merge branch master into next

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,60 @@
+name: Bug Report
+description: Report a bug in freud.
+labels: ['bug']
+body:
+  - type: textarea
+    attributes:
+      label: Description
+      description: A clear and concise description of the bug.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to Reproduce
+      description: Please provide a *minimal* script to reproduce the bug.
+      render: python
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Error Output
+      description: Please indicate the output from the above script and what you expect the output to be.
+      render: shell
+    validations:
+      required: true
+  - type: input
+    attributes:
+      label: freud Version
+      description: What version of freud are you using?
+      placeholder: v2.12.0
+    validations:
+      required: true
+  - type: input
+    attributes:
+      label: Python Version
+      description: What version of python are you using?
+      placeholder: v3.8.2
+  - type: dropdown
+    attributes:
+      label: System Platform
+      description: What platform are you using?
+      options:
+        - MacOS
+        - Linux
+        - Windows
+  - type: dropdown
+    attributes:
+      label: Installation method
+      description: How did you install freud?
+      options:
+        - Download from PyPI
+        - Download from conda-forge
+        - glotzerlab-software container
+        - built from source
+  - type: dropdown
+    attributes:
+      label: Developer
+      description: Who should fix this?
+      options:
+        - I will submit a pull request that fixes this problem.
+        - Would someone else please fix this?

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: freud users mailing list
+    url: https://groups.google.com/d/forum/freud-users
+    about: Ask for support from the freud user community.
+  - name: freud documentation
+    url: https://freud.readthedocs.io/
+    about: User documentation.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,27 @@
+name: Feature Request
+description: Suggest a new feature for freud
+labels: ['enhancement']
+body:
+  - type: textarea
+    attributes:
+      label: Description
+      description: What new feature would be useful to add to freud?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed Solution
+      description: How should this new feature be implemented? What should a script using this feature look like?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+        label: Additional Context
+        description: What additional information is useful to understand this request?
+  - type: dropdown
+    attributes:
+      label: Developer
+      description: Who should implement the new feature?
+      options:
+        - I will submit a pull request that implements this feature.
+        - Would someone else please implement this?

.github/ISSUE_TEMPLATE/task.yml

@@ -0,0 +1,16 @@
+name: Task
+description: A task that needs to be done
+labels: ['task']
+body:
+  - type: textarea
+    attributes:
+      label: Description
+      description: What task needs to be done?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Motivation and Context
+      description: Please describe why this task needs to be done.
+    validations:
+      required: true

.github/dependabot.yml

@@ -1,6 +1,6 @@
 version: 2
 updates:
-  - package-ecosystem: pip
+  - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "monthly"

.github/workflows/build_wheels.yml

@@ -30,12 +30,12 @@ jobs:
         pyver: ["3.6", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v3.0.2
+      - uses: actions/checkout@v3.1.0
         with:
           submodules: "recursive"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.8.1
+        uses: pypa/cibuildwheel@v2.11.2
         env:
           # Build for cpython >= 3.6.
           CIBW_PROJECT_REQUIRES_PYTHON: "==${{ matrix.pyver }}.*"
@@ -72,7 +72,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ contains(github.event.pull_request.labels.*.name, 'build_wheels') || github.event_name != 'pull_request' }}
     steps:
-      - uses: actions/checkout@v3.0.2
+      - uses: actions/checkout@v3.1.0
         with:
           submodules: "recursive"
 

.github/workflows/cibuildwheel-before-test.sh

@@ -8,12 +8,12 @@ PACKAGE_DIR=$1
 
 if [[ $(python --version 2>&1) == *"3.6."* ]]; then
   # Python 3.6 is only supported with oldest requirements
-  pip install -U -r "${PACKAGE_DIR}/.github/workflows/env-files/oldest-test-reqs.txt" --progress-bar=off
+  pip install -U -r "${PACKAGE_DIR}/.github/workflows/oldest-test-reqs.txt" --progress-bar=off
 elif [[ $(python --version 2>&1) == *"3.7."* ]]; then
   # Python 3.7 was dropped by NEP 29 so not compatible with some of the newest dependencies
-  pip install -U -r "${PACKAGE_DIR}/.github/workflows/env-files/requirements-test-compatible.txt" --progress-bar=off
+  pip install -U -r "${PACKAGE_DIR}/requirements/requirements-test-compatible.txt" --progress-bar=off
 else
-  pip install -U -r "${PACKAGE_DIR}/.github/workflows/env-files/requirements-test.txt" --progress-bar=off
+  pip install -U -r "${PACKAGE_DIR}/requirements/requirements-test.txt" --progress-bar=off
 fi
 
 # Allow parallel tests to speed up CI

.github/workflows/env-files/test-compatible_env.yaml

@@ -8,4 +8,4 @@ dependencies:
   - ninja
   - pip
   - pip:
-    - -r requirements-test-compatible.txt
+    - -r ../../../requirements/requirements-test-compatible.txt

.github/workflows/env-files/test-oldest_env.yaml

@@ -8,4 +8,4 @@ dependencies:
   - ninja
   - pip
   - pip:
-    - -r oldest-test-reqs.txt
+    - -r ../oldest-test-reqs.txt

.github/workflows/env-files/test_env.yaml

@@ -8,4 +8,4 @@ dependencies:
   - ninja
   - pip
   - pip:
-    - -r requirements-test.txt
+    - -r ../../../requirements/requirements-test.txt

.github/workflows/run_tests.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v2.3.4
+        uses: actions/checkout@v3.1.0
         with:
           submodules: true
 

.github/workflows/style_check.yml

@@ -23,7 +23,7 @@ jobs:
     container:
       image: glotzerlab/ci:2021.11-clang10_py38
     steps:
-      - uses: actions/checkout@v3.0.2
+      - uses: actions/checkout@v3.1.0
         with:
           submodules: true
       - name: Install pre-commit

.mailmap

@@ -45,6 +45,7 @@ Jiwoong Yu <jiwoongs0510@gmail.com> yjw0510 <jiwoongs0510@gmail.com>
 Kelly Wang <kelwang@umich.edu> Kelly Wang <47036428+klywang@users.noreply.github.com>
 Michael Stryk <mstryk@umich.edu> mstryk <60406122+mstryk@users.noreply.github.com>
 Tommy Waltmann <tomwalt@umich.edu> tommy-waltmann <53307607+tommy-waltmann@users.noreply.github.com>
+Tommy Waltmann <tomwalt@umich.edu> Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>
 Patrick Lawton <plawton@umich.edu> patricklawton <plawton@umich.edu>
 dependabot <dependabot[bot]@users.noreply.github.com> dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 Pavel Buslaev <pbuslaev@gmail.com> pbuslaev <pbuslaev@gmail.com>
@@ -59,3 +60,4 @@ DomFijan <domagoj.fijan@gmail.com> domagoj <domagoj.fijan@gmail.com>
 DomFijan <domagoj.fijan@gmail.com> Domagoj Fijan <50439291+DomFijan@users.noreply.github.com>
 DomFijan <domagoj.fijan@gmail.com> Domagoj Fijan <domagoj.fijan@gmail.com>
 Dylan Marx <marxd1@umich.edu> marxd1 <93282247+marxd1@users.noreply.github.com>
+Alain Kadar <alaink@umich.edu> AlainKadar <73320455+AlainKadar@users.noreply.github.com>

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
       - id: debug-statements
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v2.37.3'
+    rev: 'v3.2.0'
     hooks:
       - id: pyupgrade
         args:
@@ -39,7 +39,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '22.6.0'
+    rev: '22.10.0'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8

ChangeLog.md

@@ -9,6 +9,15 @@ and this project adheres to
 ### Changed
 * The `normalize` argument to `freud.density.RDF` is now `normalization_mode`.
 
+## v2.12.0 -- 2022-11-09
+
+### Added
+* Mass dependence in `freud.cluster.ClusterProperties`.
+* Inertia tensor calculation in `freud.cluster.ClusterProperties`.
+
+### Fixed
+* Compatibility with new namespace for `MDAnalysis.coordinates.timestep.Timestep`.
+
 ## v2.11.0 -- 2022-08-09
 
 ### Added

contributors.txt

@@ -1,19 +1,19 @@
-  2356	Bradley Dice <bdice@bradleydice.com>
+  2357	Bradley Dice <bdice@bradleydice.com>
   2146	Vyas Ramasubramani <vramasub@umich.edu>
   1030	Eric Harper <harperic@umich.edu>
+   462	Tommy Waltmann <tomwalt@umich.edu>
    456	Jin Soo Ihm <jinihm@umich.edu>
-   379	Tommy Waltmann <tomwalt@umich.edu>
    316	Joshua A. Anderson <joaander@umich.edu>
    240	Matthew Spellings <mspells@umich.edu>
    167	Kelly Wang <kelwang@umich.edu>
-   138	dependabot <dependabot[bot]@users.noreply.github.com>
+   163	dependabot <dependabot[bot]@users.noreply.github.com>
    137	DomFijan <domagoj.fijan@gmail.com>
    110	Erin Teich <erteich@umich.edu>
     97	Brandon Butler <butlerbr@umich.edu>
     89	Charlotte Shiqi Zhao <zshiqi@umich.edu>
     66	M. Eric Irrgang <eirrgang@umich.edu>
+    54	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
     53	Chrisy Du <xiyudu@umich.edu>
-    52	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
     41	Yezhi Jin <jinyezhi@umich.edu>
     40	Antonio Osorio <aosorio@umich.edu>
     35	Michael Stryk <mstryk@umich.edu>
@@ -22,6 +22,7 @@
     25	Andrew Kerr <andrewghkerr@gmail.com>
     25	Carl Simon Adorf <csadorf@umich.edu>
     22	Jens Glaser <jsglaser@umich.edu>
+    21	Alain Kadar <alaink@umich.edu>
     20	Tim Moore <mtimc@umich.edu>
     18	Kody Takada <ktakada@umich.edu>
     13	Pavel Buslaev <pbuslaev@gmail.com>