Merge branch 'refs/heads/development' into publish_docker

.github/workflows/publish_on_pypi.yml

@@ -0,0 +1,107 @@
+on:
+  workflow_dispatch:
+    inputs:
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5)'
+        required: true
+
+name: Publish on PyPi
+
+env:
+  PYTHON_VERSION: "3.9"
+
+jobs:
+  Create_PyPi_Release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.tag_to_release }}
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Conda info
+        shell: bash -le {0}
+        run: conda info
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+      - name: Prepare distribution
+        shell: bash -le {0}
+        run: |
+          conda create -n alphadia_build python=${{ env.PYTHON_VERSION }} -y
+          conda activate alphadia_build
+          python -m pip install --upgrade pip
+          pip install build twine
+          rm -rf dist
+          rm -rf build
+          python -m build
+          twine check dist/*
+          conda deactivate
+      - name: Publish distribution to Test-PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      - name: Test Test-PyPI loose installation
+        shell: bash -le {0}
+        run: |
+          conda create -n pip_loose_test python=${{ env.PYTHON_VERSION }} -y
+          conda activate pip_loose_test
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia"
+          alphadia -v
+          conda deactivate
+      - name: Test Test-PyPI stable installation
+        shell: bash -le {0}
+        run: |
+          conda create -n pip_stable_test python=${{ env.PYTHON_VERSION }} -y
+          conda activate pip_stable_test
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia[stable]"
+          alphadia -v
+          conda deactivate
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+  Test_PyPi_Release:
+    name: Test_PyPi_version_on_${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: Create_PyPi_Release
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Conda info
+        shell: bash -le {0}
+        run: conda info
+      - uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+      - name: Test PyPI stable installation
+        shell: bash -le {0}
+        run: |
+          conda create -n pip_stable python=${{ env.PYTHON_VERSION }} -y
+          conda activate pip_stable
+          pip install "alphadia[stable]"
+          alphadia -v
+          conda deactivate
+      - name: Test PyPI loose installation
+        shell: bash -le {0}
+        run: |
+          conda create -n pip_loose python=${{ env.PYTHON_VERSION }} -y
+          conda activate pip_loose
+          pip install alphadia
+          alphadia -v
+          conda deactivate

.github/workflows/release.yml

@@ -1,7 +1,6 @@
 on:
   pull_request:
     branches: [ main ]
-  workflow_dispatch:
 
 name: Release bundled installer
 

README.md

@@ -1,4 +1,4 @@
-![Release](https://img.shields.io/badge/release-v1.5.5-brightgreen)
+![Release](https://img.shields.io/badge/release-v1.6.0-brightgreen)
 ![License](https://img.shields.io/badge/License-Apache-brightgreen)
 ![Tests](https://github.com/MannLabs/alphadia/workflows/Default%20installation%20and%20tests/badge.svg)
 ![Deployment](https://github.com/MannLabs/alphadia/workflows/Publish%20on%20PyPi%20and%20release%20on%20GitHub/badge.svg)
@@ -88,7 +88,7 @@ conda activate alphadia
 
 Finally, alphaDIA and all its dependencies can be installed by
 ```bash
-pip install alphadia[stable]
+pip install "alphadia[stable]"
 ```
 We strongly recommend using the `stable` version, which has all dependencies fixed,
 for reasons of reproducibility and integrity.

alphadia/__init__.py

@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.5.5"
+__version__ = "1.6.0"

docs/index.md

@@ -1,6 +1,6 @@
 
 # AlphaDIA Documentation
-**Version:** 1.5.5 | [Github](https://github.com/MannLabs/alphadia)
+**Version:** 1.6.0 | [Github](https://github.com/MannLabs/alphadia)
 
 Open-source DIA search engine built with the alphaX ecosystem. Built with [alpharaw](https://github.com/MannLabs/alpharaw) and [alphatims](https://github.com/MannLabs/alphatims) for raw file acces. Spectral libraries are predicted with [peptdeep](https://github.com/MannLabs/alphapeptdeep) and managed by [alphabase](https://github.com/MannLabs/alphabase). Quantification is powered by [directLFQ](https://github.com/MannLabs/directLFQ).
 

docs/installation.md

@@ -143,28 +143,4 @@ Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-proj
 Install alphaDIA using pip as described [here](../README.md#3-installation).
 
 Afterwards, verify the alphaDIA installation by running:
-`alphadia -h`
-which should give an output like this ```1.5.5```.
-
-#### Obsolete once available on pip:
-As long as there is no public release yet, we can't use `pip install alphadia`.
-Below you can find hosted `.tar.gz` versions for now.
-- [alphadia-v1.5.4](https://datashare.biochem.mpg.de/s/Llz4lEJhQacZWGr/download)
-- [alphadia-v1.5.5](https://datashare.biochem.mpg.de/s/nryp3IUrVs9jucg/download)
-
-Copy the link for the most recent version and download it using wget.
-```bash
-wget https://datashare.biochem.mpg.de/s/nryp3IUrVs9jucg/download -O alphadia.tar.gz
-```
-
-Untar the file
-```bash
-tar -xf ./alphadia.tar.gz
-```
-
-You should get a folder named `alphadia-x.x.x`
-
-Install alphaDIA using pip, this might take some time.
-```bash
-pip install -e ./alphadia-1.5.5
-```
+`alphadia -h` which should give an output like this ```1.5.5```.

gui/package.json

@@ -1,7 +1,7 @@
 {
   "name": "alphadia",
   "productName": "alphadia-gui",
-  "version": "1.5.5",
+  "version": "1.6.0",
   "description": "Graphical user interface for DIA data analysis",
   "main": "dist/electron.js",
   "homepage": "./",

gui/src/main/modules/profile.js

@@ -7,7 +7,7 @@ const { dialog } = require('electron')
 const Profile = class {
 
     config = {
-        "version": "1.5.5",
+        "version": "1.6.0",
         "conda": {
             "envName": "alpha",
             "path": ""

misc/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.5.5
+current_version = 1.6.0
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

pyproject.toml

@@ -3,24 +3,28 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "alphadia"
+name = "alphaDIA"
 requires-python = ">=3.9.0"
 dynamic = ["version", "dependencies", "optional-dependencies"]
 
 authors = [
-    {name = "Mann Labs", email = "[email protected]"},
+    {name = "Mann Labs", email = "[email protected]"}
 ]
-description = "An open-source Python package of the AlphaPept ecosystem"
+description = "A novel proteomics search engine for DIA data based on end-to-end transfer learning."
 readme = "README.md"
 keywords = [
+    "mass spectrometry",
+    "proteomics",
+    "search engine",
+    "DIA",
+    "data-independent acquisition",
     "bioinformatics",
-    "software",
+    "AlphaPept",
     "AlphaPept ecosystem",
 ]
 license = {file = "LICENSE.txt"}
 classifiers = [
-     "Development Status :: 3 - Alpha",
-    # "Development Status :: 4 - Beta",
+    "Development Status :: 4 - Beta",
     # "Development Status :: 5 - Production/Stable",
     # "Development Status :: 6 - Mature",
     # "Development Status :: 7 - Inactive"
@@ -32,11 +36,13 @@ classifiers = [
 ]
 
 [project.urls]
-"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann"
-#Documentation = "https://readthedocs.org"
+
+"Paper preprint" = "https://www.biochem.mpg.de/mann"
 Repository = "https://github.com/MannLabs/alphadia"
-Issues = "https://github.com/MannLabs/alphadia/issues"
+#Documentation = "https://readthedocs.org"
 #Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
+Issues = "https://github.com/MannLabs/alphadia/issues"
+"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann"
 
 [tool.setuptools.packages]
 find = {}

release/macos/build_backend_macos.sh

@@ -6,7 +6,7 @@ python -c "from huggingface_hub import get_full_repo_name; print('success')"
 
 pip install build
 python -m build
-pip install "dist/alphadia-1.5.5-py3-none-any.whl"
+pip install "dist/alphadia-1.6.0-py3-none-any.whl"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller

release/macos/build_pkg_macos.sh

@@ -2,7 +2,7 @@
 
 # Set up package name and version
 PACKAGE_NAME="alphadia"
-PACKAGE_VERSION="1.5.5"
+PACKAGE_VERSION="1.6.0"
 
 ARCH=$(uname -m)
 if [ "$ARCH" == "x86_64" ]; then

release/macos/build_zip_macos.sh

@@ -2,7 +2,7 @@
 
 # Set up package name and version
 PACKAGE_NAME="alphadia"
-PACKAGE_VERSION="1.5.5"
+PACKAGE_VERSION="1.6.0"
 
 ARCH=$(uname -m)
 if [ "$ARCH" == "x86_64" ]; then

release/macos/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>alphaDIA 1.5.5</title>
+    <title>alphaDIA 1.6.0</title>
     <background mime-type="image/png" file="alphadia.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

release/macos/info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alphadia.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphadia.1.5.5</string>
+	<string>alphadia.1.6.0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.5.5</string>
+	<string>1.6.0</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/windows/alphadia_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "AlphaDIA"
-#define MyAppVersion "1.5.5"
+#define MyAppVersion "1.6.0"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphadia"
 #define MyAppExeName "alphadia-gui.exe"
@@ -25,7 +25,7 @@ LicenseFile=..\..\LICENSE.txt
 PrivilegesRequired=lowest
 PrivilegesRequiredOverridesAllowed=dialog
 OutputDir=..\..\dist
-OutputBaseFilename=alphadia-1.5.5-win-x64
+OutputBaseFilename=alphadia-1.6.0-win-x64
 SetupIconFile=..\logos\alphadia.ico
 Compression=lzma
 SolidCompression=yes

release/windows/build_backend.ps1

@@ -6,7 +6,7 @@ python -c 'from huggingface_hub import get_full_repo_name; print("success")'
 
 pip install build
 python -m build
-pip install "dist/alphadia-1.5.5-py3-none-any.whl"
+pip install "dist/alphadia-1.6.0-py3-none-any.whl"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller tbb