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<title>Take-Home Messages from Adding Code Quality Measures to GRASS GIS</title>
<meta name="description" content="Take-Home Messages from Adding Code Quality Measures to GRASS GIS - slides for FOSS4G 2022, August 25">
<meta name="author" content="Vaclav Petras">
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<!--
The message is not surprising: You should quality check your code, too, even if you are writing a small script for your own needs!
However, maybe you wondered if all the warning messages are relevant to you or got discouraged after getting a flood of messages
from tools like Pylint. Perhaps you were even annoyed by it. This talk will help you get motivated and get started
and how to automate that with continuous integration tools such as GitHub Actions.
In this talk, I will share my experience with adding various code and non-code checks to GRASS GIS which is primarily
written in C, C++, and Python. Checking a mixed code base with over 30 years of development is not easy, but not impossible.
The talk will cover code quality measures in GRASS GIS such as tests, Pylint, Black, GCC, CodeQL, and Super-Linter
and how this compares to my experience with new and small organizational repositories.
-->
<section>
<h1>Take-Home Messages from Adding Code Quality Measures to GRASS GIS</h1>
<p style="margin-top: 0.5em">
<a href="http://wenzeslaus.github.io/" style="font-weight: bold">
Vaclav (Vashek) Petras
</a>
</p>
<p class="title-foot">
<a href="http://geospatial.ncsu.edu/geoforall/" title="NCSU GeoForAll Lab">NCSU GeoForAll Lab</a>
at the
<a href="http://geospatial.ncsu.edu/" title="NCSU Center for Geospatial Analytics">Center for Geospatial Analytics</a>
<br>
<a href="http://www.ncsu.edu/" title="North Carolina State University">North Carolina State University</a>
</p>
<img src="img/grass_gis.svg" class="stretch" alt="GRASS GIS logo">
<p><small>FOSS4G Firenze, August 25, 2022</small></p>
<p>
<a href="https://wenzeslaus.github.io/code-quality-measures-foss4g-2022/">wenzeslaus.github.io/code-quality-measures-foss4g-2022</a>
</section>
<section class="textimg">
<h2>Vaclav (Vashek) Petras</h2>
<div>
Geospatial Research Software Engineer at North Carolina State University
<p>
<img src="img/ncsu.svg" alt="North Carolina State University">
<img src="img/ncsu_cga.svg" alt="Center for Geospatial Analytics at NC State">
</p>
<p><small>
Research software engineering as a service, Tangible Landscape support, open source development, skill-transfer at
<a href="https://cnr.ncsu.edu/geospatial/engage/service-center/">geospatial.ncsu.edu</a>
</small></p>
</div>
<img src="img/cli_tangible.png">
</section>
<section>
<h2>Credit to the Community</h2>
<p>
Large contributions by:
Nicklas Larsson, Anna Petrasova, Carmen Tawalika, Loïc Bartoletti, Vaclav Petras
</p>
<img src="img/osgeo_codesprint_2018.jpg" class="stretch">
</section>
<section>
<h2>General Features</h2>
<ul>
<li>
Command line tools:
<b>500+</b> <a href="https://grass.osgeo.org/grass82/manuals/full_index.html">in core</a>,
<b>400+</b> <a href="https://grass.osgeo.org/grass82/manuals/addons/">addons</a>
<!-- (C, C++, Python) -->
</li>
<li>Dynamic libraries (C, C++): <b>50+</b></li>
<li>Python (sub-)packages (<em> grass.* </em>): <b>10+</b></li>
<li>Interfaces (native): graphical, command line, Python, C</li>
<li>Innovation with Stability & All-in-one Software Suite
<small>mission: <em>Bringing advanced geospatial technologies to the world</em></small>
</ul>
<img src="img/github_languages_combined.png" class="stretch">
</section>
<section>
<h2>Development Centered Around GitHub</h2>
<ul>
<li>Git</li>
<li>PRs</li>
<li>Issues</li>
<li>
GitHub Actions <small>(A lot of free CI time since 2018.)</small>
</li>
</ul>
<br>
<img src="img/laptops.jpg" class="stretch">
</section>
<section>
<h2>Python Tools Used in GRASS GIS</h2>
<ul>
<li>Python code formatted by Black.</li>
<li>Checked against Flake8.</li>
<li>Some code checked with Pylint.</li>
</ul>
<img src="img/code_in_vscodium.png" class="stretch">
</section>
<section>
<h2>C and C++ Tools Used in GRASS GIS</h2>
<ul>
<li>GCC, Clang <small>(locally)</small>, Coverity Scan <small>(mostly in the past)</small></li>
<li>Many GCC and Clang warnings fixed <small>for 8.0 and 8.2</small>.</li>
<li>Compiler warning compliance not yet enforced.</li>
<li>
GCC runs in CI with GNU C 99-17 and C++ 11-17.
<small>Checks mostly C++ language variations.</small>
</li>
</ul>
<img src="img/code_in_qtcreator.png" class="stretch">
</section>
<section>
<h2>General Tools Used in GRASS GIS</h2>
<ul>
<li>CodeQL checks for Python, C, and C++ enabled.</li>
<li>
Super-Linter checks for JSON, Perl, Powershell, XML, and YAML.
<small>Wanted: Bash, CSS, Docker, JavaScript, Markdown, HTML, MegaLinter</small>
</li>
<li>
Spellcheck scripts are in the <code>utils</code> directory <small>(to be used locally)</small>.
<small>Wanted: CSpell (possibly through MegaLinter)</small>
</li>
</ul>
<img src="img/markdown_in_gedit.png" class="stretch">
</section>
<section>
<h2>Statistics for GRASS GIS</h2>
<table>
<thead>
<tr>
<th></th>
<th>7.8.0</th>
<th>main branch</th>
</tr>
</thead>
<tbody>
<tr>
<td>PEP 8 formatting</td>
<td>25518</td>
<td>0*</td>
</tr>
<tr>
<td>Flake8</td>
<td>10590</td>
<td>3018**</td>
</tr>
<tr>
<td>GCC -Wall -Wextra</td>
<td>1200</td>
<td>959***</td>
</tr>
</tbody>
</table>
<small>
<p>*Assuming Black compliance equals PEP 8 compliance.</p>
<p>** Flake8 issues remaining: comments, start imports, unused variables, invalid escape sequences.</p>
<p>*** GCC critical issues fixed: dangling-else, discarded-qualifiers, format, logical-op, parentheses, pointers, restrict, tautological-compare, uninitialized.</p>
</small>
<!--
Flake8 now 3018, before 10590, 36108 including formatting
Flake8 now: comments, start imports, unused, invalid escape sequence
GCC -Wall -Wextra
present: unused, sign-compare, shadow, implicit-fallthrough, uninitialized, builtin-declaration-mismatch, type-limits
fixed: dangling-else, discarded-qualifiers, format, logical-op, parentheses, pointers, restrict, tautological-compare, uninitialized
-->
<img src="img/grass_logo_development.png" alt="GRASS GIS logo" class="stretch">
</section>
<section>
<h2>Work In Progress in GRASS GIS</h2>
<ul>
<li>
Pylint
<ul>
<li>
Runs for:
<ul>
<li>grass.jupyter & grass.benchmark</li>
<li>parts of gui/wxpython</li>
<li>all other files except gunittest's testsuite directories</li>
</ul>
</li>
<li>Different configuration for each group</li>
</ul>
</li>
<li>
CodeQL
<ul>
<li>
C and C++: 217 issues
<ul>
<li>Some are false positives for security, but show real issues.</li>
<li>Hard to communicate with contributors, although present in forks.</li>
<li>Cppcheck may work well as an alternative which can run locally.</li>
</ul>
</li>
<li>
Python: 2 issues
<ul>
<li>Bandit may be a better fit for Python and may find more, but will require a lot of configuration.</li>
</ul>
</li>
</ul>
</li>
</ul>
</section>
<section>
<h2>Two Linting Tool Examples</h2>
</section>
<section>
<h2>Python: Black</h2>
<ul>
<li>Unified Python formatting</li>
<li>Simplest to configure, apply, enforce</li>
<li>PEP 8 formatting compliance</li>
<li>Developed with "<code>git diff</code>" in mind</li>
</ul>
<p>
Apply formatting to all code:
<pre><code data-trim class="no-highlight">
black .
</code></pre>
Check in CI:
<pre><code data-trim class="no-highlight">
black --check .
</code></pre>
</section>
<section>
<h2>C & C++: valgrind</h2>
<ul>
<li>Memcheck is the default tool</li>
<li>Check memory usage of a program</li>
<li>Detects segmentation faults, leaked memory, …</li>
<li>Runs the program</li>
</ul>
<p>
In a GRASS session:
<pre><code data-trim class="no-highlight">
valgrind --leak-check=yes r.stats.quantile base=zipcodes cover=elevation quantiles=3 -p
valgrind --track-origins=yes --redzone-size=2048 d.legend soil_loss
</code></pre>
Using <code>--exec</code>:
<pre><code data-trim class="no-highlight">
grass --tmp-mapset ~/data/nc_spm/ --exec valgrind r.stats.quantile base=zipcodes cover=elevation quantiles=3 -p
</code></pre>
</section>
<section>
<h2>Benefits</h2>
</section>
<section>
<h2>Automated Formatting Is Easier</h2>
<ul>
<li>
Manual formatting according to a standard is hard or impossible,
while automatic formatting is easy.
<ul>
<!--<li>Using a command, editor configuration, GitHub Action, …</li>-->
<li>But: Should really be done using the tool.</li>
<!--<li>But: Auto-formatting in PRs confuses contributors</li>-->
</ul>
</li>
<li>
No need to discuss style with every change.
<ul>
<li>...or at least formatting is a separate discussion.</li>
<!--<li>…after the configuration has been created</li>-->
<!--<li>Separates the formatting discussion from specific code contributions</li>-->
</ul>
</li>
</ul>
<br>
<img src="img/prague_isprs_sprint_cafe_discussion.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Another endless discussion about code formatting style</small>
</section>
<section>
<h2>Code Checks Ensure Consistent Quality</h2>
<ul>
<li>
Common code quality level, defined, enforced.
<ul>
<li>Simple rule: <em>If the tools flags it, it needs to be fixed.</em></li>
</ul>
</li>
<li>
No need to check basic coding issues in PR reviews.
<ul>
<li>Reviewers focus on functionality and project-specific issues.</li>
<li>Reviews are hard and cost time, make them simpler!</li>
</ul>
</li>
</ul>
<img src="img/sprint_prague_2019.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Czechs happy after reviewing their code</small>
</section>
<section>
<h2>Checks Run On All Code</h2>
<ul>
<li>Manual testing is always incomplete.</li>
<li>Tests need to be written for specific parts of code.</li>
<li>
Linting has 100% coverage.
<ul>
<li>if configured that way</li>
<li>often with default settings</li>
<li>includes old and forgotten helper scripts</li>
</ul>
</li>
</ul>
<br>
<img src="img/sprint_boston.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Czechs looking into their code <small>(photo credit: Jody Garnett)</small></small>
</section>
<section>
<h2>Even Unrelated Warnings Expose Bugs</h2>
Code:
<pre><code data-trim>
gs.fatal(_("File does not exist: {name}".format(name=filename)))
</code></pre>
Pylint reports:
<pre><code data-trim class="no-highlight">
Formatting a regular string which could be a f-string (consider-using-f-string)
</code></pre>
<p>
Analysis:
<ul>
<li>
Looks like useless warning about not using the latest f-string syntax.
</li>
<li>
Draws attention to a line where a translate function
named <code>_</code> (underscore) is used.
</li>
<li>
The <em>format</em> function is called on the string,
but it should be called on the result of the translation function.
</li>
</ul>
</p>
Fixed code:
<pre><code data-trim class="python language-python">
gs.fatal(_("File does not exist: {name}").format(name=filename))
</code></pre>
</section>
<section>
<h2>Introducing Linters to a Project</h2>
</section>
<section>
<h2>Start Early</h2>
<p>
It is much easier start right at the beginning, than later on.
</p>
<p>
Even for small projects!
</p>
<p><small>It was hard to get started in GRASS GIS, but it is hard even for projects which are couple years old.</small></p>
<p style="font-size: 500%;">Now!</p>
<p>… but better late than never and certainly possible.</p>
<aside class="notes">
Why they just didn't use GitHub Actions from the beginning? …or something like that?
Initial release of CVS 1990, of Subversion (SVN) 2000, of Git 2005, of GitHub 2008, of GitHub Actions 2018 of GRASS GIS 1983.
</aside>
</section>
<section>
<h2>Enforce the Standards in CI</h2>
<ul>
<li>Don't rely on contributors running the checks locally.</li>
<li>With many checks, you can't even ask for that.</li>
<li>But: Have a way to run the checks locally.</li>
</ul>
<br>
<img src="img/prague_isprs_sprint_box.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Coding in a protective box</small>
</section>
<section>
<h2>Consider Warnings To Be Errors</h2>
<ul>
<li>Bad practice warning is useless if it is not enforced.</li>
<li>Some tools warn, but don't report that as a failure.</li>
<!--<li>Plain warnings are for good for transitional period.</li>-->
</ul>
<p><small>
Example for GCC and Clang:
</small></p>
<pre><code data-trim class="no-highlight">
gcc -Wall -Werror ...
</code></pre>
<img src="img/prague_isprs_sprint_cafe.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Minimize errors from spilled beer. You have been warned.</small>
</section>
<section>
<h2>Tips and Tricks</h2>
</section>
<section>
<h2>Be Specific in Excluding and Ignoring</h2>
Exclude only specific files or specific checks for specific files.
<p><small>
Flake8 can ignore warnings per file or directory:
</small></p>
<pre><code data-trim class="no-highlight">
per-file-ignores =
lib/init/grass.py: E501, E722, F821, F841, W605
gui/wxpython/vnet/*: F841, E501
</code></pre>
<p><small>
Warnings can be easily enabled again later from a single place.
</small></p>
<img src="img/meetup_fishbowl.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Be transparent in what is ignored</small>
</section>
<section>
<h2>Minimize Where Warning is Ignored</h2>
Disable only a specific warning for a specific directory, file, or line.
<p>
Yes — only one line:
<pre><code data-trim class="python language-python">
apple._refresh_core() # pylint: disable=protected-access
</code></pre>
No — everything after the line:
<pre><code data-trim class="python language-python">
# pylint: disable=protected-access
apple._refresh_core()
</code></pre>
Also: Line ignores and in-file ignores are best for ignores which are there to stay, i.e., the code just has to be that way or the warning does not apply
(e.g., access to private or protected methods in tests).
</section>
<section>
<h2>Refine Ignores</h2>
Continue improving your configuration and make it specific to your project.
<p>
Code:
<pre><code data-trim class="python language-python">
gs.fatal(_("File does not exist: {name}").format(name=filename))
</code></pre>
Original error from Pylint:
<pre><code data-trim class="no-highlight">
Undefined variable '_' (undefined-variable)
</code></pre>
Quick fix for Pylint by disabling the reported message:
<pre><code data-trim class="no-highlight">
disable=undefined-variable
</code></pre>
Full fix for Pylint by telling it about our code:
<pre><code data-trim class="no-highlight">
additional-builtins=_
</code></pre>
</section>
<section>
<h2>Explain Why You Ignore Warnings</h2>
<p>
For permanent ignores, include explanation.
</p>
<p>
<small>
Example: Pylint disable in a theoretical GUI application:
</small>
<pre><code data-trim class="python language-python">
# Always show an error message window even when the code is broken.
# This avoids tracebacks appearing without context.
except Exception as error: # pylint: disable=broad-except
show_error_window(error)
</code></pre>
<img src="img/prague_isprs_sprint_ctu_box_closeup.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Developers thinking hard what the code means</small>
<aside class="notes">
For all ignores in files and others which are meant to be permanent,
include explanation for why it is that way.
<p>
Later on, it will be clear, if the warning should be enabled or not.
</aside>
</section>
<section>
<h2>Contribute Time</h2>
<ul>
<li>
Fix the code.
<ul>
<li>Great learning experience: small and independent issues.</li>
<!-- with both general and GRASS-specific take-home messages-->
<li>
Submit a good PR:
<ul>
<li>Separate unrelated fixes into multiple PRs for easier review.</li>
<!--
<li>Separate fixes into PRs for easier review.</li>
<li>Group fixes into PRs (by error id or component).</li>--> <!--to avoid many similar PRs-->
<!--<li>Don't assume all errors just need to be ignored (leave it as is if needed).</li>-->
<li>Remove ignores from configuration.</li>
</ul>
</li>
<li>Join <em>Hour with the developer</em> at the Community Sprint.</li>
</ul>
</li>
<li>
Do another task to free someone's time for coding.
</li>
</ul>
<br>
<img src="img/sprint_boston_2017_tshirts.jpg" class="stretch">
<br>
<small style="font-size: 50%;">Feeling great after contributing to GRASS GIS</small>
</section>
<section>
<h2>Contribute Money</h2>
<ul>
<li>
Pay for fixing the code.
<ul>
<li><a href="https://opencollective.com/grass">opencollective.com/grass</a> → GRASS GIS Mini Grants, …</li>
<li>Pay a developer or company (we are here, talk to us).</li>
<li>Ask your employer to donate your or your colleague's time.</li>
</ul>
</li>
</ul>
<p style="font-size: 500%;">$</p>
</section>
<section>
<img src="img/grass_gis.svg" alt="GRASS GIS logo" class="stretch">
<p>
<a href="https://github.com/OSGeo/grass/"><small>Contribute:</small> github.com/OSGeo/grass</a>
</p>
<p>
<small>Get support from NC State University:</small> vpetras@ncsu.edu
</p>
<p>
<a href="https://twitter.com/vaclavpetras/"><small>Twitter:</small> vaclavpetras</a>
<br>
<a href="https://www.linkedin.com/in/vaclav-petras-a24a1b114/"><small>LinkedIn:</small> Vaclav Petras</a>
</p>
<p>
<a href="https://wenzeslaus.github.io/code-quality-measures-foss4g-2022/">wenzeslaus.github.io/code-quality-measures-foss4g-2022</a>
</section>
<section>
<h2>Bonus Content</h2>
</section>
<section>
<h2>Changes in Mindset</h2>
</section>
<section>
<h2>If It Ain't Broke, Don't Fix It, Or?</h2>
<p>
Why to Change Code which Works?
</p>
<p>
With languages, dependencies, operating systems changing fasts,
even stable code needs modifications.
So, you may as well update the code to latest standard because:
</p>
<ul>
<li>Non-compliant code broken.</li>
</ul>
<p>
Even if you don't care about best practices:
<p>
<ul>
<li>Hard to maintain code is broken.</li>
<li>Hard to change code is broken.</li>
</ul>
<p>
When you can apply automatic linters, maintaining and changing the code is simpler
because there is more checks in place.
</p>
</section>
<section>
<h2>Correctness Over Consistency</h2>
<p>
Should I changing surrounding code only because it is ugly?
</p>
<p>
Don't add bad code because the surrounding code is bad.
</p>
<p>
Leave the code in a better condition than when you found it.
</p>
</section>
<section>
<h2>Best Practices Change</h2>
Best practices are a moving target.
<ul>
<li>Black formatting may change with new version of Black (each year).</li>
<li>What is best formatting changes as new issues or use cases are discovered.</li>
<li>Formatting may change with new syntax available.</li>
<li>Best practices may change with new libraries, syntax, or security concerns.</li>
</ul>
<p>
So, the code will change (and that's fine).
</p>
</section>
<section>
<h2>Please, test!</h2>
<quote>
<em>The day when all manual testing will be obsolete because of some tool is very far away.</em>
<br>
<div style="text-align: right; padding-top: 1ex;">
— <a href="https://cppcheck.sourceforge.io">Cppcheck documentation</a>
</div>
</quote>
<p>
Linters work together with, not instead of manual testing and written tests.
</p>
</section>
<section>
<h2>More Linting Tools</h2>
</section>
<section>
<h2>Python: Flake8</h2>
<ul>
<li>Checks for errors and best practices in Python code</li>
<li>General PEP 8 compliance</li>
<li>
Combines:
<ul>
<li>PyFlakes (error checker), pycodestyle (formerly pep8), mccabe (complexity checker)</li>
</ul>
</li>
<li>
Some configuration required
<ul>
<li>Conflicts with Black</li>
<li>Special files may need special handling (e.g., <code>__init__.py</code>)</li>
</ul>
</li>
<li>Changes in code likely required</li>
</ul>
<p>
Check all code:
<pre><code data-trim class="no-highlight">
flake8
</code></pre>
</section>
<section>
<h2>Python: pydocstyle</h2>
<ul>
<li>Checks Python docstring conventions</li>
<li>PEP 257 Docstring Conventions (PEP 8 docstring parts)</li>
<li>Missing docstrings for public methods, "Return" versus "Returns", …</li>
</ul>
<p>
Check all code:
<pre><code data-trim class="no-highlight">
pydocstyle
</code></pre>
</section>
<section>
<h2>Python: isort</h2>
<ul>
<li>Sorts imports in a unified, configurable way</li>
<li>Configuration needed for Black compatibility</li>
</ul>
<p>
Apply formatting to all code:
<pre><code data-trim class="no-highlight">
isort .
</code></pre>
Check in CI:
<pre><code data-trim class="no-highlight">
isort --check-only .
</code></pre>
</section>
<section>
<h2>Python: Pylint</h2>
<ul>
<li>Errors, best practices, code smells in Python code</li>
<li>Makes suggestions for changes, refactoring</li>
<li>Complex configuration, runs long time</li>
<li>Imports the code (but does not run it)</li>
<li>Teaches how to write better code</li>
<li>Unlikely you will get it right without running it</li>
</ul>
<p>
General use:
<pre><code data-trim class="no-highlight">
pylint scripts/v.db.univar/v.db.univar.py
</code></pre>
In GRASS GIS with environment variables:
<pre><code data-trim class="no-highlight">
PYTHONPATH=$(grass --config python_path) \
LD_LIBRARY_PATH=$(grass --config path)/lib \
pylint scripts/v.db.univar/v.db.univar.py
</code></pre>
Or using <code>--exec</code>:
<pre><code data-trim class="no-highlight">
grass --tmp-location XY --exec pylint scripts/v.db.univar/v.db.univar.py
</code></pre>
</section>
<section>
<h2>C & C++: GCC, CLang</h2>
<ul>
<li>Errors, warnings, standards</li>
<li>During compilation, just enable additional switches</li>
<li>Steady increase in warnings enabled by Linux distributions</li>
<li>Warnings on one platform may be bugs on another</li>
</ul>