cool-seq-tool 0.4.0.dev3__tar.gz → 0.5.0__tar.gz

cool_seq_tool-0.5.0/.coveragerc

@@ -0,0 +1,7 @@
+[run]
+source =
+   cool_seq_tool/
+   tests/
+omit =
+   setup.py
+   docs/*

cool_seq_tool-0.5.0/.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

cool_seq_tool-0.5.0/.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

cool_seq_tool-0.5.0/.github/workflows/checks.yaml

@@ -0,0 +1,58 @@
+name: checks
+on: [push, pull_request]
+jobs:
+  deps:
+    name: deps py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install pipenv
+          pipenv install --dev
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        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 .
+
+  docs:
+    runs-on: ubuntu-latest
+    env:
+      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install '.[docs]'
+
+      - name: Attempt docs build
+        working-directory: ./docs
+        run: make html

cool_seq_tool-0.5.0/.github/workflows/close_issue.yml

@@ -0,0 +1,18 @@
+name: Close issues related to a merged pull request based on staging branch.
+
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - staging
+
+jobs:
+  closeIssueOnPrMergeTrigger:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Closes issues related to a merged pull request.
+        uses: ldez/gha-mjolnir@v1.0.3
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

cool_seq_tool-0.5.0/.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

cool_seq_tool-0.5.0/.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@v4
+        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@v3
+        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/cool-seq-tool
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v3
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

cool_seq_tool-0.5.0/.github/workflows/stale.yaml

@@ -0,0 +1,28 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * *"
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v9
+        with:
+          remove-stale-when-updated: true
+          days-before-close: 14
+
+          days-before-issue-stale: 60
+          stale-issue-label: stale
+          stale-issue-message: "This issue is stale because it has been open 45 days with no activity. Please make a comment for triaging or closing the issue."
+          close-issue-label: closed-by-stale
+          close-issue-message: "This issue was closed because it has been stalled for 14 days with no activity."
+
+          days-before-pr-stale: 7
+          stale-pr-label: stale
+          stale-pr-message: "This PR is stale because it has been open 7 days with no activity. Please review this PR."
+          days-before-pr-close: -1

cool_seq_tool-0.5.0/.gitignore

@@ -0,0 +1,137 @@
+# 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/
+pip-wheel-metadata/
+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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# 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/
+
+.DS_Store
+
+# Data files
+src/cool_seq_tool/data/seqrepo/
+src/cool_seq_tool/data/*.txt
+src/cool_seq_tool/data/LRG_RefSeqGene*
+src/cool_seq_tool/data/MANE*
+src/cool_seq_tool/data/notebooks/
+
+# Autogenerated docs
+docs/source/reference/api
+
+# Files created by doctests
+tpm3.fasta

cool_seq_tool-0.5.0/.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: detect-private-key
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+  - 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 ]

cool_seq_tool-0.5.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.11"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  configuration: docs/source/conf.py

cool_seq_tool-0.5.0/CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Kuzma
+    given-names: Kori
+  - family-names: Stevenson
+    given-names: James
+  - family-names: Wagner
+    given-names: Alex
+title: Cool Seq Tool
+version: v0.1.1
+date-released: 2022-05-11

{cool_seq_tool-0.4.0.dev3 → cool_seq_tool-0.5.0}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2023 Wagner Lab
+Copyright (c) 2021-2024 Wagner Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{cool_seq_tool-0.4.0.dev3/src/cool_seq_tool.egg-info → cool_seq_tool-0.5.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.4.0.dev3
+Version: 0.5.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
         
-        Copyright (c) 2021-2023 Wagner Lab
+        Copyright (c) 2021-2024 Wagner Lab
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -26,12 +26,11 @@ License: MIT License
         SOFTWARE.
         
 Project-URL: Homepage, https://github.com/genomicmedlab/cool-seq-tool
-Project-URL: Documentation, https://coolseqtool.readthedocs.io/en/latest/index.html
+Project-URL: Documentation, https://coolseqtool.readthedocs.io/
 Project-URL: Changelog, https://github.com/genomicmedlab/cool-seq-tool/releases
 Project-URL: Source, https://github.com/genomicmedlab/cool-seq-tool
 Project-URL: Bug Tracker, https://github.com/genomicmedlab/cool-seq-tool/issues
 Classifier: Development Status :: 3 - Alpha
-Classifier: Framework :: FastAPI
 Classifier: Framework :: Pydantic
 Classifier: Framework :: Pydantic :: 2
 Classifier: Intended Audience :: Science/Research
@@ -39,30 +38,29 @@ 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 :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: aiofiles
 Requires-Dist: boto3
 Requires-Dist: agct>=0.1.0-dev1
-Requires-Dist: polars
+Requires-Dist: polars~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
-Requires-Dist: uvicorn
-Requires-Dist: fastapi
 Requires-Dist: ga4gh.vrs
+Requires-Dist: wags-tails~=0.1.3
+Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff==0.2.0; extra == "dev"
+Requires-Dist: ruff==0.5.0; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -81,8 +79,14 @@ Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 CoolSeqTool
 </h1>
 
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
 **[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
+---
+
 ## Overview
 
 <!-- description -->
@@ -113,6 +117,7 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ```pycon
 >>> from cool_seq_tool.app import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
 >>> cst = CoolSeqTool()
 >>> result = await cst.mane_transcript.get_mane_transcript(
 ...     "NP_004324.2",

{cool_seq_tool-0.4.0.dev3 → cool_seq_tool-0.5.0}/README.md

@@ -2,8 +2,14 @@
 CoolSeqTool
 </h1>
 
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
 **[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
+---
+
 ## Overview
 
 <!-- description -->
@@ -34,6 +40,7 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ```pycon
 >>> from cool_seq_tool.app import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
 >>> cst = CoolSeqTool()
 >>> result = await cst.mane_transcript.get_mane_transcript(
 ...     "NP_004324.2",

cool_seq_tool-0.5.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

cool_seq_tool-0.5.0/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd