deploy: f4694a9

.dockerignore

@@ -0,0 +1,33 @@
+*__pycache__*
+*.log
+docs/build
+.python-version
+*.DS_Store
+htmlcov
+.coverage
+venv
+.ipynb_checkpoints
+*.pt
+*.onnx
+*.csv
+mlruns
+.profile
+.env
+*.html
+_extract
+*.gzip
+*checkpoint*
+*.parquet
+*.npy
+*.pkl
+*.npz
+*.csv
+*.pickle
+dist/
+outputs/
+multirun/
+_autosummary
+*cyclops_report*
+*dummy_reports*
+.mypy_cache
+*code-workspace*

.gitattributes

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+# Exclude jupyter notebooks for language stats.
+*.ipynb linguist-vendored

.gitignore

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+*__pycache__*
+*.log
+docs/build
+.python-version
+*.DS_Store
+htmlcov
+.coverage
+venv
+.ipynb_checkpoints
+*.pt
+*.onnx
+*.csv
+mlruns
+.profile
+.env
+*.html
+_extract
+*.gzip
+*checkpoint*
+*.parquet
+*.npy
+*.pkl
+*.npz
+*.csv
+*.pickle
+dist/
+outputs/
+multirun/
+_autosummary
+*cyclops_report*
+*dummy_reports*
+.mypy_cache
+*code-workspace*

.gitmodules

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+[submodule "docs/cyclops-webpage"]
+	path = docs/cyclops-webpage
+	url = [email protected]:VectorInstitute/cyclops-webpage.git

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # Use the ref you want to point at
+    hooks:
+    - id: trailing-whitespace
+    - id: check-ast
+    - id: check-builtin-literals
+    - id: check-docstring-first
+    - id: check-executables-have-shebangs
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+      args: [--fix=lf]
+    - id: requirements-txt-fixer
+    - id: check-yaml
+    - id: check-toml
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.4.10'
+    hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      types_or: [python, jupyter]
+    - id: ruff-format
+      types_or: [python, jupyter]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+    - id: mypy
+      entry: python3 -m mypy --config-file pyproject.toml
+      language: system
+      types: [python]
+      exclude: "tests|cyclops/(models|monitor|report/plot)"
+
+  - repo: local
+    hooks:
+    - id: nbstripout
+      name: nbstripout
+      language: system
+      entry: python3 -m nbstripout
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.8.5
+    hooks:
+    - id: nbqa-black
+    - id: nbqa-ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+  - repo: local
+    hooks:
+    - id: doctest
+      name: doctest
+      entry: python3 -m doctest -o NORMALIZE_WHITESPACE
+      files: "^cyclops/"
+      language: system
+
+  - repo: local
+    hooks:
+    - id: pytest
+      name: pytest
+      entry: python3 -m pytest -m "not integration_test" -n auto --dist loadscope
+      language: system
+      pass_filenames: false
+      always_run: true
+
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] Add auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: true
+    autoupdate_branch: ''
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: weekly
+    skip: [pytest,doctest,nbstripout,mypy]
+    submodules: false

CODE_OF_CONDUCT.md

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+# 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, 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.
+
+## 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 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

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+# Contributing to cyclops
+
+Thanks for your interest in contributing to cyclops!
+
+To submit PRs, please fill out the PR template along with the PR. If the PR
+fixes an issue, don't forget to link the PR to the issue!
+
+## Pre-commit hooks
+
+Once the python virtual environment is setup, you can run pre-commit hooks using:
+
+```bash
+pre-commit run --all-files
+```
+
+## Coding guidelines
+
+For code style, we recommend the [PEP 8 style guide](https://peps.python.org/pep-0008/).
+
+For docstrings we use [numpy format](https://numpydoc.readthedocs.io/en/latest/format.html).
+
+We use [ruff](https://docs.astral.sh/ruff/) for code formatting and static code
+analysis. Ruff checks various rules including [flake8](https://docs.astral.sh/ruff/faq/#how-does-ruff-compare-to-flake8). The pre-commit hooks show errors which you need to fix before submitting a PR.
+
+Last but not the least, we use type hints in our code which is then checked using
+[mypy](https://mypy.readthedocs.io/en/stable/).

Dockerfile

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+FROM python:3.9.7
+
+
+WORKDIR /app/cyclops
+ARG DEBIAN_FRONTEND=noninteractive
+ENV LANG C.UTF-8
+
+
+RUN apt-get update \
+    && apt-get install -y git software-properties-common \
+    && rm -rf /var/lib/apt/lists/*
+
+
+RUN python3 -m pip install --upgrade pip
+RUN pip install poetry
+
+
+COPY * /app/cyclops/
+RUN poetry config virtualenvs.create false \
+   && poetry install --no-interaction --no-ansi --with test,docs