From f9b53c669c2da13c76240e7f9c4215d821205adf Mon Sep 17 00:00:00 2001 From: Tommy Waltmann Date: Thu, 14 Sep 2023 10:54:15 -0400 Subject: [PATCH 1/6] update submodules, put date in changelog --- ChangeLog.md | 2 +- doc/source/gettingstarted/examples | 2 +- doc/source/gettingstarted/installation.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index e0c845481..d40489869 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,7 +4,7 @@ The format is based on and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.13.1 -- YYYY-MM-DD +## v2.13.1 -- 2023-09-14 ### Added * The `gsd.hoomd.Frame` class is supported as a system-like input. diff --git a/doc/source/gettingstarted/examples b/doc/source/gettingstarted/examples index afd4316b1..ea5305887 160000 --- a/doc/source/gettingstarted/examples +++ b/doc/source/gettingstarted/examples @@ -1 +1 @@ -Subproject commit afd4316b1a412973cf3fe71900755db8f23cd2dd +Subproject commit ea53058875509dbad50094329e574e8830e678a8 diff --git a/doc/source/gettingstarted/installation.rst b/doc/source/gettingstarted/installation.rst index 737166abe..af5067a84 100644 --- a/doc/source/gettingstarted/installation.rst +++ b/doc/source/gettingstarted/installation.rst @@ -36,7 +36,7 @@ The following are **required** for building and installing **freud** from source - `Python `__ (>=3.7) - `NumPy `__ (>=1.14) - `Intel Threading Building Blocks `__ (>=2019.7) -- `Cython `__ (>=0.29.14) +- `Cython `__ (>=3.0.2) - `scikit-build `__ (>=0.10.0) - `CMake `__ (>=3.13.0) From 8c0b8e8bb611bb0b9dba02be869aa4dec3a1c37b Mon Sep 17 00:00:00 2001 From: Tommy Waltmann Date: Thu, 14 Sep 2023 10:57:10 -0400 Subject: [PATCH 2/6] update contributors list --- contributors.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/contributors.txt b/contributors.txt index 6545fc2a3..bf0683dd2 100644 --- a/contributors.txt +++ b/contributors.txt @@ -1,17 +1,17 @@ 2357 Bradley Dice 2148 Vyas Ramasubramani 1030 Eric Harper - 690 Tommy Waltmann + 786 Tommy Waltmann 456 Jin Soo Ihm 318 Joshua A. Anderson 240 Matthew Spellings - 207 dependabot - 168 DomFijan + 235 dependabot + 173 DomFijan 167 Kelly Wang 110 Erin Teich 98 Brandon Butler 94 Charlotte Shiqi Zhao - 72 pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> + 76 pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 66 M. Eric Irrgang 53 Chrisy Du 41 Yezhi Jin From 5f967e24d843d0dff08b6ce7f524228af87c997e Mon Sep 17 00:00:00 2001 From: Tommy Waltmann Date: Thu, 14 Sep 2023 11:04:11 -0400 Subject: [PATCH 3/6] update pre commit hook versions --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 677ed960e..0525333c3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -56,7 +56,7 @@ repos: - --add=This file is from the freud project, released under the BSD 3-Clause License. - --comment-prefix=// - repo: https://github.com/asottile/pyupgrade - rev: 'v3.8.0' + rev: 'v3.10.1' hooks: - id: pyupgrade args: @@ -66,11 +66,11 @@ repos: hooks: - id: isort - repo: https://github.com/psf/black - rev: '23.3.0' + rev: '23.9.1' hooks: - id: black - repo: https://github.com/PyCQA/flake8 - rev: '6.0.0' + rev: '6.1.0' hooks: - id: flake8 types: ["file"] From 562ebaaed47bb753306bee8ae8a615f76a9b97ae Mon Sep 17 00:00:00 2001 From: Tommy Waltmann Date: Thu, 14 Sep 2023 16:39:34 -0400 Subject: [PATCH 4/6] appease newest flake8 version --- freud/density.pyx | 4 ++-- freud/diffraction.pyx | 8 ++++---- freud/locality.pyx | 16 ++++++++-------- tests/test_order_Steinhardt.py | 2 +- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/freud/density.pyx b/freud/density.pyx index 59c917876..c0556dcb2 100644 --- a/freud/density.pyx +++ b/freud/density.pyx @@ -611,7 +611,7 @@ cdef class RDF(_SpatialHistogram1D): def __cinit__(self, unsigned int bins, float r_max, float r_min=0, normalize=False): - if type(self) == RDF: + if type(self) is RDF: self.thisptr = self.histptr = new freud._density.RDF( bins, r_max, r_min, normalize) @@ -621,7 +621,7 @@ cdef class RDF(_SpatialHistogram1D): self.r_max = r_max def __dealloc__(self): - if type(self) == RDF: + if type(self) is RDF: del self.thisptr def compute(self, system, query_points=None, neighbors=None, diff --git a/freud/diffraction.pyx b/freud/diffraction.pyx index e6558a069..c831da5b0 100644 --- a/freud/diffraction.pyx +++ b/freud/diffraction.pyx @@ -144,14 +144,14 @@ cdef class StaticStructureFactorDebye(_StaticStructureFactor): cdef freud._diffraction.StaticStructureFactorDebye * thisptr def __cinit__(self, unsigned int num_k_values, float k_max, float k_min=0): - if type(self) == StaticStructureFactorDebye: + if type(self) is StaticStructureFactorDebye: self.thisptr = self.ssfptr = new \ freud._diffraction.StaticStructureFactorDebye(num_k_values, k_max, k_min) def __dealloc__(self): - if type(self) == StaticStructureFactorDebye: + if type(self) is StaticStructureFactorDebye: del self.thisptr @property @@ -371,13 +371,13 @@ cdef class StaticStructureFactorDirect(_StaticStructureFactor): def __cinit__(self, unsigned int bins, float k_max, float k_min=0, unsigned int num_sampled_k_points=0): - if type(self) == StaticStructureFactorDirect: + if type(self) is StaticStructureFactorDirect: self.thisptr = self.ssfptr = \ new freud._diffraction.StaticStructureFactorDirect( bins, k_max, k_min, num_sampled_k_points) def __dealloc__(self): - if type(self) == StaticStructureFactorDirect: + if type(self) is StaticStructureFactorDirect: del self.thisptr @property diff --git a/freud/locality.pyx b/freud/locality.pyx index f53aa314b..e373532a5 100644 --- a/freud/locality.pyx +++ b/freud/locality.pyx @@ -43,7 +43,7 @@ cdef class _QueryArgs: def __cinit__(self, mode=None, r_min=None, r_max=None, r_guess=None, num_neighbors=None, exclude_ii=None, scale=None, **kwargs): - if type(self) == _QueryArgs: + if type(self) is _QueryArgs: self.thisptr = new freud._locality.QueryArgs() self.mode = mode if r_max is not None: @@ -67,7 +67,7 @@ cdef class _QueryArgs: err_str) def __dealloc__(self): - if type(self) == _QueryArgs: + if type(self) is _QueryArgs: del self.thisptr def update(self, qargs): @@ -854,7 +854,7 @@ def _make_default_nlist(system, neighbors, query_points=None): NeighborQuery nq NeighborList nlist - if type(neighbors) == NeighborList: + if type(neighbors) is NeighborList: return neighbors else: query_args = neighbors.copy() @@ -1008,10 +1008,10 @@ cdef class _PairCompute(_Compute): return (nq, nlist, qargs, l_query_points, num_query_points) def _resolve_neighbors(self, neighbors, query_points=None): - if type(neighbors) == NeighborList: + if type(neighbors) is NeighborList: nlist = neighbors qargs = _QueryArgs() - elif neighbors is None or type(neighbors) == dict: + elif neighbors is None or type(neighbors) is dict: # The default_query_args property must raise a NotImplementedError # if no query arguments were passed in and the class has no # reasonable choice of defaults. @@ -1359,7 +1359,7 @@ cdef class Filter(_PairCompute): This class is abstract and should not be instantiated directly. """ def __cinit__(self): - if type(self) == Filter: + if type(self) is Filter: raise RuntimeError( "The Filter class is abstract and should not be instantiated directly." ) @@ -1460,7 +1460,7 @@ cdef class FilterSANN(Filter): new freud._locality.FilterSANN(allow_incomplete_shell) def __dealloc__(self): - if type(self) == FilterSANN: + if type(self) is FilterSANN: del self._thisptr cdef class FilterRAD(Filter): @@ -1521,5 +1521,5 @@ cdef class FilterRAD(Filter): ) def __dealloc__(self): - if type(self) == FilterRAD: + if type(self) is FilterRAD: del self._thisptr diff --git a/tests/test_order_Steinhardt.py b/tests/test_order_Steinhardt.py index ebd26b823..0d396b44e 100644 --- a/tests/test_order_Steinhardt.py +++ b/tests/test_order_Steinhardt.py @@ -223,7 +223,7 @@ def test_weighted(self, wt): # Skip test sets without an explicit neighbor list for nq, neighbors in filter( - lambda ts: type(ts[1]) == freud.locality.NeighborList, test_set + lambda ts: type(ts[1]) is freud.locality.NeighborList, test_set ): nlist = neighbors From 1dfe85bde380c3ec4ccd0058543922e10e3308e0 Mon Sep 17 00:00:00 2001 From: Tommy Waltmann Date: Thu, 14 Sep 2023 16:42:08 -0400 Subject: [PATCH 5/6] Bump up to version 2.13.1. --- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- doc/source/conf.py | 4 ++-- freud/__init__.py | 2 +- setup.cfg | 3 ++- setup.py | 2 +- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index c1ede9967..30e606b2d 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -26,7 +26,7 @@ body: attributes: label: freud Version description: What version of freud are you using? - placeholder: v2.13.0 + placeholder: v2.13.1 validations: required: true - type: input diff --git a/doc/source/conf.py b/doc/source/conf.py index 773b95f2d..44b018fb2 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -72,8 +72,8 @@ # built documents. # # version and release are set the same for this package. -version = "2.13.0" -release = "2.13.0" +version = "2.13.1" +release = "2.13.1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/freud/__init__.py b/freud/__init__.py index 95aea03ec..443994c69 100644 --- 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__ = "2.13.0" +__version__ = "2.13.1" __all__ = [ "__version__", diff --git a/setup.cfg b/setup.cfg index ea0fcf95a..e2695174e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 2.13.0 +current_version = 2.13.1 commit = True tag = False message = Bump up to version {new_version}. @@ -36,3 +36,4 @@ ignore_errors = True [coverage:html] directory = coverage_html_report + diff --git a/setup.py b/setup.py index 03b56f992..e0a56112e 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ from skbuild import setup -version = "2.13.0" +version = "2.13.1" # Read README for PyPI, fallback to short description if it fails. description = "Powerful, efficient trajectory analysis in scientific Python." From dad014e52406c4125b1ab3efd712ed59bc31c9d5 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 14 Sep 2023 20:45:00 +0000 Subject: [PATCH 6/6] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- setup.cfg | 1 - 1 file changed, 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e2695174e..abb9dff91 100644 --- a/setup.cfg +++ b/setup.cfg @@ -36,4 +36,3 @@ ignore_errors = True [coverage:html] directory = coverage_html_report -