.travis.yml

@@ -2,4 +2,7 @@ language: cpp
 compiler:
   - gcc
   - clang
+before_script:
+  - pip install --upgrade --user pip
+  - pip install --user networkx
 script: make; make dependencies; make test
\ No newline at end of file

README.md

 Ragout
 ======
 
-Version: 2.1.1
+Version: 2.2
 
 
 [![Build Status](https://travis-ci.org/fenderglass/Ragout.svg?branch=master)](https://travis-ci.org/fenderglass/Ragout)
@@ -35,20 +35,21 @@ Manuals
 - [Usage](docs/USAGE.md)
 
 
-Authors
--------
-- Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD)
-- Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences)
-- Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences)
-- Son Pham (UCSD)
+Code contributions
+------------------
+* Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD)
+* Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences)
+* Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences)
+* Son Pham (UCSD)
+* Tatiana Malygina
 
 
 Publications
 ------------
-- Kolmogorov et al., "Chromosome assembly of large and complex genomes using multiple references",
-bioRxiv preprint, 2016
+* Kolmogorov et al., "Chromosome assembly of large and complex genomes using multiple references",
+Genome Research, 2018
 
-- Kolmogorov et al., "Ragout: A reference-assisted assembly tool for bacterial genomes",
+* Kolmogorov et al., "Ragout: A reference-assisted assembly tool for bacterial genomes",
 Bioinformatics, 2014
 
 
@@ -62,19 +63,20 @@ Acknowledgments
 ---------------
 The work was partially supported by VP Foundation.
 
-We would like to thank:
-- Anna Liosnova (benchmarks and useful suggestions)
-- Nikolay Vyahhi (testing and useful suggestions)
-- Aleksey Gurevich (testing)
+We also would like to thank:
+* Anna Liosnova (benchmarks and useful suggestions)
+* Nikolay Vyahhi (testing and useful suggestions)
+* Aleksey Gurevich (testing)
 
 
 Third-party
 -----------
-Ragout package includes some third-patry software (see INSTALL.md for details)
+Ragout is using some third-patry software (see INSTALL.md for details):
 
-* Networkx 1.8 Python library [http://networkx.github.io/]
-* Newick 1.3 [http://www.daimi.au.dk/~mailund/newick.html]
+* Networkx Python library [http://networkx.github.io/]
+* Newick parser by Thomas Mailund [https://www.mailund.dk/]
 * Sibelia [http://github.com/bioinf/Sibelia]
+* HAL Tools [https://github.com/ComparativeGenomicsToolkit/hal]
 
 
 License

bin/ragout

@@ -12,7 +12,6 @@ and invokes Ragout
 import os
 import sys
 
-LIB_DIR = "lib"
 BIN_DIR = "bin"
 
 #Check Python version
@@ -23,8 +22,6 @@ if sys.version_info[:2] != (2, 7):
 
 #Setting executable paths
 ragout_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
-lib_absolute = os.path.join(ragout_root, LIB_DIR)
-sys.path.insert(0, lib_absolute)
 sys.path.insert(0, ragout_root)
 
 bin_absolute = os.path.join(ragout_root, BIN_DIR)

debian/changelog

+ragout (2.2-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Use 2to3 to port to Python3
+    Closes: #938330
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Sep 2019 10:06:47 +0200
+
 ragout (2.1.1+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #925527)

debian/compat

-12

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-dev,
-               python-networkx (>= 2.2)
-Standards-Version: 4.3.0
+               python3-dev,
+               python3-networkx (>= 2.2)
+Standards-Version: 4.4.0
 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/
@@ -15,10 +15,10 @@ Homepage: https://github.com/fenderglass/Ragout/
 Package: ragout
 Architecture: any
 Depends: ${shlibs:Depends},
-         ${python:Depends},
+         ${python3:Depends},
          ${misc:Depends},
          sibelia,
-         python-networkx (>= 2.2)
+         python3-networkx (>= 2.2)
 Description: Reference-Assisted Genome Ordering UTility
  Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
  chromosome-level scaffolding using multiple references. Given initial
@@ -37,7 +37,7 @@ Description: Reference-Assisted Genome Ordering UTility
 Package: ragout-examples
 Architecture: all
 Depends: ${shlibs:Depends},
-         ${python:Depends},
+         ${python3:Depends},
          ${misc:Depends}
 Description: Reference-Assisted Genome Ordering UTility (example data)
  Ragout (Reference-Assisted Genome Ordering UTility) is a tool for

debian/patches/d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch

-From d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0 Mon Sep 17 00:00:00 2001
-From: Tatiana Malygina <merlettaia@gmail.com>
-Date: Mon, 25 Mar 2019 16:09:21 +0300
-Origin: https://github.com/fenderglass/Ragout/pull/41
-Subject: [PATCH] replace edges_iter iterator with edges iterator in networkx
- graphs
-
----
- ragout/breakpoint_graph/breakpoint_graph.py | 2 +-
- ragout/breakpoint_graph/chimera_detector.py | 2 +-
- ragout/breakpoint_graph/inferer.py          | 4 ++--
- ragout/scaffolder/merge_iters.py            | 4 ++--
- scripts/debug-report.py                     | 6 +++---
- 5 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/ragout/breakpoint_graph/breakpoint_graph.py b/ragout/breakpoint_graph/breakpoint_graph.py
-index c9aa6c2..e73afd9 100644
---- a/ragout/breakpoint_graph/breakpoint_graph.py
-+++ b/ragout/breakpoint_graph/breakpoint_graph.py
-@@ -272,7 +272,7 @@ def _output_graph(graph, out_file):
-     """
-     with open(out_file, "w") as fout:
-         fout.write("graph {\n")
--        for v1, v2, data in graph.edges_iter(data=True):
-+        for v1, v2, data in graph.edges(data=True):
-             fout.write("{0} -- {1}".format(v1, v2))
-             if len(data):
-                 extra = list(map(lambda (k, v) : "{0}=\"{1}\"".format(k, v),
-diff --git a/ragout/breakpoint_graph/chimera_detector.py b/ragout/breakpoint_graph/chimera_detector.py
-index d72440f..06b8f08 100644
---- a/ragout/breakpoint_graph/chimera_detector.py
-+++ b/ragout/breakpoint_graph/chimera_detector.py
-@@ -98,7 +98,7 @@ def _get_contig_breaks(self, bp_graph):
-                 logger.debug("Processing component of size {0}"
-                              .format(len(subgr.bp_graph)))
- 
--            for (u, v, data) in subgr.bp_graph.edges_iter(data=True):
-+            for (u, v, data) in subgr.bp_graph.edges(data=True):
-                 if data["genome_id"] != subgr.target:
-                     continue
- 
-diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py
-index a2c8134..7cdc5c3 100644
---- a/ragout/breakpoint_graph/inferer.py
-+++ b/ragout/breakpoint_graph/inferer.py
-@@ -115,7 +115,7 @@ def _trim_known_edges(self, graph):
-         Removes edges with known target adjacencies (red edges from paper)
-         """
-         trimmed_graph = graph.copy()
--        for v1, v2 in graph.edges_iter():
-+        for v1, v2 in graph.edges():
-             if not trimmed_graph.has_node(v1) or not trimmed_graph.has_node(v2):
-                 continue
- 
-@@ -142,7 +142,7 @@ def _min_weight_matching(graph):
-     """
-     Finds a perfect matching with minimum weight
-     """
--    for v1, v2 in graph.edges_iter():
-+    for v1, v2 in graph.edges():
-         graph[v1][v2]["weight"] = -graph[v1][v2]["weight"] #want minimum weght
- 
-     MIN_LOG_SIZE = 20
-diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py
-index fd6c9cd..66be623 100644
---- a/ragout/scaffolder/merge_iters.py
-+++ b/ragout/scaffolder/merge_iters.py
-@@ -179,7 +179,7 @@ def project(self):
- 
-             red_edges = []
-             black_edges = []
--            for (u, v, data) in subgr.edges_iter(data=True):
-+            for (u, v, data) in subgr.edges(data=True):
-                 if data["scf_set"] == "old":
-                     red_edges.append((u, v))
-                 else:
-@@ -201,7 +201,7 @@ def project(self):
- 
-         logger.debug("Made {0} k-breaks".format(num_kbreaks))
-         adjacencies = {}
--        for (u, v, data) in self.bp_graph.edges_iter(data=True):
-+        for (u, v, data) in self.bp_graph.edges(data=True):
-             if data["scf_set"] == "old":
-                 gap, support = 0, []
-                 if not data["infinity"]:
-diff --git a/scripts/debug-report.py b/scripts/debug-report.py
-index 017d3c8..e118f46 100755
---- a/scripts/debug-report.py
-+++ b/scripts/debug-report.py
-@@ -113,11 +113,11 @@ def compose_breakpoint_graph(base_dot, predicted_dot, true_edges):
-     predicted_edges = nx.read_dot(predicted_dot)
-     out_graph = nx.MultiGraph()
- 
--    for v1, v2, data in base_graph.edges_iter(data=True):
-+    for v1, v2, data in base_graph.edges(data=True):
-         color = g2c(data["genome_id"])
-         label = "oo" if data["infinity"] == "True" else ""
-         out_graph.add_edge(v1, v2, color=color, label=label)
--    for v1, v2 in predicted_edges.edges_iter():
-+    for v1, v2 in predicted_edges.edges():
-         out_graph.add_edge(v1, v2, color="red", style="dashed")
-     for (v1, v2, infinite) in true_edges:
-         label = "oo" if infinite else ""
-@@ -140,7 +140,7 @@ def output_graph(graph, output_dir, only_predicted):
- 
-         if only_predicted:
-             to_show = False
--            for v1, v2, data in subgr.edges_iter(data=True):
-+            for v1, v2, data in subgr.edges(data=True):
-                 if data.get("style") == "dashed":
-                     to_show = True
-                     break

debian/patches/e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch

-From e3a06ef1256cf132903bbf19c9d4e11ea846e6df Mon Sep 17 00:00:00 2001
-From: Tatiana Malygina <merlettaia@gmail.com>
-Date: Mon, 25 Mar 2019 16:19:40 +0300
-Origin: https://github.com/fenderglass/Ragout/pull/41
-Subject: [PATCH] fix TypeError: object of type 'dictionary-keyiterator' has no
- len()
-
----
- ragout/scaffolder/merge_iters.py | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py
-index 66be623..3536f5c 100644
---- a/ragout/scaffolder/merge_iters.py
-+++ b/ragout/scaffolder/merge_iters.py
-@@ -174,7 +174,7 @@ def project(self):
-         subgraphs = list(nx.connected_component_subgraphs(self.bp_graph))
-         for subgr in subgraphs:
-             #this is a cycle
--            if any(len(subgr.neighbors(node)) != 2 for node in subgr.nodes()):
-+            if any(len(subgr[node]) != 2 for node in subgr.nodes()):
-                 continue
- 
-             red_edges = []
-@@ -193,6 +193,7 @@ def project(self):
-                 self.bp_graph.remove_edge(u, v)
-                 self.adj_graph.remove_edge(u, v)
-             for u, v in black_edges:
-+                print(self.bp_graph[u][v])
-                 link = self.bp_graph[u][v][0]["link"]
-                 infinity = self.bp_graph[u][v][0]["infinity"]
-                 self.bp_graph.add_edge(u, v, scf_set="old",

debian/patches/f4d4e2223a337abdbc5873fd6560e1494e55342d.patch

-From f4d4e2223a337abdbc5873fd6560e1494e55342d Mon Sep 17 00:00:00 2001
-From: Tatiana Malygina <merlettaia@gmail.com>
-Date: Mon, 25 Mar 2019 17:08:08 +0300
-Origin: https://github.com/fenderglass/Ragout/pull/41
-Subject: [PATCH] fix AttributeError: 'set' object has no attribute 'items'
-
----
- ragout/breakpoint_graph/inferer.py         | 2 +-
- ragout/breakpoint_graph/repeat_resolver.py | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py
-index 7cdc5c3..eb47032 100644
---- a/ragout/breakpoint_graph/inferer.py
-+++ b/ragout/breakpoint_graph/inferer.py
-@@ -151,7 +151,7 @@ def _min_weight_matching(graph):
-                      "size {0}".format(len(graph)))
-     edges = nx.max_weight_matching(graph, maxcardinality=True)
-     unique_edges = set()
--    for v1, v2 in edges.items():
-+    for v1, v2 in edges:
-         if not (v2, v1) in unique_edges:
-             unique_edges.add((v1, v2))
- 
-diff --git a/ragout/breakpoint_graph/repeat_resolver.py b/ragout/breakpoint_graph/repeat_resolver.py
-index b3054e5..a20ea11 100644
---- a/ragout/breakpoint_graph/repeat_resolver.py
-+++ b/ragout/breakpoint_graph/repeat_resolver.py
-@@ -362,7 +362,7 @@ def _profile_similarity(profile, genome_ctx, repeats, same_len):
- def _max_weight_matching(graph):
-     edges = nx.max_weight_matching(graph, maxcardinality=True)
-     unique_edges = set()
--    for v1, v2 in edges.items():
-+    for v1, v2 in edges:
-         if not (v2, v1) in unique_edges:
-             unique_edges.add((v1, v2))
- 

debian/patches/install_newick.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
-Description: Make sure newick is installed as well
- Remark: This needs a hack in debian/rules - no idea how to do this more elegantly
-
---- a/setup.py
-+++ b/setup.py
-@@ -37,7 +37,8 @@ setup(name='ragout',
-       packages=['ragout', 'ragout/assembly_graph', 'ragout/breakpoint_graph',
-                 'ragout/maf2synteny', 'ragout/overlap', 'ragout/parsers',
-                 'ragout/phylogeny', 'ragout/scaffolder', 'ragout/shared',
--                'ragout/synteny_backend'],
-+                'ragout/synteny_backend',
-+                'newick'],
-       package_data={'ragout': ['LICENSE']},
-       scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],
-       cmdclass={'build': MakeBuild}

debian/patches/series

-install_newick.patch
-d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
-e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
-f4d4e2223a337abdbc5873fd6560e1494e55342d.patch
+2to3.patch

debian/rules

@@ -8,15 +8,7 @@ include /usr/share/dpkg/default.mk
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --with python2 --buildsystem=pybuild
-
-override_dh_auto_clean:
-	dh_auto_clean
-	if [ -L newick  ] ; then rm newick ; fi
-
-override_dh_auto_configure:
-	ln -s lib/newick .
-	dh_auto_configure
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_install:
 	dh_install

docs/INSTALL.md

@@ -26,29 +26,44 @@ Runtime Depenencies
 
 * Python 2.7
 * Sibelia [http://github.com/bioinf/Sibelia]
-* HAL Tools [https://github.com/glennhickey/hal] (alternatively to Sibelia)
+* python-networkx >= 2.2
+* HAL Tools (optionally) [https://github.com/ComparativeGenomicsToolkit/hal]
 
 
-Building
---------
+Local installation
+------------------
 
-To build Ragout binaries, type:
+If you don't want to use bioconda release, you can build
+Ragout repository clone and run it locally without installing
+into system. To do this, perform:
 
+    git clone https://github.com/fenderglass/Ragout.git
+	cd Ragout
 	python setup.py build
+	pip install -r requirements.txt --user
+    python scripts/install-sibelia.py
 
-You will also need either Sibelia or HAL Tools installed
+This will also build and install Sibelia and all Python dependencies.
+See below for HAL installation instructions.
 
-To build and install Sibelia, use:
+Once installed, you can invoke Ragout from the cloned directory by using:
 
-        python scripts/install-sibelia.py
+    bin/ragout
 
-If you already have Sibelia installed into your system, it will
-be picked up automatically.
+System installation
+-------------------
 
-Optionally, you may isntall Ragout into your system by typing:
+To integrate Ragout into your system, run:
 
+    git clone https://github.com/fenderglass/Ragout.git
+	cd Ragout
+	python setup.py build
     python setup.py install
 
+This assumes that you already have python-networkx package
+installed into your system (using the respective package manager).
+Sibelia / HAL tools should also be installed / integrated separately.
+
 
 HAL Tools
 ---------
@@ -57,7 +72,7 @@ HAL alignment produced by Progressive Cactus could be used for synteny
 blocks decomposition instead of Sibelia (recommended for large genomes). 
 
 If you want to use HAL alignment as input,
-you need to install HAL Tools package [https://github.com/glennhickey/hal]
+you need to install HAL Tools package [https://github.com/ComparativeGenomicsToolkit/hal]
 as it is described in the manual. Do not forget to properly set PATH and PYTHONPATH
 environment variables.
 
@@ -68,8 +83,8 @@ Troubleshooting
 Q: Many compilation errors, possibly with 
 "unrecognized command line option '-std=c++0x'" message:
 
-A: Probably your compiler is too old and does not support C++0x. Minimum required
-versions of GCC and Clang are given in the beginning of this document.
+A: Probably your compiler is too old and does not support C++0x. Make
+sure you have at least GCC 4.6+ / Clang 3.2+
 
 
 Q: "libstdc++.so.6: version `CXXABI_1.3.5' not found" or similar error when running

ragout/__version__.py

-__version__ = "2.1.1"
+__version__ = "2.2"

ragout/assembly_graph/assembly_refine.py

@@ -53,7 +53,7 @@ def _load_dot(filename):
 
 
 def _check_overaps_number(graph, contigs_fasta):
-    rate = float(len(graph.edges())) / len(contigs_fasta)
+    rate = float(len(graph.edges)) / len(contigs_fasta)
     if rate < config.vals["min_overlap_rate"]:
         logger.warning("Too few overlaps ({0}) between contigs were detected "
                        "-- refine procedure will be useless. Possible reasons:"
@@ -61,7 +61,7 @@ def _check_overaps_number(graph, contigs_fasta):
                        "2. Contigs overlap not on a constant value "
                        "(like k-mer for assemblers which use debruijn graph)\n"
                        "3. Contigs ends are trimmed/postprocessed\n"
-                       .format(len(graph.edges())))
+                       .format(len(graph.edges)))
 
 
 def _insert_from_graph(graph, scaffolds_in, max_path_len, contigs_fasta):

ragout/breakpoint_graph/breakpoint_graph.py

@@ -101,9 +101,9 @@ class BreakpointGraph(object):
         """
         assert len(self.bp_graph) >= 2
         g = nx.Graph()
-        g.add_nodes_from(self.bp_graph.nodes())
+        g.add_nodes_from(self.bp_graph.nodes)
 
-        for node in self.bp_graph.nodes():
+        for node in self.bp_graph.nodes:
             adjacencies = {}
             for neighbor in self.bp_graph.neighbors(node):
                 for edge in self.bp_graph[node][neighbor].values():
@@ -272,7 +272,7 @@ def _output_graph(graph, out_file):
     """
     with open(out_file, "w") as fout:
         fout.write("graph {\n")
-        for v1, v2, data in graph.edges_iter(data=True):
+        for v1, v2, data in graph.edges(data=True):
             fout.write("{0} -- {1}".format(v1, v2))
             if len(data):
                 extra = list(map(lambda (k, v) : "{0}=\"{1}\"".format(k, v),

ragout/breakpoint_graph/chimera_detector.py

@@ -98,7 +98,7 @@ class ChimeraDetector(object):
                 logger.debug("Processing component of size {0}"
                              .format(len(subgr.bp_graph)))
 
-            for (u, v, data) in subgr.bp_graph.edges_iter(data=True):
+            for (u, v, data) in subgr.bp_graph.edges(data=True):
                 if data["genome_id"] != subgr.target:
                     continue
 
@@ -130,7 +130,7 @@ class ChimeraDetector(object):
         """
         assert len(bp_graph) == 4
         red_1, red_2 = red_edge
-        cand_1, cand_2 = tuple(set(bp_graph.nodes()) - set(red_edge))
+        cand_1, cand_2 = tuple(set(bp_graph.nodes) - set(red_edge))
         if abs(cand_1) == abs(cand_2):
             return False
 

ragout/breakpoint_graph/inferer.py

@@ -76,7 +76,7 @@ class AdjacencyInferer(object):
         """
         adjacency = subgraph.to_weighted_graph(self.phylogeny)
         trimmed_graph = self._trim_known_edges(adjacency)
-        unused_nodes = set(trimmed_graph.nodes())
+        unused_nodes = set(trimmed_graph.nodes)
 
         chosen_edges = []
         for trim_subgraph in nx.connected_component_subgraphs(trimmed_graph):
@@ -84,8 +84,8 @@ class AdjacencyInferer(object):
                 continue
 
             if len(trim_subgraph) == 2:
-                chosen_edges.append(tuple(trim_subgraph.nodes()))
-                for n in trim_subgraph.nodes():
+                chosen_edges.append(tuple(trim_subgraph.nodes))
+                for n in trim_subgraph.nodes:
                     unused_nodes.remove(n)
                 continue
 
@@ -115,7 +115,7 @@ class AdjacencyInferer(object):
         Removes edges with known target adjacencies (red edges from paper)
         """
         trimmed_graph = graph.copy()
-        for v1, v2 in graph.edges_iter():
+        for v1, v2 in graph.edges:
             if not trimmed_graph.has_node(v1) or not trimmed_graph.has_node(v2):
                 continue
 
@@ -142,7 +142,7 @@ def _min_weight_matching(graph):
     """
     Finds a perfect matching with minimum weight
     """
-    for v1, v2 in graph.edges_iter():
+    for v1, v2 in graph.edges:
         graph[v1][v2]["weight"] = -graph[v1][v2]["weight"] #want minimum weght
 
     MIN_LOG_SIZE = 20
@@ -151,7 +151,7 @@ def _min_weight_matching(graph):
                      "size {0}".format(len(graph)))
     edges = nx.max_weight_matching(graph, maxcardinality=True)
     unique_edges = set()
-    for v1, v2 in edges.items():
+    for v1, v2 in edges:
         if not (v2, v1) in unique_edges:
             unique_edges.add((v1, v2))
 

ragout/breakpoint_graph/repeat_resolver.py

@@ -362,7 +362,7 @@ def _profile_similarity(profile, genome_ctx, repeats, same_len):
 def _max_weight_matching(graph):
     edges = nx.max_weight_matching(graph, maxcardinality=True)
     unique_edges = set()
-    for v1, v2 in edges.items():
+    for v1, v2 in edges:
         if not (v2, v1) in unique_edges:
             unique_edges.add((v1, v2))