When using Git
pre-commit hooks
with the wide range of files typical of scientific computing, it may occur that the hooks modify files that should be excluded, such as FITS files that have a text header and a binary data part.
Exclude such files by using case-insensitive regex patterns in the .pre-commit-config.yaml file by top level
exclude key, for example to case-insensitively exclude files with the .fit or .fits extension, use:
exclude: (?i)\.fits?$To compile legacy Fortran code, certain compiler flags can be used to enable non-standard Fortran syntax that was common before the Fortran 95 standard became widely adopted. It’s hard to pin an exact year for when developers transitioned to more standard Fortran code, but the mid-2000s is a reasonable estimate for when Fortran codebases started to modernize in significant numbers. Gfortran took over from g77 as the default Fortran compiler circa 2005 and was the first widely used free Fortran compiler capable of the Fortran 95 standard. Here are legacy-enabling flags for currently maintained Fortran compilers.
In addition to the flags below, it may be necessary to provide default real and / or integer precision flags to compile old code that relies on the default precision being different than the modern default of 4 bytes for real and 4 bytes for integer.
-std=legacy enables pre-Fortran 77 arbitrary length arrays, where A(1) was declared instead of A(*) in Fortran 77 or A(:) in modern Fortran.Flang compiler flags have a “-std” option that might be checked to see if the project sets it too restrictively.
The ftn compiler
can disable some checks with flags like -d C
Git uses per-user ~/.gitconfig, per-repository .git/config configuration files, and environment variables to customize Git behavior. The system gitconfig file is not covered here. A common pattern is a developer makes most of their settings in the per-user Git config file, occasionally overriding them in the per-repository config file.
We have several articles on Git configuration, leading to a per-user Git config file with sections like:
pull HTTPS for speed, push SSH for security
[url "ssh://github.com/"]
pushInsteadOf = https://github.com/
[url "ssh://gitlab.com/"]
pushInsteadOf = https://gitlab.com/
[url "ssh://gist.github.com/"]
pushInsteadOf = https://gist.github.com/scivision/
[url "ssh://gitlab.kitware.com/"]
pushInsteadOf = https://gitlab.kitware.com/[diff]
tool = meld
[merge]
tool = meldMaintain linear Git history with fast-forward only by default with
pull.ff only
[pull]
ff = onlyCheck upon “git push” if all Git submodules have first been “git push” before the consuming repository, to avoid broken builds for others with
push.recurseSubmodules check
[push]
recurseSubmodules = checkFor any Git operation (except “git clone”) that changs references to Git submodules commit hashes, automatically update the Git submodules to match the new commit hashes with option
submodules.recurse true
[submodule]
recurse = trueMaintain default linear Git history with “git pull” by default
allowing fast-forward only.
If encountering a Git remote that cannot be fast-forwarded, the user can then either git rebase or git merge to resolve the conflict and / or create a merge commit.
git config --global pull.ff onlyGit services such as GitHub allow enforcing linear history.
Reference: Git: rebase vs. merge
Downloading the latest release of CMake is usually easy. Admin / sudo is not required.
snap install cmakewinget install Kitware.CMakepython -m pip install cmakeFor platforms where CMake binaries aren’t easily available, build CMake using scripts/build_cmake.cmake.
To see the merge requests for a certain release, use a URL like: https://gitlab.kitware.com/cmake/cmake/-/merge_requests?milestone_title=3.32.0&scope=all&state=all
CMake 4.3 additions include:
install(EXPORT) and consumable by other build systems.cmake --version=json-v1 tells details of the libraries vendored into CMake, which is useful for debugging and reporting issues with CMake’s bundled dependencies. This is complementary to cmake -E capabilities which reports specific capabilities of the CMake.CMake 4.2 additions include:
CMake 4.1 additions include:
CMake 4.0 additions include:
LINKER: prefix to abstract options.CMake 3.31 additions include:
cmake_minimum_required() is
< 3.10.file(DOWNLOAD), ExternalProject, FetchContent, and similar.WORKING_DIRECTORY parameter that is essentially necessary to avoid machine-specific paths being embedded in the archive.CMake 3.30 additions include:
CMake 3.29 additions include:
cmake -DCMAKE_INSTALL_PREFIX= option.target_link_options() based on the particular linker.ctest --parallel without a number or 0 will use unbounded
test run parallelism.CMake 3.28 additions include:
changes PATH behavior for
Windows find_{library,path,file}()
to no longer search PATH.
This may break some projects that rely on PATH for finding libraries.
MSYS2-distributed CMake is patched to include PATH like earlier CMake, which can be confusing for CI etc. not using MSYS CMake with that patch.
Windows CI/user may need to specify CMAKE_PREFIX_PATH like
cmake -DCMAKE_PREFIX_PATH=$Env:SYSTEMDRIVE/msys64/ucrt64/lib -B buildSupport for C++20 modules is considerably improved and most users will want at least CMake 3.28 to make C++ modules usable.
Generator expressions $<IF> $<AND> $<OR> now short circuit.
Test properties now have a DIRECTORY parameter, useful for setting test parameters from the project’s top level CMakeLists.txt.
CMake 3.28.4 fixed a long-standing bug in Ninja Fortran targets that use include statements.
CMake 3.27 additions include:
cmake --debugger
is used with an IDE such as
Visual Studio.ℹ️ Note
Fortran + Ninja was broken for OBJECT libraries in CMake 3.27.0..3.27.8 and fixed in 3.27.9.
The Matlab version can be obtained “brute force” by running Matlab, but this can take tens of seconds on a network drive system such as HPC.
matlab -batch "disp(version)"A much faster way to get the Matlab version is to read the VersionInfo.xml file that is included in the Matlab installation directory. This file contains the version information in XML format, as is available at least back to Matlab R2016a.
This
Python script
quickly parses the VersionInfo.xml file to extract the Matlab version information without needing to run Matlab itself.
Environment variables that start with DYLD_ are
restricted by macOS,
and are not passed to child processes by default for security reasons.
A workaround for this is to use a dummy environment variable that does not start with DYLD_, and then use a wrapper script to read that variable and set the DYLD_LIBRARY_PATH environment variable accordingly.
This is necessary because DYLD_LIBRARY_PATH is read at program startup, and setting it within a program will not have any effect on the dynamic linker used by that program.
The wrapper script can be used to set the DYLD_LIBRARY_PATH environment variable before executing the desired program, allowing it to find the necessary libraries without being blocked by macOS security restrictions.
Continuous integration (CI) systems generally rely on an integer return code to detect success (== 0) or failure (!= 0). The error() and assert() functions of Matlab / GNU Octave return non-zero status that works well with CI systems. The Matlab unittest framework is the primary method for testing Matlab code.
Matlab -batch option to run from the command line completely replaces -r and is more robust.
matlab -batch "assertSuccess(runtests)"For pre-buildtool releases of matlab (< R2022b) we use a helper script that invokes runtests with appropriate parameters for the Matlab release used. To test across Matlab releases without a specific CI Matlab version fanout, we can use Python Pytest as in this wrapper script that tests Matlab from R2017a to R2025b and beyond.
There are several ways to reboot a computer from the terminal.
For
Linux
or
macOS
the “reboot” command (or shutdown -r) is commonly used.
For Windows, the PowerShell command
Restart-Computer
is a standard way to reboot the system from Terminal.
Within Windows Subsystem for Linux (WSL), the “reboot” command is only for the particular WSL instance and actually results in a shutdown of the WSL instance, not the entire Windows system. One can verify this by before and after the standard 8 second WSL shutdown time, running in Windows Terminal:
wsl.exe --list --runningThe Anytone AT-5000 radio has three modes: Ham, HF, and CB. 99 memories are available in each of Ham mode and HF mode. 16 memories are available in CB mode (even after moving the jumper that enables Ham and HF modes). MEM channels are not shared between frequency modes, so there are 99 Ham and 99 HF channels and 16 CB MEM channels. The radio cover screws are T9 Torx.
Anytone AT-5000 quirks:
Anytone (Qixiang Electronics) provides a programming cable for the Anytone AT-5000 radio, which connects via the 8P8C modular microphone jack to USB. This is a USB to serial adapter. If the comm port does not appear in the AT-5000 CPS software or in Device Manager under “Ports (COM & LPT)” as “USB-SERIAL CH340 (COMx)”, check Windows Device Manager under “Other devices” for “USB Serial” with a yellow warning icon.
The driver necessary is the GD USB Virtual Comm Port driver, which can be downloaded as part of the Anytone D878 programming software package if not seen as part of the Anytone AT-5000 CPS install package. Don’t install the D878 CPS software, just extract the Zip archive folder titled like “Virtual GD USB Com Drivers (Only If Needed)” and extract the “GD_VirtualComDriver v2.0.2.4944.rar” file to get the driver installer under the “x64” folder. After installing the driver, unplug and replug the programming cable. If it’s still showing a yellow warning icon, right-click on the “USB Serial” entry, select “Update driver”, and choose to browse for drivers on the computer by “let me pick from a list of available drivers on my computer”. Under USB Devices look for “USB-SERIAL CH340” and select it to install the driver. It might be necessary to unplug and replug the programming cable again after installing the driver for it to be recognized properly. There should no longer be a yellow warning icon, and the comm port should appear in the AT-5000 CPS software as “USB-SERIAL CH340 (COMx)” under the “Port” dropdown menu.
These bugs were present in the first release of the AT-5000 CPS software.