Scientific Computing

Save figure SVG from Matlab or Matplotlib

Matlab or Matplotlib will save infinite resolution vector graphics SVG format, viewable in web browsers. SVG is usable by LaTeX.

  • vector graphics (SVG or EPS) allow nearly infinite zooming without loss of quality–excellent for line plots and contour plots
  • SVG is viewable by any web browser, and is usable from LaTeX
  • EPS is more commonly used in LaTeX
  • PNG is raster graphics, so has finite (blocky) resolution

Here are examples of saving figures to SVG from Matlab and Matplotlib.

Python

To save figure handle fg, simply do fg.savefig('myfig.svg').

from pathlib import Path
from matplotlib.figure imoprt Figure

fn = Path('~/Documents/mycoolfig.svg').expanduser()

data = [1,2,3,4]

fg = Figure(constrained_layout=True)
ax = fg.gca()
ax.plot(data)

fg.savefig(fn, bbox_inches='tight')

Matlab

Matlab figures in general are saved by exportgraphics.

data = [1,2,3,4]

fg = figure();
plot(data)

exportgraphics(fg, 'matfig.svg')

NetCDF4 segfault on file open

NetCDF4 Fortran library may compile successfully and run for simple programs but segfault on programs where HDF5 is linked directly as well as NetCDF4.

A reason one might directly link both HDF5 and NetCDF is a program that need to read / write files in HDF5 as well as NetCDF format. The symptom observe thus far is the program segfault on nf90_open().

The fix is to compile HDF5 and NetCDF for yourself.

GFortran duplicate use of submodule / module

Gfortran 9.3.0 is sensitive to overlapping / duplicated use elements in a module - submodule hierarchy. That is, if a procedure is used in multiple places in the module - submodule hierarchy, only use the procedure once at the highest necessary level of the hierarchy.

This is perhaps best shown by example:

module foo
implicit none (type, external)
contains
subroutine bar()
end subroutine bar
end module foo

module parent
use foo, only : bar
implicit none (type, external)
interface
module subroutine baz
end subroutine baz
end interface
end module parent

submodule (parent) child
use foo, only : bar  !< this is unnecessary and triggers the Gfortran 9.3.0 error
implicit none (type, external)
contains
module procedure baz
end procedure baz
end submodule child

The error message from Gfortran 9.3.0 is like:

$ gfortran -c .\dupe.f90

dupe.f90:17:17:

   17 | submodule (parent) child
      |                 1
   18 | use foo, only : bar
      |                   2

Pytest ignoring Meson subprojects

Meson projects may contain Python code, including Meson subprojects. However, the Meson subproject code may not be relevant to the top-level Meson project Python code. Then, Pytest Python test suites may fail when the subprojects/ directory tree is searched and unwanted tests are run.

Ignore directories with Pytest: while this example is for Meson subprojects, it is obviously applicable to many other Python projects.

Add to file “pyproject.toml” in project top-level directory:

[tool.pytest.ini_options]
norecursedirs = subprojects .* build dist CVS _darcs {arch} *.egg venv

Python paramiko SFTP example

Paramiko Python SSH library provides a convenient SFTPClient that allows easy transfer of files over SSH. A distinction from the command line utility sftp is that “put"ing a file must include the full destination path including filename, to avoid OSError.

This Paramiko example shows copying a file from local computer to remote computer over SSH in Python.

from paramiko import SSHClient

source = "foo.txt"
dest = "~/Documents/foo.txt"

with SSHClient() as ssh:

    ssh.load_system_host_keys()
    ssh.connect("server.invalid")
    with ssh.open_sftp() as sftp:
        sftp.put(source, dest)

Matlab dependency graph

Matlab can generate dependency graphs and export to GraphML files. The GUI dependency analyzer also shows missing variable and function definitions for the whole project in one view. The implicit static analysis of the dependency analyzer seems to be more thorough than the command requiredFilesAndProducts.

Even if you don’t typically use the Matlab “Project” feature, it’s useful for quality assurance to run this tool on Matlab code to find hidden problems that escape the imperfect nature of unit tests. Regardless of coding language, we use a layered approach for code quality assurance including static analysis, unit tests and integration tests.

Silence Pytest DeprecationWarning

Pytest by default: shows DeprecationWarning and PendingDeprecationWarning.

Warning clutter can be filtered by adding to “pyproject.toml” in the top-level project directory:

[tool.pytest.ini_options]
filterwarnings =
  ignore::DeprecationWarning

We might choose to suppress DeprecationWarning in a repo’s test suite because the warnings are coming from modules developed by others (e.g. Numpy or Xarray).

However, don’t be too carte blanche about suppressing DeprecationWarning.

Related: find source of PyTest warning

Python breakpoint() debugging

Python breakpoint() abstracts away pdb.set_trace() and allows use of other debuggers. breakpoint() also works well with Pytest to conditionally break into code.

x=1
y=0

breakpoint()

z = x/y

breakpoint() is immediately clear as to its purpose.

Reference: PEP0553 breakpoint()