serhii.net

github/git-sizer: Compute various size metrics for a Git repository, flagging those that might cause problems (linked by Repository limitations and recommendations)

TL;DR too many files? too large one? too many tags? Find out!

yay took forever to compress pycharm. Like, 5-10 mins at least.

TODO documentation, but if you don’t care about package size but care about speed, this will speed up everything considerably:

PKGEXT='.pkg.tar' yay -S pycharm-professional

• You can share lists in Google Maps, making them editable by everyone with a google account
• Google My Maps is much cooler, with layers etc

Google My Maps

• Really nice tutorial on everything: Visualize your data on a custom map using Google My Maps – Google Earth Outreach
• To share it editable, you share -> Share on Drive
• drag and drop doesn’t always work
• style and colors
  • layer can be styled uniformly (easy)
  • style by data column: per-field, e.g. description, like a groupby
  • individual styles per element
• you can drag and drop items between layers only if they’re styled individually??
• If you style by e.g. description, assign icons/colors, then style individually to move them, then back to style by description, it seems to save the previous settings

So Slicer seems to use both and I need to as well, so I’ll have to learn that sooner or later.

• VTK
  • VTK advertises their Book, available online, which looks like an excellent intro about everything, terminology etc.
    • Chapter 5 - Data Representation — VTK Book
  • wiki: VTK/Tutorials - KitwarePublic but superficially less useful to me?..
• ITK

  • open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis (About | ITK)

  • Python Quick Start - ITK’s documentation

  • Examples — v5.4.0

    • Common especially has interesting things like add noise etc.: Examples — v5.4.0

  • there’s a python package docu:

    • Quick start guide — ITKPythonPackage documentation
• Slicer
  • Slicer examples as usual as always: Script repository — 3D Slicer documentation
    • Segment effects! Script repository — 3D Slicer documentation
      • Fills all internal holes inside segments. For example, fills in empty regions inside vertebral bodies segmented with Grow from seeds with intensity-based masking.
        • shows many other cool useful things as well, incl. adding segments

In pycharm, updated black to use these args: --preview --enable-unstable-feature string_processing $FilePath$

The (future of the) Black code style - Black 24.8.0 documentation has both the preview style and the unstable features one can enable (by passing the flag multilple times).

string_processing breaks long strings into multiple shorter ones, one on each line.

• Useful:

  • Running mypy and managing imports - mypy 1.12.0+dev.ecfab6a02415c46eda5717ec6ee9bfac8115c1e9.dirty documentation evergreen
  • Error codes - mypy 1.12.0+dev.ecfab6a02415c46eda5717ec6ee9bfac8115c1e9.dirty documentation
  • The mypy configuration file - mypy 1.12.0+dev.ecfab6a02415c46eda5717ec6ee9bfac8115c1e9.dirty documentation

• mypy cares about packages, especially __init__.py files — the uppermost dir with such a file will be the root package. See Mapping files to modules - Running mypy and managing imports - mypy 1.12.0+dev.ecfab6a02415c46eda5717ec6ee9bfac8115c1e9.dirty documentation

• This is needed to do per-package configs

[mypy-mycode.package.etc]
disable_error_code = attr-defined, union-attr

• Misc
  • tuple[Path, ...] means tuple containing any number of Path objects

• Problem: the pycharm extension I have crashes in the last version. :(

• Main and best: python - How to run Pylint with PyCharm - Stack Overflow

  • idea of multiple ’external tools’ for diff pylint options: HOWTO - Setup pylint with PyCharm and the PyLint Plugin

My changes:

• arguments: --msg-template="{abspath}:{line:5d},{column:2d}: {C}/{msg} ({symbol})" --output-format=colorized "$FilePath$"
  • note ", otherwise it failed for me, and {C} — for the message class see man page (or below) for list of format string options.
• output filters for on-click: $FILE_PATH$:\s*$LINE$\,\s*$COLUMN$

I had two options as separate tools:

• pylint for a single file
• pylint for the module — same as above, but
  • with $FileParentDir$ at the end.
  • --recursive=y — fails on no __init__.py otherwise

Worked neatly with a .pylintrc file in repo root with e.g.

[tool.pylint.main]

[tool.pylint.basic]
# "too-few-public-methods", disable
min-public-methods=0

function-naming-style="camelCase"
argument-naming-style="camelCase"
method-naming-style="camelCase"
variable-naming-style="camelCase"
attr-naming-style="camelCase"

[tool.pylint."messages control"]
disable = [
    "fixme",  # TODOs
    "import-error",  # runner has them in its environment
    "import-outside-toplevel",  # explicit requirement of XXX to import where used
    "duplicate-code"  # entangling different extensions/modules is not the solution
]

Pylint format string options from man pylint:

path   relative path to the file

abspath
	  absolute path to the file

line   line number

column column number

end_line
	  line number of the end of the node

end_column
	  column number of the end of the node

module module name

obj    object within the module (if any)

msg    text of the message

msg_id the message code (eg. I0011)

symbol symbolic name of the message (eg. locally-disabled)

C      one letter indication of the message category

category
	  fullname of the message category

For example, the former (pre 1.0) default format can be obtained with:

  pylint --msg-template='{msg_id}:{line:3d},{column}: {obj}: {msg}'

Bonus

If I have this post open, I’ll need this one anyway: Messages control - Pylint 4.0.0-dev0 documentation

Also here’s more randomness that I have nowhere else to put:

[tool.pylint.main]
load-plugins=pylint_pydantic

[tool.pylint.basic]
disable=logging-fstring-interpolation

uv run pylint --max-line-length=88 --fail-under=9 (find src -regextype egrep -regex '(.*.py)$') --output-format=colorized --msg=template="{path}:{line}:{category}: {msg_id}: {msg} ({symbol})"

Is ‘file’ a keyword in python? - Stack Overflow

TL;DR python3 doesn’t care about file, regardless of what syntax highlighters think about this.

TL;DR:

• pydocstyle != flake8-docstrings · PyPI!
• read the pypy documentation
• docstring-convention=google in flake8 config file, ignores there as well together with the rest.

pydocstyle / python-flake8-docstrings is a thing. Forgot I had it installed and spent a lot of time trying to understand pycharm’s output

Usage — pydocstyle 0.0.0.dev0 documentation flake8-docstrings · PyPI

To ignore things, you don’t do:

[pydocstyle]
convention = google
ignore = D401

It’s either ignore or convention. Which quietly happened in the background, and I thought it doesn’t read my config file since D401 was still shown.

Correct would be this:

[pydocstyle]
convention = google
add-ignore = D401

EDIT GodDAMN it, pydocsyle parsing a config file doesn’t mean that flake8(-..docstring) will.

Reading the flake8 plugin docs, I should add THIS and to flake8 config file. Ignores also are set up there using the usual way.

docstring-convention=google

And the pydoctest config file search and add-ignore is irrelevant. God lost so much time to this

EDIT: this may be all wrong, in the debugger I can just edit the code and it gets automatically used by slicer — logical, since it’s just a CLI script.

It’s the .xml with the interface that’s problematic and it can’t be reloaded using the method below, or at least I couldn’t.

A scriptedcli module imported to Slicer doesn’t show for me the usual “reload” buttons as seen in scripted modules in dev. mode. To develop, I need my changes I need to reload it w/o restarting 3dslicer.

Based on this more complete example¹ linked in the script repository²

>>> mpath = "/full/path/to/the/my_module.py"
>>> factoryManager = slicer.app.moduleManager().factoryManager()
>>> factoryManager.registerModule(qt.QFileInfo(mpath))
>>> factoryManager.loadModules(["my_module"])
True

BONUS:

• To debug such a module using pycharm, adding the pydev lines inside it works (and official slicer debug extension doesn’t):

import pydevd_pycharm
pydevd_pycharm.settrace('localhost', port=5678, stdoutToServer=True, stderrToServer=True)