Merge remote-tracking branch 'origin/main' into add-two-step-classifier

.bumpversion.toml

@@ -0,0 +1,61 @@
+[tool.bumpversion]
+current_version = "1.9.3-dev0"
+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
+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.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"
+
+[[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/control"
+
+[[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"

.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:

.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}}

.github/workflows/e2e_testing.yml

@@ -1,22 +1,56 @@
+name: End to end testing
+
 on:
   pull_request:
     types: [ labeled ]
-  push:
-    branches: [ main, development ]
+#  push:
+#    branches: [ main ]
+  schedule:
+    - cron: "0 0 * * *"   # daily on 12:00 AM
   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'
+      commitish_to_test:
+        type: string
+        description: 'Enter commit hash or branch to test (default: main).'
+        default: "main"
 
 jobs:
-  end2end_testing:
-    name: End to end test
-    runs-on: self-hosted
+  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.parse-test-cases.outputs.test_cases }}
+      commitish_to_test: ${{ steps.parse-commitish-to-test.outputs.commitish_to_test }}
+    steps:
+      - id: parse-test-cases
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ] && [ "${{ github.event.inputs.test_case }}" != "all" ]; then
+            echo "test_cases=[\"${{ github.event.inputs.test_case }}\"]" >> $GITHUB_OUTPUT
+          else
+            # NEW TEST CASES ARE ADDED HERE:
+            echo 'test_cases=["basic", "synchropasef", "astral", "astral_automatic_calibration", "multistep"]' >> $GITHUB_OUTPUT
+          fi
+
+      - id: parse-commitish-to-test
+        run: |
+          if [ "${{ 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
+          fi
+
+  end2end_tests:
+    name: End to end tests
+    needs: parse_inputs
+    runs-on: self-hosted
     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: ${{ fromJson(needs.parse_inputs.outputs.test_cases) }}
     env:
       RUN_NAME: alphadia-${{github.sha}}-${{github.run_id}}-${{github.run_attempt}}
       BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
@@ -28,23 +62,23 @@ jobs:
       TQDM_MININTERVAL: 10  # avoid lots of tqdm outputs
     steps:
       - uses: actions/checkout@v4
-      - name: Conda info
-        shell: bash -el {0}
-        run: conda info
-      - name: Pip installation with stable dependencies
+        with:
+          ref: ${{ needs.parse_inputs.outputs.commitish_to_test }}
+      - name: Pip installation (stable)
         id: pip_installation
         shell: bash -el {0}
         run: |
+          conda info
           cd misc
           . ./pip_install.sh stable $RUN_NAME
       - name: Run e2e tests
         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 -el {0}
+        shell: bash -l {0}
         run: |
           conda remove -n $RUN_NAME --all -y
       - name: Delete Caches on Error

.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
@@ -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
@@ -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,test
+          . ./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 }}

.github/workflows/pip_installation.yml

@@ -1,15 +1,12 @@
 # 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, development ]
-  pull_request:
     branches: [ main ]
   workflow_dispatch:
 
@@ -23,25 +20,27 @@ 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"]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh stable,test
-      test-script: ./run_unit_tests.sh
+      install-script: ./pip_install.sh stable,tests
+      test-script: ./run_unit_tests.sh true
 
   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"]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: ./pip_install.sh test
-      test-script: ./run_unit_tests.sh
+      install-script: ./pip_install.sh tests
+      test-script: ./run_unit_tests.sh true

.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 }}

.pre-commit-config.yaml

@@ -13,5 +13,3 @@ repos:
     - id: ruff-format
     - id: ruff
       args: [ '--fix' ]
-
-exclude: .bumpversion.cfg

.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

alphadia/__init__.py

@@ -1,3 +1,3 @@
 #!python
 
-__version__ = "1.9.2"
+__version__ = "1.9.3-dev0"

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"))

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.")

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 [email protected]:MannLabs/alphadia.git
-cd alphadia
+git clone [email protected]: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

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": "./",