From afe828495e8a399cc7d31156e74e70cc5e6d8082 Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 10:24:58 +0100
Subject: [PATCH 1/9] [#126]: Update ubuntu version in docker

---
 docker/static_analysis.dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/static_analysis.dockerfile b/docker/static_analysis.dockerfile
index 1f380e9..3d60501 100644
--- a/docker/static_analysis.dockerfile
+++ b/docker/static_analysis.dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:23.04 as base
+FROM ubuntu:24.04 as base
 
 # Define versions as environment variables
 ENV CLANG_VERSION=18 \

From dd723bf3bbedffca9b1a87dcdd46ececdbb92f5d Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 10:25:31 +0100
Subject: [PATCH 2/9] [#126]: Update llvm script

---
 llvm.sh | 40 +++++++++++++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 11 deletions(-)

diff --git a/llvm.sh b/llvm.sh
index 491c785..2f58e83 100644
--- a/llvm.sh
+++ b/llvm.sh
@@ -27,12 +27,12 @@ BASE_URL="http://apt.llvm.org"
 needed_binaries=(lsb_release wget add-apt-repository gpg)
 missing_binaries=()
 for binary in "${needed_binaries[@]}"; do
-    if ! which "$binary" &>/dev/null ; then
-        missing_binaries+=("$binary")
+    if ! which $binary &>/dev/null ; then
+        missing_binaries+=($binary)
     fi
 done
 if [[ ${#missing_binaries[@]} -gt 0 ]] ; then
-    echo "You are missing some tools this script requires: " "${missing_binaries[@]}"
+    echo "You are missing some tools this script requires: ${missing_binaries[@]}"
     echo "(hint: apt install lsb-release wget software-properties-common gnupg)"
     exit 4
 fi
@@ -40,12 +40,12 @@ fi
 # Set default values for commandline arguments
 # We default to the current stable branch of LLVM
 LLVM_VERSION=$CURRENT_LLVM_STABLE
+ALL=0
 DISTRO=$(lsb_release -is)
 VERSION=$(lsb_release -sr)
 UBUNTU_CODENAME=""
 CODENAME_FROM_ARGUMENTS=""
 # Obtain VERSION_CODENAME and UBUNTU_CODENAME (for Ubuntu and its derivatives)
-# shellcheck disable=SC1091
 source /etc/os-release
 DISTRO=${DISTRO,,}
 case ${DISTRO} in
@@ -76,18 +76,21 @@ esac
 if [ "$#" -ge 1 ] && [ "${1::1}" != "-" ]; then
     if [ "$1" != "all" ]; then
         LLVM_VERSION=$1
+    else
+        # special case for ./llvm.sh all
+        ALL=1
     fi
     OPTIND=2
     if [ "$#" -ge 2 ]; then
       if [ "$2" == "all" ]; then
           # Install all packages
+          ALL=1
           OPTIND=3
       fi
     fi
 fi
 
 while getopts ":hm:n:" arg; do
-    # shellcheck disable=SC2220
     case $arg in
     h)
         usage
@@ -124,7 +127,9 @@ LLVM_VERSION_PATTERNS[15]="-15"
 LLVM_VERSION_PATTERNS[16]="-16"
 LLVM_VERSION_PATTERNS[17]="-17"
 LLVM_VERSION_PATTERNS[18]="-18"
-LLVM_VERSION_PATTERNS[19]=""
+LLVM_VERSION_PATTERNS[19]="-19"
+LLVM_VERSION_PATTERNS[20]="-20"
+LLVM_VERSION_PATTERNS[21]=""
 
 if [ ! ${LLVM_VERSION_PATTERNS[$LLVM_VERSION]+_} ]; then
     echo "This script does not support LLVM version $LLVM_VERSION"
@@ -138,7 +143,7 @@ if [[ -n "${CODENAME}" ]]; then
     REPO_NAME="deb ${BASE_URL}/${CODENAME}/  llvm-toolchain${LINKNAME}${LLVM_VERSION_STRING} main"
 
     # check if the repository exists for the distro and version
-    if ! wget -q --method=HEAD "${BASE_URL}/${CODENAME}" &> /dev/null; then
+    if ! wget -q --method=HEAD ${BASE_URL}/${CODENAME} &> /dev/null; then
         if [[ -n "${CODENAME_FROM_ARGUMENTS}" ]]; then
             echo "Specified codename '${CODENAME}' is not supported by this script."
         else
@@ -156,12 +161,25 @@ if [[ ! -f /etc/apt/trusted.gpg.d/apt.llvm.org.asc ]]; then
     wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
 fi
 
-# shellcheck disable=SC2006
 if [[ -z "`apt-key list 2> /dev/null | grep -i llvm`" ]]; then
     # Delete the key in the old format
-    apt-key del AF4F7421
+    apt-key del AF4F7421 || true
 fi
+if [[ "${VERSION_CODENAME}" == "bookworm" ]]; then
+    # add it twice to workaround:
+    # https://github.com/llvm/llvm-project/issues/62475
+    add-apt-repository -y "${REPO_NAME}"
+fi
+
 add-apt-repository -y "${REPO_NAME}"
 apt-get update
-PKG="clang-$LLVM_VERSION lld-$LLVM_VERSION clangd-$LLVM_VERSION clang-tidy-$LLVM_VERSION"
-apt-get install -y "$PKG"
+PKG="clang-$LLVM_VERSION lldb-$LLVM_VERSION lld-$LLVM_VERSION clangd-$LLVM_VERSION"
+if [[ $ALL -eq 1 ]]; then
+    # same as in test-install.sh
+    # No worries if we have dups
+    PKG="$PKG clang-tidy-$LLVM_VERSION clang-format-$LLVM_VERSION clang-tools-$LLVM_VERSION llvm-$LLVM_VERSION-dev lld-$LLVM_VERSION lldb-$LLVM_VERSION llvm-$LLVM_VERSION-tools libomp-$LLVM_VERSION-dev libc++-$LLVM_VERSION-dev libc++abi-$LLVM_VERSION-dev libclang-common-$LLVM_VERSION-dev libclang-$LLVM_VERSION-dev libclang-cpp$LLVM_VERSION-dev libunwind-$LLVM_VERSION-dev"
+    if test $LLVM_VERSION -gt 14; then
+        PKG="$PKG libclang-rt-$LLVM_VERSION-dev libpolly-$LLVM_VERSION-dev"
+    fi
+fi
+apt-get install -y $PKG

From 632aa67f2b46a488dc20228ed2ce490d3701e6cc Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 10:26:33 +0100
Subject: [PATCH 3/9] [#126]: Update cppcheck and clang versions

---
 docker/static_analysis.dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker/static_analysis.dockerfile b/docker/static_analysis.dockerfile
index 3d60501..a8a52d9 100644
--- a/docker/static_analysis.dockerfile
+++ b/docker/static_analysis.dockerfile
@@ -1,8 +1,8 @@
 FROM ubuntu:24.04 as base
 
 # Define versions as environment variables
-ENV CLANG_VERSION=18 \
-    CPPCHECK_VERSION=2.14.0 \
+ENV CLANG_VERSION=20 \
+    CPPCHECK_VERSION=2.16.0 \
     CXX=clang++ \
     CC=clang \
     DEBIAN_FRONTEND=noninteractive

From 7e2854fe8f1e5c3b56a72055b8ccc78891343897 Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 10:38:23 +0100
Subject: [PATCH 4/9] [#126]: Fix docker warning

---
 docker/static_analysis.dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/static_analysis.dockerfile b/docker/static_analysis.dockerfile
index a8a52d9..57ddc9f 100644
--- a/docker/static_analysis.dockerfile
+++ b/docker/static_analysis.dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:24.04 as base
+FROM ubuntu:24.04 AS base
 
 # Define versions as environment variables
 ENV CLANG_VERSION=20 \

From 09864cb4c13356d48db6becb4c216bcb00709c9e Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 10:41:18 +0100
Subject: [PATCH 5/9] [#126]: Exclude llvm.sh from shellcheck

---
 .github/workflows/shellcheck.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/shellcheck.yml b/.github/workflows/shellcheck.yml
index 7855743..4d3ffd0 100644
--- a/.github/workflows/shellcheck.yml
+++ b/.github/workflows/shellcheck.yml
@@ -13,4 +13,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Run ShellCheck
-        uses: ludeeus/action-shellcheck@master
\ No newline at end of file
+        uses: ludeeus/action-shellcheck@master
+        with:
+          ignore_names: llvm.sh # External file
\ No newline at end of file

From 12461d3b1bd4edbbaae9eff4bffa5aac91d23e1a Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 11:24:41 +0100
Subject: [PATCH 6/9] [#126]: Update usage of clang-tidy

---
 entrypoint_cpp.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/entrypoint_cpp.sh b/entrypoint_cpp.sh
index d8851d8..d840545 100644
--- a/entrypoint_cpp.sh
+++ b/entrypoint_cpp.sh
@@ -67,16 +67,16 @@ else
         cat cppcheck_*.txt > cppcheck.txt
 
         # Excludes for clang-tidy are handled in python script
-        debug_print "Running run-clang-tidy-18 $CLANG_TIDY_ARGS -p $(pwd) $files_to_check >>clang_tidy.txt 2>&1"
-        eval run-clang-tidy-18 "$CLANG_TIDY_ARGS" -p "$(pwd)" "$files_to_check" >clang_tidy.txt 2>&1 || true
+        debug_print "Running run-clang-tidy-20 $CLANG_TIDY_ARGS -p $(pwd) $files_to_check >>clang_tidy.txt 2>&1"
+        eval run-clang-tidy-20 "$CLANG_TIDY_ARGS" -p "$(pwd)" "$files_to_check" >clang_tidy.txt 2>&1 || true
 
     else
         # Excludes for clang-tidy are handled in python script
         debug_print "Running cppcheck -j $num_proc $files_to_check $CPPCHECK_ARGS --output-file=cppcheck.txt ..."
         eval cppcheck -j "$num_proc" "$files_to_check" "$CPPCHECK_ARGS" --output-file=cppcheck.txt || true
 
-        debug_print "Running run-clang-tidy-18 $CLANG_TIDY_ARGS $files_to_check >>clang_tidy.txt 2>&1"
-        eval run-clang-tidy-18 "$CLANG_TIDY_ARGS" "$files_to_check" >clang_tidy.txt 2>&1 || true
+        debug_print "Running run-clang-tidy-20 $CLANG_TIDY_ARGS $files_to_check >>clang_tidy.txt 2>&1"
+        eval run-clang-tidy-20 "$CLANG_TIDY_ARGS" "$files_to_check" >clang_tidy.txt 2>&1 || true
     fi
 
     cd /

From ef5110299124815f3092bac3cdf4f8a60c52c8b7 Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 14:01:42 +0100
Subject: [PATCH 7/9] [#126]: Fix issues

---
 llvm.sh                    | 2 +-
 src/sa_utils.py            | 6 +++---
 src/static_analysis_cpp.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/llvm.sh b/llvm.sh
index 2f58e83..2066ab3 100644
--- a/llvm.sh
+++ b/llvm.sh
@@ -173,7 +173,7 @@ fi
 
 add-apt-repository -y "${REPO_NAME}"
 apt-get update
-PKG="clang-$LLVM_VERSION lldb-$LLVM_VERSION lld-$LLVM_VERSION clangd-$LLVM_VERSION"
+PKG="clang-$LLVM_VERSION lldb-$LLVM_VERSION lld-$LLVM_VERSION clangd-$LLVM_VERSION clang-tidy-$LLVM_VERSION clang-format-$LLVM_VERSION clang-tools-$LLVM_VERSION"
 if [[ $ALL -eq 1 ]]; then
     # same as in test-install.sh
     # No worries if we have dups
diff --git a/src/sa_utils.py b/src/sa_utils.py
index 9b13f22..075f03e 100644
--- a/src/sa_utils.py
+++ b/src/sa_utils.py
@@ -318,7 +318,7 @@ def create_or_edit_comment(comment_body):
         pull_request.create_issue_comment(body=comment_body)
 
 
-def generate_output(is_note, file_path, file_line_start, file_line_end, description):
+def generate_output(is_note, file_path, file_line_start, file_line_end, description, prefix=""):
     """
     Generate a formatted output string based on the details of a code issue.
 
@@ -347,11 +347,11 @@ def generate_output(is_note, file_path, file_line_start, file_line_end, descript
         if TARGET_REPO_NAME != REPO_NAME:
             if file_path not in FILES_WITH_ISSUES:
                 try:
-                    with open(f"{file_path}", encoding="utf-8") as file:
+                    with open(f"{prefix}/{file_path}", encoding="utf-8") as file:
                         lines = file.readlines()
                         FILES_WITH_ISSUES[file_path] = lines
                 except FileNotFoundError:
-                    print(f"Error: The file '{file_path}' was not found.")
+                    print(f"Error: The file '{prefix}/{file_path}' was not found.")
 
             modified_content = FILES_WITH_ISSUES[file_path][
                 file_line_start - 1 : file_line_end - 1
diff --git a/src/static_analysis_cpp.py b/src/static_analysis_cpp.py
index ff39a6a..ca23f9a 100644
--- a/src/static_analysis_cpp.py
+++ b/src/static_analysis_cpp.py
@@ -64,7 +64,7 @@ def create_comment_for_output(
                 )
                 was_note = is_note
                 new_line = utils.generate_output(
-                    is_note, file_path, file_line_start, file_line_end, description
+                    is_note, file_path, file_line_start, file_line_end, description, prefix
                 )
 
                 if utils.check_for_char_limit(new_line):

From 7af4f7e9dc1fc31b59e9f55a5c616544b1810d2a Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 14:55:12 +0100
Subject: [PATCH 8/9] [#126]: Fix pylint warning

---
 src/sa_utils.py               | 3 ++-
 src/static_analysis_cpp.py    | 2 +-
 src/static_analysis_python.py | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/sa_utils.py b/src/sa_utils.py
index 075f03e..251da29 100644
--- a/src/sa_utils.py
+++ b/src/sa_utils.py
@@ -318,7 +318,7 @@ def create_or_edit_comment(comment_body):
         pull_request.create_issue_comment(body=comment_body)
 
 
-def generate_output(is_note, file_path, file_line_start, file_line_end, description, prefix=""):
+def generate_output(is_note, prefix_and_file_path, file_line_start, file_line_end, description):
     """
     Generate a formatted output string based on the details of a code issue.
 
@@ -344,6 +344,7 @@ def generate_output(is_note, file_path, file_line_start, file_line_end, descript
     """
 
     if not is_note:
+        prefix, file_path = prefix_and_file_path
         if TARGET_REPO_NAME != REPO_NAME:
             if file_path not in FILES_WITH_ISSUES:
                 try:
diff --git a/src/static_analysis_cpp.py b/src/static_analysis_cpp.py
index ca23f9a..0a0b301 100644
--- a/src/static_analysis_cpp.py
+++ b/src/static_analysis_cpp.py
@@ -64,7 +64,7 @@ def create_comment_for_output(
                 )
                 was_note = is_note
                 new_line = utils.generate_output(
-                    is_note, file_path, file_line_start, file_line_end, description, prefix
+                    is_note, (prefix, file_path), file_line_start, file_line_end, description
                 )
 
                 if utils.check_for_char_limit(new_line):
diff --git a/src/static_analysis_python.py b/src/static_analysis_python.py
index b5fce05..0a420b9 100644
--- a/src/static_analysis_python.py
+++ b/src/static_analysis_python.py
@@ -104,7 +104,7 @@ def create_comment_for_output(tool_output, files_changed_in_pr, output_to_consol
             )
 
             new_line = utils.generate_output(
-                False, file_path, file_line_start, file_line_end, description
+                False, ("", file_path), file_line_start, file_line_end, description
             )
 
             if utils.check_for_char_limit(new_line):

From 6379f8a1638df7bfae57feef9998cefa7cb12ba2 Mon Sep 17 00:00:00 2001
From: JacobDomagala <domagala.jacob@gmail.com>
Date: Wed, 19 Feb 2025 15:17:49 +0100
Subject: [PATCH 9/9] [#126]: Run black

---
 .github/workflows/linter.yml      | 2 --
 .github/workflows/shellcheck.yml  | 2 +-
 .github/workflows/test_action.yml | 1 -
 .github/workflows/unit_tests.yml  | 2 --
 src/sa_utils.py                   | 4 +++-
 src/static_analysis_cpp.py        | 6 +++++-
 6 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml
index fc0c240..0469509 100644
--- a/.github/workflows/linter.yml
+++ b/.github/workflows/linter.yml
@@ -35,5 +35,3 @@ jobs:
           extra-mypy-options: "--ignore-missing-imports --show-error-codes"
           extra-flake8-options: "--max-line-length=120 --ignore=E203,E402"
           extra-pycodestyle-options: "--max-line-length=120 --ignore=E203,E402"
-
-
diff --git a/.github/workflows/shellcheck.yml b/.github/workflows/shellcheck.yml
index 4d3ffd0..5699a54 100644
--- a/.github/workflows/shellcheck.yml
+++ b/.github/workflows/shellcheck.yml
@@ -15,4 +15,4 @@ jobs:
       - name: Run ShellCheck
         uses: ludeeus/action-shellcheck@master
         with:
-          ignore_names: llvm.sh # External file
\ No newline at end of file
+          ignore_names: llvm.sh # External file
diff --git a/.github/workflows/test_action.yml b/.github/workflows/test_action.yml
index c29f311..3af048c 100644
--- a/.github/workflows/test_action.yml
+++ b/.github/workflows/test_action.yml
@@ -74,4 +74,3 @@ jobs:
 
             ***
             ### [Result for pull_request_target (non CMake)](https://github.com/JacobDomagala/TestRepo/pull/7#issuecomment-1404101648)
-
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index 44bab2d..74957e3 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -23,5 +23,3 @@ jobs:
       - name: Test with pytest
         run: |
           pytest
-
-
diff --git a/src/sa_utils.py b/src/sa_utils.py
index 251da29..e6b376d 100644
--- a/src/sa_utils.py
+++ b/src/sa_utils.py
@@ -318,7 +318,9 @@ def create_or_edit_comment(comment_body):
         pull_request.create_issue_comment(body=comment_body)
 
 
-def generate_output(is_note, prefix_and_file_path, file_line_start, file_line_end, description):
+def generate_output(
+    is_note, prefix_and_file_path, file_line_start, file_line_end, description
+):
     """
     Generate a formatted output string based on the details of a code issue.
 
diff --git a/src/static_analysis_cpp.py b/src/static_analysis_cpp.py
index 0a0b301..ff8fa5b 100644
--- a/src/static_analysis_cpp.py
+++ b/src/static_analysis_cpp.py
@@ -64,7 +64,11 @@ def create_comment_for_output(
                 )
                 was_note = is_note
                 new_line = utils.generate_output(
-                    is_note, (prefix, file_path), file_line_start, file_line_end, description
+                    is_note,
+                    (prefix, file_path),
+                    file_line_start,
+                    file_line_end,
+                    description,
                 )
 
                 if utils.check_for_char_limit(new_line):