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Merge branch 'development' into adapt_to_new_alphabase
# Conflicts: # requirements/development-stable.txt # requirements/development.txt # requirements/gui-stable.txt # requirements/gui.txt
2 parents be77e63 + 4a4a6a0 commit c1c358c

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-338
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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 1.3.0
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current_version = 1.3.1
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commit = True
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tag = False
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parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

‎.github/release.yml‎

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# https://docs.github.com/en/repositories/releasing-projects-on-github/automatically-generated-release-notes#configuring-automatically-generated-release-notes
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changelog:
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exclude:
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# labels:
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# - ignore-for-release
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authors:
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- octocat
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categories:
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- title: Breaking Changes
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labels:
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- breaking-change
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- title: Bug fixes
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labels:
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- bug
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- title: New Features
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labels:
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- enhancement
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- title: Other Changes / unlabeled
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labels:
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- "*"

‎.github/workflows/create_release.yml‎

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# Create a draft release and build and upload all installers to it.
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name: Create Draft Release
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on:
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workflow_dispatch:
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inputs:
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commitish_to_release:
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type: string
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description: 'Enter commit hash or branch to release (default: main).'
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default: "main"
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jobs:
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create-release:
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uses: MannLabs/alphashared/.github/workflows/create_release.yml@v1
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secrets: inherit
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permissions:
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contents: write
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with:
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package_name: peptdeep
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commitish_to_release: ${{ inputs.commitish_to_release }}
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build_nodejs_ui: false
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python_version: 3.9

‎.github/workflows/publish_on_pypi.yml‎

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# Publish and test releases on Test-PyPI and PyPI.
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name: Publish on PyPi
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on:
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workflow_dispatch:
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inputs:
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tag_to_release:
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description: 'Enter tag to release (example: v1.5.5). A tag with the same name must exist in the repository.'
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type: string
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required: true
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jobs:
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publish_on_pypi:
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uses: MannLabs/alphashared/.github/workflows/publish_on_pypi.yml@v1
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with:
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# see the documentation of the workflow for more information on the parameters
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package_name: peptdeep
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tag_to_release: ${{ inputs.tag_to_release }}
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python_version: 3.9
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secrets:
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test_pypi_api_token: ${{ secrets.TEST_PYPI_PEPTDEEP_API_TOKEN }}
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pypi_api_token: ${{ secrets.PYPI_PEPTDEEP_API_TOKEN }}

‎MANIFEST.in‎

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recursive-include peptdeep *
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include LICENSE.txt
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include README.md
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recursive-exclude peptdeep/logs *
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recursive-exclude logs *
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recursive-exclude tests *
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global-exclude */__pycache__/*
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global-exclude *.pyc *.nbi *.nbc

‎README.md‎

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@@ -112,10 +112,10 @@ The GUI of peptdeep is a completely stand-alone tool that requires no
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knowledge of Python or CLI tools. Click on one of the links below to
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download the latest release for:
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- [**Windows**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.0-windows-amd64.exe)
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- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.0-macos-darwin-x64.pkg)
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- [**macOS ARM**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.0-macos-darwin-arm64.pkg )
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- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.0-linux-x64.deb)
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- [**Windows**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-windows-amd64.exe)
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- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-macos-darwin-x64.pkg)
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- [**macOS ARM**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-macos-darwin-arm64.pkg )
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- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-linux-x64.deb)
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Older releases remain available on the [release
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page](https://github.com/MannLabs/alphapeptdeep/releases), but no
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Finally, peptdeep and all its [dependancies](requirements) need to be
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installed. To take advantage of all features and allow development (with
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the `-e` flag), this is best done by also installing the [development
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dependencies](requirements/requirements_development.txt) instead of only
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the [core dependencies](requirements/requirements.txt):
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dependencies](requirements/requirements_development_loose.txt) instead of only
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the [core dependencies](requirements/requirements_loose.txt):
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``` bash
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pip install -e ".[development]"
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```
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By default this installs loose dependancies (no explicit versioning),
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By default this installs 'loose' dependencies (no pinned versions),
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although it is also possible to use stable dependencies
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(e.g. `pip install -e ".[stable,development-stable]"`).
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‎docs/conf.py‎

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copyright = "2022, Mann Labs, MPIB"
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author = "Mann Labs, MPIB"
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release = "1.3.0"
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release = "1.3.1"
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# -- General configuration ---------------------------------------------------
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‎peptdeep/__init__.py‎

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#!python
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# try:
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# from . import (
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# model, spec_lib
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# )
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# from . import protein # rely on spec_lib, import after
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# except (ImportError,RuntimeError, OSError):
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# # happends when installation
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# pass
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__project__ = "peptdeep"
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__version__ = "1.3.0"
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__license__ = "Apache 2.0"
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__description__ = "The AlphaX deep learning framework for Proteomics"
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__author__ = "Mann Labs"
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__version__ = "1.3.1"
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# This information is duplicated in pyproject.toml:
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__author_email__ = "jalew.zwf@qq.com"
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__github__ = "https://github.com/MannLabs/peptdeep"
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__doc__ = "https://alphapeptdeep.readthedocs.io/en/latest/"
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__pypi__ = "https://pypi.org/project/peptdeep/"
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__keywords__ = [
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"deep learning",
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"proteomics",
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"AlphaX ecosystem",
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]
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__python_version__ = ">=3.8"
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__classifiers__ = [
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# "Development Status :: 1 - Planning",
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# "Development Status :: 2 - Pre-Alpha",
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# "Development Status :: 3 - Alpha",
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# "Development Status :: 4 - Beta",
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"Development Status :: 5 - Production/Stable",
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# "Development Status :: 6 - Mature",
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# "Development Status :: 7 - Inactive"
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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__console_scripts__ = [
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"peptdeep=peptdeep.cli:run",
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]
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__urls__ = {
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"Mann Labs at MPIB": "https://www.biochem.mpg.de/mann",
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"Mann Labs at CPR": "https://www.cpr.ku.dk/research/proteomics/mann/",
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"GitHub": __github__,
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"Docs": __doc__,
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"PyPi": __pypi__,
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}
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__extra_requirements__ = {
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"development-stable": "development-stable.txt",
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"gui-stable": "gui-stable.txt",
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"hla-stable": "hla-stable.txt",
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"stable": "base-stable.txt",
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"development": "development.txt",
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"gui": "gui.txt",
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"hla": "hla.txt",
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}
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__license__ = "Apache 2.0"

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "peptdeep"
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requires-python = ">=3.8.0"
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dynamic = ["version", "dependencies", "optional-dependencies"]
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authors = [
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{name = "Mann Labs", email = "jalew.zwf@qq.com"}
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]
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description = "The AlphaX deep learning framework for Proteomics"
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readme = "README.md"
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keywords = [
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"mass spectrometry",
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"proteomics",
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"search engine",
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"DIA",
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"data-independent acquisition",
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"bioinformatics",
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"AlphaPept",
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"AlphaPept ecosystem",
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"deep learning",
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"AlphaX ecosystem",
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]
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license = {file = "LICENSE.txt"}
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classifiers = [
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"Development Status :: 5 - Production/Stable",
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# "Development Status :: 6 - Mature",
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# "Development Status :: 7 - Inactive"
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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[project.urls]
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"Paper preprint" = "https://www.biochem.mpg.de/mann"
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Repository = "https://github.com/MannLabs/peptdeep"
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#Documentation = "https://readthedocs.org"
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#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
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Issues = "https://github.com/MannLabs/peptdeep/issues"
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"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann"
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Docs = "https://alphapeptdeep.readthedocs.io/en/latest/"
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PyPi = "https://pypi.org/project/peptdeep/"
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[tool.setuptools.packages]
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find = {}
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[tool.setuptools.dynamic]
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# https://stackoverflow.com/a/73600610
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dependencies = {file = ["requirements/requirements_loose.txt"]}
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optional-dependencies = { stable = { file = ["requirements/requirements.txt",
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] }, gui = { file = [ "requirements/requirements_gui_loose.txt",
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] }, gui-stable = { file = [ "requirements/requirements_gui.txt",
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] }, development = { file = ["requirements/requirements_development_loose.txt",
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] }, development-stable = { file = ["requirements/requirements_development.txt",
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] }, hla = { file = ["requirements/requirements_hla_loose.txt",
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] }, hla-stable = { file = ["requirements/requirements_hla.txt",
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] }}
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version = {attr = "peptdeep.__version__"}
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[project.scripts]
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peptdeep = "peptdeep.cli:run"
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[tool.ruff]
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extend-exclude = [".bumpversion.cfg"]
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[tool.ruff.lint]
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select = ["E", "F"]

‎release/linux/build_installer_linux.sh‎

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rm -rf dist_pyinstaller build_pyinstaller
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# Creating the wheel
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python setup.py sdist bdist_wheel
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python -m build
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# Setting up the local package
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# Make sure you include the required extra packages and always use the stable or very-stable options!
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pip install "dist/peptdeep-1.3.0-py3-none-any.whl[stable]"
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pip install "dist/peptdeep-1.3.1-py3-none-any.whl[stable, gui-stable]"
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if [ "${CPU_OR_GPU}" != "GPU" ]; then
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pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu

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