Scientific Computing

Convert GitHub Gist to GitHub Repository

GitHub Gists give good visibility in search engines and GitHub Search. Gists integrate well using site generators including Hugo. However, GitHub Gists do not support GitHub Actions, Discussions, etc. Gists also do not allow directory structure. Once a Gist reaches a certain feature level or number of files, it may be more useful to share the content as a GitHub Repository.

Simply import the Gist URL to a new Repository. Once satisfied with the imported Repository, the Gist can be deleted, or leave a simple note with Repository URL.

An advantage of importing rather than just copying the files over is the Gist history is preserved as Git commits. If Git was used to manage the Gist, commit messages are preserved. Edits made to the Gist in the web editor don’t have commit messages.

CMake / Meson run check DLL Hell

CMake check_source_runs and Meson compiler.run check if source code compiles, links, and runs correctly. If the checked program uses shared libraries (DLLs) such as libstdc++ on Windows, the program may fail to run due to conflicting DLLs in the Path environment variable. In CMakeConfigureLog.yaml or meson-logs/meson-log.txt, the error code may be 0xc0000139 STATUS_ENTRYPOINT_NOT_FOUND or 3221225785 corresponding to a conflicting DLL. Error code 0xc0000135 STATUS_DLL_NOT_FOUND corresponds to a missing DLL.

The general solution is to avoid unnecessary paths in the Path environment variable. Ensure the compiler and runtime library path are in the Path environment variable before conflicting DLL paths. Check if libstdc++ has multiple entries in the Path, particularly before the compiler and runtime libraries DLL directory. From Terminal:

where.exe libstdc++*.dll

If this prints

INFO: Could not find files for the given pattern(s).

then the libstdc++ DLL is not in the Path, which may result in error code 0xc0000135. If the libstdc++ DLL is in the Path, check if it is in multiple locations. The ideal is to have one path result. At least the desired compiler/library path must be the first result.

For example, Meld is a program that causes DLL conflicts if put on the Path.

Examples of using small PowerShell scripts for GCC and Clang.

Java catch Ctrl+D EOF

REPL and other command line programs can catch Ctrl+D EOF in Java in a platform-independent way. Assuming java.util.Scanner is used to read input from the command line, the code for Ctrl+D EOF detection works by catching EOF by scanner.hasNextLine() method, and also catches Ctrl+D EOF by checking for Unicode character \u0004 in stdin pipe.

import java.util.Scanner;

public class MyClass {
    public static void main(String[] args) {
        Scanner scanner = new Scanner(System.in);

        String argument = "";
        final String prompt = "MyREPL> ";

        System.out.print(prompt);

        while (scanner.hasNextLine()) {
            String input = scanner.nextLine();

            String[] inputArray = input.split(" ");
            String command = inputArray[0];

            if (inputArray.length > 1) {
                argument = inputArray[1];
            } else {
                argument = "";
            }

            if (command.equals("exit") || command.equals("\u0004")) {
                break;
            }

           // main program logic here
            }
    }
}

Windows set WiFi preference order

Windows can control WiFi from the Command Prompt, including WiFi AP preference order. Via the Windows WiFi settings GUI page, the latest added WiFi pushes to the top of the preference stack. This is typically not desired, as when setting up a device in general, one usually connects to the most needed WiFi AP first, and over time adds temporary or less desired WiFi, which Windows keeps at the top of the WiFi preference list. This netsh command prompt procedure allows correcting the Windows WiFi preference order.

Show known WiFi AP

This command lists the known (previously connected) WiFi AP, just like shown in the Windows WiFi settings GUI:

netsh wlan show profiles

The WiFi AP are listed in preference order, from most preferred at the top to least preferred at the bottom. A key piece of information needed from this command is:

Profiles on interface “Wi-Fi”

The name might be “Wi-Fi 2” or other if multiple WiFi adapters are in the PC.

Set WiFi preference order

Using the information from:

netsh wlan show profiles

Put the WiFi APs in the desired priority order like:

netsh wlan set profileorder my_work_wifi Wi-Fi 1

netsh wlan set profileorder my_home_wifi Wi-Fi 2

where the trailing integer is the position in the Windows WiFi preference.

Notes

  • show graphical report of WiFi AP signal

    sudo netsh wlan show wlanreport

  • Python example parsing netsh wlan signal under netsh.py

Matlab arrays to / from Python

Passing N-dimensional arrays to / from Python from Matlab is straightforward with Matlab. Matlab can work with Python classes including list(), dict(), set(), Numpy.ndarray and Xarray.DataArray.

Matlab using Numpy example:

filtered clown image

Filter an image in Python and display in Matlab

Matlab using Xarray: see example glow.m.

function M = xarray2mat(V)
M = double(py.numpy.asfortranarray(V));
end

function I = xarrayind2vector(V,key)
% convert xarray index to Matlab 1-D vector

I = cell2mat(cell(V.indexes{key}.values.tolist));

end

Related:

Build GPSTest app with Android Studio

The GPSTest app is currently (December 2024) not available to most devices on the Google Play store due to the app temporarily being configured for a too-old minimum Android version. This is a security measure enforced by Google Play store to all apps to preserve security of devices. App stores of other operating systems enforce similar restrictions for security.

A workaround until the GPSTest app authors update the app configuration is to build and install the app using Android Studio. Android Studio is free to use and works on Windows, macOS, or Linux equally well. Default settings were used, including setting up an optional emulator. Any reasonably current Android Studio version should be suitable.

This method doesn’t make any changes to the app, but bypasses the Google Play store restrictions by building and installing GPSTest directly from the laptop onto an Android phone. An inconvenience is lack of easy app distribution as every phone needs to one-time plug into a laptop with USB-C to install the GPSTest app. If the phone isn’t detected, try another USB cable as some cables are power-only and don’t have data lines. A message will popup on the phone asking to authorize the laptop to connect in USB Debugging mode. The app can be used indefinitely after the one-time plugin and install.

Download and Build GPSTest

Use Git as in any other project from the Terminal:

git clone https://github.com/barbeau/gpstest

From Android Studio, open that “gpstest” directory from “File > Open” menu.

Try to build the app with the “Build > Make Project” menu – or click the hammer icon in the upper right toolbar of Android Studio. Failures like

Unknown Kotlin JVM target: 21

may result upon building. This stems from the default JVM version in Android Studio. For repeatability, it is typical across code languages and platforms to have a project manifest specifying exact library versions. Android apps manifests are typically “build.gradle” file(s). We don’t edit the manifest at this time, because maybe we’ll break something unexpectedly in the app. Instead, set Android Studio to use JVM 17 as specified by manifest file “GPSTest/build.gradle”:

compileOptions {
   sourceCompatibility JavaVersion.VERSION_17
   targetCompatibility JavaVersion.VERSION_17
}
kotlinOptions {
   jvmTarget = JavaVersion.VERSION_17
}

This is accomplished under Android Studio’s Settings icon (geared wheel) in the upper right corner of the Android Studio main window. Select “Build, Execution, Development > Build Tools > Gradle” in the left hand Settings panel. Under “Gradle Projects” in the right panel, “Gradle JDK” may be set to 21 or so. Select in that menu to “Download JDK and selection “Amazon Coretto 17” or JetBrains 17 or similar. This will take a couple minutes to download and install, then click OK.

Again try to build the app with the “Build > Make Project” menu – or click the hammer icon. There will be a number of warnings, but the app should build successfully. If the optional emulator is present, clicking “Run > Run GPSTest” or clicking the green right arrow in the top Android Studio menu bar will run the app in the emulator.

Connecting Phone

The phone needs to have Developer Mode enabled to upload apps from Android Studio. Under Developer Mode settings, USB Debugging needs to be enabled, at least for the brief time the phone is connected to the laptop to upload the app. If this is a personal phone, consider disabling USB Debugging at all other times to help the security of the phone from physical hacking (someone steals/takes the phone and wants to break into it). In Android Studio Device Manager, clicking “+” will add the phone, or it may appear automatically. Clicking the Android Studio “Run” green arrow will install the app automatically if the physical phone is selected in Android Studio Device Manager. After the app is installed, unplug USB at any time and turn off USB Debugging under the phone’s Developer Mode settings if desired.

GPSTest Caveats

Android 14 and newer will not have the “Share” icon at the top of GPSTest app due to enhanced security in Android 14. The GPSTest maintainers will need to update the GPSTest app to work fully with newer Android versions.

CTest stdin pipe

CTest can be used to run test executables that require input from stdin. This is accomplished by having add_test call a CMake script that uses execute_process to run the test executable with the input piped in from a file. Null stdin is also possible.

Suppose CMakeLists.txt contains:

enable_testing()

add_executable(main main.c)

add_test(NAME stdin_null
  COMMAND ${CMAKE_COMMAND} -Dexe:FILEPATH=$<TARGET_FILE:main> -P ${CMAKE_CURRENT_SOURCE_DIR}/stdin_null.cmake
)

add_test(NAME stdin_pipe
  COMMAND ${CMAKE_COMMAND} -Dexe:FILEPATH=$<TARGET_FILE:main> -P ${CMAKE_CURRENT_SOURCE_DIR}/stdin_pipe.cmake
)

In the non-CMakeLists.txt *.cmake script files, we set a reasonable cmake_minimum_required(VERSION) to avoid issues with defaulting to pre-CMake 3.0 behavior for strings, especially for regular expressions.

The null input to stdin may be required for some executables that may hang forever waiting for stdin.

cmake_minimum_required(VERSION 3.19)

if(UNIX)
  set(devnull INPUT_FILE /dev/null)
elseif(WIN32)
  set(devnull INPUT_FILE NUL)
endif()

execute_process(COMMAND ${exe}
${devnull}
COMMAND_ERROR_IS_FATAL ANY
)

A file (typically a text file) may be piped to stdin to replace interactive input.

cmake_minimum_required(VERSION 3.19)

execute_process(COMMAND ${exe}
INPUT_FILE ${CMAKE_CURRENT_LIST_DIR}/cli_exercise.txt
COMMAND_ERROR_IS_FATAL ANY
OUTPUT_VARIABLE out
ERROR_VARIABLE err
)

if(out MATCHES "TRACE")
  message(FATAL_ERROR "TRACE found in stdout")
endif()

if(err MATCHES "TRACE")
  message(FATAL_ERROR "TRACE found in stderr")
endif()

if(NOT err STREQUAL "")
  message(FATAL_ERROR "stderr output is not empty:
  ${err}")
endif()

message(STATUS "stdout:
${out}")

In this example, the developer wishes to ensure the program ran with no unexpected stdout text and no stderr text at all. This can be helpful to catch debugging output that should not be in the final program output.

Hash of empty file

Checking the hash checksum of downloaded files can help indicate if a file has been tampered with. Hash collisions are possible by intentionally manipulating a harmful file to have the same hash as the expected file. The simpler the hash function, the more likely hash collisions are. Hash collisions have been demonstrated for MD5 and SHA-1.

SHA-256 is a popular SHA-2 hash function for which it takes longer to generate collisons.

Example empty file hash

We use CMake command tool as a platform-independent command line tool to generate and compute hashes. The results are the same regardless of the tool used.

In general, the hash length is fixed for a given hash function. The input file size does not affect the hash length.

First create an empty file:

cmake -E touch empty-file

SHA-512 hash of an empty file:

cmake -E sha512sum empty-file
cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e  empty-file

SHA-256 hash of an empty file:

cmake -E sha256sum empty-file
e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855  empty-file

SHA-1 hash of an empty file:

cmake -E sha1sum empty-file
da39a3ee5e6b4b0d3255bfef95601890afd80709  empty-file

MD5 hash of an empty file:

cmake -E md5sum empty-file
d41d8cd98f00b204e9800998ecf8427e  empty-file