glotzerlab · vyasr · Apr 2, 2022 · Apr 2, 2022 · Apr 2, 2022 · Apr 2, 2022
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,130 +1,127 @@
 version: 2.1
 
+orbs:
+  codecov: codecov/codecov@3.2.2
+
 references:
-  imtox: &imtox
-    docker:
-      - image: cimg/python:3.8
+  install_dependencies: &install_dependencies
+    name: Install dependencies
+    command: |
+      python -m pip install --progress-bar off -U virtualenv --user
+      mkdir -p ./venv
+      python -m virtualenv ./venv --clear
+      . venv/bin/activate
+      python -m pip install --progress-bar off -U -r requirements/requirements-testing.txt
 
-  wd: &wd
-    working_directory: ~/repo
+  run_tests: &run_tests
+    name: run tests
+    command: |
+      # Run with coverage
+      . venv/bin/activate
+      python -m pytest -v --cov=rowan/ --cov-report=xml
 
-  runall: &runall
+jobs:
+  linux-python-37:
+    docker:
+      - image: cimg/python:3.7
+    working_directory: ~/repo
     steps:
       - checkout
-
-      - restore_cache:
-          keys:
-          - v1-dependencies-{{ checksum "requirements.txt" }}
-          # fallback to using the latest cache if no exact match is found
-          - v1-dependencies-
-
       - run:
-          name: run tests
-          command: |
-            # Faster to just test one env first
-            pip3.8 install --progress-bar off --user -U flake8 flake8-black flake8-bugbear flake8-docstrings flake8-rst-docstrings pep8-naming flake8-isort numpy scipy
-            python3.8 -m flake8 --show-source rowan
-            # Ignore isort errors in tests that are due to ambiguity over whether or not rowan is third party.
-            python3.8 -m flake8 --extend-ignore=I001,I004 --show-source tests/
-            python3.8 -m unittest discover tests -v
-
-            ## Test python-dependency matrix with tox
-            #pip3.8 install --progress-bar off --user tox
-            #tox
-            #
-            # Run with coverage
-            pip3.8 install --progress-bar off --user coverage
-            export PATH=~/.local/bin:${PATH}
-            coverage run -m unittest discover tests
-            apt-get -yq update
-            apt-get -yq install curl
-            bash <(curl -s https://codecov.io/bash)
-            coverage xml
+          <<: *install_dependencies
+      - run:
+          <<: *run_tests
 
-      - save_cache:
-          paths:
-            - ~/.local
-          key: v1-dependencies-{{ checksum "requirements.txt" }}
+  linux-python-38:
+    docker:
+      - image: cimg/python:3.8
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run:
+          <<: *install_dependencies
+      - run:
+          <<: *run_tests
 
-  run_tests_only: &run_tests_only
+  linux-python-39:
+    docker:
+      - image: cimg/python:3.9
+    working_directory: ~/repo
     steps:
       - checkout
+      - run:
+          <<: *install_dependencies
+      - run:
+          <<: *run_tests
 
-      - restore_cache:
-          keys:
-          - v1-dependencies-{{ checksum "requirements.txt" }}
-          # fallback to using the latest cache if no exact match is found
-          - v1-dependencies-
+  linux-python-310:
+    docker:
+      - image: cimg/python:3.10
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run:
+          <<: *install_dependencies
+      - run:
+          <<: *run_tests
 
+  linux-oldest:
+    # Run tests against a set of the oldest dependencies we support.
+    docker:
+      - image: cimg/python:3.6
+    working_directory: ~/repo
+    steps:
+      - checkout
+      - run:
+          name: Install oldest dependencies
+          command: |
+            python -m pip install --progress-bar off -U virtualenv --user
+            mkdir -p ./venv
+            python -m virtualenv ./venv --clear
+            . venv/bin/activate
+            python -m pip install --progress-bar off -U -r requirements/requirements-oldest.txt
+            python -m pip install --progress-bar off -U pytest
       - run:
           name: run tests
           command: |
-            # Faster to just test one env first
-            pip3.8 install --progress-bar off --user -U flake8 flake8-black flake8-bugbear flake8-docstrings flake8-rst-docstrings pep8-naming flake8-isort numpy scipy
-            python3.8 -m flake8 --show-source rowan
-            # Ignore isort errors in tests that are due to ambiguity over whether or not rowan is third party.
-            python3.8 -m flake8 --extend-ignore=I001,I004 --show-source tests/
-            python3.8 -m unittest discover tests -v
+            . venv/bin/activate
+            python -m pytest -v tests
 
-      - save_cache:
-          paths:
-            - ~/.local
-          key: v1-dependencies-{{ checksum "requirements.txt" }}
-
-  pypi_wheels: &pypi_wheels
+  build_and_deploy:
+    docker:
+      - image: cimg/python:3.8
+    working_directory: ~/repo
     steps:
       - checkout
-
+      - run:
+          <<: *install_dependencies
+      - run:
+          <<: *run_tests
       - run:
           name: Deploy dist and wheels
           command: |
-            pip3.8 install --progress-bar off --user -U flake8 flake8-black flake8-bugbear flake8-docstrings flake8-rst-docstrings pep8-naming flake8-isort numpy scipy
-            python3.8 -m flake8 --show-source rowan
-            # Ignore isort errors in tests that are due to ambiguity over whether or not rowan is third party.
-            python3.8 -m flake8 --extend-ignore=I001,I004 --show-source tests/
-            python3.8 -m unittest discover tests -v
-            python3.8 --version
-            pip3.8 --version
-            pip3.8 install --progress-bar off --user -U twine wheel setuptools
-            export PATH=~/.local/bin:${PATH}
-            twine --version
-            wheel version
-            python3.8 setup.py sdist
-            python3.8 setup.py bdist_wheel
-            twine upload --username vramasub --password ${PYPI_PASSWORD} dist/*
-
-jobs:
-  complete:
-    <<: *imtox
-    <<: *wd
-    <<: *runall
-  test_only:
-    <<: *imtox
-    <<: *wd
-    <<: *run_tests_only
-  build_and_deploy:
-    <<: *imtox
-    <<: *wd
-    <<: *pypi_wheels
+            . venv/bin/activate
+            python -m unittest discover tests -v
+            python --version
+            python -m pip --version
+            python -m pip install --progress-bar off --user -U twine wheel setuptools
+            python -m twine --version
+            python -m wheel version
+            python setup.py sdist
+            python setup.py bdist_wheel
+            twine upload --username ${PYPI_USERNAME} --password ${PYPI_PASSWORD} dist/*
 
 workflows:
   version: 2
   testing:
     jobs:
-      - complete:
-          filters:
-            branches:
-              only:
-                - master
-                - develop
-                - /release-.*/
-      - test_only:
-          filters:
-            branches:
-              ignore:
-                - master
-                - develop
-                - /release-.*/
+      - linux-python-37
+      - linux-python-38
+      - linux-python-39
+      - linux-python-310:
+          post-steps:
+            - codecov/upload
+      - linux-oldest
   deploy:
     jobs:
       - build_and_deploy:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 ci:
   autoupdate_schedule: quarterly
 
-# TODO: Add mypy, pyupgrade, and check-yaml
+# TODO: Add mypy, pyupgrade
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 'v4.1.0'
@@ -13,7 +13,7 @@ repos:
       - id: check-builtin-literals
       - id: check-executables-have-shebangs
       - id: check-json
-      #- id: check-yaml
+      - id: check-yaml
       - id: debug-statements
       - id: requirements-txt-fixer
   - repo: https://github.com/PyCQA/isort

diff --git a/README.rst b/README.rst
@@ -65,7 +65,7 @@ To install the package from PyPI, execute:
 
 .. code-block:: bash
 
-    $ pip install rowan --user
+    $ pip install rowan
 
 To install the package from conda, first add the **conda-forge** channel and
 then install rowan:
@@ -89,6 +89,10 @@ The minimum requirements for using rowan are:
 * Python >= 3.6
 * NumPy >= 1.15
 
+To use the mapping subpackage, rowan also requires
+
+* SciPy >= 1.0
+
 Quickstart
 ----------
 

diff --git a/doc/development.rst b/doc/development.rst
@@ -30,23 +30,24 @@ Code contributions should keep these ideals in mind and adhere to the following
   * Preserve backwards-compatibility whenever possible. Make clear if something must change, and notify package maintainers that merging such changes will require a major release.
   * Enable broadcasting if at all possible. Functions for which broadcasting is not available must be documented as such.
 
-To provide a reasonable balance between a high level of backwards compatibility and a reasonable maintenance burden, **rowan** has adopted `NEP 29`_ to limit the Python and NumPy versions that will be supported.
-
 
 .. _github: https://github.com/glotzerlab/rowan
 .. _OneFlow: https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow
-.. _NEP 29: https://numpy.org/neps/nep-0029-deprecation_policy.html
 
 .. tip::
 
-    During continuous integration, the code is checked automatically with `Flake8`_.
-    To ensure your code is compliant before committing, you can set up a pre-commit hook using `pre-commit`_ (recommended) or use flake8's built-in hooks installation:
+    During continuous integration, the code is checked automatically with `pre-commit`_.
+    To run these checks locally, you can install and run pre-commit like so:
 
     .. code-block:: bash
 
-        flake8 --install-hook git
-        git config --bool flake8.strict true
+        python -m pip install pre-commit
+        pre-commit run --all-files
+
+    To avoid having commits fail in case you forget to run this, you can set up a git pre-commit hook using `pre-commit`_:
 
+    .. code-block:: bash
+        pre-commit install
 
 .. _Flake8: http://flake8.pycqa.org/en/latest/
 .. _pre-commit: https://pre-commit.com/
@@ -59,7 +60,6 @@ To provide a reasonable balance between a high level of backwards compatibility
 Source Code Conventions
 -----------------------
 
-
 The **rowan** package adheres to a relatively strict set of style guidelines.
 All code in **rowan** should be formatted using `black`_; a notable consequence of this is that the recommended max line length is 88, not the more common 80.
 Imports should be formatted using `isort`_.
@@ -68,17 +68,6 @@ All code should also follow the principles in `PEP 20 <https://www.python.org/de
 In particular, always prefer simple, explicit code where possible, avoiding unnecessary convolution or complicated code that could be written more simply.
 Avoid writing code in a manner that will be difficult for others to understand.
 
-.. tip::
-
-    Developers should format their code using black and isort locally using the commands:
-
-    .. code-block:: bash
-
-        black --exclude "coxeter/[polytri|bentley_ottman]" coxeter/ tests/
-        isort -rc coxeter/ tests/
-
-.. _black: https://black.readthedocs.io/
-.. _isort: https://timothycrosley.github.io/isort/
 
 Documentation
 -------------

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1 @@
-###### Requirements without Version Specifiers ######
-
-###### Requirements with Version Specifiers ######
-numpy>=1.15
+numpy>=1.15.0
diff --git a/requirements/requirements-oldest.txt b/requirements/requirements-oldest.txt
@@ -0,0 +1,2 @@
+numpy==1.15.0
+scipy==1.0.0
diff --git a/requirements/requirements-testing.txt b/requirements/requirements-testing.txt
@@ -0,0 +1,5 @@
+coverage==6.3.2
+numpy>=1.15.0
+pytest==7.0.1
+pytest-cov==3.0.0
+scipy>=1.0.0
diff --git a/setup.py b/setup.py
@@ -31,12 +31,15 @@
     zip_safe=True,
     install_requires=["numpy>=1.15"],
     python_requires=">=3.6, <4",
+    extras_require={"mapping": "scipy>=1.0.0"},
     classifiers=[
         "Development Status :: 6 - Mature",
         "License :: OSI Approved :: BSD License",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Scientific/Engineering :: Mathematics",
     ],
 )