Other: Script improvements

.github/workflows/spell_check.yml

@@ -38,7 +38,7 @@ jobs:
       - name: check macros
         run: |
           for file in $(git diff --name-only --diff-filter=A); do
-            ./scripts/check_macros.sh "$file" &>> check_macros.txt
+            ./scripts/internal/check_macros.sh "$file" &>> check_macros.txt
           done
       - name: Archive script output
         if: failure()

.github/workflows/test_valgrind.yml

@@ -122,4 +122,4 @@ jobs:
     # Execute script that runs a Valgrind check for all test binaries.
     # We use 4 parallel processes to run the binaries in parallel with MPI.
     - name: Valgrind check
-      run: cd scripts && bash ./check_all_test_binaries_valgrind.sh --ntasks=4
+      run: cd scripts && bash ./check_all_test_binaries_valgrind.sh ../build/test/ --ntasks=4

.typos.toml

@@ -3,4 +3,4 @@ eles = "eles"
 packageid = "packageid"
 
 [files]
-extend-exclude = ["scripts/t8indent.sh", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake", "src/t8_misc/t8_with_macro_error.h", "doc/Doxyfile.in"]
+extend-exclude = ["scripts/indent.sh", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake", "src/t8_misc/t8_with_macro_error.h", "doc/Doxyfile.in"]

pull_request_template.md

@@ -25,7 +25,7 @@ If the Pull request introduces code that is not covered by the github action (fo
   - [ ] Should this use case be added to the github action?
   - [ ] If not, does the specific use case compile and all tests pass (check manually).
 #### Scripts and Wiki
-- [ ] If a new directory with source files is added, it must be covered by the `script/find_all_source_files.scp` to check the indentation of these files.
+- [ ] If a new directory with source files is added, it must be covered by the `scripts/internal/find_all_source_files.sh` to check the indentation of these files.
 - [ ] If this PR introduces a new feature, it must be covered in an example or tutorial and a Wiki article.
 #### License
 - [ ] The author added a BSD statement to `doc/` (or already has one).

scripts/README.md

@@ -6,26 +6,21 @@ This folder contains several scripts that are useful for t8code users and develo
 
 The purpose of the indentation scripts is to help t8code developers to indent their code according to the t8code [indentation guidelines](https://github.com/DLR-AMR/t8code/wiki/Coding-Guideline#indentation). Please read these guidelines before using these scripts.
 
-#### t8indent.sh
+#### indent.sh
 
 Apply this script to a `.c`, `.cxx`, `.h` or `.hxx` file to indent it according to the guidelines.
 You can also provide a list of files and all will get indented.
 
 This script uses the `clang-format` program with t8code specific settings.
-Sometimes `t8indent.sh` does produce undesired results. Therefore, after indenting use `git add -p` or similar to check all changes before committing. You can protect code lines from being changed by the script by enclosing them in `/* clang-format off */` and `/* clang-format on */` comments.
+Sometimes `indent.sh` does produce undesired results. Therefore, after indenting use `git add -p` or similar to check all changes before committing. You can protect code lines from being changed by the script by enclosing them in `/* clang-format off */` and `/* clang-format on */` comments.
 
+#### internal/indent_ignore
 
-#### t8indent_ignore.sh
-
-A list of files that will be ignored by `t8indent.sh`.
-
-#### pre-commit
-
-This script should be copied to your `.git/hooks` folder. `git` then automatically checks the indentation of committed files and prevents you from committing wrongly indented files. See [Git indentation workflow](https://github.com/DLR-AMR/t8code/wiki/Coding-Guideline#git-indentation-workflow).
+A list of files that will be ignored by `indent.sh`.
 
 #### check_if_file_indented.sh
 
-Check for a single source file whether it is indented according to `t8indent.sh`.
+Check for a single source file whether it is indented according to `indent.sh`.
 
 #### check_if_all_files_indented.sh
 
@@ -35,30 +30,23 @@ Check whether all t8code source files are properly indented.
 
 This script indents all t8code source files at once. This script should only be used by the main developers of t8code. Handle with care.
 
-#### find_all_source_files.sh
+## Software development
+
+#### pre-commit
 
-List all source files of t8code in the `src/`, `example/` and `test/` subfolders.
+This script should be copied to your `.git/hooks` folder. `git` then automatically checks the indentation of committed files and prevents you from committing wrongly indented files. See [Git indentation workflow](https://github.com/DLR-AMR/t8code/wiki/Coding-Guideline#git-indentation-workflow).
 
 #### check_valgrind.sh
 
 This script runs Valgrind on a binary path provided as a parameter with specified memory leak detection flags. The Valgrind output is parsed. Using `--supp=[FILE]`, you can provide a path to a suppression file that is used by Valgrind to suppress certain errors (e.g. [valgrind_suppressions_file](valgrind_suppressions_file.supp)). With `--ntasks=[NUMBER]`, you can provide the number of processes to use with mpi (default is 1).
 
-#### find_all_test_binary_paths.sh
-
-This file lists all paths to test binaries that exist in the build/test directory.
-The paths are relative paths assuming an execution from the test/ folder in the build directory.
-
 #### check_all_test_binaries_valgrind.sh
 
-This script performs a valgrind check on each test binary found by [find_all_test_binary_paths.sh](find_all_test_binary_paths.sh).
+This script performs a valgrind check on each test binary found by [find_all_test_binary_paths.sh](internal/find_all_test_binary_paths.sh).
 The valgrind check is done by [check_valgrind.sh](check_valgrind.sh). It is assumed that the build folder ../build/test/ with the correct test binaries exists. With `--ntasks=[NUMBER]`, you can provide the number of processes to use with mpi for parallel tests (default is 1).
 
 ## Others
 
-#### su2_mesh_to_gmsh.py
-
-Used to convert coarse meshes from an su2 format into msh format.
-
 #### create_todo_list.sh
 
 Parses through the code and collects comments containing the `TODO` keyword.

scripts/check_all_test_binaries_valgrind.sh

@@ -4,7 +4,7 @@
 #  t8code is a C library to manage a collection (a forest) of multiple
 #  connected adaptive space-trees of general element classes in parallel.
 #
-#  Copyright (C) 2025 the developers
+#  Copyright (C) 2026 the developers
 #
 #  t8code is free software; you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
@@ -23,16 +23,34 @@
 #
 # This script performs a valgrind check on each test binary given by find_all_test_binary_paths.sh.
 # The valgrind check is done by the check_valgrind.sh script.
-# The script returns 1 if an error is found and 0 otherwise. 
-# This script must be executed from the scripts/ folder.
-# It is assumed that the build folder ../build/test/ with the correct test binaries exists.
+# The script returns 1 if an error is found and 0 otherwise.
+# You need to provide the path to the test binaries. So the test folder inside the build directory.
 # With "--ntasks=[NUMBER]", you can provide the number of processes to use with MPI for parallel tests (default is 1).
 #
 
 USAGE="\nUSAGE: This script executes valgrind in parallel on each test binary available. Use the syntax \n
-$0 --ntasks=[NUM_TASKS]\n 
+$0 [TEST_BINARY_PATH] --ntasks=[NUM_TASKS]\n
 Providing the number of parallel processes to use with MPI for parallel tests is optional.\n"
 
+# Check directory exists
+if [ -z "$1" ]; then
+  echo "ERROR: Need to provide a directory as first argument."
+  echo -e "$USAGE"
+  exit 1
+fi
+
+# Check if it is a directory
+if [ -d "$1" ]; then
+  TEST_BINARY_PATH="$1"
+else
+  echo "ERROR: Directory does not exist: $1"
+  echo -e "$USAGE"
+  exit 1
+fi
+
+#convert to abspath
+TEST_BINARY_ABSPATH=$(realpath $TEST_BINARY_PATH)
+
 # Check if a number of processes is provided. If not, set to 1.
 num_procs=1
 for arg in "$@"; do
@@ -61,20 +79,22 @@ if [ `basename $PWD` != scripts ]; then
 fi
 
 # Find all test binary paths.
-test_bin_paths=`bash ./find_all_test_binary_paths.sh`
-num_paths=$(echo $test_bin_paths | wc -w)
+test_bin_paths=$(bash ./internal/find_all_test_binary_paths.sh "$TEST_BINARY_ABSPATH")
+status=$?
 
-# This is necessary because some tests use test files specified by relative paths. 
-# These tests only work when run from the build/test/ directory. 
-if [ -d ../build/test ]; then
-  # The directory stack is automatically reset on script exit.
-  pushd ../build/test/ > /dev/null
-else
-  echo "ERROR: Couldn't find a the directory ../build/test/."
-  echo -e "$USAGE"
-  exit 1
+if [ $status -ne 0 ]; then
+  echo "$test_bin_paths"
+  echo "Failed to collect test binaries."
+  exit $status
 fi
 
+num_paths=$(echo $test_bin_paths | wc -w)
+
+# This is necessary because some tests use test files specified by relative paths.
+# These tests only work when run from the test directory.
+# The directory stack is automatically reset on script exit.
+pushd $TEST_BINARY_ABSPATH > /dev/null
+
 status=0
 counter=0
 valgrind_suppressions_file=../../scripts/valgrind_suppressions_file.supp

scripts/check_if_all_files_indented.sh

@@ -44,7 +44,7 @@ fi
 
 # Find all files with the appropriate suffix.
 # Excluding the sc/ and p4est/ subfolders.
-files=`./find_all_source_files.sh`
+files=`./internal/find_all_source_files.sh`
 
 notallindented=0
 for file in $files

scripts/check_if_file_indented.sh

@@ -21,14 +21,14 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
 #
-# This script checks if a given file is correctly indented according to the t8indent.sh script.
-# 
+# This script checks if a given file is correctly indented according to the indent.sh script.
+#
 
 GIT_REPO_PATH=$(git rev-parse --show-toplevel)
 
-INDENT_SCRIPT=${GIT_REPO_PATH}/scripts/t8indent.sh
+INDENT_SCRIPT=${GIT_REPO_PATH}/scripts/indent.sh
 
-usage="USAGE:$0 [FILE_TO_CHECK]\n\nWill check if [FILE_TO_CHECK] is correctly indentend according to the script t8indent.sh."
+usage="USAGE:$0 [FILE_TO_CHECK]\n\nWill check if [FILE_TO_CHECK] is correctly indentend according to the script indent.sh."
 
 # Check if first argument given
 if [ ${1-x} = x ]

scripts/check_valgrind.sh

@@ -21,7 +21,7 @@
 #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
 #
-# This script runs Valgrind on an input binary paths with specified memory leak detection flags. 
+# This script runs Valgrind on an input binary paths with specified memory leak detection flags.
 # The Valgrind output is parsed. If any errors are found, they are printed and the script exits with a status of 1.
 # If errors are found, the Valgrind output is kept in the file valgrind-output.log for further inspection.
 # Using "--supp=[FILE]", you can provide a path to a suppression file that is used by Valgrind to suppress certain errors.
@@ -32,7 +32,7 @@ $0 [FILE] --supp=[SUPPRESSION_FILE] --ntasks=[NUM_TASKS]\n
 to run valgrind on FILE. Optionally you can provide a suppression file and the number of parallel processes to use with MPI.\n"
 
 # Check that an argument is given and that the argument is a file.
-if [ ${1-x} = x ]; then
+if [ -z "$1" ]; then
   echo "ERROR: Need to provide a file as first argument."
   echo -e "$USAGE"
   exit 1

scripts/configure_for_rtd.sh

@@ -20,6 +20,8 @@
 #  along with t8code; if not, write to the Free Software Foundation, Inc.,
 #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
+pushd "$(git rev-parse --show-toplevel)" > /dev/null
+
 git submodule init
 git submodule update
 

scripts/find_disabled_tests.sh

@@ -1,25 +1,24 @@
 #!/bin/bash
 
-
-#This file is part of t8code.
-#t8code is a C library to manage a collection (a forest) of multiple
-#connected adaptive space-trees of general element classes in parallel.
-
-#Copyright (C) 2024 the developers
-
-#t8code is free software; you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation; either version 2 of the License, or
-#(at your option) any later version.
-
-#t8code is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#GNU General Public License for more details.
-
-#You should have received a copy of the GNU General Public License
-#along with t8code; if not, write to the Free Software Foundation, Inc.,
-#51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#  This file is part of t8code.
+#  t8code is a C library to manage a collection (a forest) of multiple
+#  connected adaptive space-trees of general element classes in parallel.
+#
+#  Copyright (C) 2024 the developers
+#
+#  t8code is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  t8code is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with t8code; if not, write to the Free Software Foundation, Inc.,
+#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
 
 

scripts/t8indent.sh → scripts/indent.sh

@@ -66,12 +66,12 @@ fi
 #
 #  Parsing of input files and throwing out files to be ignored
 #
-# Read all lines from the IGNORE_FILE 
+# Read all lines from the IGNORE_FILE
 # that are not empty and are not comments (i.e. start with '#').
 # Determine base directory of git repo
 GIT_REPO_PATH=$(git rev-parse --show-toplevel)
 
-IGNORE_FILE=${GIT_REPO_PATH}/scripts/t8indent_ignore.sh
+IGNORE_FILE=${GIT_REPO_PATH}/scripts/internal/indent_ignore
 files_to_ignore=()
 while read line; do
     if [[ ${line:0:1} != "#" ]] && [[ $line != "" ]]
@@ -112,7 +112,7 @@ do
     do
       echo Checking "$arg" against "${GIT_REPO_PATH}/$ignore_file"
     if [[ "$arg" -ef "${GIT_REPO_PATH}/$ignore_file" ]]
-    then 
+    then
       # arg matches and will be ignored
       echo The file \"$arg\" will be ignored by indentation as specified in \"$IGNORE_FILE\".
       ignore_arg=1
@@ -136,7 +136,7 @@ then
 else
   $FORMAT $FORMAT_OPTIONS ${newargs[@]}
   status=$?
-fi  
+fi
 
 # If the file content was not changed, the return
 # value determines whether or not the file was

scripts/indent_all_files.sh

@@ -43,13 +43,13 @@ fi
 
 # Find all files with the appropriate suffix.
 # Excluding the sc/ and p4est/ subfolders.
-files=`./find_all_source_files.sh`
+files=`./internal/find_all_source_files.sh`
 
 notallindented=0
 
-INDENT=./t8indent.sh
+INDENT=./indent.sh
 
-echo This script will change all source files found in 
+echo This script will change all source files found in
 echo	$PWD/../src/
 echo	$PWD/../example/
 echo	$PWD/../test/
@@ -72,14 +72,14 @@ then
     then
       $INDENT $file
       status=$?
-      if test $status -ne 0 
+      if test $status -ne 0
       then
         echo "File $file is not indented."
         notallindented=1
       fi
     fi
   done
-  
+
   if test $notallindented -eq 0
   then
     echo All files are indented.

scripts/check_macros.sh → scripts/internal/check_macros.sh

@@ -35,19 +35,19 @@ then
   exit 0
 fi
 
-# 
-# This script searches for lines containing a macro definition in the style of '#ifdef T8_ENABLE_' 
+#
+# This script searches for lines containing a macro definition in the style of '#ifdef T8_ENABLE_'
 # in the specified file and processes each matching line.
-# It uses 'grep' to find all occurrences of '#ifdef T8_ENABLE_' in the file located 
-# at the path stored in the variable 'file_path'. The '-n' option with 'grep' 
+# It uses 'grep' to find all occurrences of '#ifdef T8_ENABLE_' in the file located
+# at the path stored in the variable 'file_path'. The '-n' option with 'grep'
 # ensures that the line numbers of the matching lines are included in the output.
-# The output of 'grep' is then piped into a 'while' loop, which reads each line 
+# The output of 'grep' is then piped into a 'while' loop, which reads each line
 # and splits it into the line number and the line content using ':' as the delimiter.
 # Variables:
 # - file_path: The path to the file to be searched.
 # - line_number: The line number where the macro definition is found.
 # - line: The content of the line where the macro definition is found.
-# 
+#
 
 found_macros=FALSE