[med-svn] [Git][med-team/sourmash][master] 4 commits: Added patch to remove timeout for two tests that were too slow on riscv64.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / sourmash


Commits:
2cc8b1a3 by Michael R. Crusoe at 2025-01-20T10:46:53+01:00
Added patch to remove timeout for two tests that were too slow on riscv64.

- - - - -
df4e3296 by Michael R. Crusoe at 2025-01-20T10:48:30+01:00
d/rules: delete ".gitignore" files from the binary packages

- - - - -
15f1102d by Michael R. Crusoe at 2025-01-20T11:34:56+01:00
Build and install the manual page for sourmash, using sphinx.

- - - - -
53bb82e6 by Michael R. Crusoe at 2025-01-20T12:05:47+01:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/control
- + debian/manpages
- debian/patches/series
- + debian/patches/tests-no-timeout
- debian/rules
- + debian/sourmash.lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+sourmash (4.8.14-2) unstable; urgency=medium
+
+  * Added patch to remove timeout for two tests that were too slow on
+    riscv64.
+  * d/rules: delete ".gitignore" files from the binary packages
+  * Build and install the manual page for sourmash, using sphinx.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 20 Jan 2025 11:50:45 +0100
+
 sourmash (4.8.14-1) unstable; urgency=medium
 
   * Initial release. (Closes: #919681)


=====================================
debian/control
=====================================
@@ -9,6 +9,12 @@ Build-Depends: debhelper-compat (= 13),
                cargo,
                dh-cargo,
                dh-sequence-python3,
+               dh-sequence-sphinxdoc <!nodoc>,
+               python3-nbsphinx <!nodoc>,
+               python3-ipython <!nodoc>,
+               python3-myst-parser <!nodoc>,
+               python3-sphinx-design <!nodoc>,
+               pandoc <!nodoc>,
                librust-az-dev,
                librust-byteorder-dev,
                librust-counter-dev,


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+./build/man/sourmash.1


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 skip_from-finch_feature
 soften-deps
+tests-no-timeout


=====================================
debian/patches/tests-no-timeout
=====================================
@@ -0,0 +1,31 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Remove timeout on two tests that are too slow on RISCV64
+Forwarded: not-needed
+
+Example error: "Data generation is extremely slow: Only produced 6 valid examples in 1.41 seconds"
+--- sourmash.orig/tests/test__minhash_hypothesis.py
++++ sourmash/tests/test__minhash_hypothesis.py
+@@ -1,6 +1,6 @@
+ import pytest
+ 
+-from hypothesis import given, example
++from hypothesis import given, example, settings, HealthCheck
+ import hypothesis.strategies as st
+ 
+ from sourmash import MinHash
+@@ -12,6 +12,7 @@
+     st.lists(st.integers(min_value=0, max_value=2**64 - 1), min_size=10, max_size=1000),
+     st.integers(min_value=10, max_value=1000),
+ )
++ at settings(suppress_health_check=[HealthCheck.too_slow])
+ @example([1, 2], [3, 4], 2)
+ def test_set_abundance_num_hypothesis(hashes, abundances, sketch_size):
+     a = MinHash(sketch_size, 10, track_abundance=True)
+@@ -32,6 +33,7 @@
+     st.lists(st.integers(min_value=0, max_value=2**64 - 1), min_size=10, max_size=1000),
+     st.integers(min_value=1000, max_value=10000),
+ )
++ at settings(suppress_health_check=[HealthCheck.too_slow])
+ @example([0], [0], 1000)
+ def test_set_abundance_scaled_hypothesis(hashes, abundances, scaled):
+     a = MinHash(0, 10, track_abundance=True, scaled=scaled)


=====================================
debian/rules
=====================================
@@ -22,6 +22,9 @@ export PYBUILD_TEST_ARGS=-k 'not (test_sqlite_lca_db_create_readonly or test_com
 %:
 	dh $@ --buildsystem=pybuild
 
+execute_after_dh_auto_build:
+	PYTHONPATH=$(shell pybuild --pyver $$(py3versions -dv) --print build_dir | awk "-F:\ " '{print $$2}') python3 -m sphinx -bman doc build/man
+
 execute_after_dh_auto_clean:
 	rm -rf debian/cargo_registry
 
@@ -33,6 +36,7 @@ execute_before_dh_auto_configure:
 
 execute_after_dh_auto_install:
 	/usr/share/cargo/bin/dh-cargo-built-using sourmash
+	find debian -name .gitignore -delete
 
 override_dh_python3:
 	dh_python3 --no-ext-rename


=====================================
debian/sourmash.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# false positive; examples show tracebacks on purpose
+sourmash: python-traceback-in-manpage [usr/share/man/man1/sourmash.1.gz]



View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/a7523810afe7288bb4a44761a1c6c4edbadefbaf...53bb82e6f38eacdc942b564aa437d111474cd5fa

-- 
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/a7523810afe7288bb4a44761a1c6c4edbadefbaf...53bb82e6f38eacdc942b564aa437d111474cd5fa
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