DFSG, Licensing & New Packages Team

Hi,

A couple of issues were found in the review that you might want to fix...

1. [important] [packaging] nodoc doc build is keyed to the wrong switch and is fragile; both nodoc modes can break the build

• Files: debian/rules, debian/control, debian/python-piqtree-doc.docs
• Evidence: execute_after_dh_auto_build: contains ifeq (,$(findstring nodoc, $(DEB_BUILD_OPTIONS))) then python3 -m mkdocs build -v -d html, while Build-Depends gate mkdocs* with <!nodoc> (a build profile); debian/python-piqtree-doc.docs is html. The mkdocs step also sets PYTHONPATH=\dirname $(find .pybuild/ -type d -name "piqtreedist-info" | head -n1)``.
• Problem: Two independent switches control the same resource. With DEB_BUILD_PROFILES=nodoc the mkdocs packages are not installed but debian/rules still runs mkdocs (fails with ModuleNotFoundError); with DEB_BUILD_OPTIONS=nodoc mkdocs is skipped, html/ is never produced, and dh_installdocs then fails because debian/python-piqtree-doc.docs lists a missing html. Policy 4.9.1 makes nodoc an official DEB_BUILD_OPTIONS tag and requires the package to still build. Separately, python3-all-dev builds the extension for every supported CPython; find .pybuild/ ... | head -n1 picks whichever build dir the filesystem presents first, which is not guaranteed to match the interpreter python3 -m mkdocs uses, so from _piqtree import __iqtree_version__ (src/piqtree/init.py) can fail on ABI mismatch and abort the build.
• Fix: Gate the mkdocs step on the nodoc build profile exactly like the Build-Depends (DEB_BUILD_PROFILES), since dh_installdocs already honours the nodoc profile and will then skip the doc install consistently. Point PYTHONPATH at the build dir of the default interpreter (e.g. derive it from python3 -c 'import sys; ...' or a fixed .pybuild/... layout) instead of an unsorted find, and confirm with a clean normal and nodoc build.

2. [minor] [packaging] The pytest suite is never executed during build or autopkgtest

• Files: debian/control, debian/rules
• Evidence: Testsuite: autopkgtest-pkg-pybuild, no debian/tests/control, no PYBUILD_TEST_ARGS/--test-pytest; pybuild's pyproject plugin runs python{version} -m unittest discover -v by default and "No test runner selected ... ignoring test discovery problems" (dhpython/build/base.py:329).
• Problem: The tests are pytest-style (they rely on pytest fixtures in tests/conftest.py, e.g. three_otu, protein_four_otu), so unittest discovery finds no TestCase classes and, because discovery is allowed to find zero tests, the build passes without running anything. python3-pytest/-cov/-mock (and python3-loky) Build-Depends are therefore dead weight and regressions in this scientific package go undetected.
• Fix: Add a debian/tests/control that runs the pytest suite under autopkgtest-pkg-pybuild, or set PYBUILD_TEST_ARGS=--test-pytest and keep the pytest Build-Depends; then verify dh_auto_test actually executes the tests.

Thanks!