[med-svn] [Git][med-team/gubbins][master] 4 commits: d/control: gubbins depends on python3-pkg-resources.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Feb 28 10:10:04 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / gubbins
Commits:
de391ab4 by Étienne Mollier at 2025-02-28T10:55:12+01:00
d/control: gubbins depends on python3-pkg-resources.
- - - - -
478655e5 by Étienne Mollier at 2025-02-28T10:55:20+01:00
numpy2.patch: new: fix further autopkgtest failure with numpy 2.
Closes: #1098693
- - - - -
3e217dba by Étienne Mollier at 2025-02-28T11:09:16+01:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
f5035c35 by Étienne Mollier at 2025-02-28T11:09:38+01:00
d/changelog: ready for upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/numpy2.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+gubbins (3.4-2) unstable; urgency=medium
+
+ * d/control: gubbins depends on python3-pkg-resources.
+ * numpy2.patch: new: fix further autopkgtest failure with numpy 2.
+ (Closes: #1098693)
+ * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org> Fri, 28 Feb 2025 11:09:34 +0100
+
gubbins (3.4-1) unstable; urgency=medium
* New upstream version 3.4
=====================================
debian/control
=====================================
@@ -22,7 +22,7 @@ Build-Depends: debhelper-compat (= 13),
python3-scipy <!nocheck>,
python3-multiprocess <!nocheck>,
python3-wheel <!nocheck>
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/gubbins
Vcs-Git: https://salsa.debian.org/med-team/gubbins.git
Homepage: https://sanger-pathogens.github.io/gubbins/
@@ -34,6 +34,7 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3,
+ python3-pkg-resources,
raxml
# FIXME: python3-numba is disabled until version 0.59 makes it back to testing.
# Delete also remove-numba-temporarily.patch when the time comes to bring back
=====================================
debian/patches/numpy2.patch
=====================================
@@ -0,0 +1,73 @@
+Description: fix runtime failures with Numpy ≥ 2.
+ This patch fixes the following symptom when running gubbins with Numpy
+ version 2 and more:
+ .
+ Running joint ancestral reconstruction with pyjar
+ Traceback (most recent call last):
+ File "/usr/bin/run_gubbins", line 33, in <module>
+ sys.exit(load_entry_point('gubbins==3.4', 'console_scripts', 'run_gubbins.py')())
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
+ File "/usr/share/gubbins/gubbins/run_gubbins.py", line 166, in main
+ gubbins.common.parse_and_run(parser.parse_args(), parser.description)
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ File "/usr/share/gubbins/gubbins/common.py", line 373, in parse_and_run
+ jar(sequence_names = ordered_sequence_names, # complete polymorphism alignment
+ ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ base_patterns = base_pattern_bases_array, # array of unique base patterns in alignment
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ ...<8 lines>...
+ verbose = input_args.verbose,
+ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+ max_pos = max_pos)
+ ^^^^^^^^^^^^^^^^^^
+ File "/usr/share/gubbins/gubbins/pyjar.py", line 646, in jar
+ node_pij = numpy.full((num_nodes,16), numpy.NINF, dtype=numpy.float32)
+ ^^^^^^^^^^
+ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__
+ raise AttributeError(
+ ...<3 lines>...
+ )
+ AttributeError: `np.NINF` was removed in the NumPy 2.0 release. Use `-np.inf` instead.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/nickjcroucher/gubbins/pull/426
+Last-Update: 2025-02-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- gubbins.orig/python/gubbins/pyjar.py
++++ gubbins/python/gubbins/pyjar.py
+@@ -64,7 +64,7 @@
+ #Calculate Pij from Q matrix and branch length
+ def calculate_pij(branch_length,rate_matrix):
+ if branch_length==0:
+- pij = numpy.full((4,4), numpy.NINF, dtype = numpy.float32)
++ pij = numpy.full((4,4), -numpy.inf, dtype = numpy.float32)
+ numpy.fill_diagonal(pij, 0.0)
+ else:
+ pij = numpy.array(numpy.log(linalg.expm(numpy.multiply(branch_length,rate_matrix))), dtype = numpy.float32) # modified
+@@ -328,7 +328,7 @@
+ Cmat_null = numpy.array([0,1,2,3], dtype = numpy.uint8)
+
+ # Reset matrices
+- Lmat.fill(numpy.NINF)
++ Lmat.fill(-numpy.inf)
+ Cmat[:] = Cmat_null
+
+ # Count unknown bases
+@@ -537,7 +537,7 @@
+
+ # Generate data structures for reconstructions
+ num_nodes = len(tree.nodes())
+- Lmat = numpy.full((num_nodes,4), numpy.NINF, dtype = numpy.float32)
++ Lmat = numpy.full((num_nodes,4), -numpy.inf, dtype = numpy.float32)
+ Cmat = numpy.full((num_nodes,4), [0,1,2,3], dtype = numpy.uint8)
+ reconstructed_base_indices = numpy.full(num_nodes, 8, dtype = numpy.uint8)
+
+@@ -643,7 +643,7 @@
+ child_nodes_array = numpy.empty(num_nodes, dtype=object)
+ leaf_node_list = []
+ node_labels = numpy.empty(num_nodes, dtype=object)
+- node_pij = numpy.full((num_nodes,16), numpy.NINF, dtype=numpy.float32)
++ node_pij = numpy.full((num_nodes,16), -numpy.inf, dtype=numpy.float32)
+ postordered_nodes = numpy.arange(num_nodes, dtype=numpy.int32)
+ seed_node = None
+ seed_node_edge_truncation = True
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ iqtree2.patch
autoupdate_configure.ac.patch
python3-shebang.patch
remove-numba-temporarily.patch
+numpy2.patch
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/ed2d2ea4d007e24f13e667ea8b0b404499bddc95...f5035c35635aa2418d9c759cfbe6f5c10e3d7641
--
View it on GitLab: https://salsa.debian.org/med-team/gubbins/-/compare/ed2d2ea4d007e24f13e667ea8b0b404499bddc95...f5035c35635aa2418d9c759cfbe6f5c10e3d7641
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