Update repo with template version v1.2.8

feat: update repository with copier changes for gitea migration

See merge request bec/addams_bec!4

.copier-answers.yml

@@ -0,0 +1,9 @@
+# Do not edit this file!
+# It is needed to track the repo template version, and editing may break things.
+# This file will be overwritten by copier on template updates.
+
+_commit: v1.2.8
+_src_path: https://github.com/bec-project/plugin_copier_template.git
+make_commit: false
+project_name: addams_bec
+widget_plugins_input: []

.gitea/workflows/ci.yml

@@ -0,0 +1,102 @@
+name: CI for addams_bec
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      BEC_WIDGETS_BRANCH:
+        description: "Branch of BEC Widgets to install"
+        required: false
+        type: string
+        default: "main"
+      BEC_CORE_BRANCH:
+        description: "Branch of BEC Core to install"
+        required: false
+        type: string
+        default: "main"
+      OPHYD_DEVICES_BRANCH:
+        description: "Branch of Ophyd Devices to install"
+        required: false
+        type: string
+        default: "main"
+      BEC_PLUGIN_REPO_BRANCH:
+        description: "Branch of the BEC Plugin Repository to install"
+        required: false
+        type: string
+        default: "main"
+      PYTHON_VERSION:
+        description: "Python version to use"
+        required: false
+        type: string
+        default: "3.12"
+
+permissions:
+  pull-requests: write
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      QTWEBENGINE_DISABLE_SANDBOX: 1
+      QT_QPA_PLATFORM: "offscreen"
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "${{ inputs.PYTHON_VERSION || '3.12' }}"
+
+      - name: Checkout BEC Plugin Repository
+        uses: actions/checkout@v4
+        with:
+          repository: bec/addams_bec
+          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
+          path: ./addams_bec
+
+      - name: Lint for merge conflicts from template updates
+        shell: bash
+        # Find all Copier conflicts except this line
+        run: '! grep -r "<<<<<<< before updating" | grep -v "grep -r \"<<<<<<< before updating"'
+
+      - name: Checkout BEC Core
+        uses: actions/checkout@v4
+        with:
+          repository: bec/bec
+          ref: "${{ inputs.BEC_CORE_BRANCH || 'main' }}"
+          path: ./bec
+
+      - name: Checkout Ophyd Devices
+        uses: actions/checkout@v4
+        with:
+          repository: bec/ophyd_devices
+          ref: "${{ inputs.OPHYD_DEVICES_BRANCH || 'main' }}"
+          path: ./ophyd_devices
+
+      - name: Checkout BEC Widgets
+        uses: actions/checkout@v4
+        with:
+          repository: bec/bec_widgets
+          ref: "${{ inputs.BEC_WIDGETS_BRANCH || 'main' }}"
+          path: ./bec_widgets
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgl1 libegl1 x11-utils libxkbcommon-x11-0 libdbus-1-3 xvfb
+          sudo apt-get -y install libnss3 libxdamage1 libasound2t64 libatomic1 libxcursor1
+
+      - name: Install Python dependencies
+        shell: bash
+        run: |
+          pip install uv
+          uv pip install --system -e ./ophyd_devices
+          uv pip install --system -e ./bec/bec_lib[dev]
+          uv pip install --system -e ./bec/bec_ipython_client
+          uv pip install --system -e ./bec/bec_server[dev]
+          uv pip install --system -e ./bec_widgets[dev,pyside6]
+          uv pip install --system -e ./addams_bec
+
+      - name: Run Pytest with Coverage
+        id: coverage
+        run: pytest --random-order --cov=./addams_bec --cov-config=./addams_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./addams_bec/tests/ || test $? -eq 5

.gitea/workflows/create_update_pr.yml

@@ -0,0 +1,62 @@
+name: Create template upgrade PR for addams_bec
+on:
+  workflow_dispatch:
+
+permissions:
+  pull-requests: write
+
+jobs:
+  create_update_branch_and_pr:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+    
+      - name: Install tools
+        run: |
+          pip install copier PySide6
+
+      - name: Checkout
+        uses: actions/checkout@v4
+    
+      - name: Perform update
+        run: |
+          git config --global user.email "bec_ci_staging@psi.ch"
+          git config --global user.name "BEC automated CI"
+
+          branch="chore/update-template-$(python -m uuid)"
+          echo "switching to branch $branch"
+          git checkout -b $branch
+
+          echo "Running copier update..."
+          output="$(copier update --trust --defaults --conflict inline 2>&1)"
+          echo "$output"
+          msg="$(printf '%s\n' "$output" | head -n 1)"
+
+          if ! grep -q "make_commit: true" .copier-answers.yml ; then
+            echo "Autocommit not made, committing..."
+            git add -A
+            git commit -a -m "$msg"
+          fi
+
+          if diff-index --quiet HEAD ; then
+            echo "No changes detected"
+            exit 0
+          fi
+
+          git push -u origin $branch
+          curl -X POST "https://gitea.psi.ch/api/v1/repos/${{ gitea.repository }}/pulls" \
+            -H "Authorization: token ${{ secrets.CI_REPO_WRITE }}" \
+            -H "Content-Type: application/json" \
+            -d "{
+                  \"title\": \"Template: $(echo $msg)\",
+                  \"body\": \"This PR was created by Gitea Actions\",
+                  \"head\": \"$(echo $branch)\",
+                  \"base\": \"main\"
+                }"

.gitlab-ci.yml

@@ -1,4 +0,0 @@
-include:
-- file: /templates/plugin-repo-template.yml
-  inputs: {name: addams_bec, target: addams_bec}
-  project: bec/awi_utils

LICENSE

@@ -1,6 +1,7 @@
+
 BSD 3-Clause License
 
-Copyright (c) 2024, Paul Scherrer Institute
+Copyright (c) 2025, Paul Scherrer Institute 
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
@@ -25,4 +26,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

addams_bec/bec_ipython_client/high_level_interface/hkl_hli.py

@@ -1,75 +1,57 @@
 import builtins
 import collections
-import functools
 import json
 import math
 import pathlib
 
-import numpy
-from bec_ipython_client.main import BECClientPrompt
-
 from bec_ipython_client.prettytable import PrettyTable
 
 __all__ = [
-    'setlat',
-    'setlambda',
-    'setmode',
-    'freeze',
-    'unfreeze',
-    'br',
-    'ubr',
-    'mvhkl',
-    'umvhkl',
-    'ca',
-    'wh',
-    'pa',
-    'orientAdd',
-    'orientRemove',
-    'orientShow',
-    'orientFit',
-    'ct'
+    "setlat",
+    "setlambda",
+    "setmode",
+    "freeze",
+    "unfreeze",
+    "br",
+    "ubr",
+    "mvhkl",
+    "umvhkl",
+    "ca",
+    "wh",
+    "pa",
+    "orientAdd",
+    "orientRemove",
+    "orientShow",
+    "orientFit",
+    "ct",
 ]
 
 bec = builtins.__dict__.get("bec")
 dev = builtins.__dict__.get("dev")
 scans = builtins.__dict__.get("scans")
 
-class BECClientPromptDiffractometer(BECClientPrompt):
-
-    @property
-    def username(self):
-        """current username"""
-        if "x04v" in dev:
-            return "x04v"
-        if "x04h" in dev:
-            return "x04h"
-        return "demo"
-
-bec._ip.prompts = BECClientPromptDiffractometer(ip=bec._ip, username="demo", client=bec._client, status=1)
-
 
 # check for diffractometer device
 diffract = None
 if dev is not None:
-    if 'x04h' in dev:
+    if "x04h" in dev:
         diffract = dev.x04h
-    elif 'x04v' in dev:
+    elif "x04v" in dev:
         diffract = dev.x04v
 
 if diffract is not None:
-    RealPosition = collections.namedtuple('RealPosition', ' '.join(diffract.get_real_positioners()))
+    RealPosition = collections.namedtuple("RealPosition", " ".join(diffract.get_real_positioners()))
 
 
-def freeze(
-    angle: float | None
-):
+def freeze(angle: float | None):
     """
-    Freeze the value of the mode dependent angle, so when calculating motor positions 
-    corresponding to an arbitrary (H, K, L ), the angle will be reset to the frozen value 
+    Freeze the value of the mode dependent angle, so when calculating motor positions
+    corresponding to an arbitrary (H, K, L ), the angle will be reset to the frozen value
     before the calculation no matter what the current position of the diffractometer.
     """
     diffract.freeze(angle)
 
+
 def unfreeze():
     """
     Subsequent angle calculations will use whatever the current value of the associated
@@ -77,74 +59,69 @@ def unfreeze():
     """
     diffract.unfreeze()
 
-def setlat(
-        a: float, b: float, c: float, alpha: float, beta: float, gamma: float
-):
+
+def setlat(a: float, b: float, c: float, alpha: float, beta: float, gamma: float):
     """
     Set sample lattice parameters
     """
     diffract.set_lattice((a, b, c, alpha, beta, gamma))
 
-def setlambda(
-        wavelength: float
-):
+
+def setlambda(wavelength: float):
     """
     Set the x-ray wavelength (in Angstroms)
     """
     if wavelength <= 0:
-        print('Invalid input: wavelength <=0!')
+        print("Invalid input: wavelength <=0!")
         return
 
     current_wavelength = diffract.get_wavelength()
     if math.isclose(wavelength, current_wavelength):
-        print(f'Still using {current_wavelength} A')
+        print(f"Still using {current_wavelength} A")
     else:
         diffract.set_wavelength(wavelength)
-        print(f'Lambda reset from {current_wavelength} to {wavelength} A')
+        print(f"Lambda reset from {current_wavelength} to {wavelength} A")
 
-def setmode(
-        mode: int
-):
+
+def setmode(mode: int):
     """
     Set the geometry mode
     """
     if mode < 0 or mode > 2:
-        print('Valid mode is from 0 to 2')
+        print("Valid mode is from 0 to 2")
         return
 
     current_mode = diffract.get_mode()
     if mode == current_mode:
-        print(f'Still using mode {current_mode}')
+        print(f"Still using mode {current_mode}")
     else:
         diffract.set_mode(mode)
-        print(f'Mode reset from {current_mode} to {mode}')
+        print(f"Mode reset from {current_mode} to {mode}")
 
-def mvhkl(
-        h: float, k: float, l: float, auto=False
-):
+
+def mvhkl(h: float, k: float, l: float, auto=False):
     """
     Move to the reciprocol space coordinates
     """
     try:
         angles = diffract.forward(h, k, l)[:-2]
     except Exception as exc:
-        print(f'{h} {k} {l} is not obtainable: {exc}')
+        print(f"{h} {k} {l} is not obtainable: {exc}")
         return
 
     if not auto:
         for axis, current, target in zip(RealPosition._fields, _currentPosition(), angles):
-            print('%7s = %9.4f --> %9.4f' % (axis, current, target))
+            print("%7s = %9.4f --> %9.4f" % (axis, current, target))
 
-        answer = input('Move to these values? [Y/n]: ')
-        if answer.startswith(('N', 'n')):
-            print('Move abandoned.')
+        answer = input("Move to these values? [Y/n]: ")
+        if answer.startswith(("N", "n")):
+            print("Move abandoned.")
             return
-        
+
     br(h, k, l)
 
-def br(
-        h: float, k: float, l: float
-):
+
+def br(h: float, k: float, l: float):
     """
     Move to the reciprocol space coordinates
     """
@@ -156,9 +133,8 @@ def br(
 
     scans.mv(*args, relative=False)
 
-def ubr(
-        h: float, k: float, l: float
-):
+
+def ubr(h: float, k: float, l: float):
     """
     Move to the reciprocol space coordinates with updates
     """
@@ -170,44 +146,43 @@ def ubr(
 
     scans.umv(*args, relative=False)
 
-def umvhkl(
-        h: float, k: float, l: float, auto=False
-):
+
+def umvhkl(h: float, k: float, l: float, auto=False):
     """
     Move to the reciprocol space coordinates with updates
     """
     try:
         angles = diffract.forward(h, k, l)[:-2]
     except Exception as exc:
-        print(f'{h} {k} {l} is not obtainable: {exc}')
+        print(f"{h} {k} {l} is not obtainable: {exc}")
         return
 
     if not auto:
         for axis, current, target in zip(RealPosition._fields, _currentPosition(), angles):
-            print('%7s = %9.4f --> %9.4f' % (axis, current, target))
+            print("%7s = %9.4f --> %9.4f" % (axis, current, target))
 
-        answer = input('Move to these values? [Y/n]: ')
-        if answer.startswith(('N', 'n')):
-            print('Move abandoned.')
+        answer = input("Move to these values? [Y/n]: ")
+        if answer.startswith(("N", "n")):
+            print("Move abandoned.")
             return
-        
+
     ubr(h, k, l)
 
-def ca(
-        h: float, k: float, l: float
-):
+
+def ca(h: float, k: float, l: float):
     """
     Calculate angle positions for a given point in reciprocol space
     """
     angles = diffract.forward(h, k, l)
     print("\nCalculated positions:\n")
-    print(f'H K L = {h} {k} {l}')
-    print('BetaIn = %.5f  BetaOut = %.5f' %(angles[-2], angles[-1]))
-    print('Lambda = %.3f' % diffract.get_wavelength())
+    print(f"H K L = {h} {k} {l}")
+    print("BetaIn = %.5f  BetaOut = %.5f" % (angles[-2], angles[-1]))
+    print("Lambda = %.3f" % diffract.get_wavelength())
 
     print()
     _showAngles(angles[:-2])
 
+
 def wh():
     """
     Show where principal axes and reciprocal space
@@ -218,41 +193,45 @@ def wh():
     betaIn = diffract.betaIn.position
     betaOut = diffract.betaOut.position
 
-    print(f'H K L = {h:.4f} {k:.4f} {l:.4f}')
-    print('BetaIn = %.5f  BetaOut = %.5f' %(betaIn, betaOut))
-    print('Lambda = %.3f' % diffract.get_wavelength())
+    print(f"H K L = {h:.4f} {k:.4f} {l:.4f}")
+    print("BetaIn = %.5f  BetaOut = %.5f" % (betaIn, betaOut))
+    print("Lambda = %.3f" % diffract.get_wavelength())
 
     print()
     _showAngles()
 
+
 def pa():
     """
     Show geometry parameters
     """
-    if diffract.name == 'x04v':
-        print('x04v (Newport Microcontrols 2+3 at SLS) vertical geometry')
-    elif diffract.name == 'x04h':
-        print('x04h (Newport Microcontrols 2+3 at SLS) horizontal geometry')
+    if diffract.name == "x04v":
+        print("x04v (Newport Microcontrols 2+3 at SLS) vertical geometry")
+    elif diffract.name == "x04h":
+        print("x04h (Newport Microcontrols 2+3 at SLS) horizontal geometry")
 
     match mode := diffract.get_mode():
         case 0:
-            print(f'  BetaIn Fixed (mode {mode})')
+            print(f"  BetaIn Fixed (mode {mode})")
         case 1:
-            print(f'  BetaOut Fixed (mode {mode})')
+            print(f"  BetaOut Fixed (mode {mode})")
         case 2:
-            print(f'  BetaIn equals BetaOut (mode {mode})')
-    
+            print(f"  BetaIn equals BetaOut (mode {mode})")
+
     if beta_frozen := diffract.get_frozen():
-        print(f'  Frozen coordinate: {beta_frozen}')
+        print(f"  Frozen coordinate: {beta_frozen}")
+
 
 def orientShow():
     """
     Display list of measured reflections
     """
-    print('\n(Using lattice constants:)')
+    print("\n(Using lattice constants:)")
     lattice = diffract.get_lattice()
-    print('a = %.4g, b = %.4g, b = %.4g, alpha = %.6g, beta = %.6g, gamma = %.6g' %
-          (lattice[0], lattice[1], lattice[2], lattice[3], lattice[4], lattice[5]))
+    print(
+        "a = %.4g, b = %.4g, b = %.4g, alpha = %.6g, beta = %.6g, gamma = %.6g"
+        % (lattice[0], lattice[1], lattice[2], lattice[3], lattice[4], lattice[5])
+    )
 
     print("\n------------------------------------------------\n")
 
@@ -263,17 +242,15 @@ def orientShow():
 
     _showUB()
 
-def orientRemove(
-        h: float, k: float, l: float
-):
+
+def orientRemove(h: float, k: float, l: float):
     """
     Remove a measured reflection from the list
     """
     diffract.remove_reflection(h, k, l)
 
-def orientAdd(
-        h: float, k: float, l: float, *args
-):
+
+def orientAdd(h: float, k: float, l: float, *args):
     """
     Add a reflection to the list of measured reflections
     """
@@ -282,63 +259,67 @@ def orientAdd(
         response = diffract.real_position
         # The original return value is of namedtuple type,
         # which gets serialized to a dictionary by the device server.
-        angles = tuple(response['values'][axis] for axis in response['fields'] if axis != 'nu')
+        angles = tuple(response["values"][axis] for axis in response["fields"] if axis != "nu")
 
     if len(angles) < 4:
-        print('Please specify all angles')
+        print("Please specify all angles")
         return
 
     diffract.add_reflection(h, k, l, angles)
 
-def orientSave(
-        filename: str
-):
+
+def orientSave(filename: str):
     """
     Save the current reflections
     """
     configuration = {}
-    configuration['geometry'] = diffract.name
-    configuration['wavelength'] = diffract.get_wavelength()
-    configuration['lattice'] = diffract.get_lattice()
-    configuration['reflections'] = diffract.get_reflections()
-    
+    configuration["geometry"] = diffract.name
+    configuration["wavelength"] = diffract.get_wavelength()
+    configuration["lattice"] = diffract.get_lattice()
+    configuration["reflections"] = diffract.get_reflections()
+
     filepath = pathlib.Path(filename)
     if filepath.exists():
-        answer = input('File "%s" already exists. Do you want to overwrite it? [y/N]: ' %(filepath.absolute()))
-        if not answer.startswith(('Y', 'y')):
+        answer = input(
+            'File "%s" already exists. Do you want to overwrite it? [y/N]: ' % (filepath.absolute())
+        )
+        if not answer.startswith(("Y", "y")):
             return
 
-    with open(filepath, 'w') as f:
+    with open(filepath, "w") as f:
         json.dump(configuration, f)
 
-def orientLoad(
-        filename: str
-):
+
+def orientLoad(filename: str):
     """
     Load relfections from file
     """
-    with open(filename, 'r') as f:
+    with open(filename, "r") as f:
         configuration = json.load(f)
-        if configuration['geometry'] != diffract.name:
-            print('Saved orientation is for a different geometry "%s", current is "%s".' % configuration['geometry'], diffract.name)
+        if configuration["geometry"] != diffract.name:
+            print(
+                'Saved orientation is for a different geometry "%s", current is "%s".'
+                % configuration["geometry"],
+                diffract.name,
+            )
             return
 
         # save current wavelength, lattice and reflections
         saved_wavelength = diffract.get_wavelength()
         saved_lattice = diffract.get_lattice()
         saved_reflections = diffract.get_reflections()
-    
+
         try:
-            diffract.set_lattice(configuration['lattice'])
-            
+            diffract.set_lattice(configuration["lattice"])
+
             diffract.clear_reflections()
-            for reflection in configuration['reflections']:
+            for reflection in configuration["reflections"]:
                 diffract.add_reflection(*reflection)
 
-            _showReflections(configuration['reflections'])
+            _showReflections(configuration["reflections"])
             print("\n------------------------------------------------\n")
             # set wavelength temporarily for orientFit and restore later
-            diffract.set_wavelength(configuration['wavelength'])
+            diffract.set_wavelength(configuration["wavelength"])
             orientFit()
         except Exception as exc:
             # restore saved lattice and reflections
@@ -352,6 +333,7 @@ def orientLoad(
             # restore wavelength
             diffract.set_wavelength(saved_wavelength)
 
+
 def orientFit():
     """
     Fit UB matrix from given reflections
@@ -364,19 +346,22 @@ def orientFit():
     diffract.compute_UB()
     _showUB()
 
+
 def ct(exp_time: float):
     """
     Acquire all detectors
     """
     scans.acquire(exp_time=exp_time)
 
+
 def _showUB():
     UB = diffract.get_UB()
-    
-    print('Orientation matrix by row:')
-    print('  Row 1: %8.5f %8.5f %8.5f' % (UB[0,0], UB[0,1], UB[0,2]))
-    print('  Row 2: %8.5f %8.5f %8.5f' % (UB[1,0], UB[1,1], UB[1,2]))
-    print('  Row 3: %8.5f %8.5f %8.5f' % (UB[2,0], UB[2,1], UB[2,2]))
+
+    print("Orientation matrix by row:")
+    print("  Row 1: %8.5f %8.5f %8.5f" % (UB[0, 0], UB[0, 1], UB[0, 2]))
+    print("  Row 2: %8.5f %8.5f %8.5f" % (UB[1, 0], UB[1, 1], UB[1, 2]))
+    print("  Row 3: %8.5f %8.5f %8.5f" % (UB[2, 0], UB[2, 1], UB[2, 2]))
+
 
 def _showAngles(angles=None):
     if angles is None:
@@ -384,23 +369,25 @@ def _showAngles(angles=None):
 
     table = PrettyTable(RealPosition._fields, padding=12)
     print(table.get_header())
-    text = tuple(f'{x:9.4f}' for x in angles)
+    text = tuple(f"{x:9.4f}" for x in angles)
     print(table.get_row(*text))
 
+
 def _currentPosition():
     response = diffract.real_position
     # The original return value is of namedtuple type,
     # which gets serialized to a dictionary by the device server.
-    angles = RealPosition(*(response['values'][axis] for axis in response['fields']))
+    angles = RealPosition(*(response["values"][axis] for axis in response["fields"]))
     return angles
 
+
 def _showReflections(reflections):
-    print('The defined reflections are:')
-    header = ['h', 'k', 'l'] + diffract.real_position['fields'][:-1]
+    print("The defined reflections are:")
+    header = ["h", "k", "l"] + diffract.real_position["fields"][:-1]
     table = PrettyTable(header, padding=12)
-    print('  ', table.get_header())
+    print("  ", table.get_header())
 
     for reflection in reflections:
         h, k, l, angles = reflection
-        text = [f'{h:9.4f}', f'{k:9.4f}', f'{l:9.4f}'] + [f'{x:9.4f}' for x in angles]
-        print('  ', table.get_row(*text))
+        text = [f"{h:9.4f}", f"{k:9.4f}", f"{l:9.4f}"] + [f"{x:9.4f}" for x in angles]
+        print("  ", table.get_row(*text))

addams_bec/bec_ipython_client/plugins/energy_optimizer/addams_energy_optimizer.py

@@ -0,0 +1,83 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, List, Tuple
+
+if TYPE_CHECKING:  # pragma: no cover
+    from bec_lib.devicemanager import DeviceManagerBase as DeviceManager
+
+
+class EnergyOptimizer:
+    def __init__(self, device_manager: DeviceManager):
+        self.device_manager = device_manager
+        self.strips = {
+            "Si": {"energy_range": [5, 10]},
+            "Rh": {"energy_range": [8, 23]},
+            "Pt": {"energy_range": [20, 40]},
+        }
+        self.overlap_energyies = {"Si": {"Rh": 9}, "Rh": {"Si": 9, "Pt": 22}, "Pt": {"Rh": 22}}
+
+    @staticmethod
+    def get_transition_steps(start_energy: float, target_energy: float) -> List[Tuple[float, str]]:
+        """
+        Get the required steps to transition from one energy to another.
+
+        Args:
+            start_energy: The starting energy in keV.
+            target_energy: The target energy in keV.
+
+        Returns:
+            A list of tuples containing the energy and the strip name for each step.
+        """
+        strips = {"Si": (5, 10), "Rh": (8, 23), "Pt": (20, 40)}
+        overlap_energyies = {"Si": {"Rh": 9}, "Rh": {"Si": 9, "Pt": 22}, "Pt": {"Rh": 22}}
+
+        def get_strip(energy: float) -> str:
+            for strip, (low, high) in strips.items():
+                if low <= energy <= high:
+                    return strip
+            return ""
+
+        def find_overlap(from_strip: str, to_strip: str) -> float:
+            return overlap_energyies[from_strip][to_strip]
+
+        path = []
+
+        if get_strip(start_energy) == "":
+            raise ValueError("Start energy is out of range for available strips")
+        if not any(low <= target_energy <= high for low, high in strips.values()):
+            raise ValueError("End energy is out of range for available strips")
+
+        current_energy = start_energy
+
+        # TODO: this should be replaced with a readout from the PV
+        current_strip = get_strip(current_energy)
+
+        # if the target energy is covered by the current strip, return the path
+        if strips[current_strip][0] <= target_energy <= strips[current_strip][1]:
+            return [(target_energy, current_strip)]
+
+        target_strip = get_strip(target_energy)
+
+        available_strips = list(strips.keys())
+        current_index = available_strips.index(current_strip)
+        target_index = available_strips.index(target_strip)
+        step = 1 if target_index > current_index else -1
+
+        for i in range(current_index, target_index, step):
+            next_strip = available_strips[i + step]
+            overlap_energy = find_overlap(available_strips[i], next_strip)
+            path.append((overlap_energy, next_strip))
+            current_strip = next_strip
+
+        path.append((target_energy, target_strip))
+
+        return path
+
+
+if __name__ == "__main__":  # pragma: no cover
+    from unittest.mock import MagicMock
+
+    device_manager = MagicMock()
+    optimizer = EnergyOptimizer(device_manager)
+    steps = optimizer.get_transition_steps(30, 20)
+    print(steps)

addams_bec/bec_ipython_client/startup/post_startup.py

@@ -34,7 +34,27 @@ to setup the prompts.
 """
 
 # pylint: disable=invalid-name, unused-import, import-error, undefined-variable, unused-variable, unused-argument, no-name-in-module
+import builtins
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from bec_ipython_client.main import BECIPythonClient
+
+    bec: BECIPythonClient = BECIPythonClient()
+    dev = bec.device_manager.devices
+    scans = bec.scans
+
+else:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    scans = builtins.__dict__.get("scans")
 
 bec.load_high_level_interface("bec_hli")
 bec.load_high_level_interface("spec_hli")
 bec.load_high_level_interface("hkl_hli")
+
+
+if "x04v" in dev:
+    bec._ip.prompts.session_name = "x04v"
+elif "x04h" in dev:
+    bec._ip.prompts.session_name = "x04h"

addams_bec/bec_ipython_client/startup/pre_startup.py

@@ -1,10 +1,14 @@
 """
 Pre-startup script for BEC client. This script is executed before the BEC client
-is started. It can be used to add additional command line arguments. 
+is started. It can be used to add additional command line arguments.
 """
 
+import os
+
 from bec_lib.service_config import ServiceConfig
 
+import addams_bec
+
 
 def extend_command_line_args(parser):
     """
@@ -15,9 +19,13 @@ def extend_command_line_args(parser):
 
     return parser
 
-
-# def get_config() -> ServiceConfig:
-#     """
-#     Create and return the service configuration.
-#     """
-#     return ServiceConfig(redis={"host": "localhost", "port": 6379})
+def get_config() -> ServiceConfig:
+    """
+    Create and return the ServiceConfig for the plugin repository
+    """
+    deployment_path = os.path.dirname(os.path.dirname(os.path.dirname(addams_bec.__file__)))
+    files = os.listdir(deployment_path)
+    if "bec_config.yaml" in files:
+        return ServiceConfig(config_path=os.path.join(deployment_path, "bec_config.yaml"))
+    else:
+        return ServiceConfig(redis={"host": "localhost", "port": 6379})

addams_bec/devices/detector.py

@@ -1,5 +1,3 @@
-import os
-
 from ophyd import (
     ADComponent as ADCpt,
     Device,
@@ -53,14 +51,6 @@ class Eiger500KSetup(CustomDetectorMixin):
             self.parent.cam.acquire.put(1, wait=False) # arm
 
         # file writer
-        # TODO: enable this when new storage path is consistent on bec server and consoles.
-        # self.parent.filepath.set(
-        #     self.parent.filewriter.compile_full_filename(f"{self.parent.name}")
-        # ).wait()
-        # file_path, file_name = os.path.split(self.parent.filepath.get())
-        # self.parent.hdf.file_path.put(file_path)
-        # self.parent.hdf.file_name.put(file_name)
-        # self.parent.hdf.file_template.put("%s%s")
         self.parent.hdf.lazy_open.put(1)
         self.parent.hdf.num_capture.put(num_points)
         self.parent.hdf.file_write_mode.put(2) # Stream
@@ -109,8 +99,7 @@ class Eiger500KSetup(CustomDetectorMixin):
 
         # publish timeseries data
         metadata = self.parent.scaninfo.scan_msg.metadata
-        metadata.update({"async_update": "append", "max_shape": [None, None]})
-
+        metadata.update({"async_update": "append", "num_lines": self.parent.roistat.ts_current_point.get()})
         msg = messages.DeviceMessage(
             signals={
                 self.parent.roistat.roi1.name_.get(): {

addams_bec/devices/profileMove.py

@@ -143,11 +143,11 @@ class ProfileMoveAxisXPS(ProfileMoveAxis):
 
 
 class ProfileMoveXPSX04SA(ProfileMoveControllerXPS):
-    ov = Cpt(ProfileMoveAxisXPS, '', motor='1')
-    xv = Cpt(ProfileMoveAxisXPS, '', motor='2')
-    oh = Cpt(ProfileMoveAxisXPS, '', motor='3')
-    phi = Cpt(ProfileMoveAxisXPS, '', motor='4')
-    nu = Cpt(ProfileMoveAxisXPS, '', motor='5')
-    alp = Cpt(ProfileMoveAxisXPS, '', motor='6')
-    gam = Cpt(ProfileMoveAxisXPS, '', motor='7')
-    delta = Cpt(ProfileMoveAxisXPS, '', motor='8')
+    alp = Cpt(ProfileMoveAxisXPS, '', motor='1')
+    delta = Cpt(ProfileMoveAxisXPS, '', motor='2')
+    gam = Cpt(ProfileMoveAxisXPS, '', motor='3')
+    ov = Cpt(ProfileMoveAxisXPS, '', motor='4')
+    xv = Cpt(ProfileMoveAxisXPS, '', motor='5')
+    phi = Cpt(ProfileMoveAxisXPS, '', motor='6')
+    oh = Cpt(ProfileMoveAxisXPS, '', motor='7')
+    nu = Cpt(ProfileMoveAxisXPS, '', motor='8')

addams_bec/macros/README.md

@@ -0,0 +1,6 @@
+# Macros
+
+This directory is intended to store macros which will be loaded automatically when starting BEC.
+Macros are small functions to make repetitive tasks easier. Functions defined in python files in this directory will be accessible from the BEC console.
+Please do not put any code outside of function definitions here. If you wish for code to be automatically run when starting BEC, see the startup script at addams_bec/bec_ipython_client/startup/post_startup.py
+For a guide on writing macros, please see: https://bec.readthedocs.io/en/latest/user/command_line_interface.html#how-to-write-a-macro

addams_bec/scans/__init__.py

@@ -1,4 +1,2 @@
-from .hkl_scan import HklScan
 from .fly_scan import HklFlyScan
-from .mesh_scan import HklMeshScan, HklMeshFlyScan
-from .profilemove_scan import LineProfileMove, GridProfileMove
+from .hkl_scan import HklScan

addams_bec/scans/fly_scan.py

@@ -64,7 +64,6 @@ class HklFlyScan(AsyncFlyScanBase):
             self.positions.append(position[:-2])
 
     def scan_core(self):
-        all_motors = self.device_manager.devices[self.controller].axes.get()
         scan_motors = self.device_manager.devices[self.diffract].real_axes.get()
         hkls = numpy.linspace(self.start, self.stop, self.points).tolist()
         positions = yield from self.stubs.send_rpc_and_wait(self.diffract, 'angles_from_hkls', hkls)
@@ -81,15 +80,11 @@ class HklFlyScan(AsyncFlyScanBase):
             yield from self.stubs.send_rpc_and_wait(self.controller, 'time_mode.put', 1)
             yield from self.stubs.send_rpc_and_wait(self.controller, 'times.put', [total_time, total_time])
 
-            for axis_name in all_motors:
-                if axis_name not in scan_motors:
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 0)
-                else:
-                    index = scan_motors.index(axis_name)
-                    yield from self.stubs.send_rpc_and_wait(self.controller,
-                                                            f'{axis_name}.positions.put',
-                                                            (positions[0, index], positions[-1, index]))
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
+            for index, axis_name in enumerate(scan_motors):
+                yield from self.stubs.send_rpc_and_wait(self.controller,
+                                                    f'{axis_name}.positions.put',
+                                                    (positions[0, index], positions[-1, index]))
+                yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
 
         else:
             yield from self.stubs.send_rpc_and_wait(self.controller, 'num_points.put', num_points)
@@ -99,15 +94,11 @@ class HklFlyScan(AsyncFlyScanBase):
             yield from self.stubs.send_rpc_and_wait(self.controller, 'time_mode.put', 0)
             yield from self.stubs.send_rpc_and_wait(self.controller, 'fixed_time.put', self.exp_time)
 
-            for axis_name in all_motors:
-                if axis_name not in scan_motors:
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 0)
-                else:
-                    index = scan_motors.index(axis_name)
-                    yield from self.stubs.send_rpc_and_wait(self.controller,
-                                                            f'{axis_name}.positions.put',
-                                                            (positions[0, index], positions[-1, index]))
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
+            for index, axis_name in enumerate(scan_motors):
+                yield from self.stubs.send_rpc_and_wait(self.controller,
+                                                    f'{axis_name}.positions.put',
+                                                    positions[:, index])
+                yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
 
         yield from self.stubs.send_rpc_and_wait(self.controller, 'build_profile')
         build_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'build_status.get')
@@ -145,7 +136,7 @@ class HklFlyScan(AsyncFlyScanBase):
         logger.success(f'{self.scan_name} finished')
 
     def _publish_readbacks(self, device, readbacks):
-        metadata = {"async_update": "append", "max_shape": [None, None]}
+        metadata = {"async_update": "append", "num_lines": len(readbacks)}
         msg = messages.DeviceMessage(
             signals={device: {'value': readbacks} }, metadata=metadata
         )

addams_bec/scans/mesh_scan.py

@@ -1,266 +0,0 @@
-import itertools
-
-import numpy
-
-# from bec_lib.endpoints import MessageEndpoints
-from typing import Literal
-from bec_lib import messages
-from bec_lib.endpoints import MessageEndpoints
-from bec_lib.devicemanager import DeviceManagerBase
-from bec_lib.logger import bec_logger
-# from bec_lib import messages
-# from bec_server.scan_server.errors import ScanAbortion
-from bec_server.scan_server.scans import ScanAbortion, ScanArgType, ScanBase, AsyncFlyScanBase
-
-logger = bec_logger.logger
-
-class HklMeshScan(ScanBase):
-    scan_name = 'hklmesh_scan'
-    arg_input = {
-        'index': ScanArgType.DEVICE,
-        'start': ScanArgType.FLOAT,
-        'stop': ScanArgType.FLOAT,
-        'points': ScanArgType.INT
-    }
-    arg_bundle_size = {"bundle": len(arg_input), "min": 2, "max": 2}
-    required_kwargs = ['diffract', 'exp_time']
-
-    def __init__(self, *args,  diffract: str, **kwargs):
-        self.diffract = diffract
-        super().__init__(**kwargs)
-
-        if any(m not in ['h', 'k', 'l'] for m in self.caller_args):
-            raise ValueError("Invalid name. Must be 'h', 'k', or 'l'.")
-        if len(self.caller_args) != 2:
-            raise ValueError("Only 2 names can be given.")
-
-        self.scan_report_devices = ['h', 'k', 'l'] + self.scan_motors + self.readout_priority['monitored']
-
-    def update_scan_motors(self):
-        self.scan_motors = self.device_manager.devices[self.diffract].real_axes.get()
-
-    def prepare_positions(self):
-        """
-        Override base method to yield from _calculate_position method
-        """
-        yield from self._calculate_positions()
-        self._optimize_trajectory()
-        self.num_pos = len(self.positions) * self.burst_at_each_point
-        yield from self._set_position_offset()
-        self._check_limits()
-
-    def _calculate_positions(self):
-        inner_name, outer_name =  [x for x in self.caller_args if x in ['h','k','l']]
-        fixed_name = [x for x in ['h', 'k', 'l'] if x not in self.caller_args][0]
-        fixed_value = yield from self.stubs.send_rpc_and_wait(self.diffract, f'{fixed_name}.position')
-
-        print(f"{inner_name=}, {outer_name=}, {fixed_name=}")
-
-        inner_ind, outer_ind, fixed_ind = (['h', 'k', 'l'].index(x) for x in [inner_name, outer_name, fixed_name])
-
-        hkls = []
-        outer_start, outer_stop, outer_points = self.caller_args[outer_name]
-        inner_start, inner_stop, inner_points = self.caller_args[inner_name]
-
-        outer_vect = numpy.linspace(outer_start, outer_stop, outer_points, dtype=float)
-        for i, outer in enumerate(outer_vect):
-            if i % 2 == 0:
-                inner_vect = numpy.linspace(inner_start, inner_stop, inner_points, dtype=float)
-            else:
-                inner_vect = numpy.linspace(inner_stop, inner_start, inner_points, dtype=float)
-
-            for inner in inner_vect:
-                hkl = [0, 0, 0]
-                hkl[inner_ind] = inner
-                hkl[outer_ind] = outer
-                hkl[fixed_ind] = fixed_value
-                hkls.append(hkl)
-
-        positions = yield from self.stubs.send_rpc_and_wait(self.diffract, 'angles_from_hkls', hkls)
-        # the last two positions 'betaIn' and 'betaOut' are not real motors
-        self.positions = []
-        for position in positions:
-            self.positions.append(position[:-2])
-
-
-class HklMeshFlyScan(AsyncFlyScanBase):
-    scan_name = 'hklmesh_flyscan'
-    scan_type = 'fly'
-    arg_input = {
-        'index': ScanArgType.DEVICE,
-        'start': ScanArgType.FLOAT,
-        'stop': ScanArgType.FLOAT,
-        'points': ScanArgType.INT
-    }
-    arg_bundle_size = {"bundle": len(arg_input), "min": 2, "max": 2}
-    required_kwargs = ['diffract', 'controller']
-    use_scan_progress_report = False
-
-    def __init__(self, *args, diffract: str, controller: str, **kwargs):
-        self.diffract = diffract
-        self.controller = controller
-        super().__init__(**kwargs)
-
-        if any(m not in ['h', 'k', 'l'] for m in self.caller_args):
-            raise ValueError("Invalid name. Must be 'h', 'k', or 'l'.")
-        if len(self.caller_args) != 2:
-            raise ValueError("Only 2 names can be given.")
-
-        self.scan_report_devices = ['h', 'k', 'l'] + self.scan_motors + self.readout_priority['monitored']
-
-    @property
-    def monitor_sync(self):
-        return self.diffract
-
-    def update_scan_motors(self):
-        self.scan_motors = self.device_manager.devices[self.diffract].real_axes.get()
-
-    def update_readout_priority(self):
-        self.readout_priority['async'].extend(['h', 'k', 'l'])
-        self.readout_priority['async'].extend(self.scan_motors)
-
-    def prepare_positions(self):
-        """
-        Override base method to yield from _calculate_position method
-        """
-        yield from self._calculate_positions()
-        self._optimize_trajectory()
-        self.num_pos = len(self.positions) * self.burst_at_each_point
-        yield from self._set_position_offset()
-        self._check_limits()
-
-    def _calculate_positions(self):
-        inner_name, outer_name =  [x for x in self.caller_args if x in ['h','k','l']]
-        fixed_name = [x for x in ['h', 'k', 'l'] if x not in self.caller_args][0]
-        fixed_value = yield from self.stubs.send_rpc_and_wait(self.diffract, f'{fixed_name}.position')
-
-        inner_ind, outer_ind, fixed_ind = (['h', 'k', 'l'].index(x) for x in [inner_name, outer_name, fixed_name])
-
-        hkls = []
-        outer_start, outer_stop, outer_points = self.caller_args[outer_name]
-        inner_start, inner_stop, inner_points = self.caller_args[inner_name]
-
-        outer_vect = numpy.linspace(outer_start, outer_stop, outer_points, dtype=float)
-        for i, outer in enumerate(outer_vect):
-            if i % 2 == 0:
-                inner_vect = numpy.linspace(inner_start, inner_stop, inner_points, dtype=float)
-            else:
-                inner_vect = numpy.linspace(inner_stop, inner_start, inner_points, dtype=float)
-
-            for inner in inner_vect:
-                hkl = [0, 0, 0]
-                hkl[inner_ind] = inner
-                hkl[outer_ind] = outer
-                hkl[fixed_ind] = fixed_value
-                hkls.append(hkl)
-
-        positions = yield from self.stubs.send_rpc_and_wait(self.diffract, 'angles_from_hkls', hkls)
-        # the last two positions 'betaIn' and 'betaOut' are not real motors
-        self.positions = []
-        for position in positions:
-            self.positions.append(position[:-2])
-
-    def scan_core(self):
-        all_motors = self.device_manager.devices[self.controller].axes.get()
-
-        inner_name, outer_name =  [x for x in self.caller_args if x in ['h','k','l']]
-        fixed_name = [x for x in ['h', 'k', 'l'] if x not in self.caller_args][0]
-        fixed_value = yield from self.stubs.send_rpc_and_wait(self.diffract, f'{fixed_name}.position')
-
-        inner_ind, outer_ind, fixed_ind = (['h', 'k', 'l'].index(x) for x in [inner_name, outer_name, fixed_name])
-
-        num_pos = 0
-        hkls = []
-        outer_start, outer_stop, outer_points = self.caller_args[outer_name]
-        inner_start, inner_stop, inner_points = self.caller_args[inner_name]
-
-        outer_vect = numpy.linspace(outer_start, outer_stop, outer_points, dtype=float)
-        for i, outer in enumerate(outer_vect):
-            if i % 2 == 0:
-                start, stop = inner_start, inner_stop
-            else:
-                start, stop = inner_stop, inner_start
-
-            hkls = [[0, 0, 0], [0, 0, 0]]
-            hkls[0][inner_ind] = start
-            hkls[0][outer_ind] = outer
-            hkls[0][fixed_ind] = fixed_value
-
-            hkls[1][inner_ind] = stop
-            hkls[1][outer_ind] = outer
-            hkls[1][fixed_ind] = fixed_value
-
-            positions = yield from self.stubs.send_rpc_and_wait(self.diffract, 'angles_from_hkls', hkls)
-
-            # Move motors to start position, the last two positions 'betaIn' and 'betaOut' are not real motors
-            yield from self.stubs.set(device=self.scan_motors, value=positions[0][:-2])
-
-            inner_time = inner_points * self.exp_time
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'num_points.put', 2)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'num_pulses.put', inner_points)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'start_pulses.put', 1)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'end_pulses.put', 2)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'time_mode.put', 1)
-            print(f"{inner_time=} {inner_points=} {self.exp_time=}")
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'times.put', [inner_time, inner_time])
-
-            for axis_name in all_motors:
-                if axis_name not in self.scan_motors:
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 0)
-                else:
-                    index = self.scan_motors.index(axis_name)
-                    yield from self.stubs.send_rpc_and_wait(self.controller,
-                                                            f'{axis_name}.positions.put',
-                                                            (positions[0][index], positions[-1][index]))
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
-
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'build_profile')
-            build_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'build_status.get')
-            if build_status != 1:
-                raise ScanAbortion('Profile build failed')
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_profile')
-            execute_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_status.get')
-            if  execute_status != 1:
-                raise ScanAbortion('Profile execute failed')
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'readback_profile')
-            readback_status = yield from self.stubs.send_rpc_and_wait(self.controller,'readback_status.get')
-            if readback_status != 1:
-                raise ScanAbortion('Profile readback failed')
-
-            angle_readbacks = []
-            for index, axis_name in enumerate(self.scan_motors):
-                readbacks = yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.readbacks.get')
-                self._publish_readbacks(axis_name, readbacks)
-                angle_readbacks.append(readbacks)
-            # motor readbacks are aranged column-wise
-            angle_readbacks = [list(x) for x in zip(*angle_readbacks)]
-
-            hkls = yield from self.stubs.send_rpc_and_wait(self.diffract, 'hkls_from_angles', angle_readbacks)
-            hkls = numpy.array(hkls)
-
-            for index, name in enumerate(['h', 'k', 'l', 'betaIn', 'betaOut']):
-                self._publish_readbacks(name, hkls[:, index])
-
-            # motor readbacks have more points than generated pulses
-            num_pos += len(angle_readbacks)
-
-        self.num_pos = num_pos
-        logger.success(f'{self.scan_name} finished')
-
-    def _publish_readbacks(self, device, readbacks):
-        metadata = {"async_update": "append", "max_shape": [None, None]}
-        msg = messages.DeviceMessage(
-            signals={device: {'value': readbacks} }, metadata=metadata
-        )
-
-        self.stubs.connector.xadd(
-            topic=MessageEndpoints.device_async_readback(
-                scan_id=self.scan_id, device=device
-            ),
-            msg_dict={"data": msg},
-            expire=1800,
-        )

addams_bec/scans/metadata_schema/metadata_schema_registry.py

@@ -0,0 +1,12 @@
+# from .metadata_schema_template import ExampleSchema
+
+METADATA_SCHEMA_REGISTRY = {
+    # Add models which should be used to validate scan metadata here.
+    # Make a model according to the template, and import it as above
+    # Then associate it with a scan like so:
+    # "example_scan": ExampleSchema
+}
+
+# Define a default schema type which should be used as the fallback for everything:
+
+DEFAULT_SCHEMA = None

addams_bec/scans/metadata_schema/metadata_schema_template.py

@@ -0,0 +1,34 @@
+# # By inheriting from BasicScanMetadata you can define a schema by which metadata
+# # supplied to a scan must be validated.
+# # This schema is a Pydantic model: https://docs.pydantic.dev/latest/concepts/models/
+# # but by default it will still allow you to add any arbitrary information to it.
+# # That is to say, when you run a scan with which such a model has been associated in the
+# # metadata_schema_registry, you can supply any python dictionary with strings as keys
+# # and built-in python types (strings, integers, floats) as values, and these will be
+# # added to the experiment metadata, but it *must* contain the keys and values of the
+# # types defined in the schema class.
+# #
+# #
+# # For example, say that you would like to enforce recording information about sample
+# # pretreatment, you could define the following:
+# #
+#
+# from bec_lib.metadata_schema import BasicScanMetadata
+#
+#
+# class ExampleSchema(BasicScanMetadata):
+#    treatment_description: str
+#    treatment_temperature_k: int
+#
+#
+# # If this was used according to the example in metadata_schema_registry.py,
+# # then when calling the scan, the user would need to write something like:
+# >>> scans.example_scan(
+# >>>     motor,
+# >>>     1,
+# >>>     2,
+# >>>     3,
+# >>>     metadata={"treatment_description": "oven overnight", "treatment_temperature_k": 575},
+# >>> )
+#
+# # And the additional metadata would be saved in the HDF5 file created for the scan.

addams_bec/scans/profilemove_scan.py

@@ -1,233 +0,0 @@
-import numpy
-
-from bec_lib import messages
-from bec_lib.endpoints import MessageEndpoints
-from bec_lib.devicemanager import DeviceManagerBase
-from bec_lib.logger import bec_logger
-from bec_server.scan_server.scans import ScanAbortion, ScanArgType, ScanBase, AsyncFlyScanBase
-
-logger = bec_logger.logger
-
-class LineProfileMove(AsyncFlyScanBase):
-    scan_name = 'line_profilemove'
-    scan_type = 'fly'
-    arg_input = {
-        'motor': ScanArgType.DEVICE,
-        'start': ScanArgType.FLOAT,
-        'stop': ScanArgType.FLOAT,
-    }
-    arg_bundle_size = {"bundle": len(arg_input), "min": 1, "max": None}
-    required_kwargs = ['controller', 'points']
-    use_scan_progress_report = False
-
-    def __init__(self, *args,  controller: str, points: int, **kwargs):
-        self.controller = controller
-        self.points = self.num_pos = points
-        super().__init__(**kwargs)
-
-        self.all_motors = self.device_manager.devices[self.controller].axes.get()
-        if not all(m in self.all_motors for m in self.scan_motors):
-            raise ValueError(f"Scan motors {self.scan_motors} not in {self.all_motors}")
-
-    def update_readout_priority(self):
-        self.readout_priority['async'].extend(self.scan_motors)
-
-    def update_scan_motors(self):
-        ScanBase.update_scan_motors(self)
-
-    def prepare_positions(self):
-        """prepare the positions for the scan"""
-        self._calculate_positions()
-        self._optimize_trajectory()
-        self.num_pos = len(self.positions) * self.burst_at_each_point
-        yield from self._set_position_offset()
-        self._check_limits()
-
-    def _calculate_positions(self):
-        axis = []
-        for _, val in self.caller_args.items():
-            ax_pos = numpy.linspace(val[0], val[1], self.points, dtype=float)
-            axis.append(ax_pos)
-        self.positions = numpy.array(list(zip(*axis)), dtype=float)
-
-    def scan_core(self):
-
-        total_time = self.exp_time * self.points
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'num_points.put', 2)
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'num_pulses.put', self.points)
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'start_pulses.put', 1)
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'end_pulses.put', 2)
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'time_mode.put', 1)
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'times.put', [total_time, total_time])
-
-        for axis_name in self.all_motors:
-            if axis_name not in self.scan_motors:
-                yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 0)
-            else:
-                index = self.scan_motors.index(axis_name)
-                yield from self.stubs.send_rpc_and_wait(self.controller,
-                                                        f'{axis_name}.positions.put',
-                                                        (self.caller_args[axis_name][0], self.caller_args[axis_name][1]))
-                yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
-
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'build_profile')
-        build_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'build_status.get')
-        if build_status != 1:
-            raise ScanAbortion('Profile build failed')
-
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_profile')
-        execute_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_status.get')
-        if  execute_status != 1:
-            raise ScanAbortion('Profile execute failed')
-
-        yield from self.stubs.send_rpc_and_wait(self.controller, 'readback_profile')
-        readback_status = yield from self.stubs.send_rpc_and_wait(self.controller,'readback_status.get')
-        if readback_status != 1:
-            raise ScanAbortion('Profile readback failed')
-
-        for index, axis_name in enumerate(self.scan_motors):
-            readbacks = yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.readbacks.get')
-            self._publish_readbacks(axis_name, readbacks)
-
-        logger.success(f'{self.scan_name} finished')
-
-    def _publish_readbacks(self, device, readbacks):
-        metadata = {"async_update": "append", "max_shape": [None, None]}
-        msg = messages.DeviceMessage(
-            signals={device: {'value': readbacks} }, metadata=metadata
-        )
-
-        self.stubs.connector.xadd(
-            topic=MessageEndpoints.device_async_readback(
-                scan_id=self.scan_id, device=device
-            ),
-            msg_dict={"data": msg},
-            expire=1800,
-        )
-
-
-class GridProfileMove(AsyncFlyScanBase):
-    scan_name = 'grid_profilemove'
-    scan_type = 'fly'
-    arg_input = {
-        'motor': ScanArgType.DEVICE,
-        'start': ScanArgType.FLOAT,
-        'stop': ScanArgType.FLOAT,
-        'points': ScanArgType.INT,
-    }
-    arg_bundle_size = {"bundle": len(arg_input), "min": 2, "max": 2}
-    required_kwargs = ['controller']
-    use_scan_progress_report = False
-
-    def __init__(self, *args,  controller: str, **kwargs):
-        self.controller = controller
-        super().__init__(**kwargs)
-
-        self.all_motors = self.device_manager.devices[self.controller].axes.get()
-        if not all(m in self.all_motors for m in self.scan_motors):
-            raise ValueError(f"Scan motors {self.scan_motors} not in {self.all_motors}")
-
-    def update_readout_priority(self):
-        self.readout_priority['async'].extend(self.scan_motors)
-
-    def update_scan_motors(self):
-        ScanBase.update_scan_motors(self)
-
-    def prepare_positions(self):
-        """prepare the positions for the scan"""
-        self._calculate_positions()
-        self._optimize_trajectory()
-        self.num_pos = len(self.positions) * self.burst_at_each_point
-        yield from self._set_position_offset()
-        self._check_limits()
-
-    def _calculate_positions(self):
-        inner_motor, outer_motor =  self.scan_motors
-        outer_start, outer_stop, outer_points = self.caller_args[outer_motor]
-        inner_start, inner_stop, inner_points = self.caller_args[inner_motor]
-
-        self.positions = []
-        outer_vect = numpy.linspace(outer_start, outer_stop, outer_points, dtype=float)
-        for i, outer in enumerate(outer_vect):
-            if i % 2 == 0:
-                inner_vect = numpy.linspace(inner_start, inner_stop, inner_points, dtype=float)
-            else:
-                inner_vect = numpy.linspace(inner_stop, inner_start, inner_points, dtype=float)
-
-            for inner in inner_vect:
-                self.positions.append((inner, outer))
-
-    def scan_core(self):
-        inner_motor, outer_motor =  self.scan_motors
-        outer_start, outer_stop, outer_points = self.caller_args[outer_motor]
-        inner_start, inner_stop, inner_points = self.caller_args[inner_motor]
-        
-        num_pos = 0
-        outer_vect = numpy.linspace(outer_start, outer_stop, outer_points, dtype=float)
-        for i, outer in enumerate(outer_vect):
-            if i % 2 == 0:
-                start, stop = inner_start, inner_stop
-            else:
-                start, stop = inner_stop, inner_start
-
-            # Move outer motor to start position
-            yield from self.stubs.set(device=outer_motor, value=outer)
-            outer_readback = yield from self.stubs.send_rpc_and_wait(outer_motor, "position")
-
-            inner_time = self.exp_time * inner_points
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'num_points.put', 2)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'num_pulses.put', inner_points)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'start_pulses.put', 1)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'end_pulses.put', 2)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'time_mode.put', 1)
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'times.put', [inner_time, inner_time])
-
-            for axis_name in self.all_motors:
-                if axis_name == inner_motor:
-                    yield from self.stubs.send_rpc_and_wait(self.controller,
-                                                            f'{axis_name}.positions.put',
-                                                            (start, stop))
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 1)
-                else:
-                    yield from self.stubs.send_rpc_and_wait(self.controller, f'{axis_name}.use_axis.put', 0)
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'build_profile')
-            build_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'build_status.get')
-            if build_status != 1:
-                raise ScanAbortion('Profile build failed')
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_profile')
-            execute_status = yield from self.stubs.send_rpc_and_wait(self.controller, 'execute_status.get')
-            if  execute_status != 1:
-                raise ScanAbortion('Profile execute failed')
-
-            yield from self.stubs.send_rpc_and_wait(self.controller, 'readback_profile')
-            readback_status = yield from self.stubs.send_rpc_and_wait(self.controller,'readback_status.get')
-            if readback_status != 1:
-                raise ScanAbortion('Profile readback failed')
-
-            readbacks = yield from self.stubs.send_rpc_and_wait(self.controller, f'{inner_motor}.readbacks.get')
-            self._publish_readbacks(inner_motor, readbacks)
-
-            readbacks = [outer_readback] * len(readbacks)
-            self._publish_readbacks(outer_motor, readbacks)
-
-            # motor readbacks have more points than generated pulses
-            num_pos += len(readbacks)
-
-        self.num_pos = num_pos
-        logger.success(f'{self.scan_name} finished')
-
-    def _publish_readbacks(self, device, readbacks):
-        metadata = {"async_update": "append", "max_shape": [None]}
-        msg = messages.DeviceMessage(
-            signals={device: {'value': readbacks} }, metadata=metadata
-        )
-
-        self.stubs.connector.xadd(
-            topic=MessageEndpoints.device_async_readback(
-                scan_id=self.scan_id, device=device
-            ),
-            msg_dict={"data": msg},
-            expire=1800,
-        )

bin/.gitignore

@@ -0,0 +1 @@
+# Add anything you don't want to check in to git, e.g. very large files

pyproject.toml

@@ -5,8 +5,8 @@ build-backend = "hatchling.build"
 [project]
 name = "addams_bec"
 version = "0.0.0"
-description = "Custom device implementations based on the ophyd hardware abstraction layer"
-requires-python = ">=3.10"
+description = "A plugin repository for BEC"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
@@ -17,6 +17,7 @@ dependencies = []
 [project.optional-dependencies]
 dev = [
     "black",
+    "copier",
     "isort",
     "coverage",
     "pylint",
@@ -38,12 +39,15 @@ plugin_file_writer = "addams_bec.file_writer"
 [project.entry-points."bec.scans"]
 plugin_scans = "addams_bec.scans"
 
+[project.entry-points."bec.scans.metadata_schema"]
+plugin_metadata_schema = "addams_bec.scans.metadata_schema"
+
 [project.entry-points."bec.ipython_client_startup"]
 plugin_ipython_client_pre = "addams_bec.bec_ipython_client.startup.pre_startup"
 plugin_ipython_client_post = "addams_bec.bec_ipython_client.startup"
 
 [project.entry-points."bec.widgets.auto_updates"]
-plugin_widgets_update = "addams_bec.bec_widgets.auto_updates:PlotUpdate"
+plugin_widgets_update = "addams_bec.bec_widgets.auto_updates"
 
 [project.entry-points."bec.widgets.user_widgets"]
 plugin_widgets = "addams_bec.bec_widgets.widgets"

tests/tests_bec_ipython_client/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-

tests/tests_bec_ipython_client/test_energy_optimizer.py

@@ -0,0 +1,38 @@
+from unittest import mock
+
+import pytest
+
+from addams_bec.bec_ipython_client.plugins.energy_optimizer.addams_energy_optimizer import (
+    EnergyOptimizer,
+)
+
+
+@pytest.fixture
+def optimizer():
+    dm = mock.MagicMock()
+    yield EnergyOptimizer(dm)
+
+
+@pytest.mark.parametrize(
+    "start_energy, target_energy, expected",
+    [
+        (5, 10, [(10, "Si")]),
+        (5, 20, [(9, "Rh"), (20, "Rh")]),
+        (5, 40, [(9, "Rh"), (22, "Pt"), (40, "Pt")]),
+        (5, 5, [(5, "Si")]),
+        (5, 4, ValueError),
+        (5, 41, ValueError),
+        (2, 8, ValueError),
+        (18, 40, [(22, "Pt"), (40, "Pt")]),
+        (18, 5, [(9, "Si"), (5, "Si")]),
+        (18, 10, [(10, "Rh")]),
+        (18, 20, [(20, "Rh")]),
+        (25, 7, [(22, "Rh"), (9, "Si"), (7, "Si")]),
+    ],
+)
+def test_get_transition_steps(optimizer, start_energy, target_energy, expected):
+    if expected == ValueError:
+        with pytest.raises(ValueError):
+            optimizer.get_transition_steps(start_energy, target_energy)
+    else:
+        assert optimizer.get_transition_steps(start_energy, target_energy) == expected

tests/tests_bec_widgets/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-

tests/tests_dap_services/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-

tests/tests_devices/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-

tests/tests_file_writer/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-

tests/tests_scans/README.md

@@ -1,31 +1,34 @@
 # Getting Started with Testing using pytest
 
-BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework. 
-It can be install via 
-``` bash
+BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
+It can be installed via
+
+```bash
 pip install pytest
 ```
-in your *python environment*. 
+
+in your _python environment_.
 We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
 
 ## Introduction
 
 Tests in this package should be stored in the `tests` directory.
 We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
+It is mandatory for test files to begin with `test_` for pytest to discover them.
 
-To run all tests, navigate to the directory of the plugin from the command line, and run the command 
+To run all tests, navigate to the directory of the plugin from the command line, and run the command
 
-``` bash
+```bash
 pytest -v --random-order ./tests
 ```
+
 Note, the python environment needs to be active.
 The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
-The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines. 
+The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
 
 ## Test examples
 
-Writing tests can be quite specific for the given function. 
+Writing tests can be quite specific for the given function.
 We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
 A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
 In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).
-