Scientific Computing

Matplotlib plots with datetime axes can benefit from rotating axes tick labels or concise tick labels to avoid overlapping text.

Example code used in this post with synthetic data:

from matplotlib.pyplot import Figure
import matplotlib.dates as mdates
from datetime import datetime, timedelta

def datetime_range(start: datetime, end: datetime, step: timedelta) -> list[datetime]:
    """like range() for datetime"""
    return [start + i * step for i in range((end - start) // step)]

t = datetime_range(datetime(2021, 1, 1), datetime(2021, 1, 2), timedelta(minutes=30))
y = range(len(t))

Rotate datetime tick labels

If rotating tick labels, the overall axes typically need to be positioned to allow for the rotated labels, otherwise the tick labels can be cut off the figure edges. The axes position is updated automatically with constrained_layout option of figure().

import matplotlib.pyplot as plt

fg = plt.figure(layout='constrained')
ax = fg.gca()

ax.plot(t, y)
ax.set_xlabel('time')
ax.set_ylabel('y')
ax.tick_params(axis="x", labelrotation=30)  # arbitrary rotation amount

plt.show()

Matplotlib date formatting

Matplotlib datetime axes have numerous formatting options. Here we show the ConciseFormatter, which may avoid the need to rotate tick labels.

import matplotlib.pyplot as plt

fg = plt.figure(layout='constrained')
ax = fg.gca()

ax.plot(t, y)
ax.set_xlabel('time')
ax.set_ylabel('y')

ax.xaxis.set_major_formatter(
    mdates.ConciseDateFormatter(ax.xaxis.get_major_locator()))

plt.show()

If a DLL conflicts with a programs needed DLLs, the program may quit with a specific message, or it may silently exit. The return code may correspond to segfault or other error. To help see if a DLL conflict is occurring, use gdb to run the program. This works even for general programs that weren’t built on the system. We suggest obtaining GDB via MSYS2. If there is a problem with a DLL, GDB will often print the name of the DLL. If the DLL is in an unexpected location, this may indicate a directory that should not be in environment variable Path.

Start GDB Fortran debugger: assuming executable myprog

gdb myprog.exe

Run program from (gdb) prompt:

r

CMake has built-in support for C/C++ static code analysis tools such as CppCheck. Apply CppCheck to CMake targets with CMakeLists.txt by setting CMAKE_CXX_CPPCHECK.

File “cppcheck.supp” contains suppressions for false positives. NOTE: CMake runs cppcheck from an arbitrary directory, so per-file suppressions in the file don’t work as usual. To suppress a warning for a specific file, use the --suppress option to cppcheck in CMakeLists.txt like:

set_property(TARGET MyTarget PROPERTY CXX_CPPCHECK "${CMAKE_CXX_CPPCHECK};--suppress=containerOutOfBounds")

Don’t just blindly modify code based on CppCheck output. Like any code analysis tool there are false positives and false negatives.

A Windows short path can be converted to long path and vice versa using the Windows C library as in this standalone, single source file example.

Users (or developers!) may not realize that the shell expands glob asterisk * unless enclosed in quotes. This can surprise users unfamiliar with this shell behavior, say when using Python argparse with position-based arguments. Say a user has a single file to process in a directory, and doesn’t want to type the long filename, so they type:

python myScript.py ~/data/*.h5 32

Here we assume myScript.py expects two positional arguments, the first being a filename, and the second being an integer. If more than one “*.h5” file subsequently exists and myScript.py is run, the actual input to Python would be like:

python myScript.py ~/data/file1.h5 ~/data/file2.h5 32

Which causes a Python argparse exception.

To see what the shell is going to expand to, with default keybindings and Bash or Zsh at least, press after typing the command these keys:

CMake ExternalProject works for many types of sub-projects across CMake generators. An implementation detail of Ninja is by default ExternalProject doesn’t print progress until each ExternalProject step is finished. For large external projects that take several minutes to download and build, users could be confused thinking CMake has frozen up. To make ExternalProject show live progress as it does with Makefiles generators, add the USES_TERMINAL_* true arguments to ExternalProject_Add.

ExternalProject_Add(
  BigProject
  ...
  USES_TERMINAL_DOWNLOAD true
  USES_TERMINAL_UPDATE true
  USES_TERMINAL_PATCH true
  USES_TERMINAL_CONFIGURE true
  USES_TERMINAL_BUILD true
  USES_TERMINAL_INSTALL true
  USES_TERMINAL_TEST true
)

“USES_TERMINAL* true” forces ExternalProject steps to run sequentially. For large projects this is ordinarily not significant.

CMake doesn’t print the Generator version by default. Sometimes bugs are related to a specific generator version. Reveal CMake generator version like this snippet.

PyTest can work with Matlab Engine if the Matlab Engine is setup. Use a try-catch to ensure any non-functioning Matlab Engine issue is skipped.

import pytest


def test_me():
    try:
        mateng = pytest.importorskip("matlab.engine")
    except Exception:  # can also get RuntimeError, let's just catch all
        pytest.skip("Matlab engine not available")

    eng = mateng.start_matlab("-nojvm")
    # test code

Python subprocess can be used to run a long-running program, capturing the output to a variable and printing to the screen simultaneously. This gives the user the comfort that the program is working OK and gives program status messages without waiting for the program to finish.

This example demonstrates the “tee” subprocess behavior.

Python subprocess can run inline multi-line Python code. This is useful to use Python as a cross-platform demonstration or for production code where a new Python instance is called.

import subprocess
import sys

# the -u is to ensure unbuffered output so that program prints live
cmd = [sys.executable, "-u", "-c", r"""
import sys
import datetime
import time

for _ in range(5):
    print(datetime.datetime.now())
    time.sleep(0.3)
"""]

subprocess.check_call(cmd)