Merge branch 'master' into better_network_report

.coveragerc

@@ -1,2 +1,17 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 [run]
 branch = True

.gitignore

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 /.project
 /.pydevproject
 /.idea

.ratexcludes

@@ -0,0 +1 @@
+**/*.json

.travis.yml

@@ -1,27 +1,43 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 language: python
-dist: trusty
 python:
   - 2.7
   - 3.6
+  - 3.7
+dist: xenial
 cache: pip
-
 addons:
   apt:
     packages:
       - libxml2-utils
+      - openjdk-8-jre-headless
+      - ant
 
 before_install:
   # Work around ludicrous Travis bug
   - git clone https://github.com/SpiNNakerManchester/SupportScripts.git support
   - python support/travis_blocking_stdout.py
+  - support/rat.sh download
   # Bring pip up to date 
   - pip install --upgrade pip setuptools wheel
   - pip install --only-binary=numpy,scipy numpy scipy
   # SpiNNakerManchester internal dependencies; development mode
   - support/pipinstall.sh git://github.com/SpiNNakerManchester/SpiNNUtils.git
   - support/pipinstall.sh git://github.com/SpiNNakerManchester/SpiNNMachine.git
-  # Which version of rig should we really use?
-  - pip install --upgrade git+git://github.com/project-rig/rig.git@master
 
 install:
   - pip install -r requirements-test.txt
@@ -35,7 +51,8 @@ script:
   # Code quality check
   - flake8 pacman
   - flake8 integration_tests unittests uinit_test_objects
-  - find pacman -name '*.xml' | xargs -n 1 support/validate-xml.sh 
+  - find pacman -name '*.xml' | xargs -n 1 support/validate-xml.sh
+  - support/rat.sh run
   - cd doc/source
   - sphinx-build -T -E -b html -d _build/doctrees-readthedocsdirhtml -D language=en . _build/html
   - sphinx-build -T -b json -d _build/doctrees-json -D language=en . _build/json

CITATION.cff

@@ -0,0 +1,83 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+authors:
+- affiliation: University Of Manchester
+  email: alan.stokes-2@manchester.ac.uk
+  family-names: Stokes
+  given-names: Alan
+  orcid: https://orcid.org/0000-0002-6110-1484
+  website: http://www.cs.man.ac.uk/~stokesa6/
+- affiliation: University Of Manchester
+  email: Andrew.Rowley@manchester.ac.uk
+  family-names: Rowley
+  given-names: Andrew
+  orcid: https://orcid.org/0000-0002-2646-8520
+  website: https://www.researchgate.net/profile/Andrew_Rowley2
+- affiliation: University Of Manchester
+  email: christian.brenninkmeijer@manchester.ac.uk
+  family-names: Brenninkmeijer
+  given-names: Christian Y.
+  orcid: https://orcid.org/0000-0002-2937-7819
+  website: https://www.researchgate.net/profile/Christian_Brenninkmeijer
+- affiliation: University Of Manchester
+  email: donal.k.fellows@manchester.ac.uk
+  family-names: Fellows
+  given-names: Donal
+  orcid: https://orcid.org/0000-0002-9091-5938
+  website: http://www.cs.manchester.ac.uk/about-us/staff/profile/?ea=donal.k.fellows
+- affiliation: University Of Manchester
+  email: arthur.ceccotti@student.manchester.ac.uk
+  family-names: Ceccotti
+  given-names: Arthur
+  website: https://www.linkedin.com/in/arthur-ceccotti-07359483
+- affiliation: University Of Manchester
+  email: andrew.mundy@ieee.org
+  family-names: Mundy
+  given-names: Andrew
+  website: https://www.linkedin.com/in/andrew-mundy-56422627/
+- affiliation: University Of Manchester
+  email: petrut.bogdan@manchester.ac.uk
+  family-names: Bogdan
+  given-names: Petrut
+  orcid: https://orcid.org/0000-0001-5535-7865
+  website: https://personalpages.manchester.ac.uk/staff/petrut.bogdan/
+- affiliation: University Of Manchester
+  email: sara.summerton@student.manchester.ac.uk
+  family-names: Summerton
+  given-names: Sara
+  website: https://www.linkedin.com/in/sara-summerton-67723637/
+- affiliation: University Of Manchester
+  email: sergio.davies@gmail.com
+  family-names: Davies
+  given-names: Sergio
+  orcid: https://orcid.org/0000-0001-5330-5527
+  website: http://apt.cs.manchester.ac.uk/people/daviess/
+cff-version: 1.0.3
+contact:
+- address: University of Manchester, Oxford Road
+  city: Manchester
+  country: GB
+  name: SpiNNaker Software Team
+  post-code: M13 9PL
+date-released:
+email: spinnakerusers@googlegroups.com
+identifier:
+message: If you use this software, please cite it as below.
+repository: https://github.com/SpiNNakerManchester/PACMAN
+title: The Mapping algorthims from a graph to SpiNNaker machine data structures and
+  work flow manager for executing said algorithms
+url: http://spinnakermanchester.github.io/
+version:

MANIFEST.in

@@ -0,0 +1 @@
+include CITATION.cff LICENSE.md requirements.txt pypi_to_import

doc/Makefile

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 # Minimal makefile for Sphinx documentation
 #
 

doc/doc_requirements.txt

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 six
 enum34
 -e git+https://github.com/SpiNNakerManchester/SpiNNUtils.git@master#egg=spinn_utilities

doc/make.bat

@@ -1,5 +1,20 @@
 @ECHO OFF
 
+: Copyright (c) 2017-2019 The University of Manchester
+:
+: This program is free software: you can redistribute it and/or modify
+: it under the terms of the GNU General Public License as published by
+: the Free Software Foundation, either version 3 of the License, or
+: (at your option) any later version.
+:
+: This program is distributed in the hope that it will be useful,
+: but WITHOUT ANY WARRANTY; without even the implied warranty of
+: MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+: GNU General Public License for more details.
+:
+: You should have received a copy of the GNU General Public License
+: along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 pushd %~dp0
 
 REM Command file for Sphinx documentation

doc/source/conf.py

@@ -1,5 +1,20 @@
 # -*- coding: utf-8 -*-
 #
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
 # data_allocation documentation build configuration file, created by
 # sphinx-quickstart on Tue Jun 17 08:56:46 2014.
 #

integration_tests/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.

pacman/__init__.py

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """ Provides various functions which together can be used to take a graph and\
     split it into pieces that can be loaded on to a machine, along with\
     routes between the pieces.

pacman/_version.py

@@ -1,4 +1,20 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 __version__ = "1!4.0.1"
 __version_month__ = "September"
 __version_year__ = "2017"
+__version_day__ = "25"
 __version_name__ = "Riptalon"

pacman/exceptions.py

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 import traceback
 
 
@@ -245,3 +260,21 @@ class PacmanNoMergeException(PacmanException):
     """ An exception that indicates to indicate that there are no merges worth\
         performing.
     """
+
+
+class PacmanCanNotFindChipException(PacmanException):
+    """ An exception that indicates the chip was not in the list of chips.
+    """
+    def __init__(self, problem):
+        """
+        :param problem: The problem with the partitioning
+        :type problem: str
+        """
+        super(PacmanCanNotFindChipException, self).__init__(problem)
+
+
+class MachineHasDisconnectedSubRegion(PacmanException):
+    """Some part of the machine has no paths connecting it to the rest of the
+    machine.
+    """
+    pass

pacman/executor/__init__.py

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from .algorithm_metadata_xml_reader import AlgorithmMetadataXmlReader
 from .pacman_algorithm_executor import PACMANAlgorithmExecutor
 

pacman/executor/algorithm_classes/__init__.py

@@ -1,3 +1,18 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from .abstract_algorithm import AbstractAlgorithm
 from .abstract_python_algorithm import AbstractPythonAlgorithm
 from .external_algorithm import ExternalAlgorithm