Merge pull request #50 from sigma-epsilon/nightly

Nightly

.circleci/config.yml

@@ -7,7 +7,7 @@ orbs:
   # so you dont have to copy and paste it everywhere.
   # See the orb documentation here: https://circleci.com/developer/orbs/orb/circleci/python
   python: circleci/[email protected]
-  codecov: codecov/codecov@3
+  codecov: codecov/codecov@3.3.0
 
 jobs:
   build_test:
@@ -60,7 +60,7 @@ jobs:
             python -m build
             python -m twine upload --skip-existing dist/*
 
-  test310:  # This is the name of the job, feel free to change it to better match what you're trying to do!
+  test-cov-py310:  # This is the name of the job, feel free to change it to better match what you're trying to do!
     # These next lines defines a docker executors: https://circleci.com/docs/2.0/executor-types/
     # You can specify an image from dockerhub or use one of the convenience images from CircleCI's Developer Hub
     # A list of available CircleCI docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
@@ -73,66 +73,52 @@ jobs:
     # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
     # Then run your tests!
     # CircleCI will report the results back to your VCS provider.
-
-    working_directory: ~/project
-
+
     steps:
       - checkout
-      - python/install-packages:
-          pkg-manager: pip
-          # app-dir: ~/project/package-directory/  # If you're requirements.txt isn't in the root directory.
-          # pip-dependency-file: requirements.txt  # if you have a different name for your requirements file, maybe one that combines your runtime and test requirements.
-      - python/install-packages:
-          pkg-manager: pip
-          pip-dependency-file: requirements-test.txt
       - run:
+          name: Install package for testing
           command: pip install ".[test, dev]"
       - run:
-          name: Run tests
-          # This assumes pytest is installed via the install-package step above
-          command: pytest --cov
+          name: Refresh packages
+          command: sudo apt-get update
       - run:
-          name: Generate Artifact
-          command: pytest --cov-report html
-      #- codecov/upload
-      - store_artifacts:
-          path: ~/project/htmlcov
-
-  tox-test:  # This is the name of the job, feel free to change it to better match what you're trying to do!
-    # These next lines defines a docker executors: https://circleci.com/docs/2.0/executor-types/
-    # You can specify an image from dockerhub or use one of the convenience images from CircleCI's Developer Hub
-    # A list of available CircleCI docker convenience images are available here: https://circleci.com/developer/images/image/cimg/python
-    # The executor is the environment in which the steps below will be executed - below will use a python 3.9 container
-    # Change the version below to your required version of python
-    docker:
-      - image: fkrull/multi-python
-    # Checkout the code as the first step. This is a dedicated CircleCI step.
-    # The python orb's install-packages step will install the dependencies from a Pipfile via Pipenv by default.
-    # Here we're making sure we use just use the system-wide pip. By default it uses the project root's requirements.txt.
-    # Then run your tests!
-    # CircleCI will report the results back to your VCS provider.
-
-    working_directory: ~/project
-
-    steps:
-      - checkout
+          name: Install xvfb for offline rendering
+          command: sudo apt-get install libgl1-mesa-glx xvfb
+      - run:
+          name: Run tests and generate coverage report
+          command: |
+            chmod +x ./run_pytest_cov.sh
+            ./run_pytest_cov.sh
       - run:
-          name: Test
-          command: tox
+          name: List working directory contents
+          command: ls -al
+      - run:
+          name: List home directory contents
+          command: ls -a ~
+      - codecov/upload
+      - store_artifacts:
+          name: Store coverage report as artifact
+          path: htmlcov
+      - store_test_results:
+          name: Store test results
+          path: test-results
 
 workflows:
-  version: 2
-
-  main:  # This is the name of the workflow, feel free to change it to better match your workflow.
+
+  testing-and-coverage:  # This is the name of the workflow, feel free to change it to better match your workflow.
     # Inside the workflow, you define the jobs you want to run.
     # For more details on extending your workflow, see the configuration docs: https://circleci.com/docs/2.0/configuration-reference/#workflows
     jobs:
-      #- tox-test
-      - test310
+      - test-cov-py310
 
   build_test_publish:
     jobs:
-      - build_test
+      - build_test:
+          filters:
+            branches:
+              only:
+                - main
       - test_pypi_publish:
           context:
             - TestPyPI deploy

.coveragerc

@@ -0,0 +1,36 @@
+[run]
+branch = False
+omit = */utils/*
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    def __str__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+    # Don't complain about abstract methods, they aren't run:
+    @(abc\.)?abstractmethod
+    @(abc\.)?abstractproperty
+
+    # Don't complain about numba jitted code
+    @njit
+    @jit
+    @guv
+
+ignore_errors = True
+
+[html]
+directory = htmlcov

.coveragerc_nojit

@@ -0,0 +1,30 @@
+[run]
+branch = False
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    def __str__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:
+
+    # Don't complain about abstract methods, they aren't run:
+    @(abc\.)?abstractmethod
+    @(abc\.)?abstractproperty
+
+ignore_errors = True
+
+[html]
+directory = htmlcov

.numba_config.yaml

@@ -0,0 +1,4 @@
+# 0: False, 1: True
+
+# Disable JIT compilation entirely. 
+disable_jit: 0

CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+All notable changes to this project will be documented in this file. If you are interested in bug fixes, enhancements etc., best follow the project on GitHub.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [2.0.0] - 2023-09-27
+
+### Added
+
+- Protocols for PointData, CellData, PolyData and PolyCell classes
+- Cell interpolators (#7)
+
+### Fixed
+
+- Copy and deepcopy operations (#29).
+- Cell class generation (#36).
+
+### Changed
+
+- Class architecture of data structures. Now the geometry is a nested class.
+
+### Removed
+
+- Intermediate, unnecessary geometry classes.

CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at <[email protected]>.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

CONTRIBUTING.md

@@ -0,0 +1,8 @@
+# Contributing guidelines
+
+We appreciate your contributions via issues and pull requests. Note that the [code of conduct](CODE_OF_CONDUCT.md) applies to all interactions with the project, including issues and pull requests.
+
+When submitting pull requests, please follow the style guidelines of the project, ensure that your code is tested and documented, and write good commit messages, e.g., following [these guidelines](https://chris.beams.io/posts/git-commit/).
+
+By submitting a pull request, you are licensing your code under the project [license](LICENSE.txt) and affirming that you either own copyright (automatic for most individuals) or are authorized to distribute under the project license (e.g., in case your employer retains copyright on
+your work).