Andreas Tille pushed to branch master at Debian Med / ragout
Commits: cb20c16a by Andreas Tille at 2020-03-28T18:04:30+01:00 Sibelia is now available - - - - - 078a6b5d by Andreas Tille at 2020-03-28T18:05:19+01:00 R-U: Trailing whitespace in debian/changelog - - - - - d7a5ce0a by Andreas Tille at 2020-03-28T18:05:19+01:00 routine-update: Add salsa-ci file - - - - - 527677ab by Andreas Tille at 2020-03-28T18:05:19+01:00 routine-update: Rules-Requires-Root: no - - - - - bf122aed by Andreas Tille at 2020-03-28T18:05:23+01:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. - - - - - 9d0343f7 by Andreas Tille at 2020-03-28T22:25:33+01:00 Fix "AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'" which became obvious in test suite - - - - - b56286b5 by Andreas Tille at 2020-03-28T22:29:06+01:00 lib/ragout was moved to ragout/ragout - - - - - 44a117ad by Andreas Tille at 2020-03-28T22:34:39+01:00 networkx code copy is not inluded into upstream source any more - - - - - 6671d05c by Andreas Tille at 2020-03-28T22:48:36+01:00 Upload to unstable - - - - - 9 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/connected_component_subgraphs.patch - debian/patches/series - + debian/salsa-ci.yml - debian/tests/control_needs_sibelia → debian/tests/control - debian/upstream/metadata - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,19 @@ +ragout (2.3-2) unstable; urgency=medium + + * Sibelia is now available + Closes: #953904 + * Remove trailing whitespace in debian/changelog (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. + * Fix "AttributeError: module 'networkx' has no attribute + 'connected_component_subgraphs'" which became obvious in test suite + * d/copyright: lib/ragout was moved to ragout/ragout + * networkx code copy is not inluded into upstream source any more + + -- Andreas Tille <[email protected]> Sat, 28 Mar 2020 22:34:46 +0100 + ragout (2.3-1) unstable; urgency=medium * Test-Depends: sibelia @@ -22,7 +38,7 @@ ragout (2.2+ds-1) unstable; urgency=medium d/ragout.install accordingly * bin/ragout was still about to invoke python2 * maketrans is now a static function of str - * not allowing bin/ragout to change $PATH + * not allowing bin/ragout to change $PATH * demoted sibelia to recommends runtime dependency as there are modules that don't use it. TODO: Find out what happened to ===================================== debian/control ===================================== @@ -12,6 +12,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/ragout Vcs-Git: https://salsa.debian.org/med-team/ragout.git Homepage: https://github.com/fenderglass/Ragout/ +Rules-Requires-Root: no Package: ragout Architecture: any @@ -19,8 +20,7 @@ Depends: ${shlibs:Depends}, ${python3:Depends}, ${misc:Depends}, python3-networkx (>= 2.2) -Recommends: - sibelia +Recommends: sibelia Description: Reference-Assisted Genome Ordering UTility Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial ===================================== debian/copyright ===================================== @@ -1,7 +1,6 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Ragout Source: https://github.com/fenderglass/Ragout/releases -Files-Excluded: lib/networkx Files: * Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and @@ -11,7 +10,7 @@ Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and Benedict Paten and Son Pham License: BSD-3-clause -Files: lib/newick/* +Files: ragout/newick/* Copyright: 2003-2008 Thomas Mailund <[email protected]> License: GPL-2+ This program is free software; you can redistribute it and/or modify ===================================== debian/patches/connected_component_subgraphs.patch ===================================== @@ -0,0 +1,69 @@ +Description: Fix "AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'" which became obvious in test suite +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 28 Mar 2020 18:03:41 +0100 + +--- a/ragout/breakpoint_graph/breakpoint_graph.py ++++ b/ragout/breakpoint_graph/breakpoint_graph.py +@@ -77,7 +77,7 @@ class BreakpointGraph(object): + logger.debug("Built breakpoint graph with %d nodes", len(self.bp_graph)) + + def connected_components(self): +- subgraphs = nx.connected_component_subgraphs(self.bp_graph) ++ subgraphs = list(self.bp_graph.subgraph(c) for c in nx.connected_components(self.bp_graph)) + bp_graphs = [] + for subgr in subgraphs: + bg = BreakpointGraph() +--- a/ragout/breakpoint_graph/inferer.py ++++ b/ragout/breakpoint_graph/inferer.py +@@ -81,7 +81,7 @@ class AdjacencyInferer(object): + unused_nodes = set(trimmed_graph.nodes) + + chosen_edges = [] +- for trim_subgraph in nx.connected_component_subgraphs(trimmed_graph): ++ for trim_subgraph in list(trimmed_graph.subgraph(c) for c in nx.connected_components(trimmed_graph)): + if len(trim_subgraph) < 2: + continue + +--- a/ragout/scaffolder/merge_iters.py ++++ b/ragout/scaffolder/merge_iters.py +@@ -179,7 +179,7 @@ class RearrangementProjector: + def project(self): + #look for valid k-breaks + num_kbreaks = 0 +- subgraphs = list(nx.connected_component_subgraphs(self.bp_graph)) ++ subgraphs = list(self.bp_graph.subgraph(c) for c in nx.connected_components(self.bp_graph)) + for subgr in subgraphs: + #this is a cycle + if any(len(subgr[node]) != 2 for node in subgr.nodes): +@@ -237,9 +237,9 @@ class RearrangementProjector: + new_adj_graph.add_edge(u, v) + + old_sets = [set(g.nodes) for g in +- nx.connected_component_subgraphs(self.adj_graph)] ++ list(self.adj_graph.subgraph(c) for c in nx.connected_components(self.adj_graph))] + new_sets = [set(g.nodes) for g in +- nx.connected_component_subgraphs(new_adj_graph)] ++ list(new_adj_graph.subgraph(c) for c in nx.connected_components(new_adj_graph))] + if len(old_sets) != len(new_sets): + return False + +--- a/scripts/debug-report.py ++++ b/scripts/debug-report.py +@@ -130,7 +130,7 @@ def compose_breakpoint_graph(base_dot, p + + def output_graph(graph, output_dir, only_predicted): + MAX_SIZE = 100 +- subgraphs = nx.connected_component_subgraphs(graph) ++ subgraphs = graph.subgraph(c) for c in nx.connected_components(graph) + for comp_id, subgr in enumerate(subgraphs): + if len(subgr) == 2: + continue +@@ -193,7 +193,7 @@ def add_overlap_edges(graph, overlap_dot + + overlap_graph = nx.read_dot(overlap_dot) + +- subgraphs = nx.connected_component_subgraphs(graph) ++ subgraphs = graph.subgraph(c) for c in nx.connected_components(graph) + for subgr in subgraphs: + for v1, v2 in combinations(subgr.nodes, 2): + v1, v2 = int(v1), int(v2) ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ # adjustSetupParsingBinaries.patch +connected_component_subgraphs.patch ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/tests/control_needs_sibelia → debian/tests/control ===================================== ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Bug-Database: https://github.com/fenderglass/Ragout/issues +Bug-Submit: https://github.com/fenderglass/Ragout/issues/new Reference: - Author: > Mikhail Kolmogorov and Joel Armstrong and Brian J. Raney and Ian Streeter @@ -31,3 +33,5 @@ Registry: Entry: ragout - Name: OMICtools Entry: OMICS_07883 +Repository: https://github.com/fenderglass/Ragout.git +Repository-Browse: https://github.com/fenderglass/Ragout ===================================== debian/watch ===================================== @@ -1,4 +1,3 @@ version=4 -opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \ - https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ +https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/53c2a2b557240870a13fa089da10b2fb8a3581aa...6671d05ca0915a59aa5d4be195f3b6895e7e6fba -- View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/53c2a2b557240870a13fa089da10b2fb8a3581aa...6671d05ca0915a59aa5d4be195f3b6895e7e6fba You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
