[ovito] 02/08: Refresh patches, remove old ones.
Anton Gladky
gladk at moszumanska.debian.org
Sun Aug 6 22:01:13 UTC 2017
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository ovito.
commit 7aedcd189ec7713615630d402753cb7d9fbdf90e
Author: Anton Gladky <gladk at debian.org>
Date: Sun Aug 6 19:52:36 2017 +0200
Refresh patches, remove old ones.
---
debian/patches/0001-Disable-povray-test.patch | 14 +-
...e-3-Test-suite-can-fail-when-executed-in-.patch | 160 ---------------
...e-4-Tests-that-depend-on-the-CrystalAnaly.patch | 226 ---------------------
debian/patches/0004-Use-system-pybind11.patch | 8 +-
...latest-pybind11-version.-Also-fixing-issu.patch | 69 -------
...-required-by-latest-pybind11-version.-Fix.patch | 35 ----
debian/patches/series | 6 +-
7 files changed, 13 insertions(+), 505 deletions(-)
diff --git a/debian/patches/0001-Disable-povray-test.patch b/debian/patches/0001-Disable-povray-test.patch
index 9d56ce2..2c11d2c 100644
--- a/debian/patches/0001-Disable-povray-test.patch
+++ b/debian/patches/0001-Disable-povray-test.patch
@@ -6,12 +6,12 @@ Subject: Disable povray test
tests/scripts/test_suite/povray_renderer.py | 3 +++
1 file changed, 3 insertions(+)
-diff --git a/tests/scripts/test_suite/povray_renderer.py b/tests/scripts/test_suite/povray_renderer.py
-index d2bb8f28..a37df1cf 100644
---- a/tests/scripts/test_suite/povray_renderer.py
-+++ b/tests/scripts/test_suite/povray_renderer.py
-@@ -3,6 +3,8 @@ from ovito.io import import_file
- from ovito.vis import *
+Index: ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f/tests/scripts/test_suite/povray_renderer.py
+===================================================================
+--- ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f.orig/tests/scripts/test_suite/povray_renderer.py
++++ ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f/tests/scripts/test_suite/povray_renderer.py
+@@ -6,6 +6,8 @@ import sys
+ if "ovito.plugins.POVRay" not in sys.modules: sys.exit()
test_data_dir = "../../files/"
+
@@ -19,7 +19,7 @@ index d2bb8f28..a37df1cf 100644
node1 = import_file(test_data_dir + "LAMMPS/class2.data", atom_style = "full")
node1.add_to_scene()
node1.source.particle_properties.position.display.radius = 0.3
-@@ -22,3 +24,4 @@ print("aperture:", settings.renderer.aperture)
+@@ -25,3 +27,4 @@ print("aperture:", settings.renderer.ape
print("blur_samples:", settings.renderer.blur_samples)
ovito.dataset.viewports.active_vp.render(settings)
diff --git a/debian/patches/0002-Fixing-issue-3-Test-suite-can-fail-when-executed-in-.patch b/debian/patches/0002-Fixing-issue-3-Test-suite-can-fail-when-executed-in-.patch
deleted file mode 100644
index e77462f..0000000
--- a/debian/patches/0002-Fixing-issue-3-Test-suite-can-fail-when-executed-in-.patch
+++ /dev/null
@@ -1,160 +0,0 @@
-From: Alexander Stukowski <stukowski at mm.tu-darmstadt.de>
-Date: Tue, 3 Jan 2017 19:47:32 +0100
-Subject: Fixing issue #3: Test suite can fail when executed in parallel.
-
----
- tests/scripts/test_suite/avi_output.py | 17 ++++++++------
- tests/scripts/test_suite/dataset.py | 2 --
- tests/scripts/test_suite/export_file.py | 34 ++++++++++++++--------------
- tests/scripts/test_suite/export_file_text.py | 4 ++--
- tests/scripts/test_suite/povray_exporter.py | 7 +++---
- tests/scripts/test_suite/save_scene.py | 13 +++++++----
- 6 files changed, 41 insertions(+), 36 deletions(-)
-
-diff --git a/tests/scripts/test_suite/avi_output.py b/tests/scripts/test_suite/avi_output.py
-index f9a8b722..02bd1d65 100644
---- a/tests/scripts/test_suite/avi_output.py
-+++ b/tests/scripts/test_suite/avi_output.py
-@@ -4,16 +4,19 @@ from ovito.vis import *
- import os
- import os.path
-
--import_file("../../files/LAMMPS/animation.dump.gz", multiple_frames = True)
-+node = import_file("../../files/LAMMPS/animation.dump.gz", multiple_frames = True)
-+node.add_to_scene()
-
- vp = ovito.dataset.viewports.active_vp
-
--if os.path.isfile("movie.avi"):
-- os.remove("movie.avi")
--assert(not os.path.isfile("movie.avi"))
-+output_file = "_movie.avi"
-+
-+if os.path.isfile(output_file):
-+ os.remove(output_file)
-+assert(not os.path.isfile(output_file))
-
- settings = RenderSettings(
-- filename = "movie.avi",
-+ filename = output_file,
- size = (64, 64),
- range = RenderSettings.Range.ANIMATION
- )
-@@ -21,5 +24,5 @@ if ovito.headless_mode:
- settings.renderer = TachyonRenderer(ambient_occlusion = False, antialiasing = False)
- vp.render(settings)
-
--assert(os.path.isfile("movie.avi"))
--os.remove("movie.avi")
-+assert(os.path.isfile(output_file))
-+os.remove(output_file)
-diff --git a/tests/scripts/test_suite/dataset.py b/tests/scripts/test_suite/dataset.py
-index 01c41c90..8fc04bc1 100644
---- a/tests/scripts/test_suite/dataset.py
-+++ b/tests/scripts/test_suite/dataset.py
-@@ -28,5 +28,3 @@ assert(scene_nodes[0] == o2)
-
- del scene_nodes[0]
- assert(len(scene_nodes) == 0)
--
--ovito.dataset.save("../../files/output.ovito")
-\ No newline at end of file
-diff --git a/tests/scripts/test_suite/export_file.py b/tests/scripts/test_suite/export_file.py
-index d37ed0e3..9f2ec666 100644
---- a/tests/scripts/test_suite/export_file.py
-+++ b/tests/scripts/test_suite/export_file.py
-@@ -9,22 +9,22 @@ test_data_dir = "../../files/"
-
- node1 = import_file(test_data_dir + "LAMMPS/class2.data", atom_style = "full")
- print(node1.source)
--export_file(node1, "test.data", "lammps_data", atom_style = "full")
--export_file(node1, "test.data", "lammps_data", atom_style = "bond")
--export_file(node1, "test.data", "lammps_dump", columns = ["Particle Identifier", "Particle Type", "Position.X", "Position.Y", "Position.Z"])
--export_file(node1, "test.data", "fhi-aims")
--export_file(node1, "test.data", "imd")
--export_file(node1, "test.data", "vasp")
--export_file(node1, "test.data", "povray")
--export_file(node1, "test.data", "xyz", columns = ["Position.X", "Position.Y", "Position.Z"])
-+export_file(node1, "_export_file_test.data", "lammps_data", atom_style = "full")
-+export_file(node1, "_export_file_test.data", "lammps_data", atom_style = "bond")
-+export_file(node1, "_export_file_test.data", "lammps_dump", columns = ["Particle Identifier", "Particle Type", "Position.X", "Position.Y", "Position.Z"])
-+export_file(node1, "_export_file_test.data", "fhi-aims")
-+export_file(node1, "_export_file_test.data", "imd")
-+export_file(node1, "_export_file_test.data", "vasp")
-+export_file(node1, "_export_file_test.data", "povray")
-+export_file(node1, "_export_file_test.data", "xyz", columns = ["Position.X", "Position.Y", "Position.Z"])
- ovito.dataset.anim.last_frame = 7
--export_file(node1, "test.dump", "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], multiple_frames = True)
--export_file(node1, "test.*.dump", "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], multiple_frames = True, start_frame = 1, end_frame = 5, every_nth_frame = 2)
--os.remove("test.data")
--os.remove("test.dump")
--os.remove("test.1.dump")
--os.remove("test.3.dump")
--os.remove("test.5.dump")
-+export_file(node1, "_export_file_test.dump", "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], multiple_frames = True)
-+export_file(node1, "_export_file_test.*.dump", "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], multiple_frames = True, start_frame = 1, end_frame = 5, every_nth_frame = 2)
-+os.remove("_export_file_test.data")
-+os.remove("_export_file_test.dump")
-+os.remove("_export_file_test.1.dump")
-+os.remove("_export_file_test.3.dump")
-+os.remove("_export_file_test.5.dump")
- for i in range(ovito.dataset.anim.last_frame + 1):
-- export_file(node1, "test.%i.dump" % i, "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], frame = i)
-- os.remove("test.%i.dump" % i)
-\ No newline at end of file
-+ export_file(node1, "_export_file_test.%i.dump" % i, "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z"], frame = i)
-+ os.remove("_export_file_test.%i.dump" % i)
-\ No newline at end of file
-diff --git a/tests/scripts/test_suite/export_file_text.py b/tests/scripts/test_suite/export_file_text.py
-index a792fac2..23a098d4 100644
---- a/tests/scripts/test_suite/export_file_text.py
-+++ b/tests/scripts/test_suite/export_file_text.py
-@@ -6,5 +6,5 @@ import os.path
- test_data_dir = "../../files/"
-
- node = import_file(test_data_dir + "LAMMPS/animation1.dump", multiple_frames = True)
--export_file(node, "test.data", "txt", columns = ["Timestep", "SourceFrame"], multiple_frames = True)
--os.remove("test.data")
-\ No newline at end of file
-+export_file(node, "_export_file_text.data", "txt", columns = ["Timestep", "SourceFrame"], multiple_frames = True)
-+os.remove("_export_file_text.data")
-\ No newline at end of file
-diff --git a/tests/scripts/test_suite/povray_exporter.py b/tests/scripts/test_suite/povray_exporter.py
-index c045ae8c..2d5f8160 100644
---- a/tests/scripts/test_suite/povray_exporter.py
-+++ b/tests/scripts/test_suite/povray_exporter.py
-@@ -9,6 +9,7 @@ node1 = import_file(test_data_dir + "LAMMPS/class2.data", atom_style = "full")
- node1.add_to_scene()
- node1.source.particle_properties.position.display.shape = ParticleDisplay.Shape.Square
- node1.source.particle_properties.position.display.radius = 0.3
--export_file(node1, "test.pov", "povray")
--export_file(None, "test.pov", "povray")
--os.remove("test.pov")
-+export_file(node1, "_povray_export_test.pov", "povray")
-+export_file(None, "_povray_export_test.pov", "povray")
-+assert(os.path.isfile("_povray_export_test.pov"))
-+os.remove("_povray_export_test.pov")
-diff --git a/tests/scripts/test_suite/save_scene.py b/tests/scripts/test_suite/save_scene.py
-index e02231d0..2950bb2b 100644
---- a/tests/scripts/test_suite/save_scene.py
-+++ b/tests/scripts/test_suite/save_scene.py
-@@ -3,11 +3,14 @@ from ovito.io import *
- import os
- import os.path
-
--import_file("../../files/LAMMPS/animation.dump.gz")
-+node = import_file("../../files/LAMMPS/animation.dump.gz")
-+node.add_to_scene()
-
--if os.path.isfile("scene.ovito"): os.remove("scene.ovito")
-+output_test_file = "_save_scene.ovito"
-
--ovito.dataset.save("scene.ovito")
--assert(os.path.isfile("scene.ovito"))
-+if os.path.isfile(output_test_file): os.remove(output_test_file)
-
--os.remove("scene.ovito")
-+ovito.dataset.save(output_test_file)
-+assert(os.path.isfile(output_test_file))
-+
-+os.remove(output_test_file)
diff --git a/debian/patches/0003-Fixing-issue-4-Tests-that-depend-on-the-CrystalAnaly.patch b/debian/patches/0003-Fixing-issue-4-Tests-that-depend-on-the-CrystalAnaly.patch
deleted file mode 100644
index 7459929..0000000
--- a/debian/patches/0003-Fixing-issue-4-Tests-that-depend-on-the-CrystalAnaly.patch
+++ /dev/null
@@ -1,226 +0,0 @@
-From: Alexander Stukowski <stukowski at mm.tu-darmstadt.de>
-Date: Mon, 9 Jan 2017 21:42:28 +0100
-Subject: Fixing issue #4: Tests that depend on the CrystalAnalysis module
- fail when the module was disabled in the build.
-
----
- .../example_snippets/construct_surface_modifier.py | 3 ++
- .../dislocation_analysis_modifier.py | 3 ++
- doc/python/example_snippets/surface_mesh.py | 3 ++
- src/plugins/CMakeLists.txt | 33 +++++++++++-----------
- .../crystalanalysis/scripting/PythonInterface.cpp | 9 ++++--
- .../particles/scripting/PythonInterface.cpp | 3 +-
- src/plugins/pyscript/python/ovito/__init__.py | 1 +
- .../test_suite/construct_surface_modifier.py | 3 ++
- .../test_suite/dislocation_analysis_modifier.py | 3 ++
- .../elastic_strain_calculation_modifier.py | 3 ++
- 10 files changed, 44 insertions(+), 20 deletions(-)
-
-diff --git a/doc/python/example_snippets/construct_surface_modifier.py b/doc/python/example_snippets/construct_surface_modifier.py
-index 67ceeba5..f51e45dd 100644
---- a/doc/python/example_snippets/construct_surface_modifier.py
-+++ b/doc/python/example_snippets/construct_surface_modifier.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito.io import import_file
- from ovito.modifiers import ConstructSurfaceModifier
-
-diff --git a/doc/python/example_snippets/dislocation_analysis_modifier.py b/doc/python/example_snippets/dislocation_analysis_modifier.py
-index 8affc158..b9d98164 100644
---- a/doc/python/example_snippets/dislocation_analysis_modifier.py
-+++ b/doc/python/example_snippets/dislocation_analysis_modifier.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito.io import import_file, export_file
- from ovito.modifiers import DislocationAnalysisModifier
-
-diff --git a/doc/python/example_snippets/surface_mesh.py b/doc/python/example_snippets/surface_mesh.py
-index e5934c86..26ccdc47 100644
---- a/doc/python/example_snippets/surface_mesh.py
-+++ b/doc/python/example_snippets/surface_mesh.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito.io import import_file
- from ovito.modifiers import ConstructSurfaceModifier
-
-diff --git a/src/plugins/CMakeLists.txt b/src/plugins/CMakeLists.txt
-index dd9a8cc5..7bf9af27 100755
---- a/src/plugins/CMakeLists.txt
-+++ b/src/plugins/CMakeLists.txt
-@@ -19,62 +19,63 @@
- #
- ###############################################################################
-
--# Create the plugins directory.
--FILE(MAKE_DIRECTORY ${OVITO_PLUGINS_DIRECTORY})
-+# Create the plugins library and manifest directories.
-+FILE(MAKE_DIRECTORY "${OVITO_PLUGINS_DIRECTORY}")
-+FILE(MAKE_DIRECTORY "${OVITO_PLUGIN_MANIFESTS_DIRECTORY}")
-
- IF(OVITO_BUILD_PLUGIN_PYSCRIPT)
- ADD_SUBDIRECTORY(pyscript)
- SET(OVITOS_EXECUTABLE ${OVITOS_EXECUTABLE} PARENT_SCOPE)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/PyScript.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/PyScriptGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/PyScript.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/PyScriptGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_PARTICLES)
- ADD_SUBDIRECTORY(particles)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/Particles.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/ParticlesGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/Particles.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/ParticlesGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_TACHYON)
- ADD_SUBDIRECTORY(tachyon)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/Tachyon.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/TachyonGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/Tachyon.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/TachyonGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_MESH)
- ADD_SUBDIRECTORY(mesh)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/Mesh.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/Mesh.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_CRYSTALANALYSIS)
- ADD_SUBDIRECTORY(crystalanalysis)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/CrystalAnalysis.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/CrystalAnalysisGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/CrystalAnalysis.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/CrystalAnalysisGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_NETCDFPLUGIN)
- ADD_SUBDIRECTORY(netcdf)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/NetCDFPlugin.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/NetCDFPluginGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/NetCDFPlugin.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/NetCDFPluginGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_POVRAY)
- ADD_SUBDIRECTORY(povray)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/POVRay.json)
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/POVRayGui.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/POVRay.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/POVRayGui.json)
- ENDIF()
-
- IF(OVITO_BUILD_PLUGIN_OPENBABELPLUGIN)
- ADD_SUBDIRECTORY(openbabel)
- ELSE()
-- FILE(REMOVE ${OVITO_PLUGINS_DIRECTORY}/OpenBabelPlugin.json)
-+ FILE(REMOVE ${OVITO_PLUGIN_MANIFESTS_DIRECTORY}/OpenBabelPlugin.json)
- ENDIF()
-
- # Propagate list of plugins to parent scope.
-diff --git a/src/plugins/crystalanalysis/scripting/PythonInterface.cpp b/src/plugins/crystalanalysis/scripting/PythonInterface.cpp
-index ab27d960..eb310ed2 100755
---- a/src/plugins/crystalanalysis/scripting/PythonInterface.cpp
-+++ b/src/plugins/crystalanalysis/scripting/PythonInterface.cpp
-@@ -74,7 +74,8 @@ PYBIND11_PLUGIN(CrystalAnalysis)
- " The volume of the solid region bounded by the surface mesh.\n"
- "\n\n"
- "Example:\n\n"
-- ".. literalinclude:: ../example_snippets/construct_surface_modifier.py"
-+ ".. literalinclude:: ../example_snippets/construct_surface_modifier.py\n"
-+ " :lines: 4-\n"
- )
- .def_property("radius", &ConstructSurfaceModifier::probeSphereRadius, &ConstructSurfaceModifier::setProbeSphereRadius,
- "The radius of the probe sphere used in the surface construction algorithm."
-@@ -142,7 +143,8 @@ PYBIND11_PLUGIN(CrystalAnalysis)
- " The number of particles with local hexagonal diamond structure.\n"
- "\n\n"
- "Example:\n\n"
-- ".. literalinclude:: ../example_snippets/dislocation_analysis_modifier.py"
-+ ".. literalinclude:: ../example_snippets/dislocation_analysis_modifier.py\n"
-+ " :lines: 4-\n"
- )
- .def_property("trial_circuit_length", &DislocationAnalysisModifier::maxTrialCircuitSize, &DislocationAnalysisModifier::setMaxTrialCircuitSize,
- "The maximum length of trial Burgers circuits constructed by the DXA to discover dislocations. "
-@@ -377,7 +379,8 @@ PYBIND11_PLUGIN(CrystalAnalysis)
- "the :py:attr:`~DataObject.display` attribute of the :py:class:`~DataObject` base class."
- "\n\n"
- "Example:\n\n"
-- ".. literalinclude:: ../example_snippets/dislocation_analysis_modifier.py",
-+ ".. literalinclude:: ../example_snippets/dislocation_analysis_modifier.py\n"
-+ " :lines: 4-\n",
- // Python class name:
- "DislocationNetwork")
-
-diff --git a/src/plugins/particles/scripting/PythonInterface.cpp b/src/plugins/particles/scripting/PythonInterface.cpp
-index 231dbf8e..530659c4 100755
---- a/src/plugins/particles/scripting/PythonInterface.cpp
-+++ b/src/plugins/particles/scripting/PythonInterface.cpp
-@@ -669,7 +669,8 @@ PYBIND11_PLUGIN(Particles)
- "of the :py:class:`~ovito.modifiers.ConstructSurfaceModifier` that created the surface mesh."
- "\n\n"
- "Example:\n\n"
-- ".. literalinclude:: ../example_snippets/surface_mesh.py"
-+ ".. literalinclude:: ../example_snippets/surface_mesh.py\n"
-+ " :lines: 4-\n"
- )
- .def_property("is_completely_solid", &SurfaceMesh::isCompletelySolid, &SurfaceMesh::setCompletelySolid)
- .def("export_vtk", [](SurfaceMesh& mesh, const QString& filename, SimulationCellObject* simCellObj) {
-diff --git a/src/plugins/pyscript/python/ovito/__init__.py b/src/plugins/pyscript/python/ovito/__init__.py
-index dbc9b9f1..c7b889df 100644
---- a/src/plugins/pyscript/python/ovito/__init__.py
-+++ b/src/plugins/pyscript/python/ovito/__init__.py
-@@ -1,4 +1,5 @@
- import os.path
-+import sys
- try:
- # Python 3.x
- import collections.abc as collections
-diff --git a/tests/scripts/test_suite/construct_surface_modifier.py b/tests/scripts/test_suite/construct_surface_modifier.py
-index 7cda4a8f..ad57023d 100644
---- a/tests/scripts/test_suite/construct_surface_modifier.py
-+++ b/tests/scripts/test_suite/construct_surface_modifier.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito import *
- from ovito.io import *
- from ovito.modifiers import *
-diff --git a/tests/scripts/test_suite/dislocation_analysis_modifier.py b/tests/scripts/test_suite/dislocation_analysis_modifier.py
-index 033b5f73..6b246559 100644
---- a/tests/scripts/test_suite/dislocation_analysis_modifier.py
-+++ b/tests/scripts/test_suite/dislocation_analysis_modifier.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito import *
- from ovito.io import *
- from ovito.modifiers import *
-diff --git a/tests/scripts/test_suite/elastic_strain_calculation_modifier.py b/tests/scripts/test_suite/elastic_strain_calculation_modifier.py
-index b3047cee..a44741e3 100644
---- a/tests/scripts/test_suite/elastic_strain_calculation_modifier.py
-+++ b/tests/scripts/test_suite/elastic_strain_calculation_modifier.py
-@@ -1,3 +1,6 @@
-+import sys
-+if "ovito.modifiers.crystalanalysis" not in sys.modules: sys.exit()
-+
- from ovito import *
- from ovito.io import *
- from ovito.data import *
diff --git a/debian/patches/0004-Use-system-pybind11.patch b/debian/patches/0004-Use-system-pybind11.patch
index 19c304a..1dde7cc 100644
--- a/debian/patches/0004-Use-system-pybind11.patch
+++ b/debian/patches/0004-Use-system-pybind11.patch
@@ -6,10 +6,10 @@ Subject: Use system pybind11
src/plugins/pyscript/PyScript.h | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
-diff --git a/src/plugins/pyscript/PyScript.h b/src/plugins/pyscript/PyScript.h
-index 7bc647bb..fd0ba267 100644
---- a/src/plugins/pyscript/PyScript.h
-+++ b/src/plugins/pyscript/PyScript.h
+Index: ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f/src/plugins/pyscript/PyScript.h
+===================================================================
+--- ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f.orig/src/plugins/pyscript/PyScript.h
++++ ovito-v2.9.0-d0745a5f3db3a0423c85f3f1754f2111ca43e60f/src/plugins/pyscript/PyScript.h
@@ -33,12 +33,12 @@
#endif
diff --git a/debian/patches/0005-Updated-to-latest-pybind11-version.-Also-fixing-issu.patch b/debian/patches/0005-Updated-to-latest-pybind11-version.-Also-fixing-issu.patch
deleted file mode 100644
index 95bef85..0000000
--- a/debian/patches/0005-Updated-to-latest-pybind11-version.-Also-fixing-issu.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-From: Alexander Stukowski <stukowski at mm.tu-darmstadt.de>
-Date: Mon, 9 Jan 2017 22:57:42 +0100
-Subject: Updated to latest pybind11 version. Also fixing issue #5.
-
----
- src/plugins/pyscript/binding/AnimationBinding.cpp | 11 ++++++-----
- src/plugins/pyscript/binding/FileIOBinding.cpp | 5 +++--
- src/plugins/pyscript/python/ovito/anim/__init__.py | 3 ---
- 3 files changed, 9 insertions(+), 10 deletions(-)
-
-diff --git a/src/plugins/pyscript/binding/AnimationBinding.cpp b/src/plugins/pyscript/binding/AnimationBinding.cpp
-index 28c987a1..110bfe8d 100644
---- a/src/plugins/pyscript/binding/AnimationBinding.cpp
-+++ b/src/plugins/pyscript/binding/AnimationBinding.cpp
-@@ -42,7 +42,7 @@ PYBIND11_PLUGIN(PyScriptAnimation)
-
- py::module m("PyScriptAnimation");
-
-- py::object TimeInterval_py = py::class_<TimeInterval>(m, "TimeInterval")
-+ py::class_<TimeInterval>(m, "TimeInterval", py::metaclass())
- .def(py::init<>())
- .def(py::init<TimePoint>())
- .def(py::init<TimePoint, TimePoint>())
-@@ -58,13 +58,14 @@ PYBIND11_PLUGIN(PyScriptAnimation)
- .def("intersect", &TimeInterval::intersect)
- .def_static("time_to_seconds", &TimeToSeconds)
- .def_static("seconds_to_time", &TimeFromSeconds)
-- .def_property_readonly_static("infinite", &TimeInterval::infinite)
-- .def_property_readonly_static("empty", &TimeInterval::empty)
-+ .def_property_readonly_static("infinite", [](py::object /*self*/) { return TimeInterval::infinite(); })
-+ .def_property_readonly_static("empty", [](py::object /*self*/) { return TimeInterval::empty(); })
-+ .def_property_readonly_static("TimeNegativeInfinity", [](py::object /*self*/) { return TimeNegativeInfinity(); })
-+ .def_property_readonly_static("TimePositiveInfinity", [](py::object /*self*/) { return TimePositiveInfinity(); })
-+ .def("__str__", [](TimeInterval& iv) { return py::str("({},{})").format(iv.start(), iv.end()); })
- .def(py::self == TimeInterval())
- .def(py::self != TimeInterval())
- ;
-- py::setattr(TimeInterval_py, "TimeNegativeInfinity", py::cast(TimeNegativeInfinity()));
-- py::setattr(TimeInterval_py, "TimePositiveInfinity", py::cast(TimePositiveInfinity()));
-
- ovito_class<AnimationSettings, RefTarget>(m,
- "Stores animation-related settings of the current :py:attr:`~ovito.DataSet`. You can access "
-diff --git a/src/plugins/pyscript/binding/FileIOBinding.cpp b/src/plugins/pyscript/binding/FileIOBinding.cpp
-index 3ebf7321..a19dd391 100644
---- a/src/plugins/pyscript/binding/FileIOBinding.cpp
-+++ b/src/plugins/pyscript/binding/FileIOBinding.cpp
-@@ -57,8 +57,9 @@ PYBIND11_PLUGIN(PyScriptFileIO)
- .value("ResetScene", FileImporter::ResetScene)
- ;
-
-- py::class_<FileManager>(m, "FileManager")
-- .def_property_readonly_static("instance", py::cpp_function(&FileManager::instance, py::return_value_policy::reference))
-+ py::class_<FileManager>(m, "FileManager", py::metaclass())
-+ .def_property_readonly_static("instance", py::cpp_function(
-+ [](py::object /*self*/) { return &FileManager::instance(); }, py::return_value_policy::reference))
- //.def("removeFromCache", &FileManager::removeFromCache)
- //.def("urlFromUserInput", &FileManager::urlFromUserInput)
- ;
-diff --git a/src/plugins/pyscript/python/ovito/anim/__init__.py b/src/plugins/pyscript/python/ovito/anim/__init__.py
-index bc25378f..465426bf 100644
---- a/src/plugins/pyscript/python/ovito/anim/__init__.py
-+++ b/src/plugins/pyscript/python/ovito/anim/__init__.py
-@@ -1,5 +1,2 @@
- # Load the native module.
- from PyScriptAnimation import *
--
--# Add __str__ method to TimeInterval class:
--TimeInterval.__str__ = lambda self: str((self.start,self.end))
-\ No newline at end of file
diff --git a/debian/patches/0006-Code-change-required-by-latest-pybind11-version.-Fix.patch b/debian/patches/0006-Code-change-required-by-latest-pybind11-version.-Fix.patch
deleted file mode 100644
index ff89c89..0000000
--- a/debian/patches/0006-Code-change-required-by-latest-pybind11-version.-Fix.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-From: Alexander Stukowski <stukowski at mm.tu-darmstadt.de>
-Date: Mon, 9 Jan 2017 23:53:04 +0100
-Subject: Code change required by latest pybind11 version. Fixing issue #5.
-
----
- src/plugins/particles/resources/python/ovito/data/particles/__init__.py | 2 +-
- src/plugins/pyscript/binding/PythonBinding.h | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/plugins/particles/resources/python/ovito/data/particles/__init__.py b/src/plugins/particles/resources/python/ovito/data/particles/__init__.py
-index c02b314a..c1dcdcda 100644
---- a/src/plugins/particles/resources/python/ovito/data/particles/__init__.py
-+++ b/src/plugins/particles/resources/python/ovito/data/particles/__init__.py
-@@ -380,7 +380,7 @@ class CutoffNeighborFinder(Particles.CutoffNeighborFinder):
-
- def __init__(self, cutoff, data_collection):
- """ This is the constructor. """
-- super(self.__class__, self).__init__()
-+ super(self.__class__, self).__init__()
- if not hasattr(data_collection, 'position'):
- raise KeyError("Data collection does not contain any particles.")
- if not hasattr(data_collection, 'cell'):
-diff --git a/src/plugins/pyscript/binding/PythonBinding.h b/src/plugins/pyscript/binding/PythonBinding.h
-index 0f8095e2..4f2cb497 100644
---- a/src/plugins/pyscript/binding/PythonBinding.h
-+++ b/src/plugins/pyscript/binding/PythonBinding.h
-@@ -26,7 +26,7 @@
- #include <plugins/pyscript/engine/ScriptEngine.h>
- #include <core/utilities/io/FileManager.h>
-
--PYBIND11_DECLARE_HOLDER_TYPE(T, Ovito::OORef<T>);
-+PYBIND11_DECLARE_HOLDER_TYPE(T, Ovito::OORef<T>, true);
-
- namespace pybind11 { namespace detail {
-
diff --git a/debian/patches/series b/debian/patches/series
index 9d2c0d3..97319a8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,4 @@
0001-Disable-povray-test.patch
-0002-Fixing-issue-3-Test-suite-can-fail-when-executed-in-.patch
-0003-Fixing-issue-4-Tests-that-depend-on-the-CrystalAnaly.patch
0004-Use-system-pybind11.patch
-0005-Updated-to-latest-pybind11-version.-Also-fixing-issu.patch
-0006-Code-change-required-by-latest-pybind11-version.-Fix.patch
+05_disable_avi_test.patch
+06_fix_gcc7_compiation.patch
--
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