fusor 0.0.31.dev0__tar.gz → 0.2.0__tar.gz

fusor-0.2.0/.coveragerc

@@ -0,0 +1,7 @@
+[run]
+source =
+    fusor/
+omit =
+    setup.py
+    fusor/version.py
+    tests/

fusor-0.2.0/.github/ISSUE_TEMPLATE/bug-report.yaml

@@ -0,0 +1,85 @@
+name: Bug Report
+description: Report a bug.
+labels: ["bug"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: Provide a clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Provide detailed steps to replicate the bug.
+      placeholder: |
+        1. In this environment...
+        2. With this config...
+        3. Run '...'
+        4. See error...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Current behavior
+      description: |
+        What actually happened?
+
+        Include full errors, stack traces, and/or relevant logs.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Possible reason(s)
+      description: Provide any insights into what might be causing the issue.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Suggested fix
+      description: Provide any suggestions on how to resolve the bug.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Branch, commit, and/or version
+      description: Provide the branch, commit, and/or version you're using.
+      placeholder: |
+        branch: issue-1
+        commit: abc123d
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots with descriptions to help explain your problem.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Environment details
+      description: Provide environment details (OS name and version, etc).
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional details
+      description: Provide any other additional details about the problem.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this fix."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

fusor-0.2.0/.github/ISSUE_TEMPLATE/feature-request.yaml

@@ -0,0 +1,60 @@
+name: Feature Request
+description: Suggest an idea for this project.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: Provide a clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Use case
+      description: |
+        Why do you need this feature? For example: "I'm always frustrated when..."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed solution
+      description: Provide proposed solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions you've considered.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Implementation details
+      description: Provide any technical details on how the feature might be implemented.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Potential Impact
+      description: |
+        Discuss any potential impacts of this feature on existing functionality or performance, if known.
+        Will this feature cause breaking changes?
+        What challenges might arise?
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Provide any other context or screenshots about the feature.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this feature."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

fusor-0.2.0/.github/workflows/checks.yaml

@@ -0,0 +1,18 @@
+name: run checks
+on: [push, pull_request]
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: python3 -m pip install ".[dev]"
+
+      - name: Check style
+        run: python3 -m ruff check . && python3 -m ruff format --check .

fusor-0.2.0/.github/workflows/pr-priority-label.yaml

@@ -0,0 +1,23 @@
+name: Pull Request Has Priority Label
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  pr-priority-label:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    outputs:
+      status: ${{ steps.check-labels.outputs.status }}
+    steps:
+      - id: check-labels
+        uses: mheap/github-action-required-labels@v5
+        with:
+          mode: exactly
+          count: 1
+          labels: "priority:*"
+          use_regex: true
+          add_comment: true
+          message: "PRs require a priority label. Please add one."
+          exit_type: failure

fusor-0.2.0/.github/workflows/release.yml

@@ -0,0 +1,50 @@
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish Python distribution to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/fusor
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

fusor-0.2.0/.github/workflows/stale.yaml

@@ -0,0 +1,27 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * 1-5"
+
+jobs:
+  stale-high-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 90
+      days-before-pr-stale: 1
+      labels: priority:high
+
+  stale-medium-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 135
+      days-before-pr-stale: 3
+      labels: priority:medium
+
+  stale-low-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml@main
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low

fusor-0.2.0/.gitignore

@@ -0,0 +1,162 @@
+# Ignore xlsx temp file
+\~*
+
+# Ignore system files
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# allow pytest override with pytest.ini
+pytest.ini
+
+# ignore data dir
+data/*
+therapy/data/
+
+# IDE stuff
+.idea/
+.vim/
+*.swp
+.vscode/
+
+# DynamoDB Local
+dynamodb_local_latest/*
+
+# Build files
+Pipfile.lock

fusor-0.2.0/.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # pre-commit-hooks version
+    hooks:
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: detect-aws-credentials
+        args: [ --allow-missing-credentials ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+minimum_pre_commit_version: 3.7.1

{fusor-0.0.31.dev0/src/fusor.egg-info → fusor-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fusor
-Version: 0.0.31.dev0
+Version: 0.2.0
 Summary: Computable object representation and validation for gene fusions
 Author-email: Alex Wagner <alex.wagner@nationwidechildrens.org>, Kori Kuzma <kori.kuzma@nationwidechildrens.org>, James Stevenson <james.stevenson@nationwidechildrens.org>, Katie Stahl <kathryn.stahl@nationwidechildrens.org>, Jeremy Arbesfeld <jeremy.arbesfeld@nationwidechildrens.org>
 License: 
@@ -45,22 +45,21 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pydantic==2.*
-Requires-Dist: ga4gh.vrsatile.pydantic~=0.2.0
-Requires-Dist: ga4gh.vrs~=0.8.1
+Requires-Dist: pydantic==2.4.2
+Requires-Dist: ga4gh.vrs~=2.0.0a10
 Requires-Dist: biocommons.seqrepo
-Requires-Dist: gene-normalizer~=0.1.40-dev1
-Requires-Dist: cool-seq-tool~=0.3.0-dev1
+Requires-Dist: gene-normalizer==0.4.0
+Requires-Dist: cool-seq-tool~=0.5.1
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
 Requires-Dist: pytest-asyncio; extra == "tests"
 Provides-Extra: dev
-Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pre-commit>=3.7.1; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-asyncio; extra == "dev"
-Requires-Dist: ruff==0.2.0; extra == "dev"
+Requires-Dist: ruff==0.5.0; extra == "dev"
 
 # FUSOR
 
@@ -68,6 +67,7 @@ Requires-Dist: ruff==0.2.0; extra == "dev"
 [![image](https://img.shields.io/pypi/l/fusor.svg)](https://pypi.python.org/pypi/fusor)
 [![image](https://img.shields.io/pypi/pyversions/fusor.svg)](https://pypi.python.org/pypi/fusor)
 [![Actions status](https://github.com/cancervariants/fusor/actions/workflows/checks.yaml/badge.svg)](https://github.com/cancervariants/fusor/actions/checks.yaml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12708252.svg)](https://doi.org/10.5281/zenodo.12708252)
 
 <!-- description -->
 FUSOR (**FUS**ion **O**bject **R**epresentation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.

{fusor-0.0.31.dev0 → fusor-0.2.0}/README.md

@@ -4,6 +4,7 @@
 [![image](https://img.shields.io/pypi/l/fusor.svg)](https://pypi.python.org/pypi/fusor)
 [![image](https://img.shields.io/pypi/pyversions/fusor.svg)](https://pypi.python.org/pypi/fusor)
 [![Actions status](https://github.com/cancervariants/fusor/actions/workflows/checks.yaml/badge.svg)](https://github.com/cancervariants/fusor/actions/checks.yaml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12708252.svg)](https://doi.org/10.5281/zenodo.12708252)
 
 <!-- description -->
 FUSOR (**FUS**ion **O**bject **R**epresentation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.

{fusor-0.0.31.dev0 → fusor-0.2.0}/pyproject.toml

@@ -24,19 +24,19 @@ classifiers = [
 requires-python = ">=3.10"
 description = "Computable object representation and validation for gene fusions"
 license = {file = "LICENSE"}
+# pydantic is pinned to 2.4.2 for now, since there is a change in later versions that causes a validation error for test_fusion in test_fusor.py
 dependencies = [
-    "pydantic == 2.*",
-    "ga4gh.vrsatile.pydantic ~=0.2.0",
-    "ga4gh.vrs ~=0.8.1",
+    "pydantic ==2.4.2",
+    "ga4gh.vrs ~=2.0.0a10",
     "biocommons.seqrepo",
-    "gene-normalizer ~=0.1.40-dev1",
-    "cool-seq-tool ~=0.3.0-dev1",
+    "gene-normalizer ==0.4.0",
+    "cool-seq-tool ~=0.5.1",
 ]
 dynamic=["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "pytest-asyncio"]
-dev = ["pre-commit", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.2.0"]
+dev = ["pre-commit>=3.7.1", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.5.0"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/fusor"
@@ -46,11 +46,10 @@ Source = "https://github.com/cancervariants/fusor"
 "Bug Tracker" = "https://github.com/cancervariants/fusor/issues"
 
 [build-system]
-requires = ["setuptools>=64.0"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.dynamic]
-version = {attr = "fusor.version.__version__"}
+[tool.setuptools_scm]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -85,16 +84,22 @@ select = [
     "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
     "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
     "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
     "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
     "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
     "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 fixable = [
@@ -105,15 +110,19 @@ fixable = [
     "ANN",
     "B",
     "C4",
+    "LOG",
     "G",
     "PIE",
     "PT",
     "RSE",
     "SIM",
-    "RUF"
+    "PERF",
+    "FURB",
+    "RUF",
 ]
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
+# ANN101 - missing-type-self
+# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -129,7 +138,7 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN101", "ANN003",
+    "ANN003", "ANN101", "ANN102",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
@@ -144,6 +153,13 @@ ignore = [
 # ANN102 - missing-type-cls
 # S101 - assert
 # B011 - assert-false
+# N803 - invalid-argument-name
 # N805 - invalid-first-argument-name-for-method
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
-"src/fusor/models.py" = ["ANN201", "N805", "ANN001", "ANN2", "ANN102"]
+# N815 - mixed-case-variable-in-class-scope
+# INP001 - implicit-namespace-package
+# SLF001 - private-member-access
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "SLF001"]
+"src/fusor/models.py" = ["ANN201", "N803", "N805", "N815", "ANN001", "ANN2", "ANN102"]
+
+[tool.ruff.format]
+docstring-code-format = true

fusor-0.2.0/src/fusor/__init__.py

@@ -0,0 +1,15 @@
+"""Provide computable object representation and validation for gene fusions"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from fusor.fusor import FUSOR
+
+__all__ = ["__version__", "FUSOR"]
+
+
+try:
+    __version__ = version("cool_seq_tool")
+except PackageNotFoundError:
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

fusor-0.2.0/src/fusor/examples/README.md

@@ -0,0 +1,9 @@
+# Examples
+
+* `bcr_abl1.json`: Example BCR-ABL1 categorical fusion drawn from [COSF1780](https://cancer.sanger.ac.uk/cosmic/fusion/summary?id=1780). Demonstrates structure of junction components, a linker sequence segment, critical functional domains, and reading frame preservation. Represented in nomenclature as `NM_004327.3(BCR):e.2+182::ACTAAAGCG::NM_005157.5(ABL1):e.2-173`.
+* `bcr_abl1_expanded.json`: Equivalent fusion to the above, but with expanded descriptions of genes, locations, and sequences provided by SeqRepo and the VICC Gene Normalizer.
+* `alk.json`: Example of an ALK fusion, demonstrating use of a categorical "multiple possible gene" component, retrieved from a human-curated database like [CIViC](https://civicdb.org/variants/499/summary). Represented in nomenclature as `v::ALK(hgnc:427)`.
+* `ewsr1.json`: An EWSR1 assayed fusion, demonstrating an assay description object and use of the "unknown gene" partner. Represented in nomenclature as `EWSR1(hgnc:3508)::?`.
+* `tpm3_ntrk1.json`: Example TPM3-NTRK1 assayed fusion drawn from previous VICC Fusion Curation draft material. Represented in nomenclature as `NM_152263.3(TPM3):e.1_8::NM_002529.3(NTRK1):e.10_22`.
+* `tpm3_pdgfrb.json`: Example TPM3-PDGFRB assayed fusion identified via RT-PCR. Represented in nomenclature as `NM_152263.3(TPM3):e.8::NM_002609.3(PDGFRB):e.11_22`.
+* `igh_myc.json`: Example of an enhancer-driven IGH-MYC categorical fusion. Represented in nomenclature as `reg_e_EH38E3121735@IGH(hgnc:5477)::MYC(hgnc:7553)`.

{fusor-0.0.31.dev0 → fusor-0.2.0}/src/fusor/examples/__init__.py

@@ -1,4 +1,5 @@
 """Provide programmatic access to example objects."""
+
 import json
 from pathlib import Path