examples/clustering/bubbles_validation.py | 2 1 + 1 - 0 !
examples/clustering/cluster_visualization.py | 4 2 + 2 - 0 !
examples/clustering/clustering_tree.py | 16 8 + 8 - 0 !
examples/evol/1_freeratio.py | 22 11 + 11 - 0 !
examples/evol/2_sites_model.py | 8 4 + 4 - 0 !
examples/evol/3_branchsite_test.py | 10 5 + 5 - 0 !
examples/evol/4_branch_models.py | 22 11 + 11 - 0 !
examples/evol/5_branchsite_cladetest.py | 6 3 + 3 - 0 !
examples/evol/measuring_evolution_trees.py | 108 54 + 54 - 0 !
examples/evol/test_protamine.py | 14 7 + 7 - 0 !
examples/general/add_features.py | 16 8 + 8 - 0 !
examples/general/byoperand_search.py | 8 4 + 4 - 0 !
examples/general/copy_and_paste_trees.py | 8 4 + 4 - 0 !
examples/general/create_trees_from_scratch.py | 2 1 + 1 - 0 !
examples/general/custom_search.py | 8 4 + 4 - 0 !
examples/general/custom_tree_traversing.py | 2 1 + 1 - 0 !
examples/general/get_common_ancestor.py | 18 9 + 9 - 0 !
examples/general/get_distances_between_nodes.py | 18 9 + 9 - 0 !
examples/general/get_midpoint_outgroup.py | 4 2 + 2 - 0 !
examples/general/getting_leaves.py | 10 5 + 5 - 0 !
examples/general/iterators.py | 8 4 + 4 - 0 !
examples/general/label_nodes.py | 8 4 + 4 - 0 !
examples/general/nhx_format.py | 28 14 + 14 - 0 !
examples/general/prune_tree.py | 8 4 + 4 - 0 !
examples/general/remove_and_delete_nodes.py | 12 6 + 6 - 0 !
examples/general/rooting_subtrees.py | 8 4 + 4 - 0 !
examples/general/rooting_trees.py | 12 6 + 6 - 0 !
examples/general/search_nodes.py | 4 2 + 2 - 0 !
examples/general/tree_basis.py | 16 8 + 8 - 0 !
examples/general/tree_traverse.py | 4 2 + 2 - 0 !
examples/general/write_newick.py | 2 1 + 1 - 0 !
examples/nexml/nexml_annotated_trees.py | 10 5 + 5 - 0 !
examples/nexml/nexml_parser.py | 10 5 + 5 - 0 !
examples/phylogenies/dating_evolutionary_events.py | 14 7 + 7 - 0 !
examples/phylogenies/link_sequences_to_phylogenies.py | 16 8 + 8 - 0 !
examples/phylogenies/orthology_and_paralogy_prediction.py | 20 10 + 10 - 0 !
examples/phylogenies/species_aware_phylogenies.py | 16 8 + 8 - 0 !
examples/phylogenies/tree_reconciliation.py | 10 5 + 5 - 0 !
examples/phyloxml/phyloxml_from_scratch.py | 2 1 + 1 - 0 !
examples/phyloxml/phyloxml_parser.py | 6 3 + 3 - 0 !
examples/treeview/barchart_and_piechart_faces.py | 2 1 + 1 - 0 !
examples/treeview/floating_piecharts.py | 2 1 + 1 - 0 !
examples/treeview/item_faces.py | 3 1 + 2 - 0 !
examples/treeview/new_seq_face.py | 6 3 + 3 - 0 !
examples/treeview/random_draw.py | 2 1 + 1 - 0 !
45 files changed, 267 insertions(+), 268 deletions(-)

 run 2to3 on examples

ete3/tools/ete_build_lib/apps.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/pmodeltest.py | 1 1 + 0 - 0 !
2 files changed, 2 insertions(+), 1 deletion(-)

 make pmodeltest.py a genuine python3 executable
 This issue has been caught by lintian, as an executable not ELF nor script.

ete3/test/test_arraytable.py | 4 2 + 2 - 0 !
ete3/test/test_evol.py | 28 14 + 14 - 0 !
2 files changed, 16 insertions(+), 16 deletions(-)

 fix deprecated assertions in python 3.12

ete3/webplugin/webapp.py | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 fix test failure due to missing cgi in python 3.13.
 This change fixes the following symptom while runnong the test suite:
 .
         ==================================== ERRORS ====================================
         ___ ERROR collecting .pybuild/cpython3_3.13_ete3/build/ete3/test/test_api.py ___
         ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ete3/build/ete3/test/test_api.py'.
         Hint: make sure your test modules/packages have valid Python names.
         Traceback:
         /usr/lib/python3.13/importlib/__init__.py:88: in import_module
             return _bootstrap._gcd_import(name[level:], package, level)
         ete3/__init__.py:56: in <module>
             from .webplugin.webapp import *
         ete3/webplugin/webapp.py:44: in <module>
             import cgi
         E   ModuleNotFoundError: No module named 'cgi'

ete3/coretype/tree.py | 6 3 + 3 - 0 !
ete3/evol/evoltree.py | 4 2 + 2 - 0 !
ete3/evol/model.py | 4 2 + 2 - 0 !
ete3/evol/parser/codemlparser.py | 26 13 + 13 - 0 !
ete3/parser/newick.py | 8 4 + 4 - 0 !
ete3/parser/phylip.py | 8 4 + 4 - 0 !
ete3/phylo/phylotree.py | 4 2 + 2 - 0 !
ete3/phylomedb/phylomeDB.py | 4 2 + 2 - 0 !
ete3/phylomedb/phylomeDB3.py | 12 6 + 6 - 0 !
ete3/tools/common.py | 2 1 + 1 - 0 !
ete3/tools/ete_build.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/interface.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/sge.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/iqtree.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/phyml.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/prottest.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/prottest2.py | 2 1 + 1 - 0 !
ete3/tools/ete_build_lib/task/raxml.py | 4 2 + 2 - 0 !
ete3/tools/ete_build_lib/utils.py | 8 4 + 4 - 0 !
ete3/tools/ete_build_lib/visualize.py | 4 2 + 2 - 0 !
ete3/tools/ete_build_lib/workflow/genetree.py | 2 1 + 1 - 0 !
ete3/tools/ete_view.py | 8 4 + 4 - 0 !
ete3/tools/utils.py | 2 1 + 1 - 0 !
ete3/treeview/faces.py | 2 1 + 1 - 0 !
ete3/treeview/main.py | 6 3 + 3 - 0 !
ete3/utils.py | 2 1 + 1 - 0 !
26 files changed, 65 insertions(+), 65 deletions(-)

 fix multiple invalid escape sequences.
 This change fixes multiple variations around the following symptom:
 .
         SyntaxWarning: invalid escape sequence