Initialize repository and test bioprocess, gene, and metapath data extraction

.github/workflows/run-tests.yml

@@ -0,0 +1,44 @@
+---
+# used for running tests
+name: tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre_commit_checks:
+    runs-on: ubuntu-22.04
+    steps:
+      # checks out the repo
+      - uses: actions/checkout@v4
+      # run pre-commit
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - uses: pre-commit/action@v3.0.1
+  run_tests:
+    strategy:
+      matrix:
+        python_version: ["3.11", "3.12"]
+        os: [ubuntu-22.04, macos-13]
+    runs-on: ${{ matrix.os }}
+    env:
+      OS: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Python setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python_version }}
+      - name: Setup for uv
+        run: |
+          python -m pip install uv
+      - name: Install environment
+        run: uv run poe setup
+      - name: Run pytest
+        run: uv run pytest

.gitignore

@@ -160,3 +160,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# data ignores
+src/bioprocess_metapath_to_gene_pval_and_dwpc/data/results

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
+  python: python3.11
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: detect-private-key
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "v2.5.0"
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        exclude: |
+          (?x)^(
+              .*\.lock |
+              .*\.csv
+          )$
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.18
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-gfm
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.7.2"
+    hooks:
+      - id: ruff-format
+      - id: ruff
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.4
+    hooks:
+      - id: actionlint

CODE_OF_CONDUCT.md

@@ -0,0 +1,132 @@
+# 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, socioeconomic 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,
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+- Other conduct which could reasonably be considered inappropriate in a
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+
+## 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 email 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 community leaders responsible for enforcement.
+Please open a [new security advisory notice](https://github.com/CU-DBMI/hetionet-analysis/security/advisories/new) (using defaults or "n/a" where unable to fill in the form) to privately notify us of any incidents of this nature.
+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
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+
+### 2. Warning
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+**Community Impact**: A violation through a single incident or series of
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+
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+interaction with the people involved, including unsolicited interaction with
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+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].
+
+[faq]: https://www.contributor-covenant.org/faq
+[homepage]: https://www.contributor-covenant.org
+[mozilla coc]: https://github.com/mozilla/diversity
+[translations]: https://www.contributor-covenant.org/translations
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2024, Dave Bunten
+Copyright (c) 2024, CU DBMI Community
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.md

@@ -1,10 +1,10 @@
 # Hetionet Analysis
 
-Various data analysis performed using Hetionet, a hetnet of biomedical knowledge.
+Various data analysis performed using [Hetionet](https://het.io/), a [hetnet](https://en.wikipedia.org/wiki/Heterogeneous_network) of biomedical knowledge.
 
 ## Development
 
 1. [Install `uv`](https://docs.astral.sh/uv/getting-started/installation/).
 1. Install package locally (e.g. `uv pip install -e ".[dev]"`).
 1. Run tests (e.g. `uv run poe test`, through [poethepoet](https://poethepoet.natn.io/index.html) task).
-1. Build dynamically versioned distribution (e.g. `uv build`).
+1. Run various tasks (e.g. `uv run poe run_bioproc_gene_metapath_test`)

pyproject.toml

@@ -0,0 +1,91 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [ "setuptools>=64", "setuptools-scm>=8" ]
+
+[project]
+name = "hetnet-analysis"
+description = "Demonstrating Pythonic uv usage with dynamic versioning."
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dynamic = [ "version" ]
+dependencies = [
+  "black>=24.10",
+  "hetmatpy>=0.1",
+  "ipywidgets>=8.1.5",
+  "isort>=5.13.2",
+  "joblib>=1.4.2",
+  "jupyterlab>=4.3",
+  "jupyterlab-code-formatter>=3.0.2",
+  "jupytext>=1.16.4",
+  "lancedb>=0.15",
+  "neo4j>=5.26",
+  "requests>=2.32.3",
+]
+
+[tool.setuptools_scm]
+root = "."
+
+[tool.ruff]
+target-version = "py38"
+line-length = 88
+fix = true
+lint.select = [
+  # flake8-builtins
+  "A",
+  # flake8-annotations
+  "ANN",
+  # flake8-comprehensions
+  "C4",
+  # mccabe
+  "C90",
+  # pycodestyle
+  "E",
+  # pyflakes
+  "F",
+  # isort
+  "I",
+  # pylint
+  "PL",
+  # ruff
+  "RUF",
+  # flake8-simplify
+  "SIM",
+  "W",
+]
+# Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
+lint.per-file-ignores."__init__.py" = [ "F401" ]
+
+# ignore typing rules for tests
+lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004" ]
+
+[tool.jupytext]
+formats = "ipynb,py:light"
+
+[tool.uv]
+dev-dependencies = [
+  "setuptools-scm>=8.1.0",
+  "poethepoet>=0.29",
+  "pre-commit>=4.0.1",
+  "pytest>=8.3.3",
+]
+
+[tool.poe.tasks]
+# install the project for development purposes
+setup.shell = """
+uv pip install '.[dev]'
+"""
+# run testing on development source
+test.shell = """
+uv run pre-commit run -a
+uv run pytest
+"""
+#
+run_bioproc_gene_metapath_test.shell = """
+uv run python src/bioprocess_metapath_to_gene_pval_and_dwpc/gather_subset_data_metapath_BPpGdAdG.py
+"""