pynxtools 0.2.0__tar.gz → 0.2.1__tar.gz

{pynxtools-0.2.0 → pynxtools-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynxtools
-Version: 0.2.0
+Version: 0.2.1
 Summary: Extend NeXus for experiments and characterization in Materials Science and Materials Engineering and serve as a NOMAD parser implementation for NeXus.
 Author: The NOMAD Authors
 License: 
@@ -228,6 +228,7 @@ Requires-Dist: pandas>=1.3.2
 Requires-Dist: ase>=3.19.0
 Requires-Dist: mergedeep
 Requires-Dist: importlib-metadata
+Requires-Dist: lxml>=4.9.1
 Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
@@ -235,7 +236,7 @@ Requires-Dist: mkdocs-material-extensions; extra == "docs"
 Requires-Dist: mkdocs-macros-plugin; extra == "docs"
 Provides-Extra: dev
 Requires-Dist: mypy; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: ruff==0.3.4; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
@@ -246,7 +247,11 @@ Requires-Dist: types-requests; extra == "dev"
 Requires-Dist: pip-tools; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: convert
-Requires-Dist: pynxtools[mpes,stm,xps,xrd]; extra == "convert"
+Requires-Dist: pynxtools[apm,em,mpes,stm,xps,xrd]; extra == "convert"
+Provides-Extra: apm
+Requires-Dist: pynxtools-apm; extra == "apm"
+Provides-Extra: em
+Requires-Dist: pynxtools-em; extra == "em"
 Provides-Extra: mpes
 Requires-Dist: pynxtools-mpes; extra == "mpes"
 Provides-Extra: xps

{pynxtools-0.2.0 → pynxtools-0.2.1}/dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
+# This file is autogenerated by pip-compile with Python 3.11
 # by the following command:
 #
 #    pip-compile --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
@@ -8,9 +8,9 @@ ase==3.22.1
     # via pynxtools (pyproject.toml)
 babel==2.14.0
     # via mkdocs-material
-build==1.0.3
+build==1.1.1
     # via pip-tools
-certifi==2023.11.17
+certifi==2024.2.2
     # via requests
 cfgv==3.4.0
     # via pre-commit
@@ -26,51 +26,49 @@ click-default-group==1.2.4
     # via pynxtools (pyproject.toml)
 colorama==0.4.6
     # via mkdocs-material
-contourpy==1.1.1
+contourpy==1.2.0
     # via matplotlib
-coverage[toml]==7.3.2
-    # via
-    #   coverage
-    #   pytest-cov
+coverage[toml]==7.4.4
+    # via pytest-cov
 cycler==0.12.1
     # via matplotlib
-distlib==0.3.7
+distlib==0.3.8
     # via virtualenv
-exceptiongroup==1.2.0
-    # via pytest
-filelock==3.13.1
+filelock==3.13.3
     # via virtualenv
-fonttools==4.45.1
+fonttools==4.50.0
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
 h5py==3.10.0
     # via pynxtools (pyproject.toml)
-identify==2.5.33
+identify==2.5.35
     # via pre-commit
 idna==3.6
     # via requests
-importlib-metadata==6.8.0
+importlib-metadata==7.1.0
     # via pynxtools (pyproject.toml)
 iniconfig==2.0.0
     # via pytest
-jinja2==3.1.2
+jinja2==3.1.3
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
 kiwisolver==1.4.5
     # via matplotlib
-markdown==3.5.2
+lxml==5.1.0
+    # via pynxtools (pyproject.toml)
+markdown==3.6
     # via
     #   mkdocs
     #   mkdocs-material
     #   pymdown-extensions
-markupsafe==2.1.3
+markupsafe==2.1.5
     # via
     #   jinja2
     #   mkdocs
-matplotlib==3.7.4
+matplotlib==3.8.3
     # via ase
 mergedeep==1.3.4
     # via
@@ -83,19 +81,19 @@ mkdocs==1.5.3
     #   pynxtools (pyproject.toml)
 mkdocs-macros-plugin==1.0.5
     # via pynxtools (pyproject.toml)
-mkdocs-material==9.5.10
+mkdocs-material==9.5.15
     # via pynxtools (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
     #   mkdocs-material
     #   pynxtools (pyproject.toml)
-mypy==1.7.1
+mypy==1.9.0
     # via pynxtools (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
 nodeenv==1.8.0
     # via pre-commit
-numpy==1.24.4
+numpy==1.26.4
     # via
     #   ase
     #   contourpy
@@ -105,7 +103,7 @@ numpy==1.24.4
     #   pynxtools (pyproject.toml)
     #   scipy
     #   xarray
-packaging==23.2
+packaging==24.0
     # via
     #   build
     #   matplotlib
@@ -114,48 +112,50 @@ packaging==23.2
     #   xarray
 paginate==0.5.6
     # via mkdocs-material
-pandas==2.0.3
+pandas==2.2.1
     # via
     #   pynxtools (pyproject.toml)
     #   xarray
 pathspec==0.12.1
     # via mkdocs
-pillow==10.0.1
+pillow==10.2.0
     # via matplotlib
-pip-tools==7.3.0
+pip-tools==7.4.1
     # via pynxtools (pyproject.toml)
-platformdirs==4.0.0
+platformdirs==4.2.0
     # via
     #   mkdocs
     #   virtualenv
-pluggy==1.3.0
+pluggy==1.4.0
     # via pytest
-pre-commit==3.5.0
+pre-commit==3.7.0
     # via pynxtools (pyproject.toml)
 pygments==2.17.2
     # via mkdocs-material
-pymdown-extensions==10.7
+pymdown-extensions==10.7.1
     # via mkdocs-material
-pyparsing==3.1.1
+pyparsing==3.1.2
     # via matplotlib
 pyproject-hooks==1.0.0
-    # via build
-pytest==7.4.3
+    # via
+    #   build
+    #   pip-tools
+pytest==8.1.1
     # via
     #   pynxtools (pyproject.toml)
     #   pytest-cov
     #   pytest-timeout
-pytest-cov==4.1.0
+pytest-cov==5.0.0
     # via pynxtools (pyproject.toml)
-pytest-timeout==2.2.0
+pytest-timeout==2.3.1
     # via pynxtools (pyproject.toml)
-python-dateutil==2.8.2
+python-dateutil==2.9.0.post0
     # via
     #   ghp-import
     #   matplotlib
     #   mkdocs-macros-plugin
     #   pandas
-pytz==2023.3.post1
+pytz==2024.1
     # via pandas
 pyyaml==6.0.1
     # via
@@ -171,47 +171,39 @@ regex==2023.12.25
     # via mkdocs-material
 requests==2.31.0
     # via mkdocs-material
-ruff==0.1.7
+ruff==0.3.4
     # via pynxtools (pyproject.toml)
-scipy==1.9.1
+scipy==1.12.0
     # via ase
 six==1.16.0
     # via python-dateutil
-structlog==23.2.0
+structlog==24.1.0
     # via pynxtools (pyproject.toml)
 termcolor==2.4.0
     # via mkdocs-macros-plugin
-tomli==2.0.1
-    # via
-    #   build
-    #   coverage
-    #   mypy
-    #   pip-tools
-    #   pyproject-hooks
-    #   pytest
-types-pytz==2023.3.1.1
+types-pytz==2024.1.0.20240203
     # via pynxtools (pyproject.toml)
-types-pyyaml==6.0.12.12
+types-pyyaml==6.0.12.20240311
     # via pynxtools (pyproject.toml)
-types-requests==2.31.0.10
+types-requests==2.31.0.20240311
     # via pynxtools (pyproject.toml)
-typing-extensions==4.8.0
+typing-extensions==4.10.0
     # via mypy
-tzdata==2023.3
+tzdata==2024.1
     # via pandas
-urllib3==2.1.0
+urllib3==2.2.1
     # via
     #   requests
     #   types-requests
-virtualenv==20.25.0
+virtualenv==20.25.1
     # via pre-commit
 watchdog==4.0.0
     # via mkdocs
-wheel==0.42.0
+wheel==0.43.0
     # via pip-tools
-xarray==2023.1.0
+xarray==2024.2.0
     # via pynxtools (pyproject.toml)
-zipp==3.17.0
+zipp==3.18.1
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/__init__.py

@@ -1,6 +1,3 @@
-"""init file
-
-"""
 #
 # Copyright The NOMAD Authors.
 #
@@ -18,6 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+
 import os
 import re
 from datetime import datetime

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/_build_wrapper.py

@@ -2,6 +2,7 @@
 Build wrapper for setuptools to create a nexus-version.txt file
 containing the nexus definitions verison.
 """
+
 import os
 from subprocess import CalledProcessError, run
 from typing import Optional

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/convert.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """This script runs the conversion routine using a selected reader and write out a NeXus file."""
+
 import glob
 import importlib.machinery
 import importlib.util

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/hdfdict.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Taken from: https://github.com/SiggiGue/hdfdict/blob/master/hdfdict/hdfdict.py"""
+
 from collections import UserDict
 from contextlib import contextmanager
 from datetime import datetime

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/helpers.py

@@ -20,17 +20,17 @@
 import json
 import logging
 import re
-import xml.etree.ElementTree as ET
 from datetime import datetime, timezone
 from typing import Any, Callable, List, Optional, Tuple, Union
 
 import h5py
+import lxml.etree as ET
 import numpy as np
 from ase.data import chemical_symbols
 
 from pynxtools import get_nexus_version, get_nexus_version_hash
 from pynxtools.nexus import nexus
-from pynxtools.nexus.nexus import NxdlAttributeError
+from pynxtools.nexus.nexus import NxdlAttributeNotFoundError
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -63,6 +63,9 @@ def get_all_defined_required_children_for_elem(xml_element):
     """Gets all possible inherited required children for a given NXDL element"""
     list_of_children_to_add = set()
     for child in xml_element:
+        tag = remove_namespace_from_tag(child.tag)
+        if tag not in ("group", "field", "attribute"):
+            continue
         child.set("nxdlbase_class", xml_element.get("nxdlbase_class"))
         if child.attrib and get_required_string(child) == "required":
             tag = remove_namespace_from_tag(child.tag)
@@ -572,7 +575,7 @@ def try_undocumented(data, nxdl_root: ET.Element):
             if units in data.undocumented:
                 data[get_required_string(elem)][units] = data.undocumented[units]
                 del data.undocumented[units]
-        except NxdlAttributeError:
+        except NxdlAttributeNotFoundError:
             pass
 
 
@@ -637,6 +640,8 @@ def validate_data_dict(template, data, nxdl_root: ET.Element):
 def remove_namespace_from_tag(tag):
     """Helper function to remove the namespace from an XML tag."""
 
+    if not isinstance(tag, str):
+        return ""
     return tag.split("}")[-1]
 
 

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/base/reader.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """The abstract class off of which to implement readers."""
+
 from abc import ABC, abstractmethod
 from typing import Tuple, Any
 

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/ellips/mock.py

@@ -16,6 +16,7 @@
 #
 
 """A generic class for generating duplicate outputs for ellipsometry"""
+
 import random
 import numpy as np
 import ase

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/ellips/reader.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """An example reader implementation for the DataConverter."""
+
 import math
 import os
 from importlib.metadata import PackageNotFoundError, version
@@ -439,9 +440,9 @@ class EllipsometryReader(BaseReader):
                 # using a proper unit parsing logic
                 template[f"/ENTRY[entry]/plot/DATA[{key}]/@units"] = "degree"
                 if dindx == 0 and index == 0:
-                    template[
-                        f"/ENTRY[entry]/plot/DATA[{key}]/@long_name"
-                    ] = f"{plot_name} (degree)"
+                    template[f"/ENTRY[entry]/plot/DATA[{key}]/@long_name"] = (
+                        f"{plot_name} (degree)"
+                    )
                 template[f"/ENTRY[entry]/plot/DATA[{key}_errors]"] = {
                     "link": "/entry/data_collection/data_error",
                     "shape": np.index_exp[index, dindx, :],
@@ -472,9 +473,9 @@ class EllipsometryReader(BaseReader):
             template["/ENTRY[entry]/program_name/@version"] = version("pynxtools")
         except PackageNotFoundError:
             pass
-        template[
-            "/ENTRY[entry]/program_name/@url"
-        ] = "https://github.com/FAIRmat-NFDI/pynxtools"
+        template["/ENTRY[entry]/program_name/@url"] = (
+            "https://github.com/FAIRmat-NFDI/pynxtools"
+        )
 
         return template
 

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/example/reader.py

@@ -17,6 +17,7 @@
 
 #
 """An example reader implementation for the DataConverter."""
+
 import json
 import os
 from typing import Any, Tuple
@@ -101,9 +102,9 @@ class ExampleReader(BaseReader):
                 f"{my_path}/xarray_saved_small_calibration.h5:/axes/ax2",
             ]
         }
-        template[
-            "/ENTRY[entry]/test_virtual_dataset/concatenate_datasets"
-        ] = my_datasets
+        template["/ENTRY[entry]/test_virtual_dataset/concatenate_datasets"] = (
+            my_datasets
+        )
 
         # virtual datasets slicing
         my_path = str(f"{os.path.dirname(__file__)}/../../../../tests/data/nexus")
@@ -130,9 +131,9 @@ class ExampleReader(BaseReader):
         my_compression_dict = {"compress": "string not to be compressed"}
         template["/ENTRY[entry]/test_compression/not_to_compress"] = my_compression_dict
         my_compression_dict2 = {"compress": np.array([1, 2, 3, 4])}
-        template[
-            "/ENTRY[entry]/test_compression/compressed_data"
-        ] = my_compression_dict2
+        template["/ENTRY[entry]/test_compression/compressed_data"] = (
+            my_compression_dict2
+        )
 
         # sh = h5py.File(file_names_to_concatenate[0], 'r')[entry_key].shape
         # layout = h5py.VirtualLayout(shape=(len(file_names_to_concatenate),) + sh,

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/json_map/reader.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """An example reader implementation for the DataConverter."""
+
 import json
 import pickle
 from typing import Any, Tuple

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/json_yml/reader.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """An example reader implementation for the DataConverter."""
+
 from typing import Tuple, Any, Callable, Dict, List
 import os
 

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/readers/utils.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 """Utility functions for the NeXus reader classes."""
+
 import json
 import logging
 import re

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/dataconverter/writer.py

@@ -28,8 +28,8 @@ import h5py
 import numpy as np
 
 from pynxtools.dataconverter import helpers
-from pynxtools.nexus import nexus
 from pynxtools.dataconverter.exceptions import InvalidDictProvided
+from pynxtools.nexus import nexus
 
 logger = logging.getLogger(__name__)  # pylint: disable=C0103
 logger.setLevel(logging.INFO)
@@ -222,7 +222,7 @@ class Writer:
             elem = nexus.get_node_at_nxdl_path(
                 nxdl_path, elem=copy.deepcopy(self.nxdl_data)
             )
-        except nexus.NxdlAttributeError:
+        except nexus.NxdlAttributeNotFoundError:
             return None
 
         # Remove the name attribute as we only use it to name the HDF5 entry

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/definitions/base_classes/NXbeam.nxdl.xml

@@ -1,10 +1,10 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 <!--
 # NeXus - Neutron and X-ray Common Data Format
-# 
-# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
+# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
@@ -454,7 +454,7 @@
             <attribute name="depends_on" type="NX_CHAR">
                 <doc>
                      Points to the path to a field defining the location on which this
-                     depends or the string &quot;.&quot; for origin.
+                     depends or the string "." for origin.
                 </doc>
             </attribute>
         </field>
@@ -482,9 +482,20 @@
             <attribute name="depends_on" type="NX_CHAR">
                 <doc>
                      Points to the path to a field defining the location on which this
-                     depends or the string &quot;.&quot; for origin.
+                     depends or the string "." for origin.
                 </doc>
             </attribute>
         </field>
     </group>
+    <field name="previous_device">
+        <doc>
+             Indicates the beam device from which this beam originates.
+             This defines, whether the beam in an "input" or "output" beam.
+        </doc>
+    </field>
+    <field name="next_device">
+        <doc>
+             
+        </doc>
+    </field>
 </definition>

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/definitions/base_classes/NXinstrument.nxdl.xml

@@ -61,6 +61,7 @@
     <group type="NXfilter"/>
     <group type="NXflipper"/>
     <group type="NXguide"/>
+    <group type="NXhistory"/>
     <group type="NXinsertion_device"/>
     <group type="NXmirror"/>
     <group type="NXmoderator"/>

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/definitions/base_classes/NXsample.nxdl.xml

@@ -1,10 +1,10 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 <!--
 # NeXus - Neutron and X-ray Common Data Format
-# 
-# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
+# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
@@ -481,7 +481,9 @@
         </doc>
     </group>
     <group type="NXoff_geometry">
-        <!--exists: ['min', '0']-->
+        <!--
+exists: ['min', '0']
+-->
         <doc>
              This group describes the shape of the sample
         </doc>
@@ -518,7 +520,9 @@
         </doc>
     </group>
     <group type="NXenvironment">
-        <!--eventually, this should be stored in the application definitions-->
+        <!--
+eventually, this should be stored in the application definitions
+-->
         <doc>
              Any environmental or external stimuli/measurements.
              These can include, among others:
@@ -526,7 +530,7 @@
              external electric/magnetic/mechanical fields, temperature, ...
         </doc>
     </group>
-    <group type="NXsample_history">
+    <group name="history" type="NXhistory">
         <doc>
              A set of physical processes that occurred to the sample prior/during experiment.
         </doc>
@@ -550,7 +554,7 @@
              to apply to the component starting from 0, 0, 0. The order of these operations
              is critical and forms what NeXus calls a dependency chain. The depends_on
              field defines the path to the top most operation of the dependency chain or the
-             string &quot;.&quot; if located in the origin. Usually these operations are stored in a
+             string "." if located in the origin. Usually these operations are stored in a
              NXtransformations group. But NeXus allows them to be stored anywhere.
         </doc>
     </field>

{pynxtools-0.2.0 → pynxtools-0.2.1}/pynxtools/definitions/base_classes/NXsample_component.nxdl.xml

@@ -1,10 +1,10 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version='1.0' encoding='UTF-8'?>
 <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
 <!--
 # NeXus - Neutron and X-ray Common Data Format
-# 
-# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
+# Copyright (C) 2014-2024 NeXus International Advisory Committee (NIAC)
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
@@ -212,7 +212,7 @@
              Details about the sample component vendor (company or research group)
         </doc>
     </group>
-    <group type="NXsample_history">
+    <group name="history" type="NXhistory">
         <doc>
              A set of physical processes that occurred to the sample component prior/during
              experiment.
@@ -220,7 +220,7 @@
     </group>
     <field name="depends_on">
         <doc>
-             Any NXsample_component depends on the instance of NXsample_component_set, at the same level of 
+             Any NXsample_component depends on the instance of NXsample_component_set, at the same level of
              description granularity where the component is located.
         </doc>
     </field>