.gitea/actions/install/action.yml

@@ -0,0 +1,46 @@
+name: "Install"
+description: "Setup system and python environment and install repo"
+inputs:
+  python_version:
+    required: false
+    default: "3.12"
+    description: "Python version to use"
+  index_username:
+    required: false
+    default: ""
+    description: "Username for the private psi package index"
+  index_password:
+    required: false
+    default: ""
+    description: "Token/password for the private psi package index"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install Libraries
+      shell: bash
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y \
+          libgl1 \
+          libegl1 \
+          libxkbcommon-x11-0 \
+          libdbus-1-3 \
+          libxcb-cursor0 \
+          libx11-xcb1
+
+    - name: Setup Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ inputs.python_version }}
+
+    - name: Install repo
+      shell: bash
+      env:
+        UV_INDEX_PSI_USERNAME: ${{ inputs.index_username }}
+        UV_INDEX_PSI_PASSWORD: ${{ inputs.index_password }}
+      run: |
+        pip install uv
+        uv venv
+        source .venv/bin/activate
+        uv pip install -e .[test]

.gitea/workflows/action.yaml

@@ -1,223 +0,0 @@
-name: Build and Publish
-on:
-  push:
-    tags:
-      - '*'
-    branches:
-      - master
-      - deploy
-      - 'feature/**'
-      - gitea-pages
-  pull_request:
-    branches:
-      - master
-      - deploy
-  pull_request_target:
-    types: [closed]
-
-env:
-  DEPLOY_BRANCH: gitea-pages
-  PREVIEWS_DIR: previews
-  PYTHONPATH: src
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v4
-
-      - name: Set Up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.12'
-
-      - name: Cache pip
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-test-${{ hashFiles('**/pyproject.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-test-
-
-      - name: Create virtual environment
-        run: |
-          python -m venv venv
-
-      - name: Install dependencies
-        env:
-          PIP_INDEX_URL: https://${{ secrets.GITEA_USER }}:${{ secrets.GITEA_TOKEN }}@gitea.psi.ch/api/packages/mx/pypi/simple/
-          PIP_EXTRA_INDEX_URL: https://pypi.org/simple
-        run: |
-          source venv/bin/activate
-  
-          python -m pip install --upgrade pip
-  
-          pip install pytest pytest-cov pytest-mock pytest-qt pytest-asyncio
-  
-          pip install -e .
-
-      - name: Install system dependencies for PySide6
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y \
-            libgl1 \
-            libegl1 \
-            libxkbcommon-x11-0 \
-            libdbus-1-3 \
-            libxcb-cursor0 \
-            libx11-xcb1
-
-      - name: Debug Python env
-        run: |
-          source venv/bin/activate
-          which python
-          which pytest
-          python -m pip list | grep pytest
-
-      - name: Run tests with pytest
-        env:
-          QT_QPA_PLATFORM: offscreen
-          BEAMLINE: SIMULATED
-        run: |
-          source venv/bin/activate
-  
-          python -m pytest --cov=aare --cov-report=xml tests/unit
-
-  build:
-    runs-on: ubuntu-latest
-    needs: test
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          
-      - name: Cache pip
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
-      
-      - name: Set Up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.12'
-      
-      - name: Set Up Python Environment
-        run: |
-          python3 -m venv venv  # Create a virtual environment
-          source venv/bin/activate
-          pip install twine build
-      
-      - name: Build the package
-        run: |
-          source venv/bin/activate
-          python -m build
-
-      - name: Upload Package to Gitea PyPI
-        if: startsWith(github.ref, 'refs/tags/')
-        env:
-          TWINE_USERNAME: "__token__"  # Username for Twine when using token-based auth
-          TWINE_PASSWORD: ${{ secrets.PIP_REPOSITORY_API_TOKEN }}  # Use the secret for authentication
-        run: |
-          source venv/bin/activate
-          twine upload --repository-url https://gitea.psi.ch/api/packages/mx/pypi \
-          dist/*
-  
-  docs:
-    name: Build and Deploy Docs
-    runs-on: ubuntu-latest
-    needs: [build, test]
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0  # needed for pushing branches/tags
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.12'
-
-      - name: Build Sphinx HTML
-        working-directory: docs
-        run: |
-            python3 -m venv venv
-            source venv/bin/activate
-        
-            pip install --upgrade pip
-            pip install -r requirements.txt
-        
-            pip install -e .. --no-deps
-        
-            sphinx-apidoc -o modules/ ../src/aare --separate --module-first --force --remove-old
-        
-            sphinx-build -b html . _build/html
-
-      - name: Deploy to gitea-pages branch (Gitea)
-        env:
-          GIT_USER: "Martin Appleby (Gitea)"
-          GIT_EMAIL: "martin.appleby@psi.ch"
-          DEPLOY_TOKEN: ${{ secrets.DOCS_DEPLOY_TOKEN }}
-        run: |
-          set -e
-          git config --global user.name "$GIT_USER"
-          git config --global user.email "$GIT_EMAIL"
-          
-          # Deploy strategy: create/update branch gitea-pages and replace its contents
-          # with the generated daq/docs/_build/html. This keeps only the documentation
-          # on the gitea-pages branch.
-          # Confirm build output exists (relative to repository root)
-          BUILD_DIR="docs/_build/html"
-          echo "Checking build output at: $BUILD_DIR"
-
-          if [ ! -d "$BUILD_DIR" ] || [ -z "$(ls -A "$BUILD_DIR")" ]; then
-            echo "ERROR: $BUILD_DIR does not exist or is empty"
-            echo "Listing docs/:"
-            ls -la docs || true
-            echo "Listing docs/_build:"
-            ls -la docs/_build || true
-            exit 1
-          fi
-
-          # Work in a temporary clone to avoid touching the runner workspace
-          TMPDIR=$(mktemp -d)
-          REPO_URL="https://$DEPLOY_TOKEN@gitea.psi.ch/${{ github.repository }}"
-          git clone "$REPO_URL" "$TMPDIR"
-          cd "$TMPDIR"
-
-          # Create or switch to orphan branch gitea-pages
-          if git rev-parse --verify --quiet gitea-pages >/dev/null; then
-            git checkout gitea-pages
-            # Make sure working tree matches branch (hard reset)
-            git fetch --prune origin gitea-pages || true
-            git reset --hard origin/gitea-pages || git reset --hard
-          else
-            git checkout --orphan gitea-pages
-          fi
-          # Remove all files tracked in the branch (leave .git)
-          git rm -rf . || true
-          # Also remove untracked files to ensure clean branch state
-          git clean -fdx || true
-
-          # Copy built HTML into the clone root
-          echo "Copying built HTML into branch root..."
-          (cd "${GITHUB_WORKSPACE}/${BUILD_DIR}" && tar -cf - .) | tar -xf - -C "$TMPDIR"
-
-          # Ensure index.html exists in destination as sanity check
-          if [ ! -f "$TMPDIR/index.html" ] && [ ! -f "$TMPDIR/index.htm" ]; then
-            # If site root index is not present, try to check subfolder
-            echo "Warning: no index.html found at branch root after copy. Listing files:"
-            ls -la "$TMPDIR" || true
-          fi
-         
-          git add --all
-          if git diff --quiet --cached; then
-            echo "No changes to deploy"
-            exit 0
-          fi
-          COMMIT_DATE="$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
-          git commit -m "docs: (${COMMIT_DATE}) | auto-update documentation from ${GITHUB_SHA}"
-          git push --force-with-lease origin gitea-pages

.gitea/workflows/ci.yml

@@ -0,0 +1,51 @@
+name: CI
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Setup
+        uses: ./.gitea/actions/install
+        with:
+          python_version: "3.12"
+          index_username: ${{ secrets.GITEA_USER }}
+          index_password: ${{ secrets.GITEA_TOKEN }}
+
+      - name: Format
+        run: |
+          source .venv/bin/activate
+          ruff format --check
+
+  test:
+    runs-on: ubuntu-latest
+    needs: "lint"
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Setup
+        uses: ./.gitea/actions/install
+        with:
+          python_version: ${{ matrix.python-version }}
+          index_username: ${{ secrets.GITEA_USER }}
+          index_password: ${{ secrets.GITEA_TOKEN }}
+
+      - name: Run Pytest with Coverage
+        env:
+          QT_QPA_PLATFORM: offscreen
+          BEAMLINE: SIMULATED
+        run: |
+          source .venv/bin/activate
+          pytest --cov=aare --cov-config=./pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./tests/unit

.gitea/workflows/publish.yml

@@ -0,0 +1,77 @@
+name: Build and Publish
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-release-${{ github.ref_name }}
+      cancel-in-progress: false
+    outputs:
+      release_made: ${{ steps.release_step.outputs.release_made }}
+    permissions:
+      contents: write
+    steps:
+      - name: Setup | Checkout Repository on Release Branch
+        uses: actions/checkout@v6
+        with:
+          ref: ${{ github.ref_name }}
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Setup | Force release branch to be at workflow sha
+        run: |
+          git reset --hard ${{ github.sha }}
+      - name: Evaluate | Verify upstream has NOT changed
+        shell: bash
+        run: |
+          set +o pipefail
+
+          UPSTREAM_BRANCH_NAME="$(git status -sb | head -n 1 | cut -d' ' -f2 | grep -E '\.{3}' | cut -d'.' -f4)"
+          printf '%s\n' "Upstream branch name: $UPSTREAM_BRANCH_NAME"
+
+          set -o pipefail
+
+          if [ -z "$UPSTREAM_BRANCH_NAME" ]; then
+              printf >&2 '%s\n' "::error::Unable to determine upstream branch name!"
+              exit 1
+          fi
+
+          git fetch "${UPSTREAM_BRANCH_NAME%%/*}"
+
+          if ! UPSTREAM_SHA="$(git rev-parse "$UPSTREAM_BRANCH_NAME")"; then
+              printf >&2 '%s\n' "::error::Unable to determine upstream branch sha!"
+              exit 1
+          fi
+
+          HEAD_SHA="$(git rev-parse HEAD)"
+
+          if [ "$HEAD_SHA" != "$UPSTREAM_SHA" ]; then
+              printf >&2 '%s\n' "[HEAD SHA] $HEAD_SHA != $UPSTREAM_SHA [UPSTREAM SHA]"
+              printf >&2 '%s\n' "::error::Upstream has changed, aborting release..."
+              exit 1
+          fi
+
+          printf '%s\n' "Verified upstream branch has not changed, continuing with release..."
+
+      - name: Semantic Version Release
+        id: release_step
+        env:
+          TWINE_USERNAME: "__token__"
+          TWINE_PASSWORD: ${{ secrets.MX_GITEA_BOT_TOKEN }}
+          MX_GITEA_BOT_TOKEN: ${{ secrets.MX_GITEA_BOT_TOKEN }}
+        run: |
+          pip install python-semantic-release==9.* wheel build twine
+          semantic-release --config ./ci/semantic_release.toml version
+          if [ ! -d dist ]; then echo No release will be made; echo "release_made=false" >> "$GITHUB_OUTPUT"; exit 0; fi
+          echo "release_made=true" >> "$GITHUB_OUTPUT"
+          twine upload dist/* --repository-url https://gitea.psi.ch/api/packages/mx/pypi
+          semantic-release publish

LEGACY_CHANGELOG.md

@@ -1,4 +1,7 @@
 # Changelog
+
+## Hand-written changelog is now superseded by the generated one in CHANGELOG.md; preserved for posterity.
+
 ## 0.3.2 (unreleased)
 - **Authentication & Sessions**:
     - Migrated DAQ server URLs to HTTPS with per-beamline configurable certificate paths (cacert) and mTLS; GUI now validates certificates and handles self-signed certs / SSL errors in `DAQWorker` and `SSEClient`.

VERSION

@@ -1 +0,0 @@
-0.3.2

ci/semantic_release.toml

@@ -0,0 +1,35 @@
+[tool.semantic_release]
+build_command = "python -m build"
+version_toml = [
+    "./pyproject.toml:project.version",
+]
+
+[tool.semantic_release.commit_author]
+env = "GIT_COMMIT_AUTHOR"
+default = "semantic-release <semantic-release>"
+
+[tool.semantic_release.commit_parser_options]
+allowed_tags = [
+    "build",
+    "chore",
+    "ci",
+    "docs",
+    "feat",
+    "fix",
+    "perf",
+    "style",
+    "refactor",
+    "test",
+]
+minor_tags = ["feat"]
+patch_tags = ["fix", "perf"]
+default_bump_level = 0
+
+[tool.semantic_release.remote]
+type = "gitea"
+domain = "gitea.psi.ch"
+token = { env = "MX_GITEA_BOT_TOKEN" }
+
+[tool.semantic_release.publish]
+dist_glob_patterns = ["dist/*"]
+upload_to_vcs_release = true

pyproject.toml

@@ -41,7 +41,8 @@ test = [
     "pytest-mock==3.14.0",
     "pytest-qt==4.4.0",
     "pytest-asyncio==0.25.3",
-    "pytest-timeout"
+    "pytest-timeout",
+    "ruff==0.15.*"
 ]
 
 [lint]

scripts/redis_dump.py

@@ -20,7 +20,7 @@ def decode_bulk(value: Any):
 
 
 def fetch_key(r: redis.Redis, key: bytes) -> Tuple[str, Any]:
-    key_s = decode_bulk(key)
+    decode_bulk(key)
     t = r.type(key)
     if isinstance(t, bytes):
         t = t.decode()

src/aare/daq/aaredb.py

@@ -229,7 +229,7 @@ class AareWrapper:
             experiment_params_payload = ExperimentParametersCreate(
                 type="standard", beamline_parameters=beamline_params, sample_id=s.db_id
             )
-            response = self.__sample_api.create_experiment_parameters_for_sample(
+            self.__sample_api.create_experiment_parameters_for_sample(
                 sample_id=s.db_id, experiment_parameters_create=experiment_params_payload
             )
             # logger.debug("Experiment parameters created:", response)
@@ -291,7 +291,7 @@ class AareWrapper:
             experiment_params_payload = ExperimentParametersCreate(
                 type="standard", beamline_parameters=beamline_params, sample_id=s.db_id
             )
-            response = self.__sample_api.create_experiment_parameters_for_sample(
+            self.__sample_api.create_experiment_parameters_for_sample(
                 sample_id=s.db_id, experiment_parameters_create=experiment_params_payload
             )
             # logger.info("Experiment parameters created:", response)

src/aare/daq/config.py

@@ -42,11 +42,8 @@ from aarecommon.models.models import (
 )
 from aare.daq.config_model import LocalContactConfigModel
 
-#TODO WHAT SHOULD THIS BE? This should be in the YAMl file it is beamline specific
-ABR_POS_MOUNT = AerotechCoordinate(
-    at_mm=Coordinate(x=0, y=0, z=0),
-    omega_deg=0
-)
+# TODO WHAT SHOULD THIS BE? This should be in the YAMl file it is beamline specific
+ABR_POS_MOUNT = AerotechCoordinate(at_mm=Coordinate(x=0, y=0, z=0), omega_deg=0)
 
 
 # TODO WHAT SHOULD THIS BE? This should be in the YAMl file it is beamline specific
@@ -1261,7 +1258,9 @@ class BeamlineConfig:
             logger.warning(f"Failed to read Local Contact config from Redis: {e}")
             return default
 
-    def set_local_contact_config(self, config: LocalContactConfigModel | dict) -> LocalContactConfigModel:
+    def set_local_contact_config(
+        self, config: LocalContactConfigModel | dict
+    ) -> LocalContactConfigModel:
         validated = LocalContactConfigModel.model_validate(config)
         try:
             redis_key = f"{self.__bl}:local_contact_config"

src/aare/daq/daq.py

@@ -1385,8 +1385,9 @@ class AareDAQ:
             )
             return None
 
-
-    def _execute_rotation_sequence(self, rotation_request: RotationScanRequest) -> CompletedRotationScan | None:
+    def _execute_rotation_sequence(
+        self, rotation_request: RotationScanRequest
+    ) -> CompletedRotationScan | None:
         """
         Execute rotation scan.
 
@@ -1574,19 +1575,21 @@ class AareDAQ:
         self.last_time = end - start
 
     def _expand_macros(self, name: str) -> str:
-        name = name.replace('{date}',  datetime.now().strftime('%Y%m%d'))
-        name = name.replace('{sample}', self.sample.sample_name)
-        name = name.replace('{CrystalName}', self.sample.sample_name)
-        name = name.replace('{puck}', self.sample.puck_name)
-        name = name.replace('{position}', f"{self.sample.pin:02d}")
-        name = name.replace('{sample_id}', f"{self.sample.db_id}")
-        name = name.replace('{beamline}', f"{self._beamline.value.lower()}")
-        name = name.replace('{prefix}', f"{self.sample.puck_name}/{self.sample.pin:02d}/{self.sample.sample_name}")
-        #TODO work out why clean_filename is removing slahses
-        #name = clean_filename(name)
+        name = name.replace("{date}", datetime.now().strftime("%Y%m%d"))
+        name = name.replace("{sample}", self.sample.sample_name)
+        name = name.replace("{CrystalName}", self.sample.sample_name)
+        name = name.replace("{puck}", self.sample.puck_name)
+        name = name.replace("{position}", f"{self.sample.pin:02d}")
+        name = name.replace("{sample_id}", f"{self.sample.db_id}")
+        name = name.replace("{beamline}", f"{self._beamline.value.lower()}")
+        name = name.replace(
+            "{prefix}", f"{self.sample.puck_name}/{self.sample.pin:02d}/{self.sample.sample_name}"
+        )
+        # TODO work out why clean_filename is removing slahses
+        # name = clean_filename(name)
         return name
 
-    def spreadsheet_params(self) -> tuple[Optional[SimpleScanParameters], str|None]:
+    def spreadsheet_params(self) -> tuple[Optional[SimpleScanParameters], str | None]:
         file_prefix = None
 
         if self.status.sample is None:
@@ -1979,7 +1982,7 @@ class AareDAQ:
             self.save_screenshot_db(sample_id, screenshot_name)
 
         if request.transmission is not None and request.transmission != self.__devs.transmission:
-            logger.info(f'requesting transmission to move to {request.transmission}')
+            logger.info(f"requesting transmission to move to {request.transmission}")
             self.__devs.transmission = request.transmission
 
         start_pos = getattr(request, "start", None)
@@ -2700,7 +2703,9 @@ class AareDAQ:
 
             if raster_params.filename is not None:
                 logger.info(f"Using filename {raster_params.filename}")
-                sample_prefix = "{filename}/{prefix}".format(filename=raster_params.filename, prefix=sample.sample_name)
+                sample_prefix = "{filename}/{prefix}".format(
+                    filename=raster_params.filename, prefix=sample.sample_name
+                )
 
             raster_grid = RasterGridRequest(
                 exp_time_s=raster_params.exp_time_s,
@@ -2767,17 +2772,20 @@ class AareDAQ:
 
             update_sample = self.sample
             if (
-                    update_sample is not None
-                    and update_sample.db_id is not None
-                    and update_sample.db_id == sample.db_id
+                update_sample is not None
+                and update_sample.db_id is not None
+                and update_sample.db_id == sample.db_id
             ):
-                logger.info(f"Updating sample info {sample.db_id} old run_number"
-                            f" sample.run_number {sample.run_number} new run_number {update_sample.run_number}")
-
+                logger.info(
+                    f"Updating sample info {sample.db_id} old run_number"
+                    f" sample.run_number {sample.run_number} new run_number {update_sample.run_number}"
+                )
 
             if params.filename is not None:
                 logger.info(f"Using filename {params.filename}")
-                sample_prefix = "{filename}/{prefix}".format(filename=params.filename, prefix=sample.sample_name)
+                sample_prefix = "{filename}/{prefix}".format(
+                    filename=params.filename, prefix=sample.sample_name
+                )
 
             rotation_request = RotationScanRequest(
                 start_omega_deg=start_omega,
@@ -3492,7 +3500,9 @@ class AareDAQ:
         finally:
             self.__cfg.state_busy = False
 
-    def fluorimeter_take_spectrum(self, fm: FluorescenceSpectrumParameterModel) -> FluorescenceSpectrumOutputModel:
+    def fluorimeter_take_spectrum(
+        self, fm: FluorescenceSpectrumParameterModel
+    ) -> FluorescenceSpectrumOutputModel:
         self.__cfg.try_set_busy(timeout=360)
 
         try:

src/aare/daq/operations/common/ml_bounding_box.py

@@ -3,7 +3,6 @@ from dataclasses import dataclass
 from math import ceil, floor
 from typing import Callable
 
-import cv2
 from aarecommon.config.beamline import cfg_get
 from aarecommon.config.logger_events import (
     geom_log_context,
@@ -112,7 +111,6 @@ def get_ml_bounding_box(
         preferred_class=(3, 0), return_image=True, return_bundle_meta=True
     )
     m = prediction_result.box
-    bundle_image = prediction_result.image
 
     log_ml_bundle_meta(
         logger,

src/aare/daq/operations/face_detection/service.py

@@ -53,7 +53,6 @@ class FaceDetectionService:
         beam_y = geom.beam_location_pxl.y
         beam_x = geom.beam_location_pxl.x
 
-        x1 = model.box.top_x
         y1 = model.box.top_y
         y2 = model.box.bottom_y
 

src/aare/daq/server.py

@@ -1,7 +1,6 @@
 import asyncio
 import hmac
 import importlib
-import io
 import json
 import os
 import random
@@ -9,7 +8,6 @@ import time
 from contextlib import asynccontextmanager
 from typing import AsyncGenerator, Optional
 
-import cv2
 import uvicorn
 from aarecommon.config.beamline import mx_beamline
 from aarecommon.config.logger import get_uvicorn_logging_config, setup_logger

src/aare/devices/jfjoch.py

@@ -256,7 +256,7 @@ class JFJochWrapper:
 
     def detector(self) -> jfjoch_client.models.DetectorListElement:
         try:
-            l = self.__api.config_select_detector_get()
+            detector_list = self.__api.config_select_detector_get()
         except Exception as e:
             self._raise_jfjoch_error(
                 f"JFJoch detector configuration retrieval failed: {e}",
@@ -265,7 +265,7 @@ class JFJochWrapper:
                 endpoint="config_select_detector_get",
             )
 
-        if len(l.detectors) == 0:
+        if len(detector_list.detectors) == 0:
             raise JFJochCommunicationError(
                 "JFJoch returned no configured detectors",
                 operation="GET",
@@ -275,7 +275,7 @@ class JFJochWrapper:
             )
 
         try:
-            return l.detectors[l.current_id]
+            return detector_list.detectors[detector_list.current_id]
         except Exception as e:
             self._raise_jfjoch_error(
                 "JFJoch returned an invalid selected detector entry",

src/aare/devices/smargon.py

@@ -220,7 +220,6 @@ class Smargon(object):
             sleep(poll_time)
 
     def wait_aerotech(self, timeout=60.0, tol=0.01, poll_time=0.01):
-        target = self.target
         timeout = timeout + time()
         while time() < timeout:
             if self.target_aerotech.eq(self.readback_aerotech, tol):

src/aare/devices/tell_backend.py

@@ -120,11 +120,7 @@ class PShellTellBackend:
         if e.response is not None and e.response.text:
             msg = e.response.text.strip()
         raise TellCommunicationError(
-            msg,
-            base_url=self._url,
-            endpoint=endpoint,
-            operation=operation,
-            critical=True,
+            msg, base_url=self._url, endpoint=endpoint, operation=operation, critical=True
         ) from e
 
     def eval(self, expr: str):

src/aare/devices/tell_client.py

@@ -359,7 +359,9 @@ class TellClient:
             raise
         except Exception as e:
             logger.error(f"Exception occurred: {e}")
-            raise TellCommunicationError(message=f"Error during mount {segment}{puck}-{sample}: {e}", critical=True)
+            raise TellCommunicationError(
+                message=f"Error during mount {segment}{puck}-{sample}: {e}", critical=True
+            )
 
     def unmount(self, force=False, wait=False, timeout=360.0):
         if self.is_busy():
@@ -582,7 +584,7 @@ if __name__ == "__main__":
     state = tell_client.get_robot_state()
     manual_mode = tell_client.is_manual_mode()
     print("state: ", state)
-    print("is manual mode True: ", manual_mode == True)
+    print("is manual mode True: ", manual_mode)
     print(tell_client.backend.eval("is_manual_mode()&"))
     print(tell_client.is_door_closed())
     # print("release safety: ", tell_client.backend.eval('release_safety()&'))

src/aare/devices/workflow_tools.py

@@ -14,11 +14,17 @@ def wait_position(motor, target, tolerance=None, timeout=60.0):
     elif isinstance(position, (bytes, str)):
         tst = "'%s' == '%s'"
         if isinstance(position, bytes):
-            ltst = lambda x, y, z: (
-                x.lower() == y.lower().encode() if isinstance(y, str) else x.lower() == y.lower()
-            )
+
+            def ltst(x, y, z):
+                return (
+                    x.lower() == y.lower().encode()
+                    if isinstance(y, str)
+                    else x.lower() == y.lower()
+                )
         else:
-            ltst = lambda x, y, z: x.lower() == y.lower()
+
+            def ltst(x, y, z):
+                return x.lower() == y.lower()
     else:
         raise RuntimeError("BUG: could not understand arguments: ")
 

src/aare/gui/gui.py

@@ -1,4 +1,3 @@
-import importlib
 import os
 import sys
 import traceback
@@ -20,24 +19,24 @@ logger = setup_logger(LOGGER_NAME)
 
 def main():
     """Wrapped gui as main function to make tests easier"""
-    splash = None
+    try:
+        basedir = os.path.dirname(__file__)
+        icon_path = os.path.join(basedir, "graphics/aaregui_logo.svg")
+        banner_path = os.path.join(basedir, "graphics/aare_banner.png")
+        splash_pix = QtGui.QPixmap(banner_path)
+        splash = LoadingSplashScreen(splash_pix)
+    except Exception as e:
+        logger.error(f"Failed to load resources for splash screen: {e}")
+        sys.exit(1)
     try:
         # define application
         app = QApplication(sys.argv)
+        app.setWindowIcon(QtGui.QIcon(icon_path))
         app.setApplicationName("AareGUI")
         app.setApplicationVersion("0.3.1")
         app.setOrganizationName("PSI")
         app.setOrganizationDomain("psi.ch")
 
-        # set icon
-        basedir = os.path.dirname(__file__)
-        icon_path = os.path.join(basedir, "graphics/aaregui_logo.svg")
-        app.setWindowIcon(QtGui.QIcon(icon_path))
-
-        # show splash screen
-        banner_path = os.path.join(basedir, "graphics/aare_banner.png")
-        splash_pix = QtGui.QPixmap(banner_path)
-        splash = LoadingSplashScreen(splash_pix)
         splash.show()
         splash.set_progress(10, "Initializing Application...")
 
@@ -200,16 +199,13 @@ def main():
         logger.error(f"Error starting GUI: {e}")
         logger.error(f"Traceback: {traceback.format_exc()}")
 
-        try:
-            QMessageBox.critical(
-                None,
-                "Fatal Error",
-                f"An error occurred during startup. See console for details."
-                f"\nPlease check the server is running and your network connection."
-                f"\n\n{str(e)}\n\n",
-            )
-        except:
-            pass
+        QMessageBox.critical(
+            None,
+            "Fatal Error",
+            f"An error occurred during startup. See console for details."
+            f"\nPlease check the server is running and your network connection."
+            f"\n\n{str(e)}\n\n",
+        )
 
         sys.exit(1)
 

src/aare/gui/main_window.py

@@ -1852,7 +1852,7 @@ class MainWindow(QMainWindow):
         logger.critical(f"Automation critical failure: {message}")
 
         is_detector_failure = self._is_detector_critical_failure(message)
-        banner_message = (
+        (
             self._detector_error_banner_text(automation=True, message=message)
             if is_detector_failure
             else f"Automation halted: {message}"
@@ -2493,6 +2493,6 @@ class MainWindow(QMainWindow):
                 "Idle timeout reached, but GUI remains open because beamline is busy or automation is active."
             )
             return
-        #TODO deny communication from GUI to DAQ while IDLE for too long rather than kill the GUI
+        # TODO deny communication from GUI to DAQ while IDLE for too long rather than kill the GUI
         logger.warning("Closing GUI after inactivity timeout.")
         self.close()

src/aare/gui/models/sample_queue_model.py

@@ -90,9 +90,9 @@ class SampleQueueSpreadsheet(QAbstractTableModel):
             row = parent.row()
 
         try:
-            l = SampleShortInfoList.model_validate_json(data.text())
+            sample_data = SampleShortInfoList.model_validate_json(data.text())
             self.beginResetModel()
-            for sample in l.s:
+            for sample in sample_data.s:
                 updated_row = row
                 updated_samples = []
                 for i in range(len(self.samples)):

src/aare/gui/models/user_sample_model.py

@@ -180,12 +180,12 @@ class UserSampleSpreadsheet(QAbstractTableModel):
     def mimeData(self, indexes):
         mime_data = QMimeData()
 
-        l = SampleShortInfoList(s=[])
+        sample_data = SampleShortInfoList(s=[])
 
         for i in sorted(set(index.row() for index in indexes)):
-            l.s.append(self.__sorted_samples[i])
+            sample_data.s.append(self.__sorted_samples[i])
 
-        mime_data.setText(l.model_dump_json())
+        mime_data.setText(sample_data.model_dump_json())
         return mime_data
 
     def get_id(self, row: int) -> SampleShortInfo:

src/aare/gui/panels/face_detection_panel.py

@@ -78,7 +78,7 @@ class FaceDetectionPanel(QWidget):
         samples = data.get("samples", []) or []
         running = bool(data.get("running", False))
         angle = data.get("current_angle_deg")
-        status = data.get("status", "")
+        data.get("status", "")
 
         if running:
             if self._manual_run_requested:

src/aare/gui/panels/file_path_panel.py

@@ -86,14 +86,16 @@ class FilePathPanel(QWidget):
 
     def _expand_macros(self, base: str, rn: int) -> str:
         name = f"{base}_{rn:03d}"
-        name = name.replace('{date}', self.__formatted_date)
-        name = name.replace('{sample}', self.__sample_name)
-        name = name.replace('{CrystalName}', self.__sample_name)
-        name = name.replace('{puck}', self.__puck_name)
-        name = name.replace('{position}', f"{self.__puck_pos:02d}")
-        name = name.replace('{sample_id}', f"{self.__sample_id}")
-        name = name.replace('{beamline}', f"{self.__beamline}")
-        name = name.replace('{prefix}', f"{self.__puck_name}/{self.__puck_pos:02d}/{self.__sample_name}")
+        name = name.replace("{date}", self.__formatted_date)
+        name = name.replace("{sample}", self.__sample_name)
+        name = name.replace("{CrystalName}", self.__sample_name)
+        name = name.replace("{puck}", self.__puck_name)
+        name = name.replace("{position}", f"{self.__puck_pos:02d}")
+        name = name.replace("{sample_id}", f"{self.__sample_id}")
+        name = name.replace("{beamline}", f"{self.__beamline}")
+        name = name.replace(
+            "{prefix}", f"{self.__puck_name}/{self.__puck_pos:02d}/{self.__sample_name}"
+        )
         return name
 
     def _effective_dataset_base(self, base_no_run: str) -> str:

src/aare/gui/panels/local_contact_panel.py

@@ -22,7 +22,7 @@ from PySide6.QtWidgets import (
     QTabWidget,
     QTextEdit,
     QVBoxLayout,
-    QWidget, 
+    QWidget,
 )
 
 from aare.gui.constants import LOGGER_NAME
@@ -333,11 +333,22 @@ class LocalContactPanel(QFrame):
         tools_layout.addWidget(tools)
 
         tools_layout.addWidget(
-            self._make_button("Load BEC user macros", self._daq.bec_load_user_macros, "Loading BEC user macros."))
+            self._make_button(
+                "Load BEC user macros", self._daq.bec_load_user_macros, "Loading BEC user macros."
+            )
+        )
         tools_layout.addWidget(
-            self._make_button("Show BEC user macros", self._daq.bec_list_all_user_macros, "Listing BEC user macros."))
+            self._make_button(
+                "Show BEC user macros",
+                self._daq.bec_list_all_user_macros,
+                "Listing BEC user macros.",
+            )
+        )
         tools_layout.addWidget(
-            self._make_button("Show BEC position devices", self._daq.bec_list_all_devices, "Listing BEC devices."))
+            self._make_button(
+                "Show BEC position devices", self._daq.bec_list_all_devices, "Listing BEC devices."
+            )
+        )
         tools_layout.addWidget(
             self._make_button(
                 "Reinitialise BEC planner/devices",

src/aare/gui/panels/raster_data_collection.py

@@ -31,15 +31,14 @@ class RasterDataCollectionPanel(ScanSettingsPanel):
     raster_alpha_changed = Signal(int)
 
     def __init__(
-        self,
-        raster_mgr: RasterGridManager,
-        diffraction: DiffractionGeometry,
-        parent=None,
+        self, raster_mgr: RasterGridManager, diffraction: DiffractionGeometry, parent=None
     ):
-        super().__init__(diffraction=diffraction,
-                         default_dtz=raster_mgr.active_grid.dtz,
-                         default_transmission=raster_mgr.active_grid.transmission,
-                         parent=parent)
+        super().__init__(
+            diffraction=diffraction,
+            default_dtz=raster_mgr.active_grid.dtz,
+            default_transmission=raster_mgr.active_grid.transmission,
+            parent=parent,
+        )
 
         self._previous_sample_was_none_raster = True
 

src/aare/gui/panels/rotation_data_collection.py

@@ -39,8 +39,13 @@ class RotationDataCollectionPanel(ScanSettingsPanel):
         super().__init__(
             parent=parent,
             diffraction=diffraction,
-            default_dtz=cfg_get("daq.data_collection_settings.default_rotation_settings.dtz", default_dtz),
-            default_transmission=cfg_get("daq.data_collection_settings.default_rotation_settings.transmission", default_transmission),
+            default_dtz=cfg_get(
+                "daq.data_collection_settings.default_rotation_settings.dtz", default_dtz
+            ),
+            default_transmission=cfg_get(
+                "daq.data_collection_settings.default_rotation_settings.transmission",
+                default_transmission,
+            ),
         )
 
         self.__beamline_state = None
@@ -71,8 +76,12 @@ class RotationDataCollectionPanel(ScanSettingsPanel):
         self._layout.addWidget(QLabel("°", parent=self), 5, 4)
 
         self._layout.addWidget(QLabel("Image time", parent=self), 6, 0)
-        default_screening_exp_time = cfg_get("daq.data_collection_settings.default_screening_settings.exp_time_s", 0.1)
-        self.screening_image_time_enter = NumberLineEdit(0.0005, 10.0, default_screening_exp_time, decimals=4, parent=self)
+        default_screening_exp_time = cfg_get(
+            "daq.data_collection_settings.default_screening_settings.exp_time_s", 0.1
+        )
+        self.screening_image_time_enter = NumberLineEdit(
+            0.0005, 10.0, default_screening_exp_time, decimals=4, parent=self
+        )
         self._layout.addWidget(self.screening_image_time_enter, 6, 1, 1, 3)
         self._layout.addWidget(QLabel("s", parent=self), 6, 4)
 
@@ -96,22 +105,32 @@ class RotationDataCollectionPanel(ScanSettingsPanel):
         )
 
         self._layout.addWidget(QLabel("Total angle", parent=self), 10, 0)
-        default_steps = cfg_get("daq.data_collection_settings.default_rotation_settings.steps", 1800)
-        default_increment_omega = cfg_get("daq.data_collection_settings.default_rotation_settings.increment_omega_deg", 0.2)
-        default_total_angle = default_steps*default_increment_omega
-        self.total_angle = DbOverrideLineEdit(0, 9999.0, default=default_total_angle, decimals=3, parent=self)
+        default_steps = cfg_get(
+            "daq.data_collection_settings.default_rotation_settings.steps", 1800
+        )
+        default_increment_omega = cfg_get(
+            "daq.data_collection_settings.default_rotation_settings.increment_omega_deg", 0.2
+        )
+        default_total_angle = default_steps * default_increment_omega
+        self.total_angle = DbOverrideLineEdit(
+            0, 9999.0, default=default_total_angle, decimals=3, parent=self
+        )
         self._layout.addWidget(self.total_angle, 10, 1, 1, 3)
         self._layout.addWidget(QLabel("°", parent=self), 10, 4)
         self._register_override_field(self.total_angle)
 
         self._layout.addWidget(QLabel("Image angle", parent=self), 11, 0)
-        self.image_angle = DbOverrideLineEdit(0, 10.0, default=default_increment_omega, decimals=3, parent=self)
+        self.image_angle = DbOverrideLineEdit(
+            0, 10.0, default=default_increment_omega, decimals=3, parent=self
+        )
         self._layout.addWidget(self.image_angle, 11, 1, 1, 3)
         self._layout.addWidget(QLabel("°", parent=self), 11, 4)
         self._register_override_field(self.image_angle)
         # TODO add protection on X10SA to prevent too short exposure time/ too high detector rep rate
         self._layout.addWidget(QLabel("Image time", parent=self), 12, 0)
-        default_image_exp_time = cfg_get("daq.data_collection_settings.default_rotation_settings.exp_time_s", 0.01)
+        default_image_exp_time = cfg_get(
+            "daq.data_collection_settings.default_rotation_settings.exp_time_s", 0.01
+        )
         self.image_time_enter = DbOverrideLineEdit(
             0.0005, 10.0, default=default_image_exp_time, decimals=4, parent=self
         )
@@ -145,7 +164,7 @@ class RotationDataCollectionPanel(ScanSettingsPanel):
         self.measurement_button.clicked.connect(self.run_measurement)
         self._layout.addWidget(self.measurement_button, 16, 0, 1, 6)
         self._reset_to_defaults()
-        
+
     @Slot()
     def run_screening(self):
         if self.__beamline_state != BeamlineStateEnum.SampleAlignment:

src/aare/gui/panels/scan_settings_panel.py

@@ -196,7 +196,7 @@ class ScanSettingsPanel(QWidget):
         else:
             if not self._previous_sample_was_none:
                 logger.info("Sample cleared, resetting parameters to defaults")
-                #self._reset_to_defaults()
+                # self._reset_to_defaults()
                 self._previous_sample_was_none = True  # Mark that sample is now None
 
             self._sample = None

src/aare/gui/panels/target_stability_panel.py

@@ -55,7 +55,7 @@ class InteractiveChartView(QChartView):
     def mousePressEvent(self, event: QMouseEvent) -> None:
         if event.button() == Qt.MouseButton.LeftButton:
             click_pos = event.position()
-            chart_pos = self.chart().mapToValue(click_pos.toPoint())
+            self.chart().mapToValue(click_pos.toPoint())
 
             if self._panel._try_select_series_at_point(click_pos.toPoint()):
                 event.accept()

src/aare/gui/scan_logic/raster_grid_manager.py

@@ -140,8 +140,12 @@ class RasterGridManager(QObject):
             smargon_top_left=self.__geom.smargon,
             grid_size_mm=Coordinate(x=0.8 * self.__beam_size_mm.x, y=0.8 * self.__beam_size_mm.y),
             omega_deg=self.__geom.omega_deg,
-            exp_time_s=cfg_get("daq.data_collection_settings.default_raster_settings.exp_time_s", 0.01),
-            transmission=cfg_get("daq.data_collection_settings.default_raster_settings.transmission", 1.0),
+            exp_time_s=cfg_get(
+                "daq.data_collection_settings.default_raster_settings.exp_time_s", 0.01
+            ),
+            transmission=cfg_get(
+                "daq.data_collection_settings.default_raster_settings.transmission", 1.0
+            ),
             dtz=cfg_get("daq.data_collection_settings.default_raster_settings.dtz", 200.0),
         )
         self.__completed_grids: List[CompletedRasterGridElem] = []

src/aare/gui/scan_logic/rotation_scan_manager.py

@@ -3,7 +3,6 @@ from aarecommon.models.rotation_scan import CompletedRotationScan
 from PySide6.QtCore import QObject, Signal, Slot
 
 
-
 class RotationScanManager(QObject):
     file_ready = Signal(str, int)
 

src/aare/gui/threads/jfjoch_viewer.py

@@ -64,7 +64,7 @@ class JFJochDBusClient(QObject):
             path = "/sls/mx/data/" + name + "_master.h5"
         print(f"Load dataset: {path} image: {number}")
         if self._ensure_interface():
-            reply = self.__interface.call("LoadFile", path, number, 1)
+            self.__interface.call("LoadFile", path, number, 1)
 
     @Slot()
     def load_online(self):
@@ -73,4 +73,4 @@ class JFJochDBusClient(QObject):
             return
 
         if self._ensure_interface():
-            reply = self.__interface.call("LoadFile", self.__detector_url, -1, 1)
+            self.__interface.call("LoadFile", self.__detector_url, -1, 1)

src/aare/gui/tutorials/tutorial_manager.py

@@ -554,13 +554,13 @@ class TutorialManager(QObject):
 
         return None
 
-    def _run_setup_actions(self, step: TutorialStep) -> None:
+    def _run_setup_actions(self, step: TutorialStepDefinition) -> None:
         if self.context is None:
             return
         for action in step.setup_actions:
             self.action_executor.execute_action(action, self.context)
 
-    def _run_cleanup_actions(self, step: TutorialStep) -> None:
+    def _run_cleanup_actions(self, step: TutorialStepDefinition) -> None:
         if self.context is None:
             return
         for action in step.cleanup_actions:

src/aare/gui/tutorials/tutorial_runtime.py

@@ -14,6 +14,7 @@ from aare.gui.tutorials.tutorial_models import (
     TutorialContext,
     TutorialEvent,
     TutorialScenario,
+    TutorialStepDefinition,
     TutorialTarget,
     TutorialTextRef,
 )
@@ -188,7 +189,11 @@ class CompletionEvaluator:
         self._event_bus = event_bus
 
     def is_step_complete(
-        self, step: TutorialStep, context: TutorialContext, *, target_clicked: bool = False
+        self,
+        step: TutorialStepDefinition,
+        context: TutorialContext,
+        *,
+        target_clicked: bool = False,
     ) -> bool:
         if step.completion is None:
             return True

tests/unit/daq/operations/test_ml_raster_plan.py

@@ -151,7 +151,8 @@ def test_grid_padding_fraction_scales(monkeypatch):
 
 def test_crystal_union_extends_grid_only_when_enabled(monkeypatch):
     # crystal extends well beyond the loop_face box on +x
-    mlbox = lambda: _fake_mlbox(loop_face=(150, 150, 300, 300), crystals=[(350, 150, 520, 300)])
+    def mlbox():
+        return _fake_mlbox(loop_face=(150, 150, 300, 300), crystals=[(350, 150, 520, 300)])
 
     def cfg(enabled):
         return lambda k, d=None: (

tests/unit/daq/test_auth.py

@@ -23,12 +23,7 @@ with patch.dict("os.environ", {"JWT_AAREDAQ_KEY": "test_secret"}):
         respond_to_baton_request,
     )
 from aarecommon.errors.exception_handler import AuthenticationException, UserRightsException
-from aarecommon.models.auth import (
-    BatonHolderInfo,
-    BatonRequest,
-    BatonRequestStatus,
-    BatonStatus,
-)
+from aarecommon.models.auth import BatonHolderInfo, BatonRequest, BatonRequestStatus, BatonStatus
 from aarecommon.models.models import SessionsStateEnum
 
 

tests/unit/daq/test_beamcenterfit.py

@@ -45,7 +45,7 @@ def test_beamcenter_fit_no_converge():
     # beamcenter_fit might still find some contour if there's enough noise,
     # but curve_fit might fail to converge
     # If it doesn't converge, it returns None now.
-    result = beamcenter_fit(image)
+    beamcenter_fit(image)
     # It might actually return a result if it finds a random blob,
     # but we want to test the failure path.
     # To truly force non-convergence we might need a more extreme case,

tests/unit/daq/test_server.py

@@ -2,7 +2,6 @@ import os
 from types import SimpleNamespace
 from unittest.mock import patch
 
-import numpy as np
 
 os.environ["JWT_AAREDAQ_KEY"] = "test_key_for_unit_testing"
 

tests/unit/devices/test_experimental_hutch_shutter.py

@@ -7,7 +7,7 @@ from aare.devices.experimental_hutch_shutter import ExperimentalHutchShutter
 
 @patch("aare.devices.experimental_hutch_shutter.PV")
 def test_shutter_init(mock_pv):
-    shutter = ExperimentalHutchShutter(MXBeamline.X06DA)
+    ExperimentalHutchShutter(MXBeamline.X06DA)
     assert mock_pv.call_count == 3
     # Check if PV names are correct
     args = [call.args[0] for call in mock_pv.call_args_list]

tests/unit/devices/test_filter_transmission.py

@@ -8,7 +8,7 @@ from aare.devices.filter_transmission import FilterTransmission
 
 @patch("aare.devices.filter_transmission.PV")
 def test_filter_init(mock_pv):
-    filters = FilterTransmission(MXBeamline.X06DA)
+    FilterTransmission(MXBeamline.X06DA)
     assert mock_pv.call_count == 3
 
 

tests/unit/gui/test_message_box.py

@@ -31,6 +31,7 @@ def test_timer_box_auto_accept(qtbot):
 
     assert box.result() == QMessageBox.StandardButton.Yes
 
+
 @pytest.mark.timeout(10)
 def test_ring_current_low_check_ok(qtbot):
     # Should return True immediately if current is high enough