From 610ad3f1a9399ad48f5bdf46da927c467660806c Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Mon, 13 Jan 2025 18:47:15 +0100
Subject: [PATCH 01/29] move to .bumpversion.toml

---
 .bumpversion.toml                         | 54 +++++++++++++++++++++++
 .pre-commit-config.yaml                   |  2 -
 misc/.bumpversion.cfg                     | 36 ---------------
 pyproject.toml                            |  2 +-
 requirements/requirements_development.txt |  2 +-
 5 files changed, 56 insertions(+), 40 deletions(-)
 create mode 100644 .bumpversion.toml
 delete mode 100644 misc/.bumpversion.cfg

diff --git a/.bumpversion.toml b/.bumpversion.toml
new file mode 100644
index 00000000..988c36f0
--- /dev/null
+++ b/.bumpversion.toml
@@ -0,0 +1,54 @@
+[tool.bumpversion]
+current_version = "1.9.2"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+
+[[tool.bumpversion.files]]
+filename = "./alphadia/__init__.py"
+
+[[tool.bumpversion.files]]
+filename = "./gui/src/main/modules/profile.js"
+
+[[tool.bumpversion.files]]
+filename = "./gui/package.json"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/info.plist"
+
+[[tool.bumpversion.files]]
+filename = "./release/linux/build_installer_linux.sh"
+
+[[tool.bumpversion.files]]
+filename = "./release/linux/control"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/build_installer_macos.sh"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/build_package_macos.sh"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/distribution.xml"
+
+[[tool.bumpversion.files]]
+filename = "./release/windows/alphadia_innoinstaller.iss"
+
+[[tool.bumpversion.files]]
+filename = "./release/windows/build_installer_windows.ps1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b64f17a2..cfefafb7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,5 +13,3 @@ repos:
     - id: ruff-format
     - id: ruff
       args: [ '--fix' ]
-
-exclude: .bumpversion.cfg
diff --git a/misc/.bumpversion.cfg b/misc/.bumpversion.cfg
deleted file mode 100644
index 1aa88e0f..00000000
--- a/misc/.bumpversion.cfg
+++ /dev/null
@@ -1,36 +0,0 @@
-[bumpversion]
-current_version = 1.9.2
-commit = True
-tag = True
-parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
-serialize = 
-	{major}.{minor}.{patch}
-	{major}.{minor}.{patch}
-
-[bumpversion:part:release]
-
-[bumpversion:part:build]
-
-[bumpversion:file:../alphadia/__init__.py]
-
-[bumpversion:file:../gui/src/main/modules/profile.js]
-
-[bumpversion:file:../gui/package.json]
-
-[bumpversion:file:../release/macos/info.plist]
-
-[bumpversion:file:../release/linux/build_installer_linux.sh]
-
-[bumpversion:file:../release/linux/control]
-
-[bumpversion:file:../release/macos/build_installer_macos.sh]
-
-[bumpversion:file:../release/macos/build_package_macos.sh]
-
-[bumpversion:file:../release/macos/distribution.xml]
-
-[bumpversion:file:../release/windows/alphadia_innoinstaller.iss]
-
-[bumpversion:file:../release/windows/build_installer_windows.ps1]
-search = {current_version}
-replace = {new_version}
diff --git a/pyproject.toml b/pyproject.toml
index 711b3bf1..2a687c89 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ version = {attr = "alphadia.__version__"}
 alphadia = "alphadia.cli:run"
 
 [tool.ruff]
-extend-exclude = ["misc/.bumpversion.cfg", "tests"]
+extend-exclude = ["tests"]
 
 [tool.ruff.lint]
 select =  [
diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt
index 9c13e1b2..9e6c618d 100644
--- a/requirements/requirements_development.txt
+++ b/requirements/requirements_development.txt
@@ -5,7 +5,7 @@ jupyter_contrib_nbextensions
 pyinstaller
 
 twine
-bumpversion
+bump-my-version
 pipdeptree
 ipykernel
 psutil

From e6d6cd577c9b17be190f2ab195f888beb6beb6fb Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 14 Jan 2025 12:17:46 +0100
Subject: [PATCH 02/29] include dev versions

---
 .bumpversion.toml | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index 988c36f0..92364c61 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,7 +1,19 @@
 [tool.bumpversion]
 current_version = "1.9.2"
-parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
-serialize = ["{major}.{minor}.{patch}"]
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre_l: pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre_n: pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
 search = "{current_version}"
 replace = "{new_version}"
 regex = false
@@ -19,6 +31,9 @@ setup_hooks = []
 pre_commit_hooks = []
 post_commit_hooks = []
 
+[tool.bumpversion.parts.pre_l]
+values = ["dev", "final"]
+optional_value = "final"
 
 [[tool.bumpversion.files]]
 filename = "./alphadia/__init__.py"

From 3cc33d54ef3c2eb733bb2d3f703461fbdc338be2 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 14 Jan 2025 12:19:34 +0100
Subject: [PATCH 03/29] add bump version workflow

---
 .github/workflows/bump_version.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .github/workflows/bump_version.yml

diff --git a/.github/workflows/bump_version.yml b/.github/workflows/bump_version.yml
new file mode 100644
index 00000000..03035f8e
--- /dev/null
+++ b/.github/workflows/bump_version.yml
@@ -0,0 +1,24 @@
+# Bump the version for releases
+# Requires a .bumpversion.toml file in the root of the repository
+name: Bump version
+
+on:
+  workflow_dispatch:
+    inputs:
+      bump_type:
+        description: 'Bump type'
+        required: true
+        default: 'patch'
+        type: choice
+        options:
+        - prerelease
+        - patch
+        - minor
+        - major
+
+jobs:
+  bump-version:
+    uses: MannLabs/alphashared/.github/workflows/bump_version.yml@v1
+    secrets: inherit
+    with:
+     bump_type: ${{inputs.bump_type}}

From 4931b5dfedc8aa152eba3d11c93f1132c039de56 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 14 Jan 2025 12:29:07 +0100
Subject: [PATCH 04/29] adapt to latest workflow

---
 .github/workflows/publish_on_pypi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/publish_on_pypi.yml b/.github/workflows/publish_on_pypi.yml
index 4a538d6f..91fb072f 100644
--- a/.github/workflows/publish_on_pypi.yml
+++ b/.github/workflows/publish_on_pypi.yml
@@ -16,6 +16,7 @@ jobs:
       # see the documentation of the workflow for more information on the parameters
       package_name: alphadia
       tag_to_release: ${{ inputs.tag_to_release }}
+      test_stable: true
     secrets:
       test_pypi_api_token: ${{ secrets.TEST_PYPI_API_TOKEN }}
       pypi_api_token: ${{ secrets.PYPI_API_TOKEN }}

From 187647424d14919fb9ee4f0fb3578f2f51d2744f Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 14 Jan 2025 14:47:21 +0100
Subject: [PATCH 05/29] improve docs

---
 .bumpversion.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index 92364c61..f18e425a 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -32,6 +32,7 @@ pre_commit_hooks = []
 post_commit_hooks = []
 
 [tool.bumpversion.parts.pre_l]
+# 'final' is just a dummy, but required to have the versioning compatible with the reusable alphashared workflow
 values = ["dev", "final"]
 optional_value = "final"
 

From a5a4a0522ee9ea001874657d755d37d28de0dcbb Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Thu, 16 Jan 2025 14:58:58 +0100
Subject: [PATCH 06/29] fix building wheels for prereleases

---
 release/linux/build_installer_linux.sh      | 4 +++-
 release/macos/build_installer_macos.sh      | 5 ++++-
 release/windows/build_installer_windows.ps1 | 5 ++++-
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/release/linux/build_installer_linux.sh b/release/linux/build_installer_linux.sh
index 35703bad..151131fd 100755
--- a/release/linux/build_installer_linux.sh
+++ b/release/linux/build_installer_linux.sh
@@ -10,7 +10,9 @@ rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
 python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+# substitute X.Y.Z-devN with X.Y.Z.devN
+WHL_NAME=$(echo "alphadia-1.9.2-py3-none-any.whl" | sed 's/\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\)-dev\([0-9][0-9]*\)/\1.dev\2/g')
+pip install "dist/${WHL_NAME}[stable]"
 
 if [ "${CPU_OR_GPU}" != "GPU" ]; then
     pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu
diff --git a/release/macos/build_installer_macos.sh b/release/macos/build_installer_macos.sh
index 0fd02708..33ab0170 100755
--- a/release/macos/build_installer_macos.sh
+++ b/release/macos/build_installer_macos.sh
@@ -10,7 +10,10 @@ rm -rf dist_pyinstaller build_pyinstaller
 export EAGER_IMPORT=true  # TODO check if this can be removed with newset peptdeep version w/out transformer dependenc
 
 python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+
+# substitute X.Y.Z-devN with X.Y.Z.devN
+WHL_NAME=$(echo "alphadia-1.9.2-py3-none-any.whl" | sed 's/\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\)-dev\([0-9][0-9]*\)/\1.dev\2/g')
+pip install "dist/${WHL_NAME}[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pyinstaller release/pyinstaller/alphadia.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y
diff --git a/release/windows/build_installer_windows.ps1 b/release/windows/build_installer_windows.ps1
index 1123d75f..08ed15b2 100644
--- a/release/windows/build_installer_windows.ps1
+++ b/release/windows/build_installer_windows.ps1
@@ -5,7 +5,10 @@ Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build
 Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
 
 python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+
+# substitute X.Y.Z-devN with X.Y.Z.devN
+$WHL_NAME = "alphadia-1.9.2-py3-none-any.whl" -replace '(\d+\.\d+\.\d+)-dev(\d+)', '$1.dev$2'
+pip install "dist/$WHL_NAME[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install tbb==2021.13.1

From e3d497de5e1ecef3224affc9ac05c5e67f34b59e Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:09:43 +0100
Subject: [PATCH 07/29] rename requirements: tests -> tests

---
 .github/workflows/branch-checks.yaml                 |  2 +-
 .github/workflows/fdr_performance.yml                |  2 +-
 .github/workflows/pip_installation.yml               |  2 +-
 pyproject.toml                                       | 12 ++++++++----
 requirements/requirements_development.txt            |  2 +-
 ...{requirements_test.txt => requirements_tests.txt} |  0
 6 files changed, 12 insertions(+), 8 deletions(-)
 rename requirements/{requirements_test.txt => requirements_tests.txt} (100%)

diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
index 90677094..fb87725b 100644
--- a/.github/workflows/branch-checks.yaml
+++ b/.github/workflows/branch-checks.yaml
@@ -25,7 +25,7 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh stable,test
+      install-script: ./pip_install.sh stable,tests
       test-script: ./run_unit_tests.sh
 
   get-code-review-input:
diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
index 33d7a98d..b1574fec 100644
--- a/.github/workflows/fdr_performance.yml
+++ b/.github/workflows/fdr_performance.yml
@@ -35,7 +35,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd misc
-          . ./pip_install.sh stable,test
+          . ./pip_install.sh stable,tests
       - name: Run legacy classifier
         env: # Or as an environment variable
           NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_FDR_TOKEN }}
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index 4f7711f4..b82f9f26 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.github/workflows/pip_installation.yml
@@ -30,7 +30,7 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh stable,test
+      install-script: ./pip_install.sh stable,tests
       test-script: ./run_unit_tests.sh
 
   run-unit-tests-loose:
diff --git a/pyproject.toml b/pyproject.toml
index 794d7fd2..e87a1cfe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,10 +50,14 @@ find = {}
 [tool.setuptools.dynamic]
 # https://stackoverflow.com/a/73600610
 dependencies = {file = ["requirements/requirements_loose.txt"]}
-optional-dependencies = { stable = { file = ["requirements/requirements.txt",
-] }, test = { file = [ "requirements/requirements_test.txt",
-] }, development = { file = ["requirements/requirements_development.txt", "requirements/requirements_test.txt", "requirements/requirements_docs.txt"
-] }}
+optional-dependencies.stable = { file = ["requirements/requirements.txt"] }
+optional-dependencies.tests = { file = ["requirements/requirements_test.txt"] }
+optional-dependencies.docs = { file = ["requirements/requirements_docs.txt"] }
+optional-dependencies.development = { file = [
+    "requirements/requirements_development.txt",
+    "requirements/requirements_test.txt",
+    "requirements/requirements_docs.txt"] }
+
 version = {attr = "alphadia.__version__"}
 
 [project.scripts]
diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt
index 9c13e1b2..0b4bc8c7 100644
--- a/requirements/requirements_development.txt
+++ b/requirements/requirements_development.txt
@@ -1,5 +1,5 @@
 # Dependencies required for developing alphaDIA
-# Also, `requirements_test.txt` and `requirements_docs.txt` are required for developing
+# Also, `requirements_tests.txt` and `requirements_docs.txt` are required for developing
 jupyter
 jupyter_contrib_nbextensions
 pyinstaller
diff --git a/requirements/requirements_test.txt b/requirements/requirements_tests.txt
similarity index 100%
rename from requirements/requirements_test.txt
rename to requirements/requirements_tests.txt

From 59a20b4e6bf174b179d670ef882d3510aeaa278b Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:09:55 +0100
Subject: [PATCH 08/29] fix readthedocs

---
 .readthedocs.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index c3b9ee8f..2ec64484 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -12,4 +12,7 @@ sphinx:
 # Explicitly set the version of Python and its requirements
 python:
   install:
-    - requirements: requirements/requirements_docs.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

From ad1a90ae791f13c31cce13d7ba1f74d327c66f18 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:10:23 +0100
Subject: [PATCH 09/29] update Readme

---
 docs/installation.md | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/docs/installation.md b/docs/installation.md
index 6fada45c..6afe58cf 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -69,18 +69,14 @@ See also the [developer guide](developer_guide.md) for more information on how t
 
 ### 1. Setting up the repository
 
-Navigate to a folder where you would like to install alphaDIA and
- download the alphaDIA repository. This creates a subfolder `alphadia` in your current directory
+Navigate to a folder where you would like to set up the repository and execute
 ```bash
-cd ~/work/search_engines
-git clone git@github.com:MannLabs/alphadia.git
-cd alphadia
+git clone git@github.com:MannLabs/alphadia.git && cd alphadia
 ```
 
-Optionally, to get the latest features, switch to the `development` branch and pull the most recent version
+Optionally, get the code version of the latest tag (corresponding to the latest (pre)release):
 ```bash
-git switch development
-git pull
+git fetch --tags && git checkout $(git describe --tags $(git rev-list --tags --max-count=1))
 ```
 
 ### 2. Installation: backend

From 36ca9b5f741774274eca4376e45dfd08d49bb91c Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:25:26 +0100
Subject: [PATCH 10/29] add build_wheel.sh

---
 release/common/build_wheel.sh               | 12 ++++++++++++
 release/linux/build_installer_linux.sh      |  6 +++---
 release/macos/build_installer_macos.sh      |  8 ++++----
 release/windows/build_installer_windows.ps1 | 11 ++++++-----
 4 files changed, 25 insertions(+), 12 deletions(-)
 create mode 100755 release/common/build_wheel.sh

diff --git a/release/common/build_wheel.sh b/release/common/build_wheel.sh
new file mode 100755
index 00000000..46192117
--- /dev/null
+++ b/release/common/build_wheel.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+set -e -u
+
+# Build the wheel for all os (on a linux runner).
+# This script must be run from the root of the repository.
+# If you want OS-specific wheels, add the respective scripts to the OS-specific folders,
+# the alphashared workflow will use those then:
+# e.g. release/linux/build_wheel_linux.sh
+
+rm -rf dist ./*.egg-info
+
+python -m build
diff --git a/release/linux/build_installer_linux.sh b/release/linux/build_installer_linux.sh
index 35703bad..66a661e6 100755
--- a/release/linux/build_installer_linux.sh
+++ b/release/linux/build_installer_linux.sh
@@ -5,12 +5,12 @@ CPU_OR_GPU=${1:-CPU}
 
 # Build the installer for Linux.
 # This script must be run from the root of the repository.
+# Prerequisites: wheel has been build, e.g. using build_wheel.sh
 
-rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
-python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+WHL_NAME=$(cd dist && ls ./*.whl && cd ..)
+pip install "dist/${WHL_NAME}[stable]"
 
 if [ "${CPU_OR_GPU}" != "GPU" ]; then
     pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu
diff --git a/release/macos/build_installer_macos.sh b/release/macos/build_installer_macos.sh
index 0fd02708..eb4a8b8e 100755
--- a/release/macos/build_installer_macos.sh
+++ b/release/macos/build_installer_macos.sh
@@ -3,14 +3,14 @@ set -e -u
 
 # Build the installer for MacOS.
 # This script needs to be run from the root of the repository.
+# Prerequisites: wheel has been build, e.g. using build_wheel.sh
 
-rm -rf dist build *.egg-info
 rm -rf dist_pyinstaller build_pyinstaller
 
-export EAGER_IMPORT=true  # TODO check if this can be removed with newset peptdeep version w/out transformer dependenc
+export EAGER_IMPORT=true  # TODO check if this can be removed with newest peptdeep version w/out transformer dependency
 
-python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+WHL_NAME=$(cd dist && ls ./*.whl && cd ..)
+pip install "dist/${WHL_NAME}[stable]"
 
 # Creating the stand-alone pyinstaller folder
 pyinstaller release/pyinstaller/alphadia.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y
diff --git a/release/windows/build_installer_windows.ps1 b/release/windows/build_installer_windows.ps1
index 1123d75f..6b019f46 100644
--- a/release/windows/build_installer_windows.ps1
+++ b/release/windows/build_installer_windows.ps1
@@ -1,12 +1,13 @@
 # Build the installer for Windows.
 # This script must be run from the root of the repository.
+# Prerequisites: wheel has been build, e.g. using build_wheel.sh
 
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build
-Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
+Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build_pyinstaller
+Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist_pyinstaller
 
-python -m build
-pip install "dist/alphadia-1.9.2-py3-none-any.whl[stable]"
+$WHL_NAME = (Get-ChildItem -Path "dist" -Filter "*.whl").Name
+pip install "dist/$WHL_NAME[stable]"
 
 # Creating the stand-alone pyinstaller folder
-pip install tbb==2021.13.1
+pip install tbb==2021.13.1  # TODO check if this is necessary
 pyinstaller release/pyinstaller/alphadia.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y

From e24bbacabfe0a452210c5c0376557595a7699838 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:28:52 +0100
Subject: [PATCH 11/29] remove development branch

---
 .github/workflows/e2e_testing.yml      | 2 +-
 .github/workflows/fdr_performance.yml  | 2 +-
 .github/workflows/pip_installation.yml | 2 +-
 tests/e2e_tests/e2e_slurm.sh           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 0ab2bd0d..1e1a6743 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -2,7 +2,7 @@ on:
   pull_request:
     types: [ labeled ]
   push:
-    branches: [ main, development ]
+    branches: [ main ]
   workflow_dispatch:
 
 name: End to end testing
diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
index b1574fec..801a31b4 100644
--- a/.github/workflows/fdr_performance.yml
+++ b/.github/workflows/fdr_performance.yml
@@ -2,7 +2,7 @@ on:
   pull_request:
     types: [ labeled ]
   push:
-    branches: [ main, development ]
+    branches: [ main ]
   workflow_dispatch:
 
 name: FDR performance test
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index b82f9f26..ac66e262 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.github/workflows/pip_installation.yml
@@ -8,7 +8,7 @@
 
 on:
   push:
-    branches: [ main, development ]
+    branches: [ main ]
   pull_request:
     branches: [ main ]
   workflow_dispatch:
diff --git a/tests/e2e_tests/e2e_slurm.sh b/tests/e2e_tests/e2e_slurm.sh
index ee4db7e8..34f17828 100644
--- a/tests/e2e_tests/e2e_slurm.sh
+++ b/tests/e2e_tests/e2e_slurm.sh
@@ -13,7 +13,7 @@
 
 # input parameters:
 CONDA_ENV=alphadia
-BRANCH=development  # branch to take test cases from
+BRANCH=main  # branch to take test cases from
 TEST_CASE=basic
 
 #

From f39f7a45c31b276a121d0dd3ef66614e3dc92bd5 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:35:48 +0100
Subject: [PATCH 12/29] allow to run e2e cases manually

---
 .github/workflows/e2e_testing.yml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 1e1a6743..f367c9cd 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -1,3 +1,5 @@
+name: End to end testing
+
 on:
   pull_request:
     types: [ labeled ]
@@ -5,7 +7,11 @@ on:
     branches: [ main ]
   workflow_dispatch:
 
-name: End to end testing
+inputs:
+  test_case:
+    description: 'Test case to run (see e2e_test_cases.yaml for available cases), "all" to run all test cases.'
+    required: false
+    default: 'all'
 
 jobs:
   end2end_testing:
@@ -28,23 +34,24 @@ jobs:
       TQDM_MININTERVAL: 10  # avoid lots of tqdm outputs
     steps:
       - uses: actions/checkout@v4
-      - name: Conda info
-        shell: bash -el {0}
-        run: conda info
+        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
       - name: Pip installation with stable dependencies
         id: pip_installation
+        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
         shell: bash -el {0}
         run: |
+          conda info
           cd misc
           . ./pip_install.sh stable $RUN_NAME
       - name: Run e2e tests
+        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
         shell: bash -el {0}
         run: |
           cd tests
            . ./run_e2e_tests.sh ${{ matrix.test_case }} $RUN_NAME True ${GITHUB_SHA::7} $BRANCH_NAME
       - name: Cleanup
         if: always()
-        shell: bash -el {0}
+        shell: bash -l {0}
         run: |
           conda remove -n $RUN_NAME --all -y
       - name: Delete Caches on Error

From 949c273e18dd8f34f65f48eb76c2c9c9d9df004b Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:38:21 +0100
Subject: [PATCH 13/29] allow to run e2e cases manually

---
 .github/workflows/e2e_testing.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index f367c9cd..4c8ea7cf 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -6,12 +6,11 @@ on:
   push:
     branches: [ main ]
   workflow_dispatch:
-
-inputs:
-  test_case:
-    description: 'Test case to run (see e2e_test_cases.yaml for available cases), "all" to run all test cases.'
-    required: false
-    default: 'all'
+    inputs:
+      test_case:
+        description: 'Test case to run (see e2e_test_cases.yaml for available cases), "all" to run all test cases.'
+        required: false
+        default: 'all'
 
 jobs:
   end2end_testing:

From dfb5a4047d9cc2f4c28ab3339b41644ad2dc7d3d Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:44:35 +0100
Subject: [PATCH 14/29] allow to run e2e cases manually

---
 .github/workflows/e2e_testing.yml | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 4c8ea7cf..0356092f 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -13,15 +13,29 @@ on:
         default: 'all'
 
 jobs:
+  determine_test_cases:
+    runs-on: ubuntu-latest
+    outputs:
+      test_cases: ${{ steps.set-matrix.outputs.test_cases }}
+    steps:
+      - id: set-matrix
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ] && [ "${{ github.event.inputs.test_case }}" != "all" ]; then
+            echo "test_cases=[\"${{ github.event.inputs.test_case }}\"]" >> $GITHUB_OUTPUT
+          else
+            # NEW TEST CASES ARE ADDED HERE:
+            echo 'test_cases=["basic", "synchropasef", "astral", "astral_automatic_calibration", "multistep"]' >> $GITHUB_OUTPUT
+          fi
+
   end2end_testing:
     name: End to end test
+    needs: determine_test_cases
     runs-on: self-hosted
     if: contains(github.event.pull_request.labels.*.name, 'test:e2e') || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        # test case name as defined in e2e_test_cases.yaml
-        test_case: [ "basic", "synchropasef", "astral", "astral_automatic_calibration", "multistep"]
+        test_case: ${{ fromJson(needs.determine_test_cases.outputs.test_cases) }}
     env:
       RUN_NAME: alphadia-${{github.sha}}-${{github.run_id}}-${{github.run_attempt}}
       BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
@@ -33,21 +47,18 @@ jobs:
       TQDM_MININTERVAL: 10  # avoid lots of tqdm outputs
     steps:
       - uses: actions/checkout@v4
-        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
       - name: Pip installation with stable dependencies
         id: pip_installation
-        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
         shell: bash -el {0}
         run: |
           conda info
           cd misc
           . ./pip_install.sh stable $RUN_NAME
       - name: Run e2e tests
-        if: ${{ inputs.test_case == 'all' || matrix.test_case == inputs.test_case }}
         shell: bash -el {0}
         run: |
           cd tests
-           . ./run_e2e_tests.sh ${{ matrix.test_case }} $RUN_NAME True ${GITHUB_SHA::7} $BRANCH_NAME
+          . ./run_e2e_tests.sh ${{ matrix.test_case }} $RUN_NAME True ${GITHUB_SHA::7} $BRANCH_NAME
       - name: Cleanup
         if: always()
         shell: bash -l {0}

From f2615d59291ffa191dbb97f8e1dc35bd3538db5b Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:51:12 +0100
Subject: [PATCH 15/29] don't run all tests on PRs to main

---
 .github/workflows/pip_installation.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index ac66e262..2852dec2 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.github/workflows/pip_installation.yml
@@ -1,16 +1,13 @@
 # Perform pip installation (stable, loose) and run tests on all three OS
 
 # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
-# On each push to develop, the whole test matrix runs, additionally, its success is mandatory for merging to main.
+# On each push to main, the whole test matrix runs.
 # In the (assumed to be rare case) that these full matrix tests fail but the reduced matrix tests passed,
-# we will learn about it latest before pushing to main. The merge that caused the issue can then be identified
-# from the tests that ran on develop.
+# we will learn about it latest after pushing to main.
 
 on:
   push:
     branches: [ main ]
-  pull_request:
-    branches: [ main ]
   workflow_dispatch:
 
 name: Pip install + unit tests

From 6268dd18c65af801ccc160f0cd0264926cbc2cff Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:53:12 +0100
Subject: [PATCH 16/29] run e2e only daily

---
 .github/workflows/e2e_testing.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 0356092f..25f0f2dd 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -3,8 +3,10 @@ name: End to end testing
 on:
   pull_request:
     types: [ labeled ]
-  push:
-    branches: [ main ]
+#  push:
+#    branches: [ main ]
+  schedule:
+    - cron: "0 0 0 * * *"   # daily on 12:00 AM
   workflow_dispatch:
     inputs:
       test_case:

From 15dffb45ac3a72a7251d741f999e8329a9f28352 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:56:11 +0100
Subject: [PATCH 17/29] change strategy to fail-fast: false

---
 .github/workflows/pip_installation.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index 2852dec2..66b7fa81 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.github/workflows/pip_installation.yml
@@ -20,6 +20,7 @@ jobs:
   run-unit-tests-stable:
     name: Test 'stable' on ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os:  [ubuntu-latest, macos-13, windows-latest]
         python-version: ["3.10", "3.11", "3.12"]
@@ -33,6 +34,7 @@ jobs:
   run-unit-tests-loose:
     name: Test 'loose' on ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-13, windows-latest ]
         python-version: ["3.10", "3.11", "3.12"]
@@ -40,5 +42,5 @@ jobs:
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh test
+      install-script: ./pip_install.sh tests
       test-script: ./run_unit_tests.sh

From 0b7d34fec3f391ff3c237dd6b93a56ff3cbb5e3a Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:38:32 +0100
Subject: [PATCH 18/29] fix tests

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e87a1cfe..90c3e9ac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ find = {}
 # https://stackoverflow.com/a/73600610
 dependencies = {file = ["requirements/requirements_loose.txt"]}
 optional-dependencies.stable = { file = ["requirements/requirements.txt"] }
-optional-dependencies.tests = { file = ["requirements/requirements_test.txt"] }
+optional-dependencies.tests = { file = ["requirements/requirements_tests.txt"] }
 optional-dependencies.docs = { file = ["requirements/requirements_docs.txt"] }
 optional-dependencies.development = { file = [
     "requirements/requirements_development.txt",

From 7bb2e3d5b5fef90dc207f88ea51ac74f1bcaef73 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:38:46 +0100
Subject: [PATCH 19/29] remove performance_testing workflow

---
 .github/workflows/performance_testing.yml | 30 -----------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 .github/workflows/performance_testing.yml

diff --git a/.github/workflows/performance_testing.yml b/.github/workflows/performance_testing.yml
deleted file mode 100644
index 6338ef35..00000000
--- a/.github/workflows/performance_testing.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-on:
-  pull_request:
-    branches:
-      - 'alpha'
-  workflow_dispatch:
-
-name: Performance test
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-env:
-  TEST_DATA_DIR: C:\actions-runner\_data
-  CONDA: C:\Users\wallmann\Miniconda3
-  NEPTUNE_TOKEN: ${{ secrets.NEPTUNE_TOKEN }}
-
-jobs:
-  performance_testing:
-    name: Performance testing
-    runs-on: self-hosted
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install alphadia
-        run: |
-          conda activate alpha
-      - name: Diann re extraction
-        run: |
-            python tests/performance_tests/1_brunner_2022_1ng_all.py

From 89b3854e1e88975eb553ceb35e1dee3ae6a55d35 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:38:57 +0100
Subject: [PATCH 20/29] remove tbb dependency for windows installer

---
 release/windows/build_installer_windows.ps1 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/release/windows/build_installer_windows.ps1 b/release/windows/build_installer_windows.ps1
index 6b019f46..96e98c81 100644
--- a/release/windows/build_installer_windows.ps1
+++ b/release/windows/build_installer_windows.ps1
@@ -9,5 +9,5 @@ $WHL_NAME = (Get-ChildItem -Path "dist" -Filter "*.whl").Name
 pip install "dist/$WHL_NAME[stable]"
 
 # Creating the stand-alone pyinstaller folder
-pip install tbb==2021.13.1  # TODO check if this is necessary
+# pip install tbb==2021.13.1  # TODO check if this is necessary
 pyinstaller release/pyinstaller/alphadia.spec --distpath dist_pyinstaller --workpath build_pyinstaller -y

From abeec9abe0aef686e72de560178791ca6d4a184d Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:52:11 +0100
Subject: [PATCH 21/29] fix output_path being None

---
 alphadia/search_step.py     | 2 +-
 alphadia/workflow/config.py | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/alphadia/search_step.py b/alphadia/search_step.py
index 4b40ca9f..4cbcfeb6 100644
--- a/alphadia/search_step.py
+++ b/alphadia/search_step.py
@@ -122,7 +122,7 @@ def _init_config(
 
         config.update(config_updates, do_print=True)
 
-        if ConfigKeys.OUTPUT_DIRECTORY not in config:
+        if config.get(ConfigKeys.OUTPUT_DIRECTORY, None) is None:
             config[ConfigKeys.OUTPUT_DIRECTORY] = output_folder
 
         config.to_yaml(os.path.join(output_folder, "frozen_config.yaml"))
diff --git a/alphadia/workflow/config.py b/alphadia/workflow/config.py
index 378ed2c6..c1ce539e 100644
--- a/alphadia/workflow/config.py
+++ b/alphadia/workflow/config.py
@@ -14,6 +14,7 @@
 
 import yaml
 
+from alphadia.constants.keys import ConfigKeys
 from alphadia.exceptions import KeyAddedConfigError, TypeMismatchConfigError
 
 logger = logging.getLogger()
@@ -51,7 +52,9 @@ def to_json(self, path: str) -> None:
             json.dump(self.data, f)
 
     def __setitem__(self, key, item):
-        raise NotImplementedError("Use update() to update the config.")
+        if key != ConfigKeys.OUTPUT_DIRECTORY:
+            raise NotImplementedError("Use update() to update the config.")
+        return super().__setitem__(key, item)
 
     def __delitem__(self, key):
         raise NotImplementedError("Use update() to update the config.")

From de1da63ed9ad9548de95238310b0559654378157 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 11:54:02 +0100
Subject: [PATCH 22/29] fix debug notebook

---
 nbs/debug/debug_lvl1.ipynb | 89 ++++++++++++++++++++++++--------------
 1 file changed, 57 insertions(+), 32 deletions(-)

diff --git a/nbs/debug/debug_lvl1.ipynb b/nbs/debug/debug_lvl1.ipynb
index b5140001..5c5d2b97 100644
--- a/nbs/debug/debug_lvl1.ipynb
+++ b/nbs/debug/debug_lvl1.ipynb
@@ -5,15 +5,13 @@
    "metadata": {},
    "source": [
     "# Debugging notebook for alphaDIA\n",
-    "THis notebooks allows you to run a search in a jupyter notebook and debug the results.\n",
+    "This notebooks allows you to run a search in a jupyter notebook and debug the results.\n",
     "It allows you to debug a search on the workflow level as well on the peakgroup level"
    ]
   },
   {
    "metadata": {},
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
     "%reload_ext autoreload\n",
     "%autoreload 2\n",
@@ -30,13 +28,13 @@
     "os.environ[\"NUMBA_BOUNDSCHECK\"] = \"1\"\n",
     "os.environ[\"NUMBA_DEVELOPER_MODE\"] = \"1\"\n",
     "os.environ[\"NUMBA_FULL_TRACEBACKS\"] = \"1\""
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "metadata": {},
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
     "import tempfile\n",
     "\n",
@@ -67,13 +65,13 @@
     "\n",
     "library_path = DataShareDownloader(library_url,test_folder).download()\n",
     "raw_data_path_list = [DataShareDownloader(url,test_folder).download() for url in raw_data_url_list]"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "metadata": {},
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
     "config = {\n",
     "    \"general\": {\n",
@@ -86,26 +84,29 @@
     "        \"target_ms1_tolerance\": 4,\n",
     "        \"target_ms2_tolerance\": 7,\n",
     "        \"target_rt_tolerance\": 200,\n",
-    "    }\n",
+    "    },\n",
+    "    \"raw_paths\": raw_data_path_list,\n",
+    "    \"library_path\": library_path,\n",
     "}\n",
-    "step = search_step.SearchStep(test_folder, raw_data_path_list, library_path, config=config)"
-   ]
+    "output_folder = test_folder + \"/output\"\n",
+    "step = search_step.SearchStep(output_folder, config=config)"
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "metadata": {},
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
     "for raw_name, dia_path, speclib in step.get_run_data():\n",
     "    pass"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "metadata": {},
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
     "workflow = peptidecentric.PeptideCentricWorkflow(\n",
     "    raw_name,\n",
@@ -113,31 +114,31 @@
     ")\n",
     "workflow.load(dia_path, speclib)\n",
     "workflow.search_parameter_optimization()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "workflow.extraction()"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "test_df = workflow.spectral_library.precursor_df.sample(1000)"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "from alphadia.peakgroup import search\n",
     "\n",
@@ -166,13 +167,13 @@
     "    fwhm_mobility=workflow.optimization_manager.fwhm_mobility,\n",
     ")\n",
     "candidates_df = extraction(thread_count=workflow.config[\"general\"][\"thread_count\"])"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "metadata": {},
-   "outputs": [],
    "source": [
     "from alphadia import plexscoring\n",
     "\n",
@@ -202,14 +203,38 @@
     "    thread_count=workflow.config[\"general\"][\"thread_count\"],\n",
     "    debug=True,\n",
     ")"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Multistep Search"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "from alphadia.search_plan import SearchPlan\n",
+    "\n",
+    "config = {\n",
+    "    \"raw_paths\": raw_data_path_list,\n",
+    "    \"library_path\": library_path,\n",
+    "}\n",
+    "\n",
+    "plan = SearchPlan(output_folder, config=config)\n",
+    "plan.run_plan()"
+   ],
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "alpha",
+   "display_name": "alphadia",
    "language": "python",
-   "name": "python3"
+   "name": "alphadia"
   },
   "language_info": {
    "codemirror_mode": {

From d722b10f9cebc2dce4977e246c37c0166e5c9374 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:26:27 +0100
Subject: [PATCH 23/29] fix fdr_performance.yml

---
 .github/workflows/e2e_testing.yml     | 2 +-
 .github/workflows/fdr_performance.yml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 25f0f2dd..29d0fbed 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -49,7 +49,7 @@ jobs:
       TQDM_MININTERVAL: 10  # avoid lots of tqdm outputs
     steps:
       - uses: actions/checkout@v4
-      - name: Pip installation with stable dependencies
+      - name: Pip installation (stable)
         id: pip_installation
         shell: bash -el {0}
         run: |
diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
index 801a31b4..97332bb2 100644
--- a/.github/workflows/fdr_performance.yml
+++ b/.github/workflows/fdr_performance.yml
@@ -31,11 +31,11 @@ jobs:
       - name: Conda info
         shell: bash -l {0}
         run: conda info
-      - name: Pip installation with all loose dependencies
+      - name: Pip installation (stable)
         shell: bash -l {0}
         run: |
           cd misc
-          . ./pip_install.sh stable,tests
+          . ./pip_install.sh stable,tests alphadia True
       - name: Run legacy classifier
         env: # Or as an environment variable
           NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_FDR_TOKEN }}

From eeb00aa08fc68535fa4b98b0fb4ce11349de101a Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:41:02 +0100
Subject: [PATCH 24/29] fix actions

---
 .github/workflows/e2e_testing.yml     | 2 +-
 .github/workflows/fdr_performance.yml | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 29d0fbed..84ddcf4f 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -6,7 +6,7 @@ on:
 #  push:
 #    branches: [ main ]
   schedule:
-    - cron: "0 0 0 * * *"   # daily on 12:00 AM
+    - cron: "0 0 * * *"   # daily on 12:00 AM
   workflow_dispatch:
     inputs:
       test_case:
diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
index 97332bb2..6ce844a5 100644
--- a/.github/workflows/fdr_performance.yml
+++ b/.github/workflows/fdr_performance.yml
@@ -19,8 +19,8 @@ jobs:
     env: # Or as an environment variable
       NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_FDR_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: 3.11
@@ -35,7 +35,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd misc
-          . ./pip_install.sh stable,tests alphadia True
+          . ./pip_install.sh stable,tests alphadia 3.11 True
       - name: Run legacy classifier
         env: # Or as an environment variable
           NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_FDR_TOKEN }}

From 9ee5ac7ae778d7b1d65fc26b5b6a0125dc1df8c3 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:47:48 +0100
Subject: [PATCH 25/29] fix merge issues

---
 .bumpversion.toml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index f18e425a..db4f24ff 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -48,15 +48,9 @@ filename = "./gui/package.json"
 [[tool.bumpversion.files]]
 filename = "./release/macos/info.plist"
 
-[[tool.bumpversion.files]]
-filename = "./release/linux/build_installer_linux.sh"
-
 [[tool.bumpversion.files]]
 filename = "./release/linux/control"
 
-[[tool.bumpversion.files]]
-filename = "./release/macos/build_installer_macos.sh"
-
 [[tool.bumpversion.files]]
 filename = "./release/macos/build_package_macos.sh"
 
@@ -65,6 +59,3 @@ filename = "./release/macos/distribution.xml"
 
 [[tool.bumpversion.files]]
 filename = "./release/windows/alphadia_innoinstaller.iss"
-
-[[tool.bumpversion.files]]
-filename = "./release/windows/build_installer_windows.ps1"

From 4d36da2ff951324ad34bdf41893acd6c2e070aa1 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 15:58:15 +0100
Subject: [PATCH 26/29] run also slow tests

---
 .github/workflows/fdr_performance.yml  |  2 +-
 .github/workflows/pip_installation.yml |  4 ++--
 tests/run_unit_tests.sh                | 17 ++++++++++++-----
 3 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
index 6ce844a5..0fbafaea 100644
--- a/.github/workflows/fdr_performance.yml
+++ b/.github/workflows/fdr_performance.yml
@@ -35,7 +35,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd misc
-          . ./pip_install.sh stable,tests alphadia 3.11 True
+          . ./pip_install.sh stable,tests alphadia 3.11 true
       - name: Run legacy classifier
         env: # Or as an environment variable
           NEPTUNE_API_TOKEN: ${{ secrets.NEPTUNE_FDR_TOKEN }}
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
index 66b7fa81..fac121ae 100644
--- a/.github/workflows/pip_installation.yml
+++ b/.github/workflows/pip_installation.yml
@@ -29,7 +29,7 @@ jobs:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
       install-script: ./pip_install.sh stable,tests
-      test-script: ./run_unit_tests.sh
+      test-script: ./run_unit_tests.sh true
 
   run-unit-tests-loose:
     name: Test 'loose' on ${{ matrix.os }}
@@ -43,4 +43,4 @@ jobs:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
       install-script: ./pip_install.sh tests
-      test-script: ./run_unit_tests.sh
+      test-script: ./run_unit_tests.sh true
diff --git a/tests/run_unit_tests.sh b/tests/run_unit_tests.sh
index 81ff4727..4236efa2 100755
--- a/tests/run_unit_tests.sh
+++ b/tests/run_unit_tests.sh
@@ -1,7 +1,14 @@
-conda activate alphadia
-#python -m unittest unit_tests/test_cli.py
-#python -m unittest unit_tests/test_gui.py
-coverage run --source=../alphadia -m pytest -k 'not slow'
+#!/bin/bash
+
+ENV_NAME=alphadia
+
+INCLUDE_SLOW_TESTS=${1:-false}
+
+if [ "$INCLUDE_SLOW_TESTS" == "true" ]; then
+  conda run -n $ENV_NAME --no-capture-output coverage run --source=../alphadia -m pytest
+else
+  conda run -n $ENV_NAME --no-capture-output coverage run --source=../alphadia -m pytest -k 'not slow'
+fi
+
 # coverage run --source=../alphadia -m pytest && coverage html && coverage-badge -f -o ../coverage.svg
 # coverage run --source=../alphadia -m pytest -k 'not slow' && coverage html && coverage-badge -f -o ../coverage.svg
-conda deactivate

From 4f900631716da43e6faa57b3899b256f6f1709ca Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 16:39:19 +0100
Subject: [PATCH 27/29] fix running e2e tests manually

---
 .github/workflows/e2e_testing.yml | 30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index 84ddcf4f..fe395940 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -13,14 +13,20 @@ on:
         description: 'Test case to run (see e2e_test_cases.yaml for available cases), "all" to run all test cases.'
         required: false
         default: 'all'
+      commitish_to_test:
+        type: string
+        description: 'Enter commit hash or branch to test (default: main).'
+        default: "main"
 
 jobs:
-  determine_test_cases:
+  parse_inputs:
     runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.labels.*.name, 'test:e2e') || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     outputs:
-      test_cases: ${{ steps.set-matrix.outputs.test_cases }}
+      test_cases: ${{ steps.parse-test-cases.outputs.test_cases }}
+      commitish_to_test: ${{ steps.parse-commitish-to-test.outputs.commitish_to_test }}
     steps:
-      - id: set-matrix
+      - id: parse-test-cases
         run: |
           if [ "${{ github.event_name }}" = "workflow_dispatch" ] && [ "${{ github.event.inputs.test_case }}" != "all" ]; then
             echo "test_cases=[\"${{ github.event.inputs.test_case }}\"]" >> $GITHUB_OUTPUT
@@ -29,15 +35,21 @@ jobs:
             echo 'test_cases=["basic", "synchropasef", "astral", "astral_automatic_calibration", "multistep"]' >> $GITHUB_OUTPUT
           fi
 
-  end2end_testing:
-    name: End to end test
-    needs: determine_test_cases
+      - id: parse-commitish-to-test
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+            echo "commitish_to_test=[\"${{ github.event.inputs.commitish_to_test }}\"]" >> $GITHUB_OUTPUT
+          else
+            echo "commitish_to_test=main" >> $GITHUB_OUTPUT
+
+  end2end_tests:
+    name: End to end tests
+    needs: parse_inputs
     runs-on: self-hosted
-    if: contains(github.event.pull_request.labels.*.name, 'test:e2e') || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        test_case: ${{ fromJson(needs.determine_test_cases.outputs.test_cases) }}
+        test_case: ${{ fromJson(needs.parse_inputs.outputs.test_cases) }}
     env:
       RUN_NAME: alphadia-${{github.sha}}-${{github.run_id}}-${{github.run_attempt}}
       BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
@@ -49,6 +61,8 @@ jobs:
       TQDM_MININTERVAL: 10  # avoid lots of tqdm outputs
     steps:
       - uses: actions/checkout@v4
+        with:
+          ref: ${{ needs.parse_inputs.outputs.commitish_to_test }}
       - name: Pip installation (stable)
         id: pip_installation
         shell: bash -el {0}

From 4a7615d4cb6ab90282810cb4b3639e053b3a18ad Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 16:40:34 +0100
Subject: [PATCH 28/29] fix running e2e tests manually

---
 .github/workflows/e2e_testing.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
index fe395940..99890b3a 100644
--- a/.github/workflows/e2e_testing.yml
+++ b/.github/workflows/e2e_testing.yml
@@ -41,6 +41,7 @@ jobs:
             echo "commitish_to_test=[\"${{ github.event.inputs.commitish_to_test }}\"]" >> $GITHUB_OUTPUT
           else
             echo "commitish_to_test=main" >> $GITHUB_OUTPUT
+          fi
 
   end2end_tests:
     name: End to end tests

From 26ef0dc7677fc4f8a3e352bba96ff24da7d28315 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 17 Jan 2025 17:03:28 +0100
Subject: [PATCH 29/29] =?UTF-8?q?Bump=20version:=201.9.2=20=E2=86=92=201.9?=
 =?UTF-8?q?.3-dev0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.toml                          | 2 +-
 alphadia/__init__.py                       | 2 +-
 gui/package.json                           | 2 +-
 gui/src/main/modules/profile.js            | 2 +-
 release/linux/control                      | 2 +-
 release/macos/build_package_macos.sh       | 4 ++--
 release/macos/distribution.xml             | 2 +-
 release/macos/info.plist                   | 4 ++--
 release/windows/alphadia_innoinstaller.iss | 4 ++--
 9 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index db4f24ff..ddd8ba49 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.9.2"
+current_version = "1.9.3-dev0"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.
diff --git a/alphadia/__init__.py b/alphadia/__init__.py
index e16450ce..edc69a43 100644
--- a/alphadia/__init__.py
+++ b/alphadia/__init__.py
@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.9.2"
+__version__ = "1.9.3-dev0"
diff --git a/gui/package.json b/gui/package.json
index 0c003da7..51aea7d7 100644
--- a/gui/package.json
+++ b/gui/package.json
@@ -1,7 +1,7 @@
 {
   "name": "alphadia",
   "productName": "alphadia-gui",
-  "version": "1.9.2",
+  "version": "1.9.3-dev0",
   "description": "Graphical user interface for DIA data analysis",
   "main": "dist/electron.js",
   "homepage": "./",
diff --git a/gui/src/main/modules/profile.js b/gui/src/main/modules/profile.js
index c9b7f95b..3b6d3715 100644
--- a/gui/src/main/modules/profile.js
+++ b/gui/src/main/modules/profile.js
@@ -3,7 +3,7 @@ const path = require("path")
 const { app, shell, BrowserWindow} = require("electron")
 const { dialog } = require('electron')
 
-const VERSION = "1.9.2"
+const VERSION = "1.9.3-dev0"
 
 const Profile = class {
 
diff --git a/release/linux/control b/release/linux/control
index 90fed30a..f15baab3 100644
--- a/release/linux/control
+++ b/release/linux/control
@@ -1,5 +1,5 @@
 Package: alphadia
-Version: 1.9.2
+Version: 1.9.3-dev0
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: alphadia
diff --git a/release/macos/build_package_macos.sh b/release/macos/build_package_macos.sh
index 2ae26c65..7e999c50 100755
--- a/release/macos/build_package_macos.sh
+++ b/release/macos/build_package_macos.sh
@@ -7,10 +7,10 @@ set -e -u
 # Set up package name and version
 PACKAGE_NAME="alphadia"
 APP_NAME="alphadia"
-PACKAGE_VERSION="1.9.2"
+PACKAGE_VERSION="1.9.3-dev0"
 PKG_FOLDER="dist/$APP_NAME.app"
 
-# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.2-macos-darwin-arm64 or alphadia-1.9.2-macos-darwin-x64
+# BUILD_NAME is taken from environment variables, e.g. alphadia-1.9.3-dev0-macos-darwin-arm64 or alphadia-1.9.3-dev0-macos-darwin-x64
 rm -rf ${BUILD_NAME}.pkg
 
 # Cleanup the package folder
diff --git a/release/macos/distribution.xml b/release/macos/distribution.xml
index bac68251..ded80d77 100644
--- a/release/macos/distribution.xml
+++ b/release/macos/distribution.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>AlphaDIA 1.9.2</title>
+    <title>AlphaDIA 1.9.3-dev0</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" />
diff --git a/release/macos/info.plist b/release/macos/info.plist
index 02a16ba3..2a83ccdf 100644
--- a/release/macos/info.plist
+++ b/release/macos/info.plist
@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alphadia.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphadia.1.9.2</string>
+	<string>alphadia.1.9.3-dev0</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.9.2</string>
+	<string>1.9.3-dev0</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>
diff --git a/release/windows/alphadia_innoinstaller.iss b/release/windows/alphadia_innoinstaller.iss
index a19ba8e4..ba988cc5 100644
--- a/release/windows/alphadia_innoinstaller.iss
+++ b/release/windows/alphadia_innoinstaller.iss
@@ -5,7 +5,7 @@
 ; so all paths are given relative to the location of this .iss file.
 
 #define MyAppName "AlphaDIA"
-#define MyAppVersion "1.9.2"
+#define MyAppVersion "1.9.3-dev0"
 #define MyAppPublisher "Max Planck Institute of Biochemistry, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphadia"
 #define MyAppExeName "alphadia-gui.exe"
@@ -29,7 +29,7 @@ PrivilegesRequired=lowest
 PrivilegesRequiredOverridesAllowed=dialog
 ; release workflow expects artifact at root of repository
 OutputDir=..\..\
-; example for BUILD_NAME: alphadia-1.9.2-win-x64
+; example for BUILD_NAME: alphadia-1.9.3-dev0-win-x64
 OutputBaseFilename={#GetEnv('BUILD_NAME')}
 SetupIconFile=..\logos\alphadia.ico
 Compression=lzma