Merge remote-tracking branch 'pyop2/master' into JDBetteridge/merge_p…

…yop2_tsfc

.gitattributes

@@ -1 +1,9 @@
+# Set default behaviour, in case users don't have core.autocrlf set.
+* text=auto
+
+# Whitespace
+* whitespace=tab-in-indent,space-before-tab,trailing-space,tabwidth=2
+*.{py,pyx,pxd,pxi} whitespace=tab-in-indent,space-before-tab,trailing-space,tabwidth=4
+Makefile whitespace=space-before-tab,trailing-space,tabwidth=2
+pyop2/_version.py export-subst
 firedrake/_version.py export-subst

.github/workflows/ci.yml

@@ -0,0 +1,123 @@
+name: CI
+
+# Trigger the workflow on push or pull request,
+# but only for the master branch
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      # Don't immediately kill all if one Python version fails
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    env:
+      CC: mpicc
+      PETSC_DIR: ${{ github.workspace }}/petsc
+      PETSC_ARCH: default
+      PETSC_CONFIGURE_OPTIONS: --with-debugging=1 --with-shared-libraries=1 --with-c2html=0 --with-fortran-bindings=0
+      RDMAV_FORK_SAFE: 1
+      PYOP2_CI_TESTS: 1
+    timeout-minutes: 60
+
+    steps:
+      - name: Install system dependencies
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt install build-essential mpich libmpich-dev \
+              libblas-dev liblapack-dev gfortran
+
+      - name: Set correct Python version
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Clone PETSc
+        uses: actions/checkout@v2
+        with:
+          repository: firedrakeproject/petsc
+          path: ${{ env.PETSC_DIR }}
+
+      - name: Build and install PETSc
+        shell: bash
+        working-directory: ${{ env.PETSC_DIR }}
+        run: |
+          ./configure ${PETSC_CONFIGURE_OPTIONS}
+          make
+
+      - name: Build and install petsc4py
+        shell: bash
+        working-directory: ${{ env.PETSC_DIR }}/src/binding/petsc4py
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade wheel cython numpy
+          python -m pip install --no-deps .
+
+      - name: Checkout PyOP2
+        uses: actions/checkout@v2
+        with:
+          path: PyOP2
+
+      - name: Install PyOP2 dependencies
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          # xargs is used to force installation of requirements in the order we specified.
+          xargs -l1 python -m pip install < requirements-ext.txt
+          xargs -l1 python -m pip install < requirements-git.txt
+          python -m pip install pulp
+          python -m pip install -U flake8
+          python -m pip install -U pytest-timeout
+
+      - name: Install PyOP2 (Python <3.12)
+        if: ${{ matrix.python-version != '3.12' }}
+        shell: bash
+        working-directory: PyOP2
+        run: python -m pip install .
+
+        # Not sure if this is a bug in setuptools or something PyOP2 is doing wrong
+      - name: Install PyOP2 (Python == 3.12)
+        if: ${{ matrix.python-version == '3.12' }}
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          python -m pip install -U setuptools
+          python setup.py install
+
+      - name: Run linting
+        shell: bash
+        working-directory: PyOP2
+        run: make lint
+
+      - name: Run tests
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          # Running parallel test cases separately works around a bug in pytest-mpi
+          pytest -k "not parallel" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v test
+          mpiexec -n 3 pytest -k "parallel[3]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v test
+        timeout-minutes: 10
+
+      - name: Build documentation
+        if: ${{ matrix.python-version == '3.10' }}
+        shell: bash
+        working-directory: PyOP2
+        run: |
+          python -m pip install sphinx
+          make -C doc/sphinx html
+      - name: Upload to github pages
+        if: ${{ github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.python-version== '3.10' }}
+        uses: crazy-max/[email protected]
+        with:
+          build_dir: PyOP2/doc/sphinx/build/html
+          jekyll: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -43,3 +43,34 @@ __pycache__/
 /firedrake_configuration/configuration.json
 /firedrake.egg-info
 /docs/source/element_list.csv
+
+
+# Build
+build
+dist
+MANIFEST
+PyOP2.egg-info
+*.py[cdo]
+
+# Extension modules
+sparsity.so
+sparsity.c
+sparsity.cpython*.so
+# Docs
+pyop2.coffee.rst
+pyop2.rst
+pyop2.pdf
+pyop2.aux
+pyop2.log
+
+# Testing
+.pytest-incremental
+.tox
+.vagrant
+
+# Meshes
+*.edge
+*.ele
+*.msh
+*.node
+*.geo

.mailmap

@@ -124,3 +124,22 @@ Joe Wallwork <[email protected]>
 Jingmin Xia <[email protected]>
 Jingmin Xia <[email protected]> <[email protected]>
 
+Gheorghe-Teodor Bercea <[email protected]> <foraker.doc.ic.ac.uk>
+George Boutsioukis <[email protected]>
+David A Ham <[email protected]>
+David A Ham <[email protected]> <[email protected]>
+Miklós Homolya <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Nicolas Loriant <[email protected]> <[email protected]>
+Fabio Luporini <[email protected]> <[email protected]>
+Graham Markall <[email protected]> <[email protected]>
+Graham Markall <[email protected]> <[email protected]>
+Andrew McRae <[email protected]> <[email protected]>
+Andrew McRae <[email protected]> <[email protected]>
+Lawrence Mitchell <[email protected]> <[email protected]>
+Lawrence Mitchell <[email protected]> <[email protected]>
+Kaho Sato <[email protected]>
+Reuben W. Nixon-Hill <[email protected]> <[email protected]>

AUTHORS

@@ -0,0 +1,24 @@
+PyOP2 has received contributions from the following:
+
+Institutions
+------------
+
+Imperial College London
+The University of Edinburgh
+
+Individuals
+-----------
+
+Gheorghe-Teodor Bercea  <[email protected]>
+Simon Funke             <[email protected]>
+Ben Grabham             <[email protected]>
+David A Ham             <[email protected]>
+Nicolas Loriant         <[email protected]>
+Fabio Luporini          <[email protected]>
+Graham Markall          <[email protected]>
+Lawrence Mitchell       <[email protected]>
+Florian Rathgeber       <[email protected]>
+Francis Russell         <[email protected]>
+Kaho Sato               <[email protected]>
+Reuben W. Nixon-Hill    <[email protected]>
+Nacime Bouziani         <[email protected]>

CONTRIBUTING.md

@@ -0,0 +1,60 @@
+# Contributing to PyOP2
+
+We value third-party contributions. To keep things simple for you and us,
+please adhere to the following contributing guidelines.
+
+## Getting Started
+
+* You will need a [GitHub account](https://github.com/signup/free).
+* Submit a [ticket for your issue][0], assuming one does not already exist.
+  * Clearly describe the issue including steps to reproduce when it is a bug.
+  * Make sure you specify the version that you know has the issue.
+  * Bonus points for submitting a failing test along with the ticket.
+* If you don't have push access, fork the repository on GitHub.
+
+## Making Changes
+
+* Create a topic branch for your feature or bug fix.
+* Make commits of logical units.
+* Make sure your commits adhere to the coding guidelines below.
+* Make sure your commit messages are in the [proper format][1]: The first line
+  of the message should have 50 characters or less, separated by a blank line
+  from the (optional) body. The body should be wrapped at 70 characters and
+  paragraphs separated by blank lines. Bulleted lists are also fine.
+* Make sure you have added the necessary tests for your changes.
+* Run _all_ the tests to assure nothing else was accidentally broken.
+
+## Coding guidelines
+
+[PEP 0008][2] is enforced, with the exception of [E501][3] and [E226][3]:
+* Indent by 4 spaces, tabs are *strictly forbidden*.
+* Lines should not exceed 79 characters where possible without severely
+  impacting legibility. If breaking a line would make the code much less
+  readable it's fine to overrun by a little bit.
+* No trailing whitespace at EOL or trailing blank lines at EOF.
+
+## Checking your commit conforms to coding guidelines
+
+Install a Git pre-commit hook automatically checking for tab and whitespace
+errors before committing and also calls `flake8` on your changed files. In the
+`.git/hooks` directory of your local Git repository, run the following:
+
+```
+git config --local core.whitespace "space-before-tab, tab-in-indent, trailing-space, tabwidth=4"
+wget https://gist.github.com/kynan/d233073b66e860c41484/raw/pre-commit
+chmod +x pre-commit
+```
+
+Make sure the `pre-commit.sample` hook is still in place, since it is required.
+
+## Submitting Changes
+
+* We can only accept your contribution if you have signed the Contributor
+  License Agreement (CLA).
+* Push your changes to a topic branch in your fork of the repository.
+* Submit a pull request to the repository in the OP2 organization.
+
+[0]: https://github.com/OP2/PyOP2/issues
+[1]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
+[2]: http://www.python.org/dev/peps/pep-0008/
+[3]: http://pep8.readthedocs.org/en/latest/intro.html#error-codes

LICENSE

@@ -1,3 +1,4 @@
+Firedrake:
 Firedrake is free software: you can redistribute it and/or modify it under
 the terms of the GNU Lesser General Public License as published by the
 Free Software Foundation, either version 3 of the License, or (at your
@@ -11,3 +12,33 @@ License for more details.
 You should have received a copy of the GNU Lesser General Public
 License along with Firedrake. If not, see <http://www.gnu.org/licenses/>.
 
+PyOP2:
+Copyright (c) 2012, Imperial College London and others. Please see the
+AUTHORS file in the main source directory for a full list of copyright
+holders.  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * The name of Imperial College London or that of other
+      contributors may not be used to endorse or promote products
+      derived from this software without specific prior written
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTERS
+''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.

MANIFEST.in

@@ -1,2 +1,5 @@
 include versioneer.py
 include firedrake/_version.py
+recursive-include pyop2 *.c
+include pyop2/_version.py
+

Makefile

@@ -95,3 +95,73 @@ alltest: modules lint test
 shorttest: modules lint
 	@echo "    Running short regression tests"
 	@python -m pytest --short tests $(PYTEST_ARGS)
+
+# PyOP2 Makefile
+# PYTEST = py.test
+#
+# TEST_BASE_DIR = test
+#
+# UNIT_TEST_DIR = $(TEST_BASE_DIR)/unit
+#
+# SPHINX_DIR = doc/sphinx
+# SPHINX_BUILD_DIR = $(SPHINX_DIR)/build
+# SPHINX_TARGET = html
+# SPHINX_TARGET_DIR = $(SPHINX_BUILD_DIR)/$(SPHINX_TARGET)
+# SPHINXOPTS = -a
+#
+# PORT = 8000
+#
+# MESHES_DIR = demo/meshes
+#
+# GIT_REV = $(shell git rev-parse --verify --short HEAD)
+#
+# all: ext
+#
+# .PHONY : help test lint unit doc update_docs ext ext_clean meshes
+#
+# help:
+# 	@echo "make COMMAND with COMMAND one of:"
+# 	@echo "  test               : run lint and unit tests"
+# 	@echo "  lint               : run flake8 code linter"
+# 	@echo "  unit               : run unit tests"
+# 	@echo "  unit_BACKEND       : run unit tests for BACKEND"
+# 	@echo "  doc                : build sphinx documentation"
+# 	@echo "  serve              : launch local web server to serve up documentation"
+# 	@echo "  update_docs        : build sphinx documentation and push to GitHub"
+# 	@echo "  ext                : rebuild Cython extension"
+# 	@echo "  ext_clean          : delete generated extension"
+# 	@echo "  meshes             : download demo meshes"
+# 	@echo
+# 	@echo "Available OpenCL contexts: $(OPENCL_CTXS)"
+#
+# test: lint unit
+#
+# lint:
+# 	@flake8
+#
+# unit:
+# 	cd $(TEST_BASE_DIR); $(PYTEST) unit
+#
+# doc:
+# 	make -C $(SPHINX_DIR) $(SPHINX_TARGET) SPHINXOPTS=$(SPHINXOPTS)
+#
+# serve:
+# 	make -C $(SPHINX_DIR) livehtml
+#
+# update_docs:
+# 	if [ ! -d $(SPHINX_TARGET_DIR)/.git ]; then \
+# 	mkdir -p $(SPHINX_BUILD_DIR); \
+# 	cd $(SPHINX_BUILD_DIR); git clone `git config --get remote.origin.url` $(SPHINX_TARGET); \
+# fi
+# 	cd $(SPHINX_TARGET_DIR); git fetch -p; git checkout -f gh-pages; git reset --hard origin/gh-pages
+# 	make -C $(SPHINX_DIR) $(SPHINX_TARGET) SPHINXOPTS=$(SPHINXOPTS)
+# 	cd $(SPHINX_TARGET_DIR); git add .; git commit -am "Update documentation to revision $(GIT_REV)"; git push origin gh-pages
+#
+# ext: ext_clean
+# 	python setup.py build_ext -i
+#
+# ext_clean:
+# 	rm -rf build pyop2/compute_ind.c pyop2/compute_ind.so pyop2/sparsity.c pyop2/sparsity.so
+#
+# meshes:
+# 	make -C $(MESHES_DIR) meshes

doc/Makefile

@@ -0,0 +1,2 @@
+all:
+	pdflatex pyop2.tex