fusor 0.0.30.dev1__tar.gz → 0.0.31.dev0__tar.gz

fusor-0.0.31.dev0/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.1
+Name: fusor
+Version: 0.0.31.dev0
+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: 
+        MIT License
+        
+        Copyright (c) 2021-2023 VICC
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/cancervariants/fusor
+Project-URL: Documentation, https://github.com/cancervariants/fusor
+Project-URL: Changelog, https://github.com/cancervariants/fusor/releases
+Project-URL: Source, https://github.com/cancervariants/fusor
+Project-URL: Bug Tracker, https://github.com/cancervariants/fusor/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Framework :: Pydantic
+Classifier: Framework :: Pydantic :: 2
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+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: biocommons.seqrepo
+Requires-Dist: gene-normalizer~=0.1.40-dev1
+Requires-Dist: cool-seq-tool~=0.3.0-dev1
+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: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-asyncio; extra == "dev"
+Requires-Dist: ruff==0.2.0; extra == "dev"
+
+# FUSOR
+
+[![image](https://img.shields.io/pypi/v/fusor.svg)](https://pypi.python.org/pypi/fusor)
+[![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)
+
+<!-- description -->
+FUSOR (**FUS**ion **O**bject **R**epresentation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.
+<!-- /description -->
+
+## Installation
+
+### Package
+
+To install FUSOR:
+```shell
+python3 -m pip install fusor
+```
+
+### SeqRepo and UTA
+
+FUSOR relies on data from [SeqRepo](https://github.com/biocommons/seqrepo) and the [Universal Transcript Archive (UTA)](https://github.com/biocommons/uta), supplied via [Cool-Seq-Tool](https://github.com/genomicmedlab/cool-seq-tool). See the [Cool-Seq-Tool installation instructions](https://coolseqtool.readthedocs.io/en/latest/install.html) for specifics on setting up SeqRepo and UTA.
+
+To connect to the UTA database, you can use the default url (`postgresql://uta_admin@localhost:5433/uta/uta_20210129`). If you use the default url, you must either set the password using environment variable `UTA_PASSWORD` or setting the parameter `db_pwd` in the `FUSOR` class.
+
+If you do not wish to use the default, you must set the environment variable `UTA_DB_URL` which has the format of `driver://user:pass@host:port/database/schema`.
+
+### Gene Normalizer
+
+`FUSOR` also relies on data from the [Gene Normalizer](https://github.com/cancervariants/gene-normalization), which you must download yourself. See the [README](https://github.com/cancervariants/gene-normalization#readme) for deploying the gene database.
+
+## Development
+
+### Setup
+
+Clone the repo:
+
+```shell
+git clone https://github.com/cancervariants/fusor
+cd fusor
+```
+
+Create a virtual environment, and activate it:
+
+```shell
+python3 -m virtualenv venv
+source venv/bin/activate
+```
+
+Install test and dev dependencies:
+
+```shell
+python3 -m pip install -e '.[dev,tests]'
+```
+
+### Style
+
+Code style is managed by [Ruff](https://github.com/astral-sh/ruff) and checked prior to commit.
+
+```shell
+python3 -m ruff format . && python3 -m ruff check --fix .
+```
+
+We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
+
+This performs checks for:
+
+* Code style
+* File endings
+* Added large files
+* AWS credentials
+* Private keys
+
+Before your first commit, run:
+
+```shell
+pre-commit install
+```
+
+### Unit tests
+
+Unit testing is provided via `pytest`:
+
+```shell
+pytest
+```

fusor-0.0.31.dev0/README.md

@@ -0,0 +1,87 @@
+# FUSOR
+
+[![image](https://img.shields.io/pypi/v/fusor.svg)](https://pypi.python.org/pypi/fusor)
+[![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)
+
+<!-- description -->
+FUSOR (**FUS**ion **O**bject **R**epresentation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.
+<!-- /description -->
+
+## Installation
+
+### Package
+
+To install FUSOR:
+```shell
+python3 -m pip install fusor
+```
+
+### SeqRepo and UTA
+
+FUSOR relies on data from [SeqRepo](https://github.com/biocommons/seqrepo) and the [Universal Transcript Archive (UTA)](https://github.com/biocommons/uta), supplied via [Cool-Seq-Tool](https://github.com/genomicmedlab/cool-seq-tool). See the [Cool-Seq-Tool installation instructions](https://coolseqtool.readthedocs.io/en/latest/install.html) for specifics on setting up SeqRepo and UTA.
+
+To connect to the UTA database, you can use the default url (`postgresql://uta_admin@localhost:5433/uta/uta_20210129`). If you use the default url, you must either set the password using environment variable `UTA_PASSWORD` or setting the parameter `db_pwd` in the `FUSOR` class.
+
+If you do not wish to use the default, you must set the environment variable `UTA_DB_URL` which has the format of `driver://user:pass@host:port/database/schema`.
+
+### Gene Normalizer
+
+`FUSOR` also relies on data from the [Gene Normalizer](https://github.com/cancervariants/gene-normalization), which you must download yourself. See the [README](https://github.com/cancervariants/gene-normalization#readme) for deploying the gene database.
+
+## Development
+
+### Setup
+
+Clone the repo:
+
+```shell
+git clone https://github.com/cancervariants/fusor
+cd fusor
+```
+
+Create a virtual environment, and activate it:
+
+```shell
+python3 -m virtualenv venv
+source venv/bin/activate
+```
+
+Install test and dev dependencies:
+
+```shell
+python3 -m pip install -e '.[dev,tests]'
+```
+
+### Style
+
+Code style is managed by [Ruff](https://github.com/astral-sh/ruff) and checked prior to commit.
+
+```shell
+python3 -m ruff format . && python3 -m ruff check --fix .
+```
+
+We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
+
+This performs checks for:
+
+* Code style
+* File endings
+* Added large files
+* AWS credentials
+* Private keys
+
+Before your first commit, run:
+
+```shell
+pre-commit install
+```
+
+### Unit tests
+
+Unit testing is provided via `pytest`:
+
+```shell
+pytest
+```

fusor-0.0.31.dev0/pyproject.toml

@@ -0,0 +1,149 @@
+[project]
+name = "fusor"
+authors = [
+    {name = "Alex Wagner", email = "alex.wagner@nationwidechildrens.org"},
+    {name = "Kori Kuzma", email = "kori.kuzma@nationwidechildrens.org"},
+    {name = "James Stevenson", email = "james.stevenson@nationwidechildrens.org"},
+    {name = "Katie Stahl", email = "kathryn.stahl@nationwidechildrens.org"},
+    {name = "Jeremy Arbesfeld", email = "jeremy.arbesfeld@nationwidechildrens.org"}
+]
+readme = "README.md"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Framework :: Pydantic",
+    "Framework :: Pydantic :: 2",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+requires-python = ">=3.10"
+description = "Computable object representation and validation for gene fusions"
+license = {file = "LICENSE"}
+dependencies = [
+    "pydantic == 2.*",
+    "ga4gh.vrsatile.pydantic ~=0.2.0",
+    "ga4gh.vrs ~=0.8.1",
+    "biocommons.seqrepo",
+    "gene-normalizer ~=0.1.40-dev1",
+    "cool-seq-tool ~=0.3.0-dev1",
+]
+dynamic=["version"]
+
+[project.optional-dependencies]
+tests = ["pytest", "pytest-cov", "pytest-asyncio"]
+dev = ["pre-commit", "pytest", "pytest-cov", "pytest-asyncio", "ruff==0.2.0"]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/fusor"
+Documentation = "https://github.com/cancervariants/fusor"
+Changelog = "https://github.com/cancervariants/fusor/releases"
+Source = "https://github.com/cancervariants/fusor"
+"Bug Tracker" = "https://github.com/cancervariants/fusor/issues"
+
+[build-system]
+requires = ["setuptools>=64.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "fusor.version.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"fusor.examples" = ["*.json"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
+
+[tool.ruff]
+src = ["src"]
+
+[tool.ruff.lint]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "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
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "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
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+fixable = [
+    "I",
+    "F401",
+    "D",
+    "UP",
+    "ANN",
+    "B",
+    "C4",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "SIM",
+    "RUF"
+]
+# ANN101 - missing-type-self
+# ANN003 - missing-type-kwargs
+# D203 - one-blank-line-before-class
+# D205 - blank-line-after-summary
+# D206 - indent-with-spaces*
+# D213 - multi-line-summary-second-line
+# D300 - triple-single-quotes*
+# D400 - ends-in-period
+# D415 - ends-in-punctuation
+# E111 - indentation-with-invalid-multiple*
+# E114 - indentation-with-invalid-multiple-comment*
+# E117 - over-indented*
+# E501 - line-too-long*
+# W191 - tab-indentation*
+# S321 - suspicious-ftp-lib-usage
+# *ignored for compatibility with formatter
+ignore = [
+    "ANN101", "ANN003",
+    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
+    "E111", "E114", "E117", "E501",
+    "W191",
+    "S321",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# ANN001 - missing-type-function-argument
+# ANN102 - missing-type-cls
+# ANN2 - missing-return-type
+# ANN201 - missing-return-type-undocumented-public-function
+# ANN102 - missing-type-cls
+# S101 - assert
+# B011 - assert-false
+# N805 - invalid-first-argument-name-for-method
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
+"src/fusor/models.py" = ["ANN201", "N805", "ANN001", "ANN2", "ANN102"]

fusor-0.0.31.dev0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

fusor-0.0.31.dev0/src/fusor/__init__.py

@@ -0,0 +1,6 @@
+"""Provide computable object representation and validation for gene fusions"""
+from fusor.fusor import FUSOR
+
+from .version import __version__
+
+__all__ = ["__version__", "FUSOR"]

{fusor-0.0.30.dev1 → fusor-0.0.31.dev0/src}/fusor/examples/__init__.py

@@ -1,37 +1,37 @@
 """Provide programmatic access to example objects."""
 import json
+from pathlib import Path
 
-from fusor import APP_ROOT
 from fusor.models import AssayedFusion, CategoricalFusion
 
-EXAMPLES_DIR = APP_ROOT / "examples"
+EXAMPLES_DIR = Path(__file__).resolve().parents[0]
 
-with open(EXAMPLES_DIR / "alk.json") as f:
+with (EXAMPLES_DIR / "alk.json").open() as f:
     alk = CategoricalFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "bcr_abl1.json") as f:
+with (EXAMPLES_DIR / "bcr_abl1.json").open() as f:
     bcr_abl1 = CategoricalFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "bcr_abl1_expanded.json") as f:
+with (EXAMPLES_DIR / "bcr_abl1_expanded.json").open() as f:
     bcr_abl1_expanded = CategoricalFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "ewsr1.json") as f:
+with (EXAMPLES_DIR / "ewsr1.json").open() as f:
     ewsr1 = AssayedFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "ewsr1_no_assay.json") as f:
+with (EXAMPLES_DIR / "ewsr1_no_assay.json").open() as f:
     ewsr1_no_assay = AssayedFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "ewsr1_no_causative_event.json") as f:
+with (EXAMPLES_DIR / "ewsr1_no_causative_event.json").open() as f:
     ewsr1_no_causative_event = AssayedFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "ewsr1_elements_only.json") as f:
+with (EXAMPLES_DIR / "ewsr1_elements_only.json").open() as f:
     ewsr1_elements_only = AssayedFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "igh_myc.json") as f:
+with (EXAMPLES_DIR / "igh_myc.json").open() as f:
     igh_myc = CategoricalFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "tpm3_ntrk1.json") as f:
+with (EXAMPLES_DIR / "tpm3_ntrk1.json").open() as f:
     tpm3_ntrk1 = AssayedFusion(**json.load(f))
 
-with open(EXAMPLES_DIR / "tpm3_pdgfrb.json") as f:
+with (EXAMPLES_DIR / "tpm3_pdgfrb.json").open() as f:
     tpm3_pdgfrb = AssayedFusion(**json.load(f))

{fusor-0.0.30.dev1 → fusor-0.0.31.dev0/src}/fusor/examples/tpm3_pdgfrb.json

@@ -121,4 +121,4 @@
     "method_uri": "pmid:24034314",
     "fusion_detection": "observed"
   }
-}
+}

{fusor-0.0.30.dev1 → fusor-0.0.31.dev0/src}/fusor/exceptions.py

@@ -4,10 +4,6 @@
 class IDTranslationException(Exception):  # noqa: N818
     """Indicate translation failure for provided ID value"""
 
-    pass
-
 
 class FUSORParametersException(Exception):  # noqa: N818
     """Signal incorrect or insufficient parameters for model constructor methods."""
-
-    pass