From ded833320895b9a1e0d95c8c131a3eabb88735b9 Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Wed, 14 Feb 2024 11:46:41 +0100 Subject: [PATCH 01/19] feat: add prefixattr=... argument to Graph.write_graphml(), fixes #759 --- src/_igraph/graphobject.c | 17 +++++++++++------ tests/test_foreign.py | 1 + 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/src/_igraph/graphobject.c b/src/_igraph/graphobject.c index 4315a6df0..488a55740 100644 --- a/src/_igraph/graphobject.c +++ b/src/_igraph/graphobject.c @@ -9728,18 +9728,19 @@ PyObject *igraphmodule_Graph_write_pajek(igraphmodule_GraphObject * self, PyObject *igraphmodule_Graph_write_graphml(igraphmodule_GraphObject * self, PyObject * args, PyObject * kwds) { - PyObject *fname = NULL; - static char *kwlist[] = { "f", NULL }; + PyObject *fname = NULL, *prefixattr_o = Py_True; + static char *kwlist[] = { "f", "prefixattr", NULL }; igraphmodule_filehandle_t fobj; - if (!PyArg_ParseTupleAndKeywords(args, kwds, "O", kwlist, &fname)) + if (!PyArg_ParseTupleAndKeywords(args, kwds, "O|O", kwlist, &fname, &prefixattr_o)) return NULL; if (igraphmodule_filehandle_init(&fobj, fname, "w")) return NULL; - if (igraph_write_graph_graphml(&self->g, igraphmodule_filehandle_get(&fobj), - /*prefixattr=*/ 1)) { + if (igraph_write_graph_graphml( + &self->g, igraphmodule_filehandle_get(&fobj), PyObject_IsTrue(prefixattr_o) + )) { igraphmodule_handle_igraph_error(); igraphmodule_filehandle_destroy(&fobj); return NULL; @@ -16930,9 +16931,13 @@ struct PyMethodDef igraphmodule_Graph_methods[] = { /* interface to igraph_write_graph_edgelist */ {"write_graphml", (PyCFunction) igraphmodule_Graph_write_graphml, METH_VARARGS | METH_KEYWORDS, - "write_graphml(f)\n--\n\n" + "write_graphml(f, prefixattr=True)\n--\n\n" "Writes the graph to a GraphML file.\n\n" "@param f: the name of the file to be written or a Python file handle\n" + "@param prefixattr: whether attribute names in the written file should be\n" + " prefixed with C{g_}, C{v_} and C{e_} for graph, vertex and edge\n" + " attributes, respectively. This might be needed to ensure the uniqueness\n" + " of attribute identifiers in the written GraphML file.\n" }, /* interface to igraph_write_graph_leda */ {"write_leda", (PyCFunction) igraphmodule_Graph_write_leda, diff --git a/tests/test_foreign.py b/tests/test_foreign.py index 69657062e..72047dc1a 100644 --- a/tests/test_foreign.py +++ b/tests/test_foreign.py @@ -360,6 +360,7 @@ def testGraphML(self): self.assertTrue("name" in g.vertex_attributes()) g.write_graphml(tmpfname) + g.write_graphml(tmpfname, prefixattr=False) def testGraphMLz(self): with temporary_file( From bafd4a651cc08997965adbc201fce9a0a856de9d Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Wed, 14 Feb 2024 11:47:44 +0100 Subject: [PATCH 02/19] chore: updated changelog --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03ca918b0..32d6c5702 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # igraph Python interface changelog +## [master] + +### Added + +- Added a `prefixattr=...` keyword argument to `Graph.write_graphml()` that + allows the user to strip the `g_`, `v_` and `e_` prefixes from GraphML files + written by igraph. + ## [0.11.4] ### Added From 03f9faa15eaa223d8f6f5525e4fb59b0aed5f8a5 Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Wed, 14 Feb 2024 11:52:59 +0100 Subject: [PATCH 03/19] refactor: Graph.are_connected() was renamed to Graph.are_adjacent() --- CHANGELOG.md | 6 ++++++ doc/source/analysis.rst | 2 +- src/_igraph/graphobject.c | 14 +++++++------- src/igraph/__init__.py | 8 ++++++++ tests/test_attributes.py | 2 +- tests/test_structural.py | 2 +- 6 files changed, 24 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 32d6c5702..891995ccd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,12 @@ allows the user to strip the `g_`, `v_` and `e_` prefixes from GraphML files written by igraph. +### Changed + +- `Graph.are_connected()` has now been renamed to `Graph.are_adjacent()`, + following up a similar change in the C core. The old name of the function + is deprecated but will be kept around until at least 0.12.0. + ## [0.11.4] ### Added diff --git a/doc/source/analysis.rst b/doc/source/analysis.rst index 943f719cc..bb911efad 100644 --- a/doc/source/analysis.rst +++ b/doc/source/analysis.rst @@ -63,7 +63,7 @@ To get the vertices at the two ends of an edge, use :attr:`Edge.source` and :att >>> v1, v2 = e.source, e.target Vice versa, to get the edge if from the source and target vertices, you can use :meth:`Graph.get_eid` or, for multiple pairs of source/targets, -:meth:`Graph.get_eids`. The boolean version, asking whether two vertices are directly connected, is :meth:`Graph.are_connected`. +:meth:`Graph.get_eids`. The boolean version, asking whether two vertices are directly connected, is :meth:`Graph.are_adjacent`. To get the edges incident on a vertex, you can use :meth:`Vertex.incident`, :meth:`Vertex.out_edges` and :meth:`Vertex.in_edges`. The three are equivalent on undirected graphs but not directed ones of course:: diff --git a/src/_igraph/graphobject.c b/src/_igraph/graphobject.c index 488a55740..c79b4b479 100644 --- a/src/_igraph/graphobject.c +++ b/src/_igraph/graphobject.c @@ -1445,10 +1445,10 @@ PyObject *igraphmodule_Graph_is_biconnected(igraphmodule_GraphObject *self, PyOb /** \ingroup python_interface_graph * \brief Decides whether there is an edge from a given vertex to an other one. * \return Py_True if the vertices are directly connected, Py_False otherwise - * \sa igraph_are_connected + * \sa igraph_are_adjacent */ -PyObject *igraphmodule_Graph_are_connected(igraphmodule_GraphObject * self, - PyObject * args, PyObject * kwds) +PyObject *igraphmodule_Graph_are_adjacent(igraphmodule_GraphObject * self, + PyObject * args, PyObject * kwds) { static char *kwlist[] = { "v1", "v2", NULL }; PyObject *v1, *v2; @@ -1464,7 +1464,7 @@ PyObject *igraphmodule_Graph_are_connected(igraphmodule_GraphObject * self, if (igraphmodule_PyObject_to_vid(v2, &idx2, &self->g)) return NULL; - if (igraph_are_connected(&self->g, idx1, idx2, &res)) + if (igraph_are_adjacent(&self->g, idx1, idx2, &res)) return igraphmodule_handle_igraph_error(); if (res) @@ -14554,10 +14554,10 @@ struct PyMethodDef igraphmodule_Graph_methods[] = { // STRUCTURAL PROPERTIES OF GRAPHS // ///////////////////////////////////// - // interface to igraph_are_connected - {"are_connected", (PyCFunction) igraphmodule_Graph_are_connected, + // interface to igraph_are_adjacent + {"are_adjacent", (PyCFunction) igraphmodule_Graph_are_adjacent, METH_VARARGS | METH_KEYWORDS, - "are_connected(v1, v2)\n--\n\n" + "are_adjacent(v1, v2)\n--\n\n" "Decides whether two given vertices are directly connected.\n\n" "@param v1: the ID or name of the first vertex\n" "@param v2: the ID or name of the second vertex\n" diff --git a/src/igraph/__init__.py b/src/igraph/__init__.py index c0997aa8c..7f0e328b7 100644 --- a/src/igraph/__init__.py +++ b/src/igraph/__init__.py @@ -948,6 +948,14 @@ def Incidence(cls, *args, **kwds): deprecated("Graph.Incidence() is deprecated; use Graph.Biadjacency() instead") return cls.Biadjacency(*args, **kwds) + def are_connected(self, *args, **kwds): + """Deprecated alias to L{Graph.are_adjacent()}.""" + deprecated( + "Graph.are_connected() is deprecated; use Graph.are_adjacent() " + "instead" + ) + return self.are_adjacent(*args, **kwds) + def get_incidence(self, *args, **kwds): """Deprecated alias to L{Graph.get_biadjacency()}.""" deprecated( diff --git a/tests/test_attributes.py b/tests/test_attributes.py index 4b6683d32..1299cada9 100644 --- a/tests/test_attributes.py +++ b/tests/test_attributes.py @@ -112,7 +112,7 @@ def testVertexNameIndexingBug196(self): g.add_vertices([a, b]) g.add_edges([(a, b)]) self.assertEqual(g.ecount(), 1) - self.assertTrue(g.are_connected(a, b)) + self.assertTrue(g.are_adjacent(a, b)) def testInvalidAttributeNames(self): g = Graph.Famous("bull") diff --git a/tests/test_structural.py b/tests/test_structural.py index 5ad20648c..bfda0f2e5 100644 --- a/tests/test_structural.py +++ b/tests/test_structural.py @@ -994,7 +994,7 @@ def testGetAllSimplePaths(self): self.assertEqual(15, path[-1]) curr = path[0] for next in path[1:]: - self.assertTrue(g.are_connected(curr, next)) + self.assertTrue(g.are_adjacent(curr, next)) curr = next def testPathLengthHist(self): From 055e836ba26569d59227ee3482da79707e94630c Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Mon, 19 Feb 2024 10:33:38 +0000 Subject: [PATCH 04/19] doc: clarify that we use natural logarithms for entropies --- src/igraph/clustering.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/igraph/clustering.py b/src/igraph/clustering.py index b45e6d9ce..b1fca9ab4 100644 --- a/src/igraph/clustering.py +++ b/src/igraph/clustering.py @@ -1459,6 +1459,9 @@ def _ensure_list(obj): def compare_communities(comm1, comm2, method="vi", remove_none=False): """Compares two community structures using various distance measures. + For measures involving entropies (e.g., the variation of information metric), + igraph uses natural logarithms. + B{References} - Meila M: Comparing clusterings by the variation of information. In: From 1741af467f3beb286c1d833046dac699e6855697 Mon Sep 17 00:00:00 2001 From: David R Connell Date: Wed, 6 Mar 2024 17:03:01 -0600 Subject: [PATCH 05/19] Update from deprecated PyCObject to PyCapsule --- src/_igraph/igraphmodule_api.h | 21 ++------------------- 1 file changed, 2 insertions(+), 19 deletions(-) diff --git a/src/_igraph/igraphmodule_api.h b/src/_igraph/igraphmodule_api.h index f7eeb932b..8ab364b50 100644 --- a/src/_igraph/igraphmodule_api.h +++ b/src/_igraph/igraphmodule_api.h @@ -56,25 +56,8 @@ extern "C" { /* Return -1 and set exception on error, 0 on success */ static int import_igraph(void) { - PyObject *c_api_object; - PyObject *module; - - module = PyImport_ImportModule("igraph._igraph"); - if (module == 0) - return -1; - - c_api_object = PyObject_GetAttrString(module, "_C_API"); - if (c_api_object == 0) { - Py_DECREF(module); - return -1; - } - - if (PyCObject_Check(c_api_object)) - PyIGraph_API = (void**)PyCObject_AsVoidPtr(c_api_object); - - Py_DECREF(c_api_object); - Py_DECREF(module); - return 0; + PyIGraph_API = (void **)PyCapsule_Import("igraph._igraph._C_API", 0); + return (PyIGraph_API != NULL) ? 0 : -1; } #endif From 1920c4e590bc186e5b51a2f57a3ffe826c40bbdb Mon Sep 17 00:00:00 2001 From: jpowell11 Date: Wed, 13 Mar 2024 18:30:18 -0500 Subject: [PATCH 06/19] Added clarification to the get_shortest_path() documentation --- src/_igraph/graphobject.c | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/_igraph/graphobject.c b/src/_igraph/graphobject.c index c79b4b479..b10be661f 100644 --- a/src/_igraph/graphobject.c +++ b/src/_igraph/graphobject.c @@ -15122,6 +15122,7 @@ struct PyMethodDef igraphmodule_Graph_methods[] = { METH_VARARGS | METH_KEYWORDS, "get_shortest_path(v, to, weights=None, mode=\"out\", output=\"vpath\", algorithm=\"auto\")\n--\n\n" "Calculates the shortest path from a source vertex to a target vertex in a graph.\n\n" + "This function only returns a single shortest path, to find all shortest paths consider using L{get_shortest_paths()}.\n\n" "@param v: the source vertex of the path\n" "@param to: the target vertex of the path\n" "@param weights: edge weights in a list or the name of an edge attribute\n" @@ -15139,7 +15140,8 @@ struct PyMethodDef igraphmodule_Graph_methods[] = { " algorithm automatically based on whether the graph has negative weights\n" " or not. C{\"dijkstra\"} uses Dijkstra's algorithm. C{\"bellman_ford\"}\n" " uses the Bellman-Ford algorithm. Ignored for unweighted graphs.\n" - "@return: see the documentation of the C{output} parameter.\n"}, + "@return: see the documentation of the C{output} parameter.\n" + "@see: L{get_shortest_paths()}\n"}, /* interface to igraph_get_shortest_paths */ {"get_shortest_paths", (PyCFunction) igraphmodule_Graph_get_shortest_paths, From b556e98fe983b5f4a4dd4c86b07ea7d0b73030ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tam=C3=A1s=20Nepusz?= Date: Thu, 14 Mar 2024 17:03:48 +0100 Subject: [PATCH 07/19] doc: word wrapping in improved get_shortest_path() docs for the console --- src/_igraph/graphobject.c | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/_igraph/graphobject.c b/src/_igraph/graphobject.c index b10be661f..44b617cf4 100644 --- a/src/_igraph/graphobject.c +++ b/src/_igraph/graphobject.c @@ -15122,7 +15122,8 @@ struct PyMethodDef igraphmodule_Graph_methods[] = { METH_VARARGS | METH_KEYWORDS, "get_shortest_path(v, to, weights=None, mode=\"out\", output=\"vpath\", algorithm=\"auto\")\n--\n\n" "Calculates the shortest path from a source vertex to a target vertex in a graph.\n\n" - "This function only returns a single shortest path, to find all shortest paths consider using L{get_shortest_paths()}.\n\n" + "This function only returns a single shortest path. Consider using L{get_shortest_paths()}\n" + "to find all shortest paths between a source and one or more target vertices.\n\n" "@param v: the source vertex of the path\n" "@param to: the target vertex of the path\n" "@param weights: edge weights in a list or the name of an edge attribute\n" From 17eec0abb7a6b143a73b9641b69b92910e999eff Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Thu, 14 Mar 2024 17:24:53 +0100 Subject: [PATCH 08/19] chore: updated contributors list --- .all-contributorsrc | 9 +++++++++ CONTRIBUTORS.md | 1 + 2 files changed, 10 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 78c931202..f8a0ea85d 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -531,6 +531,15 @@ "contributions": [ "code" ] + }, + { + "login": "JDPowell648", + "name": "JDPowell648", + "avatar_url": "https://avatars.githubusercontent.com/u/41934552?v=4", + "profile": "https://github.com/JDPowell648", + "contributions": [ + "doc" + ] } ], "contributorsPerLine": 7 diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 37b369f5d..5535a66ac 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -81,6 +81,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
szcf-weiya
๐Ÿ’ป
tristanlatr
๐Ÿ’ป +
JDPowell648
๐Ÿ“– From 6ad42fb0dda864cbc122ff307290fe59f4e0b8d7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 18 Mar 2024 14:03:13 +0000 Subject: [PATCH 09/19] build(deps): bump pypa/cibuildwheel from 2.16.5 to 2.17.0 Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.16.5 to 2.17.0. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](https://github.com/pypa/cibuildwheel/compare/v2.16.5...v2.17.0) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/build.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e9b7f0666..f047f808a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -30,7 +30,7 @@ jobs: python-version: '3.8' - name: Build wheels (manylinux) - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel cairo-devel && pip install -U cmake pip wheel && python setup.py build_c_core" CIBW_BUILD: "*-manylinux_${{ matrix.wheel_arch }}" @@ -39,7 +39,7 @@ jobs: CIBW_TEST_SKIP: "cp310-manylinux_i686 cp311-manylinux_i686 cp312-manylinux_i686" - name: Build wheels (musllinux) - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_BEFORE_BUILD: "apk add flex bison libxml2-dev zlib-dev cairo-dev && pip install -U cmake pip wheel && python setup.py build_c_core" CIBW_BUILD: "*-musllinux_${{ matrix.wheel_arch }}" @@ -64,7 +64,7 @@ jobs: uses: docker/setup-qemu-action@v3 - name: Build wheels (manylinux) - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel cairo-devel && pip install -U cmake pip wheel && python setup.py build_c_core" CIBW_ARCHS_LINUX: aarch64 @@ -89,7 +89,7 @@ jobs: uses: docker/setup-qemu-action@v3 - name: Build wheels (musllinux) - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_BEFORE_BUILD: "apk add flex bison libxml2-dev zlib-dev cairo-dev && pip install -U cmake pip wheel && python setup.py build_c_core" CIBW_ARCHS_LINUX: aarch64 @@ -156,7 +156,7 @@ jobs: cmake --install . - name: Build wheels - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_ARCHS_MACOS: "${{ matrix.wheel_arch }}" CIBW_BEFORE_BUILD: "python setup.py build_c_core" @@ -256,7 +256,7 @@ jobs: shell: cmd - name: Build wheels - uses: pypa/cibuildwheel@v2.16.5 + uses: pypa/cibuildwheel@v2.17.0 env: CIBW_BEFORE_BUILD: "python setup.py build_c_core" CIBW_BUILD: "*-${{ matrix.wheel_arch }}" From 82c162e7da9bbf18a53a0122992cf0afff883e10 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Monteiro=20de=20Moraes=20de=20Arruda=20Falc?= =?UTF-8?q?=C3=A3o?= Date: Wed, 20 Mar 2024 19:52:00 -0300 Subject: [PATCH 10/19] Bug fix in libraries.py The 'pop' function in line 58 is called wrongly, resulting in: TypeError: 'builtin_function_or_method' object is not subscriptable --- src/igraph/io/libraries.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/igraph/io/libraries.py b/src/igraph/io/libraries.py index 52e47b8af..f35cc9545 100644 --- a/src/igraph/io/libraries.py +++ b/src/igraph/io/libraries.py @@ -55,7 +55,7 @@ def _export_graph_to_networkx( eattr["_igraph_index"] = i if multigraph and "_nx_multiedge_key" in eattr: - eattr["key"] = eattr.pop["_nx_multiedge_key"] + eattr["key"] = eattr.pop("_nx_multiedge_key") if vertex_attr_hashable in graph.vertex_attributes(): hashable_source = graph.vs[vertex_attr_hashable][edge.source] From 19b5a45d0e987397256efa48fd447cec5e7315c9 Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Thu, 21 Mar 2024 08:35:29 +0100 Subject: [PATCH 11/19] chore: updated contributors list --- .all-contributorsrc | 45 +++++++++++++++++++++++++++++++++++++++++++++ CONTRIBUTORS.md | 7 +++++++ 2 files changed, 52 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index f8a0ea85d..6daaa80b3 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -540,6 +540,51 @@ "contributions": [ "doc" ] + }, + { + "login": "Adriankhl", + "name": "k.h.lai", + "avatar_url": "https://avatars.githubusercontent.com/u/16377650?v=4", + "profile": "https://github.com/Adriankhl", + "contributions": [ + "code" + ] + }, + { + "login": "gruebel", + "name": "Anton Grรผbel", + "avatar_url": "https://avatars.githubusercontent.com/u/33207684?v=4", + "profile": "https://github.com/gruebel", + "contributions": [ + "code" + ] + }, + { + "login": "flange-ipb", + "name": "flange-ipb", + "avatar_url": "https://avatars.githubusercontent.com/u/34936695?v=4", + "profile": "https://github.com/flange-ipb", + "contributions": [ + "code" + ] + }, + { + "login": "pmp-p", + "name": "Paul m. p. Peny", + "avatar_url": "https://avatars.githubusercontent.com/u/16009100?v=4", + "profile": "https://discuss.afpy.org/", + "contributions": [ + "code" + ] + }, + { + "login": "DavidRConnell", + "name": "David R. Connell", + "avatar_url": "https://avatars.githubusercontent.com/u/35470740?v=4", + "profile": "https://davidrconnell.github.io/", + "contributions": [ + "code" + ] } ], "contributorsPerLine": 7 diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 5535a66ac..dc02942b4 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -82,6 +82,13 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
szcf-weiya
๐Ÿ’ป
tristanlatr
๐Ÿ’ป
JDPowell648
๐Ÿ“– +
k.h.lai
๐Ÿ’ป +
Anton Grรผbel
๐Ÿ’ป +
flange-ipb
๐Ÿ’ป +
Paul m. p. Peny
๐Ÿ’ป + + +
David R. Connell
๐Ÿ’ป From dbedbcd9169a27e73cc485aaa8286050bfce6277 Mon Sep 17 00:00:00 2001 From: Kreijstal Date: Sat, 20 Apr 2024 11:08:18 +0200 Subject: [PATCH 12/19] Linking with existing igraph on msys2 I've been thinking for a while if the msys2/mingw distribution should provide a package for python-igraph itself, but these are instructions to build from source, so it should suffice --- README.md | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a94f33f5a..afa7e83e0 100644 --- a/README.md +++ b/README.md @@ -77,6 +77,8 @@ where `[arch]` is either `Win32` for 32-bit builds or `x64` for 64-bit builds. Also, when building in MSYS2, you need to set the `SETUPTOOLS_USE_DISTUTILS` environment variable to `stdlib`; this is because MSYS2 uses a patched version of `distutils` that conflicts with `setuptools >= 60.0`. +Note: You need the following packages: +`$MINGW_PACKAGE_PREFIX-python-pip $MINGW_PACKAGE_PREFIX-python-setuptools $MINGW_PACKAGE_PREFIX-cc $MINGW_PACKAGE_PREFIX-cmake` ### Enabling GraphML @@ -158,8 +160,16 @@ the packaged igraph library instead of bringing its own copy. It is also useful on macOS if you want to link to the igraph library installed from Homebrew. -Due to the lack of support of `pkg-config` on Windows, it is currently not -possible to build against an external library on Windows. +Due to the lack of support of `pkg-config` on MSVC, it is currently not +possible to build against an external library on MSVC. + +In case you are already using a MSYS2/[MinGW](https://www.mingw-w64.org/) and already have +[mingw-w64-igraph](https://packages.msys2.org/base/mingw-w64-igraph) installed, +simply type: +``` +IGRAPH_USE_PKG_CONFIG=1 SETUPTOOLS_USE_DISTUTILS=stdlib pip install igraph +``` +to build. **Warning:** the Python interface is guaranteed to work only with the same version of the C core that is vendored inside the `vendor/source/igraph` From bb8ca883c5c4b40da160cbcd0347a43ad0921239 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tam=C3=A1s=20Nepusz?= Date: Sat, 20 Apr 2024 14:35:01 +0200 Subject: [PATCH 13/19] doc: update README.md styling --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index afa7e83e0..45a127ca4 100644 --- a/README.md +++ b/README.md @@ -77,8 +77,10 @@ where `[arch]` is either `Win32` for 32-bit builds or `x64` for 64-bit builds. Also, when building in MSYS2, you need to set the `SETUPTOOLS_USE_DISTUTILS` environment variable to `stdlib`; this is because MSYS2 uses a patched version of `distutils` that conflicts with `setuptools >= 60.0`. -Note: You need the following packages: -`$MINGW_PACKAGE_PREFIX-python-pip $MINGW_PACKAGE_PREFIX-python-setuptools $MINGW_PACKAGE_PREFIX-cc $MINGW_PACKAGE_PREFIX-cmake` + +> [!TIP] +> You need the following packages: +> `$MINGW_PACKAGE_PREFIX-python-pip $MINGW_PACKAGE_PREFIX-python-setuptools $MINGW_PACKAGE_PREFIX-cc $MINGW_PACKAGE_PREFIX-cmake` ### Enabling GraphML From eb2e7e02ba92ff6940e82ac7a387829539dc297f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= Date: Tue, 23 Apr 2024 15:40:11 +0000 Subject: [PATCH 14/19] doc: clarify Weighted_Adjacency docs --- src/igraph/io/adjacency.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/igraph/io/adjacency.py b/src/igraph/io/adjacency.py index ff83df5a6..7f09ed167 100644 --- a/src/igraph/io/adjacency.py +++ b/src/igraph/io/adjacency.py @@ -78,6 +78,8 @@ def _construct_graph_from_weighted_adjacency( ): """Generates a graph from its weighted adjacency matrix. + Only edges with a non-zero weight are created. + @param matrix: the adjacency matrix. Possible types are: - a list of lists - a numpy 2D array or matrix (will be converted to list of lists) @@ -85,12 +87,12 @@ def _construct_graph_from_weighted_adjacency( to a dense matrix) @param mode: the mode to be used. Possible values are: - C{"directed"} - the graph will be directed and a matrix element - specifies the number of edges between two vertices. + specifies the weight of the corresponding edge. - C{"undirected"} - the graph will be undirected and a matrix element - specifies the number of edges between two vertices. The matrix must + specifies the weight of the corresponding edge. The matrix must be symmetric. - - C{"max"} - undirected graph will be created and the number of - edges between vertex M{i} and M{j} is M{max(A(i,j), A(j,i))} + - C{"max"} - undirected graph will be created and the weight of the + edge between vertex M{i} and M{j} is M{max(A(i,j), A(j,i))} - C{"min"} - like C{"max"}, but with M{min(A(i,j), A(j,i))} - C{"plus"} - like C{"max"}, but with M{A(i,j) + A(j,i)} - C{"upper"} - undirected graph with the upper right triangle of From 973d96153bd562ca6df497c124a024ef8a241086 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= Date: Mon, 29 Apr 2024 08:54:35 +0000 Subject: [PATCH 15/19] chore: update C core --- vendor/source/igraph | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vendor/source/igraph b/vendor/source/igraph index 2de2c37e3..8b2d1c666 160000 --- a/vendor/source/igraph +++ b/vendor/source/igraph @@ -1 +1 @@ -Subproject commit 2de2c37e353e15000d0608d2dd2f4b3c3595edb6 +Subproject commit 8b2d1c666d0f53ffe65de5fd737866724e327d86 From c9c236fd7bb0670004a034463b766b4fd58840a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= Date: Mon, 29 Apr 2024 09:15:29 +0000 Subject: [PATCH 16/19] chore: update C core (and pick up attempted fix for linking error) --- vendor/source/igraph | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vendor/source/igraph b/vendor/source/igraph index 8b2d1c666..45cb86394 160000 --- a/vendor/source/igraph +++ b/vendor/source/igraph @@ -1 +1 @@ -Subproject commit 8b2d1c666d0f53ffe65de5fd737866724e327d86 +Subproject commit 45cb86394a34021111fb6b071b48aa783930fdd9 From 1ffb0737f3267e5c9212330d383335849e0f3533 Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Tue, 7 May 2024 15:13:22 +0200 Subject: [PATCH 17/19] chore: updated C core --- vendor/source/igraph | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vendor/source/igraph b/vendor/source/igraph index 45cb86394..9e7717014 160000 --- a/vendor/source/igraph +++ b/vendor/source/igraph @@ -1 +1 @@ -Subproject commit 45cb86394a34021111fb6b071b48aa783930fdd9 +Subproject commit 9e77170146f537ad44e81ca905548738a5a086a0 From 76a98b84acd9f2350810047b6b1e4e5a5de343b1 Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Tue, 7 May 2024 15:13:38 +0200 Subject: [PATCH 18/19] chore: updated pre-commit hooks --- .pre-commit-config.yaml | 13 +++---------- pyproject.toml | 5 ++--- 2 files changed, 5 insertions(+), 13 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 516ea19ca..2b88275d5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,14 @@ fail_fast: true repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 + rev: v4.6.0 hooks: - - id: check-ast - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: v0.0.275 + rev: v0.3.5 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] - - - repo: https://github.com/psf/black - rev: 22.3.0 - hooks: - - id: black - exclude: ^doc/examples_sphinx-gallery/ - language_version: python3 + - id: ruff-format diff --git a/pyproject.toml b/pyproject.toml index 0d5932b7b..0ded74ac4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,6 +3,5 @@ requires = ["setuptools", "wheel"] build-backend = "setuptools.build_meta" [tool.ruff] -ignore = ["B905", "C901", "E402", "E501"] -line-length = 80 -select = ["B", "C", "E", "F", "W"] +lint.ignore = ["B905", "C901", "E402", "E501"] +lint.select = ["B", "C", "E", "F", "W"] From 8e7179ce3f0f2e6b1da7dcf68c54145b03e34fdb Mon Sep 17 00:00:00 2001 From: Tamas Nepusz Date: Tue, 7 May 2024 15:23:47 +0200 Subject: [PATCH 19/19] chore: bumped version to 0.11.5 --- CHANGELOG.md | 7 +++++-- src/igraph/version.py | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 891995ccd..f787db23f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # igraph Python interface changelog -## [master] +## [0.11.5] - 2024-05-07 ### Added @@ -14,6 +14,8 @@ following up a similar change in the C core. The old name of the function is deprecated but will be kept around until at least 0.12.0. +- The C core of igraph was updated to version 0.10.12. + ## [0.11.4] ### Added @@ -635,7 +637,8 @@ Please refer to the commit logs at https://github.com/igraph/python-igraph for a list of changes affecting versions up to 0.8.3. Notable changes after 0.8.3 are documented above. -[main]: https://github.com/igraph/python-igraph/compare/0.11.4...main +[main]: https://github.com/igraph/python-igraph/compare/0.11.5...main +[0.11.5]: https://github.com/igraph/python-igraph/compare/0.11.4...0.11.5 [0.11.4]: https://github.com/igraph/python-igraph/compare/0.11.3...0.11.4 [0.11.3]: https://github.com/igraph/python-igraph/compare/0.11.2...0.11.3 [0.11.2]: https://github.com/igraph/python-igraph/compare/0.11.0...0.11.2 diff --git a/src/igraph/version.py b/src/igraph/version.py index 4c4a3bf3a..92c6ba6fb 100644 --- a/src/igraph/version.py +++ b/src/igraph/version.py @@ -1,2 +1,2 @@ -__version_info__ = (0, 11, 4) +__version_info__ = (0, 11, 5) __version__ = ".".join("{0}".format(x) for x in __version_info__)