pynxtools-spm 0.2.2__tar.gz → 0.2.4__tar.gz

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynxtools-spm
-Version: 0.2.2
+Version: 0.2.4
 Summary: pynxtools-spm: A pynxtools plugin for SPM (Scanning Probe Microscopy) data readers
 Author: The NOMAD Authors
 License: 
@@ -217,7 +217,7 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pynxtools>=0.12.0
+Requires-Dist: pynxtools>=0.13.0
 Requires-Dist: findiff>=0.11.1
 Requires-Dist: matplotlib
 Requires-Dist: scipy
@@ -239,16 +239,42 @@ Requires-Dist: mkdocs-simple-hooks; extra == "docs"
 Dynamic: license-file
 
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-[![DOI](https://zenodo.org/badge/890885270.svg)](https://zenodo.org/badge/latestdoi/890885270)
 ![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/pytest.yml/badge.svg)
 ![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/pylint.yml/badge.svg)
 ![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/publish.yml/badge.svg)
 ![](https://img.shields.io/pypi/pyversions/pynxtools-spm)
 ![](https://img.shields.io/pypi/l/pynxtools-spm)
 ![](https://img.shields.io/pypi/v/pynxtools-spm)
-![](https://coveralls.io/repos/github/FAIRmat-NFDI/pynxtools_spm/badge.svg?branch=master)
+![](https://coveralls.io/repos/github/FAIRmat-NFDI/pynxtools-spm/badge.svg?branch=main)
+[![DOI](https://zenodo.org/badge/759916501.svg)](https://doi.org/10.5281/zenodo.17390485)
 
- # SPM Reader
- See full documentation at [https://fairmat-nfdi.github.io/pynxtools-spm/](https://fairmat-nfdi.github.io/pynxtools-spm/).
+# `pynxtools-spm`: A `pynxtools` reader for SPM data
 
- **Note**: This repository is an upgraded and renamed version of [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm), which is now archived. In addition to the integration of new readers (e.g., `AFM`), all functionalities of `pynxtools-stm` remain available in this repository.
+.
+
+This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/`pynxtools-plugin-template) template.
+
+## Installation
+
+It is recommended to use python 3.12 with a dedicated virtual environment for this package.
+Learn how to manage [python versions](https://github.com/pyenv/pyenv) and
+[virtual environments](https://realpython.com/python-virtual-environments-a-primer/).
+
+This package is a reader plugin for [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools) and can be installed together with `pynxtools`:
+
+```shell
+uv pip install pynxtools[spm]
+```
+
+for the latest released version.
+
+## Docs
+
+More information about this pynxtools plugin is available in the [documentation](https://fairmat-nfdi.github.io/pynxtools-spm/). You will find information about getting started, how-to guides, the supported file formats, how to get involved, and much more there.
+
+## Contact person in FAIRmat for this reader
+
+Rubel Mozumder
+
+
+**Note**: This repository is an upgraded and renamed version of [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm), which is now archived. In addition to the integration of new readers (e.g., `AFM`), all functionalities of `pynxtools-stm` remain available in this repository.

pynxtools_spm-0.2.4/README.md

@@ -0,0 +1,40 @@
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/pytest.yml/badge.svg)
+![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/pylint.yml/badge.svg)
+![](https://github.com/FAIRmat-NFDI/pynxtools-spm/actions/workflows/publish.yml/badge.svg)
+![](https://img.shields.io/pypi/pyversions/pynxtools-spm)
+![](https://img.shields.io/pypi/l/pynxtools-spm)
+![](https://img.shields.io/pypi/v/pynxtools-spm)
+![](https://coveralls.io/repos/github/FAIRmat-NFDI/pynxtools-spm/badge.svg?branch=main)
+[![DOI](https://zenodo.org/badge/759916501.svg)](https://doi.org/10.5281/zenodo.17390485)
+
+# `pynxtools-spm`: A `pynxtools` reader for SPM data
+
+.
+
+This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/`pynxtools-plugin-template) template.
+
+## Installation
+
+It is recommended to use python 3.12 with a dedicated virtual environment for this package.
+Learn how to manage [python versions](https://github.com/pyenv/pyenv) and
+[virtual environments](https://realpython.com/python-virtual-environments-a-primer/).
+
+This package is a reader plugin for [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools) and can be installed together with `pynxtools`:
+
+```shell
+uv pip install pynxtools[spm]
+```
+
+for the latest released version.
+
+## Docs
+
+More information about this pynxtools plugin is available in the [documentation](https://fairmat-nfdi.github.io/pynxtools-spm/). You will find information about getting started, how-to guides, the supported file formats, how to get involved, and much more there.
+
+## Contact person in FAIRmat for this reader
+
+Rubel Mozumder
+
+
+**Note**: This repository is an upgraded and renamed version of [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm), which is now archived. In addition to the integration of new readers (e.g., `AFM`), all functionalities of `pynxtools-stm` remain available in this repository.

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/pyproject.toml

@@ -21,7 +21,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "pynxtools>=0.12.0",
+    "pynxtools>=0.13.0",
     "findiff>=0.11.1",
     # "pySPM==0.6.2",  # SPM file reader for Bruker files use it when you have Bruker files
     "matplotlib",
@@ -59,7 +59,7 @@ spm = "pynxtools_spm.reader:SPMReader"
 sts_example = "pynxtools_spm.nomad.entrypoints:sts_example"
 stm_example = "pynxtools_spm.nomad.entrypoints:stm_example"
 afm_example = "pynxtools_spm.nomad.entrypoints:afm_example"
-spm_app = "pynxtools_spm.app:spm_app"
+spm_app = "pynxtools_spm.nomad.apps:spm_app"
 
 
 [tool.setuptools.packages.find]

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/configs/__init__.py

@@ -52,5 +52,5 @@ def load_default_config(config_type):
     elif config_type == "omicron_sm4_stm":
         config_file = omicron_sm4_stm
     if config_file is not None:
-        with open(config_file, "r", encoding="utf-8") as f:
+        with open(config_file, encoding="utf-8") as f:
             return json.load(f)

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/configs/nanonis/nanonis_sxm_generic_afm.json

@@ -365,7 +365,7 @@
             "DATA[scan_data]": [
               {
                 "data": {
-                  "name": "imput_4",
+                  "name": "input_4",
                   "raw_path": "/Input_4/forward",
                   "@units": "/DATA/INFO/Input_4/Unit"
                 },
@@ -376,7 +376,7 @@
               },
               {
                 "data": {
-                  "name": "imput_4",
+                  "name": "input_4",
                   "raw_path": "/Input_4/backward",
                   "@units": "/DATA/INFO/Input_4/Unit"
                 },
@@ -525,7 +525,7 @@
           "@units": "/DATA/INFO/Z/Unit"
         },
         "title": {
-          "raw_path": "@default:Height Plot of AFM Experiment (Foward Direction)"
+          "raw_path": "@default:Height Plot of AFM Experiment (Forward Direction)"
         },
         "grp_name": "z_forward"
       },

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/configs/nanonis/nanonis_sxm_generic_stm.json

@@ -578,7 +578,7 @@
           "@units": "@default:m"
         },
         "title": {
-          "raw_path": "@default:Height Plot of STM Experiment (Foward Direction)"
+          "raw_path": "@default:Height Plot of STM Experiment (Forward Direction)"
         },
         "grp_name": "z_forward"
       },
@@ -600,7 +600,7 @@
           "@units": "@default:A"
         },
         "title": {
-          "raw_path": "@default:Current Plot of STM Experiment (Foward Direction)"
+          "raw_path": "@default:Current Plot of STM Experiment (Forward Direction)"
         },
         "grp_name": "current_forward"
       },

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/configs/omicron/omicron_sm4_stm.json

@@ -524,7 +524,7 @@
           "@units": "/Topography_Forward/RHK_Y/@unit"
         },
         "title": {
-          "raw_path": "@default:Topography Plot of STM Experiment (Foward Direction)"
+          "raw_path": "@default:Topography Plot of STM Experiment (Forward Direction)"
         },
         "grp_name": "z_forward"
       },

pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/README.md

@@ -0,0 +1,3 @@
+# NOMAD integration
+
+This module is for integrating pynxtools-spm into [NOMAD](https://nomad-lab.eu/) as a plugin.

{pynxtools_spm-0.2.2/src/pynxtools_spm/app → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/apps}/__init__.py

@@ -99,9 +99,9 @@ map_concept_to_full_quantities = {
     "Reference Phase (Oscillator)": f"data.ENTRY.INSTRUMENT.SPM_CANTILEVER.cantilever_oscillator.reference_phase__field#{schema}#float",
 }
 
-spm_app = AppEntryPoint(
+spm_app: AppEntryPoint = AppEntryPoint(
     name="SpmApp",
-    description="A Generic NOMAD App for SPM Experimetal Technique.",
+    description="A Generic NOMAD App for SPM Experiment Technique.",
     app=App(
         # Label of the App
         label="SPM",

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/nomad/entrypoints.py

@@ -25,7 +25,7 @@ sts_example = ExampleUploadEntryPoint(
     category="NeXus Experiment Examples",
     description="""This example presents the capabilities of the NOMAD platform to store standardized Scanning Tunneling Spectroscopy (sts) data.""",
     plugin_package="pynxtools_spm",
-    resources=["nomad/examples/sts/STSExampleWithCustomization/*"],
+    resources=["nomad/example_uploads/sts/STSExampleWithCustomization/*"],
 )
 
 
@@ -34,7 +34,7 @@ stm_example = ExampleUploadEntryPoint(
     category="NeXus Experiment Examples",
     description="""This example presents the capabilities of the NOMAD platform to store standardized Scanning Tunneling Microscopy (stm) data""",
     plugin_package="pynxtools_spm",
-    resources=["nomad/examples/stm/STMExampleWithCustomization/*"],
+    resources=["nomad/example_uploads/stm/STMExampleWithCustomization/*"],
 )
 
 
@@ -43,5 +43,5 @@ afm_example = ExampleUploadEntryPoint(
     category="NeXus Experiment Examples",
     description="""This example presents the capabilities of the NOMAD platform to store standardized Atomic Force Microscopy (afm) data""",
     plugin_package="pynxtools_spm",
-    resources=["nomad/examples/afm/AFMExampleWithCustomization/*"],
+    resources=["nomad/example_uploads/afm/AFMExampleWithCustomization/*"],
 )

{pynxtools_spm-0.2.2/src/pynxtools_spm/nomad/examples → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/example_uploads}/afm/AFMExampleWithCustomization/afm.scheme.archive.yaml

@@ -5,7 +5,7 @@ definitions:
   sections:
     ELN_for_AFM:
       base_sections:
-        - pynxtools.nomad.dataconverter.NexusDataConverter
+        - pynxtools.nomad.schema_packages.dataconverter.NexusDataConverter
         - nomad.datamodel.data.EntryData
       m_annotations:
         template:
@@ -155,7 +155,7 @@ definitions:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               software:
                 section:
                   m_annotations:
@@ -183,14 +183,14 @@ definitions:
                           component: StringEditQuantity
                       description: |
                         Version or model of the component named by the manufacturer (e.g. Generic 4).
-                        Note that this should be exacty the same as in experiment file.
+                        Note that this should be exactly the same as in experiment file.
                     model_version:
                       type: str
                       m_annotations:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               height_piezo_sensor:
                 section:
                   m_annotations:

{pynxtools_spm-0.2.2/src/pynxtools_spm/nomad/examples → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/example_uploads}/afm/AFMExampleWithCustomization/config.json

@@ -368,7 +368,7 @@
             "DATA[scan_data]": [
               {
                 "data": {
-                  "name": "imput_4",
+                  "name": "input_4",
                   "raw_path": "/Input_4/forward",
                   "@units": "/DATA/INFO/Input_4/Unit"
                 },
@@ -379,7 +379,7 @@
               },
               {
                 "data": {
-                  "name": "imput_4",
+                  "name": "input_4",
                   "raw_path": "/Input_4/backward",
                   "@units": "/DATA/INFO/Input_4/Unit"
                 },
@@ -528,7 +528,7 @@
           "@units": "/DATA/INFO/Z/Unit"
         },
         "title": {
-          "raw_path": "@default:Height Plot of AFM Experiment (Foward Direction)"
+          "raw_path": "@default:Height Plot of AFM Experiment (Forward Direction)"
         },
         "grp_name": "z_forward"
       },

{pynxtools_spm-0.2.2/src/pynxtools_spm/nomad/examples → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/example_uploads}/stm/STMExampleWithCustomization/config.json

@@ -578,7 +578,7 @@
           "@units": "@default:m"
         },
         "title": {
-          "raw_path": "@default:Height Plot of STM Experiment (Foward Direction)"
+          "raw_path": "@default:Height Plot of STM Experiment (Forward Direction)"
         },
         "grp_name": "z_forward"
       },
@@ -600,7 +600,7 @@
           "@units": "@default:A"
         },
         "title": {
-          "raw_path": "@default:Current Plot of STM Experiment (Foward Direction)"
+          "raw_path": "@default:Current Plot of STM Experiment (Forward Direction)"
         },
         "grp_name": "current_forward"
       },

{pynxtools_spm-0.2.2/src/pynxtools_spm/nomad/examples → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/example_uploads}/stm/STMExampleWithCustomization/stm.scheme.archive.yaml

@@ -5,7 +5,7 @@ definitions:
   sections:
     ELN_for_STM:
       base_sections:
-        - pynxtools.nomad.dataconverter.NexusDataConverter
+        - pynxtools.nomad.schema_packages.dataconverter.NexusDataConverter
         - nomad.datamodel.data.EntryData
       m_annotations:
         template:
@@ -151,7 +151,7 @@ definitions:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               software:
                 section:
                   m_annotations:
@@ -187,7 +187,7 @@ definitions:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               height_piezo_sensor:
                 section:
                   m_annotations:

{pynxtools_spm-0.2.2/src/pynxtools_spm/nomad/examples → pynxtools_spm-0.2.4/src/pynxtools_spm/nomad/example_uploads}/sts/STSExampleWithCustomization/sts.scheme.archive.yaml

@@ -5,7 +5,7 @@ definitions:
   sections:
     ELN_for_STS:
       base_sections:
-        - pynxtools.nomad.dataconverter.NexusDataConverter
+        - pynxtools.nomad.schema_packages.dataconverter.NexusDataConverter
         - nomad.datamodel.data.EntryData
       m_annotations:
         template:
@@ -139,7 +139,7 @@ definitions:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               software:
                 section:
                   m_annotations:
@@ -175,7 +175,7 @@ definitions:
                         eln:
                           component: StringEditQuantity
                       description: |
-                        If model has a distinquishable version (e.g. BP5e).
+                        If model has a distinguishable version (e.g. BP5e).
               lockin_amplifier:
                 section:
                   m_annotations:

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/nomad/nomad_example_paths.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-List of path for nomad exmaples to run test in nomad.
+List of path for nomad examples to run test in nomad.
 """
 # -*- coding: utf-8 -*-
 #
@@ -25,22 +25,22 @@ import os
 
 
 STS_DEFAULT_CONF_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "sts", "STSDefaultExample"
+    os.path.dirname(__file__), "example_uploads", "sts", "STSDefaultExample"
 )
 STS_CUSTOMIZED_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "sts", "STSExampleWithCustomization"
+    os.path.dirname(__file__), "example_uploads", "sts", "STSExampleWithCustomization"
 )
 
 STM_DEFAULT_CONF_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "stm", "STMDefaultExample"
+    os.path.dirname(__file__), "example_uploads", "stm", "STMDefaultExample"
 )
 STM_CUSTOMIZED_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "stm", "STMExampleWithCustomization"
+    os.path.dirname(__file__), "example_uploads", "stm", "STMExampleWithCustomization"
 )
 
 AFM_DEFAULT_CONF_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "afm", "AFMDefaultExample"
+    os.path.dirname(__file__), "example_uploads", "afm", "AFMDefaultExample"
 )
 AFM_CUSTOMIZED_EXAMPLE_PATH = os.path.join(
-    os.path.dirname(__file__), "examples", "afm", "AFMExampleWithCustomization"
+    os.path.dirname(__file__), "example_uploads", "afm", "AFMExampleWithCustomization"
 )

{pynxtools_spm-0.2.2/src/pynxtools_spm/nxformatters/nanonis → pynxtools_spm-0.2.4/src/pynxtools_spm/nxformatters}/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Copyright The NOMAD Authors.
 #

{pynxtools_spm-0.2.2 → pynxtools_spm-0.2.4}/src/pynxtools_spm/nxformatters/base_formatter.py

@@ -27,7 +27,8 @@ import re
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Union
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
+from collections.abc import Callable
 
 import numpy as np
 import yaml
@@ -47,7 +48,7 @@ if TYPE_CHECKING:
     from pint import Quantity
 
 
-REPLACE_NESTED: Dict[str, str] = {}
+REPLACE_NESTED: dict[str, str] = {}
 
 CONVERT_DICT = {
     "Positioner_spm": "POSITIONER_SPM[positioner_spm]",
@@ -83,14 +84,14 @@ REPEATEABLE_CONCEPTS = ("Sample_component",)
 
 @dataclass
 class NXdata:
-    grp_name: Optional[str] = ""
-    signal: Optional[str] = None
-    auxiliary_signals: Optional[List[str]] = None
-    title: Optional[str] = None
+    grp_name: str | None = ""
+    signal: str | None = None
+    auxiliary_signals: list[str] | None = None
+    title: str | None = None
 
 
 def write_multiple_concepts_instance(
-    eln_dict: Dict, list_of_concept: tuple[str], convert_mapping: Dict[str, str]
+    eln_dict: dict, list_of_concept: tuple[str], convert_mapping: dict[str, str]
 ):
     """Write multiple concepts for variadic name in eln dict if there are multiple
     instances are requested in eln archive.json file.
@@ -133,22 +134,22 @@ class SPMformatter(ABC):
         # Put the class in the base_formatter.py under BaseFormatter class
         x_points: int
         y_points: int
-        x_offset: Union[int, float]
-        x_offset_unit: Union[str, "Quantity"]
-        y_offset: Union[int, float]
-        y_offset_unit: Union[str, "Quantity"]
-        x_start: Union[int, float]
-        x_start_unit: Union[str, "Quantity"]
-        y_start: Union[int, float]
-        y_start_unit: Union[str, "Quantity"]
-        x_range: Union[int, float]
-        x_range_unit: Union[str, "Quantity"]
-        y_range: Union[int, float]
-        y_range_unit: Union[str, "Quantity"]
-        x_end: Union[int, float]
-        x_end_unit: Union[str, "Quantity"]
-        y_end: Union[int, float]
-        y_end_unit: Union[str, "Quantity"]
+        x_offset: int | float
+        x_offset_unit: str | Quantity
+        y_offset: int | float
+        y_offset_unit: str | Quantity
+        x_start: int | float
+        x_start_unit: str | Quantity
+        y_start: int | float
+        y_start_unit: str | Quantity
+        x_range: int | float
+        x_range_unit: str | Quantity
+        y_range: int | float
+        y_range_unit: str | Quantity
+        x_end: int | float
+        x_end_unit: str | Quantity
+        y_end: int | float
+        y_end_unit: str | Quantity
         fast_axis: str  # lower case x, y
         slow_axis: str  # lower case x, y
 
@@ -171,17 +172,15 @@ class SPMformatter(ABC):
     def __init__(
         self,
         template: Template,
-        raw_file: Union[str, "Path"],
+        raw_file: str | Path,
         eln_file: str | Path,
-        config_file: Optional[
-            Union[str, Path]
-        ] = None,  # Incase it is not provided by users
-        entry: Optional[str] = None,
+        config_file: None | (str | Path) = None,  # In case it is not provided by users
+        entry: str | None = None,
     ):
         self.template: Template = template
-        self.raw_file: Union[str, "Path"] = raw_file
+        self.raw_file: str | Path = raw_file
         self.eln = self._get_eln_dict(eln_file)  # Placeholder
-        self.raw_data: Dict = self.get_raw_data_dict()
+        self.raw_data: dict = self.get_raw_data_dict()
         self.entry: str = entry
         self.config_dict = self._get_conf_dict(config_file) or None  # Placeholder
 
@@ -189,7 +188,7 @@ class SPMformatter(ABC):
     def _get_conf_dict(self, config_file: str | Path = None): ...
 
     def _get_eln_dict(self, eln_file: str | Path):
-        with open(eln_file, mode="r", encoding="utf-8") as fl_obj:
+        with open(eln_file, encoding="utf-8") as fl_obj:
             eln_dict: dict = yaml.safe_load(fl_obj)
             extended_eln: dict = write_multiple_concepts_instance(
                 eln_dict=eln_dict,
@@ -203,14 +202,14 @@ class SPMformatter(ABC):
 
     def walk_though_config_nested_dict(
         self,
-        config_dict: Dict,
+        config_dict: dict,
         parent_path: str,
         use_custom_func_prior: bool = True,
-        func_on_raw_key: Optional[Callable] = None,
+        func_on_raw_key: Callable | None = None,
     ):
         # This concept is just note where the group will be
         # handeld name of the function regestered in the self._grp_to_func
-        # or somthing like that.
+        # or something like that.
         if "#note" in config_dict:
             return
         for key, val in config_dict.items():
@@ -221,7 +220,7 @@ class SPMformatter(ABC):
                 self._resolve_link_in_config(val, f"{parent_path}/{key}")
             # Special case, will be handled in a specific function registered
             # in self._grp_to_func
-            elif retrived_key := next(
+            elif retrieved_key := next(
                 (k for k in self._grp_to_func.keys() if key.startswith(k)), None
             ):
                 if not use_custom_func_prior:
@@ -231,10 +230,10 @@ class SPMformatter(ABC):
                         func_on_raw_key=func_on_raw_key,
                     )
                     # Fill special fields first
-                    method = getattr(self, self._grp_to_func[retrived_key])
+                    method = getattr(self, self._grp_to_func[retrieved_key])
                     method(val, parent_path, key)
                 else:
-                    method = getattr(self, self._grp_to_func[retrived_key])
+                    method = getattr(self, self._grp_to_func[retrieved_key])
                     method(val, parent_path, key)
                     self.walk_though_config_nested_dict(
                         config_dict=val,
@@ -310,7 +309,7 @@ class SPMformatter(ABC):
                     val, f"{parent_path}/{key}", func_on_raw_key=func_on_raw_key
                 )
 
-    def rearrange_data_according_to_axes(self, data, is_forward: Optional[bool] = None):
+    def rearrange_data_according_to_axes(self, data, is_forward: bool | None = None):
         """Rearrange array data according to the fast and slow axes.
 
         Implement this function in other base classes (e.g., NanonisBase) where it is needed.
@@ -377,7 +376,7 @@ class SPMformatter(ABC):
         """
 
         if val.startswith("@default_link:"):
-            val = val.split("@default_link:")[-1]
+            val = val.rsplit("@default_link:", maxsplit=1)[-1]
 
             classes = val.split("/")[1:]
             pattern = ""
@@ -522,7 +521,7 @@ class SPMformatter(ABC):
         parent_path: str,
         group_name: str,
         group_index=0,
-        is_forward: Optional[bool] = None,
+        is_forward: bool | None = None,
         rearrange_2d_data: bool = True,
     ):
         """Example NXdata dict descrioption from config
@@ -671,7 +670,9 @@ class SPMformatter(ABC):
             r"active_channel$": str,
             r"model/@version$": str,
             r"/model$": str,
-            r"lockin_amplifier/(demodulated|modulation)_signal$": lambda input: input.lower(),
+            r"lockin_amplifier/(demodulated|modulation)_signal$": lambda input: (
+                input.lower()
+            ),
             r"lockin_amplifier/(hp|lp){1,}_filter_orderN\[\1_filter_order_[\w]*\]$": (
                 lambda input: input if isinstance(input, (int, float)) else ""
             ),
@@ -732,7 +733,7 @@ class SPMformatter(ABC):
         end_conf_dct: dict,
         parent_path: str,
         concept_key: str,
-        part_to_embed: Optional[str],
+        part_to_embed: str | None,
     ):
         """
         Puts the data, unit, and other attributes into the template