wheely-radiant 1.0.1__tar.gz

wheely_radiant-1.0.1/.github/workflows/black.yml

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+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

wheely_radiant-1.0.1/.github/workflows/publish.yml

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+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Deploy Packages
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  codeartifact-deploy:
+    name: Upload release to CodeArtifact
+    if: ${{ github.event_name == 'release' }}
+    runs-on: [self-hosted, aws-master, X64]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        pip config unset global.index-url || true
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine build 'awscli>=1.18.83'
+        aws codeartifact login --tool twine --repository seer_ds --domain seer --domain-owner 718843040700 --region us-west-2
+    - name: Build and publish
+      run: |
+        python -m build --sdist --wheel .
+        twine upload --repository codeartifact dist/*
+
+  pypi-deploy:
+    name: Upload release to PyPI
+    if: ${{ github.event_name == 'release' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/wheely-mammoth
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine build
+      - name: Build package
+        run: python -m build --sdist --wheel .
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

wheely_radiant-1.0.1/.github/workflows/tests.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  schedule:
+  - cron: "0 0 1 1/1 *" # Run monthly
+
+jobs:
+  build:
+    runs-on: [self-hosted, aws-master, X64]
+    #    strategy:
+    #      matrix:
+    #        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.8"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 wheel
+        aws codeartifact login --tool pip --repository seer_ds --domain seer --domain-owner 718843040700 --region us-west-2
+        pip install '.[dev]'
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --extend-exclude=build/
+    - name: Test with pytest
+      run: |
+        python -m pytest

wheely_radiant-1.0.1/.gitignore

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+.idea
+_build
+
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+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/
+pytestdebug.log
+
+# 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/
+doc/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# poetry
+#poetry.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
+.env/
+.venv/
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+pythonenv*
+
+# 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/
+
+# operating system-related files
+*.DS_Store #file properties cache/storage on macOS
+Thumbs.db #thumbnail cache on Windows
+
+# profiling data
+.prof
+
+
+# End of https://www.toptal.com/developers/gitignore/api/python

wheely_radiant-1.0.1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/psf/black
+    rev: stable # Replace by any tag/version: https://github.com/psf/black/tags
+    hooks:
+      - id: black
+        language_version: python3 # Should be a command that runs python3.6+

wheely_radiant-1.0.1/CONTRIBUTING.md

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+## Contributing to this project
+
+### Setting up for development
+
+1. Clone the repository
+
+    ```shell
+    git clone git@github.com:seerbio/repo-name.git
+    cd repo-name
+    ```
+
+    Alternatively, create a fork through GitHub and clone that repository.
+
+2. Set up `pre-commit` hook (for code formatting):
+
+    ```shell
+    pip install pre-commit
+    pre-commit install
+    ```
+
+    This will ensure all Python sources are consistently formatted whenever
+    you commit to the repository.
+
+### Developing changes
+
+1. Create a branch
+
+    ```shell
+    git checkout main
+    git pull --ff-only --tags origin main
+    git checkout -b my-feature-branch main
+    ```
+
+2. Develop your changes. Commit often, with meaningful messages for each commit.
+   Be sure to develop unit tests and ensure that all existing tests pass:
+
+    ```shell
+    pytest
+    ```
+
+3. Push changes back to the repository (or your fork).
+4. Create a pull request through GitHub. Assign yourself to it and add appropriate
+   reviewers.
+
+### Releasing a version of this project's package
+
+After changes are developed, reviewed, and merged, it's possible to create a
+release automatically using GitHub.
+
+1. Determine the appropriate [semantic version](https://semver.org/) for the
+   new release. Check the GitHub repo's "Releases" section to see what the most
+   recent release number is and consider the changes made.
+2. Create a Release through the GitHub UI. Choose to create a new tag targeting
+   the `main` branch and name it for the new version number, i.e. `v3.4.5`.
+   Use the same string as the release title. Click "generate release notes" to
+   automatically create a list of PRs since the last release.
+3. After creating the release, the package will be automatically built and
+   deployed with the new version number.

wheely_radiant-1.0.1/LICENSE.md

@@ -0,0 +1,209 @@
+**LICENSE**
+
+Use of the Fulcrum Pipeline™ framework software, including any portion
+thereof, is licensed under a Mandatory Grant-Back Apache 2.0 license, as
+modified by the Commons Clause (collectively, the "**License**").
+
+You may not use the Fulcrum Pipeline™ software, including any portion
+thereof, except in compliance with the License. See the entire License
+for specific language governing permissions and limitations under the
+License.
+
+------------------------------------------------------------------------
+
+**Mandatory Grant-Back** **Apache 2.0 License, as modified by the Commons Clause May 2026**
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+**1. Definitions**.
+
+"**License**" shall mean the terms and conditions for use,
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+this document.
+
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wheely_radiant-1.0.1/PKG-INFO

@@ -0,0 +1,81 @@
+Metadata-Version: 2.4
+Name: wheely-radiant
+Version: 1.0.1
+Summary: Reader for Radiant DIA results, compatible with wheely-mammoth
+Home-page: https://github.com/seerbio/wheely-radiant
+Author: Seth Just
+Author-email: sjust@seer.bio
+Project-URL: Bug Tracker, https://github.com/seerbio/wheely-radiant/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: pyspark[sql]<4.0.0,>=3.3.1
+Requires-Dist: wheely-mammoth<1.0.0,>=0.16.2
+Requires-Dist: importlib_metadata; python_version < "3.8"
+Provides-Extra: docs
+Requires-Dist: numpydoc>=1.0.0; extra == "docs"
+Requires-Dist: sphinx-argparse>=0.2.5; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.7.1; extra == "docs"
+Requires-Dist: ipykernel>=5.3.0; extra == "docs"
+Requires-Dist: recommonmark>=0.5.0; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: pre-commit>=2.7.1; extra == "dev"
+Requires-Dist: black>=20.8b1; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pandas; extra == "dev"
+Dynamic: license-file
+
+**wheely-radiant**: Reader for Radiant DIA results, compatible with
+[`wheely-mammoth`](https://github.com/seerbio/wheely-mammoth).
+
+## Installation  
+
+This library requires Python 3.8+ and can be installed with pip:  
+
+```shell
+pip install wheely-radiant
+```
+
+## Basic Usage
+
+This package provides a plugin for the [Fulcrum Pipeline](https://github.com/seerbio/fulcrum/)'s
+`read_existing` search backend.
+
+After installing `wheely-radiant` you may use the `radiant` engine to load
+existing Radiant DIA results:
+
+```toml
+[search]
+backend = "read_existing"
+engine = "radiant"
+location = ["uri_one", "uri_two", ...]
+```
+
+(or similar in JSON or `dict` format)
+
+## Direct Usage
+
+To load raw PSM scores from a Radiant Parquet (`.radiantDIA`) file, use the function
+`read_radiant_features()`.
+
+```pycon
+>>> from wheely_radiant import read_radiant_features
+>>> ds = read_radiant_features("data/1.mzML.subset.radiantDIA")
+>>> type(ds)
+<class 'wheely.mammoth.dataset.PsmDataset'>
+>>> ds.scores.select(ds.score_columns[1]).describe().toPandas()
+  summary            cosineSim
+0   count                 1000
+1    mean   0.3947062000000001
+2  stddev  0.15665395271892263
+3     min               0.0315
+4     max               0.9926
+```
+
+To read multiple files, pass a tuple, list, array, or series of file paths.
+Currently only full paths are supported; you can not pass wildcard ("glob")
+paths to the function.

wheely_radiant-1.0.1/README.md

@@ -0,0 +1,50 @@
+**wheely-radiant**: Reader for Radiant DIA results, compatible with
+[`wheely-mammoth`](https://github.com/seerbio/wheely-mammoth).
+
+## Installation  
+
+This library requires Python 3.8+ and can be installed with pip:  
+
+```shell
+pip install wheely-radiant
+```
+
+## Basic Usage
+
+This package provides a plugin for the [Fulcrum Pipeline](https://github.com/seerbio/fulcrum/)'s
+`read_existing` search backend.
+
+After installing `wheely-radiant` you may use the `radiant` engine to load
+existing Radiant DIA results:
+
+```toml
+[search]
+backend = "read_existing"
+engine = "radiant"
+location = ["uri_one", "uri_two", ...]
+```
+
+(or similar in JSON or `dict` format)
+
+## Direct Usage
+
+To load raw PSM scores from a Radiant Parquet (`.radiantDIA`) file, use the function
+`read_radiant_features()`.
+
+```pycon
+>>> from wheely_radiant import read_radiant_features
+>>> ds = read_radiant_features("data/1.mzML.subset.radiantDIA")
+>>> type(ds)
+<class 'wheely.mammoth.dataset.PsmDataset'>
+>>> ds.scores.select(ds.score_columns[1]).describe().toPandas()
+  summary            cosineSim
+0   count                 1000
+1    mean   0.3947062000000001
+2  stddev  0.15665395271892263
+3     min               0.0315
+4     max               0.9926
+```
+
+To read multiple files, pass a tuple, list, array, or series of file paths.
+Currently only full paths are supported; you can not pass wildcard ("glob")
+paths to the function.