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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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