rs:64: replace parse_pox_stacking_result -> std::result::Result<(PrincipalData, u128, u64), i128> with Ok((Default::default(), 1, 1))

mutation-testing/packages-output/stx-genesis/missed.txt

@@ -1,3 +1,3 @@
 stx-genesis/src/lib.rs:108: replace <impl Iterator for LinePairReader>::count -> usize with 1
-stx-genesis/src/lib.rs:100: replace <impl Iterator for LinePairReader>::next -> Option<Self::Item> with None
 stx-genesis/src/lib.rs:108: replace <impl Iterator for LinePairReader>::count -> usize with 0
+stx-genesis/src/lib.rs:100: replace <impl Iterator for LinePairReader>::next -> Option<Self::Item> with None

mutation-testing/packages-output/stx-genesis/unviable.txt

@@ -1,11 +1,11 @@
-stx-genesis/src/lib.rs:71: replace GenesisData::read_namespaces -> Box<dyn Iterator<Item = GenesisNamespace>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:148: replace read_lockups -> Box<dyn Iterator<Item = GenesisAccountLockup>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:78: replace GenesisData::read_names -> Box<dyn Iterator<Item = GenesisName>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:140: replace read_balances -> Box<dyn Iterator<Item = GenesisAccountBalance>> with Box::new(Default::default())
 stx-genesis/src/lib.rs:157: replace read_namespaces -> Box<dyn Iterator<Item = GenesisNamespace>> with Box::new(Default::default())
 stx-genesis/src/lib.rs:129: replace iter_deflated_csv -> Box<dyn Iterator<Item = Vec<String>>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:140: replace read_balances -> Box<dyn Iterator<Item = GenesisAccountBalance>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:85: replace GenesisData::read_name_zonefiles -> Box<dyn Iterator<Item = GenesisZonefile>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:78: replace GenesisData::read_names -> Box<dyn Iterator<Item = GenesisName>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:64: replace GenesisData::read_lockups -> Box<dyn Iterator<Item = GenesisAccountLockup>> with Box::new(Default::default())
-stx-genesis/src/lib.rs:115: replace read_deflated_zonefiles -> Box<dyn Iterator<Item = GenesisZonefile>> with Box::new(Default::default())
 stx-genesis/src/lib.rs:57: replace GenesisData::read_balances -> Box<dyn Iterator<Item = GenesisAccountBalance>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:115: replace read_deflated_zonefiles -> Box<dyn Iterator<Item = GenesisZonefile>> with Box::new(Default::default())
 stx-genesis/src/lib.rs:171: replace read_names -> Box<dyn Iterator<Item = GenesisName>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:148: replace read_lockups -> Box<dyn Iterator<Item = GenesisAccountLockup>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:64: replace GenesisData::read_lockups -> Box<dyn Iterator<Item = GenesisAccountLockup>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:85: replace GenesisData::read_name_zonefiles -> Box<dyn Iterator<Item = GenesisZonefile>> with Box::new(Default::default())
+stx-genesis/src/lib.rs:71: replace GenesisData::read_namespaces -> Box<dyn Iterator<Item = GenesisNamespace>> with Box::new(Default::default())

mutation-testing/scripts/append-match-package.sh

@@ -0,0 +1,88 @@
+# the append-match-package.sh
+## goes through each line in the output and based on the package ( first element before /)
+### verifies the line with the other lines in that specific folder
+#### in our case folder_name == package_name
+
+
+# goes through each PR file line by line
+# for each first_element/the_rest_of_the_line goes through it
+## search in that specific folder on all 4 files
+## if it is matchy, remove it from that file
+## based on the file it was taken from, append it to the same file in the STABLE folder
+
+
+
+#!/bin/bash
+
+PR_FOLDER="./../temp/mutants.out"
+STABLE_FOLDER_PARENT="./../packages-output"
+FILES=("caught.txt" "missed.txt" "timeout.txt" "unviable.txt")
+
+echo "Starting script..."
+echo "PR Folder: $PR_FOLDER"
+echo "STABLE Folder: $STABLE_FOLDER_PARENT"
+echo "Files to process: ${FILES[*]}"
+
+# Function to escape special characters for awk
+escape_for_awk() {
+    echo "$1" | sed -E 's/([][\/$*.^|])/\\&/g'
+}
+
+# Iterate over the specified files
+for file in "${FILES[@]}"; do
+    pr_file="$PR_FOLDER/$file"
+    stable_file="$STABLE_FOLDER_PARENT/$file"
+
+    echo "Processing file: $file"
+
+    # Check if PR file exists and is not empty
+    if [[ -s "$pr_file" ]]; then
+        # Read each line from the PR file
+        while IFS= read -r line; do
+            echo "Reading line from PR file: $line"
+
+            # Extract the core pattern without the line number and escape it for awk
+            core_pattern=$(echo "$line" | sed -E 's/^[^:]+:[0-9]+:(.+)/\1/')
+            escaped_pattern=$(escape_for_awk "$core_pattern")
+            echo "Extracted and escaped pattern: $escaped_pattern"
+
+            # Iterate over each file in the STABLE folder
+            for target_file in "${FILES[@]}"; do
+                target_path="$STABLE_FOLDER_PARENT/$target_file"
+                echo "Checking against STABLE file: $target_path"
+
+                # Remove the line matching the pattern, ignoring line numbers
+                awk -v pat="$escaped_pattern" '$0 !~ pat' "$target_path" > temp_file && mv temp_file "$target_path"
+            done
+        done < "$pr_file"
+    else
+        echo "PR file $pr_file is empty or does not exist, skipping..."
+    fi
+done
+
+# After processing all lines, append contents from PR_DIR to STABLE_DIR
+for file in "${FILES[@]}"; do
+    cat "$PR_FOLDER/$file" >> "$STABLE_FOLDER_PARENT/$file"
+done
+
+# Echo the contents of the STABLE folder for verification
+echo "Updated contents of STABLE folder:"
+for file in "${FILES[@]}"; do
+    stable_file="$STABLE_FOLDER_PARENT/$file"
+    echo "Contents of $stable_file:"
+    cat "$stable_file"
+    echo ""
+done
+
+echo "Script completed."
+
+
+
+
+# goes only through txt
+
+
+
+
+# remove temp/mutants.out
+## rm -rf ../temp/

mutation-testing/scripts/create-stable.sh

@@ -4,34 +4,52 @@
 
 #!/bin/bash
 
-# Create mutants directory
-mkdir -p mutants
+# moves to mutation-testing folder
+cd ../packages-output
 
 ### Run mutation testing on the packages uncommented
 
 # Run mutation testing for stx-genesis package
-cargo mutants --package stx-genesis --output mutants/stx-genesis
+cargo mutants --package stx-genesis --output stx-genesis
+mv stx-genesis/mutants.out/*.txt stx-genesis/
+rm -rf stx-genesis/mutants.out
 
 # Run mutation testing for pox-locking package
-cargo mutants --package pox-locking --output mutants/pox-locking
+cargo mutants --package pox-locking --output pox-locking
+mv pox-locking/mutants.out/*.txt pox-locking/
+rm -rf pox-locking/mutants.out
 
 # # Run mutation testing for libsigner package
-# cargo mutants --package libsigner --output mutants/libsigner
+# cargo mutants --package libsigner --output libsigner
+# mv libsigner/mutants.out/*.txt libsigner/
+# rm -rf libsigner/mutants.out
 
 # # Run mutation testing for libstackerdb package
-# cargo mutants --package libstackerdb --output mutants/libstackerdb
+# cargo mutants --package libstackerdb --output libstackerdb
+# mv libstackerdb/mutants.out/*.txt libstackerdb/
+# rm -rf libstackerdb/mutants.out
 
 # # Run mutation testing for stacks-common package
-# cargo mutants --package stacks-common --output mutants/stacks-common
+# cargo mutants --package stacks-common --output stacks-common
+# mv stacks-common/mutants.out/*.txt stacks-common/
+# rm -rf stacks-common/mutants.out
 
 # # Run mutation testing for clarity package
-# cargo mutants --package clarity --output mutants/clarity
+# cargo mutants --package clarity --output clarity
+# mv clarity/mutants.out/*.txt clarity/
+# rm -rf clarity/mutants.out
 
 # Run mutation testing for stacks-signer package - working, 10 min approx. 
-# cargo mutants --package stacks-signer --output mutants/stacks-signer
+# cargo mutants --package stacks-signer --output stacks-signer
+# mv stacks-signer/mutants.out/*.txt stacks-signer/
+# rm -rf stacks-signer/mutants.out
 
 # Commented out mutation testing for stacks-node package due to test errors and long compile/testing time
-# cargo mutants --package stacks-node --output mutants/stacks-node
+# cargo mutants --package stacks-node --output stacks-node
+# mv stacks-node/mutants.out/*.txt stacks-node/
+# rm -rf stacks-node/mutants.out
 
 # Commented out mutation testing for stackslib package due to long compile/testing time
-# cargo mutants --package stackslib --output mutants/stackslib
+# cargo mutants --package stackslib --output stackslib
+# mv stackslib/mutants.out/*.txt stackslib/
+# rm -rf stackslib/mutants.out

mutation-testing/scripts/git-diff.sh

@@ -1,17 +1,18 @@
 # script that makes .git for the differences
 # it saves the .git on scripts folder
 
-# it runs cargo mutants for those specific changed functions
+# run from scripts folder
+cd ..
+git diff > git.diff
 
-# it creates a new output
+# it runs cargo mutants for those specific changed functions and outputs to /temp/mutants.out
+# for faster builds: increase number to 4 if at least 16 gb ram and 6 cores CPU
+cargo mutants --no-shuffle -j 2 -vV --in-diff git.diff --output temp/
 
 
-# then the append-match-package.sh is called
-## TODO: update append-match-package.sh with what would be the output from the cargo mutants diff
+# call append-match-package.sh to update the content from the stable output
+### sh scripts/append-match-package.sh
+
 
 
-# the append-match-package.sh
-## goes through each line in the output and based on the package ( first element before /)
-### verifies the line with the other lines in that specific folder
-#### in our case folder_name == package_name