Merge pull request #734 from glotzerlab/release/2.5.0

Release/2.5.0
glotzerlab · Mar 23, 2021 · 8151715 · 8151715
2 parents 6d1b0d5 + 42ccb1b
commit 8151715
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Showing 14 changed files with 95 additions and 57 deletions.
diff --git a/.circleci/deploy-linux.sh b/.circleci/deploy-linux.sh
@@ -27,12 +27,18 @@ if [ -z $1 ]; then
 fi
 
 # Build TBB
-git clone https://github.com/intel/tbb.git
-cd tbb
+cd ~/
+git clone https://github.com/oneapi-src/oneTBB.git
+cd oneTBB
+mkdir -p build
+cd build
+cmake ../ -DTBB_TEST=OFF
 make
-BUILD_DIR=$(find build -name linux*release)
+cmake -DCOMPONENT=runtime -P cmake_install.cmake
+cmake -DCOMPONENT=devel -P cmake_install.cmake
+BUILD_DIR=$(dirname $(find . -name vars.sh))
 cd ${BUILD_DIR}
-source tbbvars.sh
+source vars.sh
 cd ~/
 
 # Build wheels for Python 3.6, 3.7, 3.8, 3.9
@@ -44,18 +50,17 @@ for PYBIN in $PYBINS; do
   # Need to export the current bin path so that scikit-build can find the pip
   # installed cmake binary.
   export PATH=${PYBIN}:${PATH}
-  "${PYBIN}/python" -m pip install cython scikit-build cmake --ignore-installed -q --progress-bar=off
-  rm -rf numpy-1.14.6
-  curl -sSLO https://github.com/numpy/numpy/archive/v1.14.6.tar.gz
-  tar -xzf v1.14.6.tar.gz
-  cd numpy-1.14.6
-  rm -f numpy/random/mtrand/mtrand.c
-  rm -f PKG-INFO
-  "${PYBIN}/python" -m pip install . --no-deps --ignore-installed -v --progress-bar=off -q
+  "${PYBIN}/python" -m pip install cython scikit-build cmake oldest-supported-numpy --ignore-installed -q --progress-bar=off
   "${PYBIN}/pip" wheel ~/ci/freud/ -w ~/wheelhouse/ --no-deps --no-build-isolation --no-use-pep517
 done
 
-# Update RPath for wheels
+# Install patched auditwheel (fixes RPATHs for libfreud/libtbb, issue #136).
+cd ~/
+git clone https://github.com/pypa/auditwheel.git -b master auditwheel
+cd auditwheel
+/opt/_internal/tools/bin/pip install -e .
+
+# Update RPATH for wheels
 for whl in ~/wheelhouse/freud*.whl; do
   auditwheel repair "$whl" -w ~/ci/freud/wheelhouse/
 done
@@ -65,9 +70,14 @@ for PYBIN in $PYBINS; do
   echo "Testing for $(${PYBIN}/python --version)"
 
   "${PYBIN}/python" -m pip install freud_analysis --no-deps --no-index -f ~/ci/freud/wheelhouse
-  "${PYBIN}/python" -m pip install -U -r ~/ci/freud/requirements/requirements-test.txt --progress-bar=off
-  cd ~/ci/freud/tests
-  "${PYBIN}/python" -m unittest discover . -v
+  if [[ $("${PYBIN}/python" --version 2>&1) == *"3.6."* ]]; then
+    # Python 3.6 is only supported with oldest requirements
+    "${PYBIN}/python" -m pip install -U -r ~/ci/freud/.circleci/ci-oldest-reqs.txt --progress-bar=off
+  else
+    "${PYBIN}/python" -m pip install -U -r ~/ci/freud/requirements/requirements-test.txt --progress-bar=off
+  fi
+  cd ~/ci/freud/tests/
+  "${PYBIN}/python" -m pytest . -v
 done
 
 # Build source distribution using whichever Python appears last

diff --git a/.circleci/deploy-macos.sh b/.circleci/deploy-macos.sh
@@ -33,18 +33,25 @@ export MACOSX_DEPLOYMENT_TARGET=10.12
 # tries to delete them again and causes errors. To avoid this issue, we update
 # manually here for the current main version of Python (required by pyenv).
 brew upgrade [email protected]
+brew install cmake
 brew install pyenv
 eval "$(pyenv init -)"
 # Check supported versions with pyenv install --list
-PY_VERSIONS=(3.6.12 3.7.9 3.8.6 3.9.0)
+PY_VERSIONS=(3.6.13 3.7.10 3.8.7 3.9.1)
 
 # Build TBB
-git clone https://github.com/intel/tbb.git
-cd tbb
+cd ~/
+git clone https://github.com/oneapi-src/oneTBB.git
+cd oneTBB
+mkdir -p build
+cd build
+cmake ../ -DTBB_TEST=OFF
 make
-BUILD_DIR=$(find build -name mac*release)
+cmake -DCOMPONENT=runtime -P cmake_install.cmake
+cmake -DCOMPONENT=devel -P cmake_install.cmake
+BUILD_DIR=$(dirname $(find . -name vars.sh))
 cd ${BUILD_DIR}
-source tbbvars.sh
+source vars.sh
 # Force the TBB path to use an absolute path to itself for others to find.
 install_name_tool -id "${PWD}/libtbb.dylib" libtbb.dylib
 cd ~/
@@ -56,20 +63,11 @@ for VERSION in ${PY_VERSIONS[@]}; do
   pyenv global ${VERSION}
 
   pip install --upgrade pip
-  pip install cython scikit-build cmake --ignore-installed -q --progress-bar=off
-  rm -rf numpy-1.14.6
-  curl -sSLO https://github.com/numpy/numpy/archive/v1.14.6.tar.gz
-  tar -xzf v1.14.6.tar.gz
-  cd numpy-1.14.6
-  rm -f numpy/random/mtrand/mtrand.c
-  rm -f PKG-INFO
-  pip install . --no-deps --ignore-installed -v -q --progress-bar=off
-
-  pip install wheel delocate --progress-bar=off
+  pip install cython scikit-build cmake oldest-supported-numpy wheel delocate --ignore-installed -q --progress-bar=off
   pip wheel ~/ci/freud/ -w ~/wheelhouse/ --no-deps --no-build-isolation --no-use-pep517
 done
 
-# Update RPath for wheels
+# Update RPATH for wheels
 for whl in ~/wheelhouse/freud*.whl; do
   delocate-wheel "$whl" -w ~/ci/freud/wheelhouse/
 done
@@ -80,10 +78,15 @@ for VERSION in ${PY_VERSIONS[@]}; do
   pyenv global ${VERSION}
 
   pip install freud_analysis --no-deps --no-index -f ~/ci/freud/wheelhouse
-  # Don't install MDAnalysis and skip the relevant tests.
-  cat ~/ci/freud/requirements/requirements-test.txt | grep -v MDAnalysis | xargs -n 1 pip install -U --progress-bar=off
-  cd ~/ci/freud/tests
-  python -m unittest discover . -v
+  if [[ $(python --version 2>&1) == *"3.6."* ]]; then
+    # Python 3.6 is only supported with oldest requirements
+    pip install -U -r ~/ci/freud/.circleci/ci-oldest-reqs.txt --progress-bar=off --no-use-pep517 --no-build-isolation
+  else
+    # Don't install MDAnalysis and skip the relevant tests
+    cat ~/ci/freud/requirements/requirements-test.txt | grep -v MDAnalysis | xargs -n 1 pip install -U --progress-bar=off --no-use-pep517 --no-build-isolation
+  fi
+  cd ~/ci/freud/tests/
+  python -m pytest . -v
 done
 
 pip install --user twine

diff --git a/.mailmap b/.mailmap
@@ -30,8 +30,9 @@ Mayank Agrawal <[email protected]> Mayank Agrawal <[email protected].
 Mayank Agrawal <[email protected]> Mayank Agrawal <[email protected]>
 Jens Glaser <[email protected]> Jens-Steffen Glaser <[email protected]>
 Bryan VanSaders <[email protected]> Bryan Vansaders <[email protected]>
-Tim Moore <[email protected]> Timothy Moore <[email protected]>
-Tim Moore <[email protected]> mootimot <[email protected]>
+Tim Moore <[email protected]> Timothy Moore <[email protected]>
+Tim Moore <[email protected]> mootimot <[email protected]>
+Tim Moore <[email protected]> Tim Moore <[email protected]>
 Andrew Karas <[email protected]> Andrew Karas <[email protected]>
 Andrew Karas <[email protected]> Andrew <[email protected]>
 Alex Dutton <[email protected]> alxdttn <[email protected]>

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -110,3 +110,7 @@ set(ignoreMe "${SKBUILD}")
 
 add_subdirectory(cpp)
 add_subdirectory(freud)
+
+if(_using_conda)
+  set_target_properties(libfreud PROPERTIES INSTALL_RPATH_USE_LINK_PATH True)
+endif()
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -4,7 +4,7 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v2.5.0 - 2021-03-xx
+## v2.5.0 - 2021-03-16
 
 ### Changed
 * NeighborList `filter` method has been optimized.

diff --git a/contributors.txt b/contributors.txt
@@ -1,8 +1,8 @@
   2066	Vyas Ramasubramani <[email protected]>
-  1773	Bradley Dice <[email protected]>
+  1862	Bradley Dice <[email protected]>
   1030	Eric Harper <[email protected]>
    456	Jin Soo Ihm <[email protected]>
-   278	Joshua A. Anderson <[email protected]>
+   281	Joshua A. Anderson <[email protected]>
    240	Matthew Spellings <[email protected]>
    159	Kelly Wang <[email protected]>
    110	Erin Teich <[email protected]>
@@ -12,13 +12,13 @@
     41	Yezhi Jin <[email protected]>
     40	Antonio Osorio <[email protected]>
     35	Michael Stryk <[email protected]>
+    35	dependabot <dependabot[bot]@users.noreply.github.com>
     31	Richmond Newman <[email protected]>
     30	Tommy Waltmann <[email protected]>
     25	Carl Simon Adorf <[email protected]>
     22	Jens Glaser <[email protected]>
-    17	dependabot <dependabot[bot]@users.noreply.github.com>
+    14	Tim Moore <[email protected]>
     13	Pavel Buslaev <[email protected]>
-    12	Tim Moore <[email protected]>
     10	Benjamin Schultz <[email protected]>
     10	Bryan VanSaders <[email protected]>
     10	Matt Palathingal <[email protected]>

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -70,8 +70,8 @@
 # built documents.
 #
 # version and release are set the same for this package.
-version = "2.4.1"
-release = "2.4.1"
+version = "2.5.0"
+release = "2.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -319,6 +319,7 @@
     "garnett": ("https://garnett.readthedocs.io/en/stable/", None),
     "MDAnalysis": ("https://docs.mdanalysis.org/stable", None),
     "ovito": ("https://www.ovito.org/docs/current/python/", None),
+    "pytest": ("https://docs.pytest.org/en/stable", None),
 }
 
 autodoc_default_options = {

diff --git a/doc/source/gettingstarted/installation.rst b/doc/source/gettingstarted/installation.rst
@@ -125,13 +125,13 @@ The **freud** CMake configuration also respects the following environment variab
 Unit Tests
 ==========
 
-The unit tests for **freud** are included in the repository and are configured to be run using the Python :mod:`unittest` library:
+The unit tests for **freud** are included in the repository and are configured to be run using the Python :mod:`pytest` library:
 
 .. code-block:: bash
 
     # Run tests from the tests directory
     cd tests
-    python -m unittest discover .
+    python -m pytest .
 
 Note that because **freud** is designed to require installation to run (i.e. it cannot be run directly out of the build directory), importing **freud** from the root of the repository will fail because it will try and import the package folder.
 As a result, unit tests must be run from outside the root directory if you wish to test the installed version of **freud**.

diff --git a/doc/source/reference/development/design.rst b/doc/source/reference/development/design.rst
@@ -26,7 +26,7 @@ In order to achieve this goal, **freud** takes the following viewpoints:
   standard for code, stressing explicitly written code which is easy
   to read.
 * To ensure correctness, **freud** employs unit testing using the
-  Python unittest framework. In addition, **freud** utilizes
+  Python :mod:`pytest` framework. In addition, **freud** utilizes
   `CircleCI <https://circleci.com>`_ for continuous integration to
   ensure that all of its code works correctly and that any changes or
   new features do not break existing functionality.

diff --git a/doc/source/reference/development/howtoadd.rst b/doc/source/reference/development/howtoadd.rst
@@ -63,7 +63,7 @@ To keep modules well-organized, **freud** implements the following structure:
 - The core Cython code for modules is contained in ``freud/MODULENAME.pyx`` (no underscore).
 - Generated Cython C++ code (e.g. ``freud/MODULENAME.cxx``) should not be committed during development. These files are generated using Cython when building from source, and are unnecessary when installing compiled binaries.
 - If a Cython module contains code that must be imported into other Cython modules (such as the :class:`freud.box.Box` class), the ``pyx`` file must be accompanied by a ``pxd`` file with the same name: ``freud/MODULENAME.pxd`` (distinguished from ``pxd`` files used to expose C++ code by the lack of a preceding underscore). For more information on how ``pxd`` files work, see the `Cython documentation <https://cython.readthedocs.io/en/latest/src/tutorial/pxd_files.html>`_.
-- All tests in **freud** are based on the Python standard :mod:`unittest` library and are contained in the ``tests`` folder. Test files are named by the convention ``tests/test_MODULENAME_CLASSNAME.py``.
+- All tests in **freud** are based on the Python :mod:`pytest` library and are contained in the ``tests`` folder. Test files are named by the convention ``tests/test_MODULENAME_CLASSNAME.py``.
 - Benchmarks for **freud** are contained in the ``benchmarks`` directory and are named analogously to tests: ``benchmarks/benchmark_MODULENAME_CLASSNAME.py``.
 
 Benchmarks

diff --git a/freud/CMakeLists.txt b/freud/CMakeLists.txt
@@ -32,6 +32,22 @@ if(${PYTHON_VERSION_MAJOR} EQUAL 3
   add_compile_options("-Wno-deprecated-declarations")
 endif()
 
+# Detect when building against a conda environment set the _using_conda variable
+# for use both in this file and in the parent
+get_filename_component(_python_bin_dir ${PYTHON_EXECUTABLE} DIRECTORY)
+if(EXISTS "${_python_bin_dir}/conda" OR DEFINED ENV{CONDA_EXE})
+  message("-- Detected conda python, setting INSTALL_RPATH_USE_LINK_PATH")
+  set(_using_conda On)
+  set(_using_conda
+      On
+      PARENT_SCOPE)
+else()
+  set(_using_conda Off)
+  set(_using_conda
+      Off
+      PARENT_SCOPE)
+endif()
+
 set(cython_modules_with_cpp
     box
     cluster
@@ -86,8 +102,11 @@ foreach(cython_module ${cython_modules_with_cpp} ${cython_modules_without_cpp})
   else()
     set_target_properties(${cython_module} PROPERTIES INSTALL_RPATH "\$ORIGIN")
   endif()
-  set_target_properties(${cython_module} PROPERTIES INSTALL_RPATH_USE_LINK_PATH
-                                                    True)
+
+  if(_using_conda)
+    set_target_properties(${cython_module}
+                          PROPERTIES INSTALL_RPATH_USE_LINK_PATH True)
+  endif()
 endforeach()
 
 # The SolidLiquid class has an instance of cluster::Cluster as a member, so

diff --git a/freud/__init__.py b/freud/__init__.py
@@ -23,7 +23,7 @@
 # automatic selection runs, the user cannot change it.
 set_num_threads(0)
 
-__version__ = "2.4.1"
+__version__ = "2.5.0"
 
 __all__ = [
     "__version__",

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.4.1
+current_version = 2.5.0
 commit = True
 tag = True
 message = Bump up to version {new_version}.
@@ -10,7 +10,7 @@ filename = *.py,*.pyx,*.pxi,*.pxd
 exclude = .eggs,*.egg,build,extern,doc/source/gettingstarted/examples
 select = E,F,W
 ignore = E203,E225,E226,E227,E741,E999,W503,W504
-per-file-ignores =
+per-file-ignores = 
 	freud/__init__.py: F401
 
 [tool:pytest]

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 from skbuild import setup as skbuild_setup
 
-version = "2.4.1"
+version = "2.5.0"
 
 # Read README for PyPI, fallback to short description if it fails.
 description = "Powerful, efficient trajectory analysis in scientific Python."
@@ -84,9 +84,9 @@ def setup(*args, **kwargs):
     },
     python_requires=">=3.6",
     install_requires=[
-        "cython>=0.29",
+        "cython>=0.29.14",
         "numpy>=1.14",
-        "rowan>=1.2",
+        "rowan>=1.2.1",
         "scipy>=1.1",
     ],
     tests_require=[