pynxtools 0.3.2__tar.gz → 0.3.3__tar.gz

{pynxtools-0.3.2 → pynxtools-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynxtools
-Version: 0.3.2
+Version: 0.3.3
 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: 
@@ -223,18 +223,20 @@ Requires-Dist: click_default_group
 Requires-Dist: h5py>=3.6.0
 Requires-Dist: xarray>=0.20.2
 Requires-Dist: PyYAML>=6.0
-Requires-Dist: numpy>=1.21.2
+Requires-Dist: numpy<2.0.0,>=1.21.2
 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
 Requires-Dist: anytree
+Requires-Dist: setuptools>=64.0.1
 Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
 Requires-Dist: mkdocs-material-extensions; extra == "docs"
 Requires-Dist: mkdocs-macros-plugin; extra == "docs"
+Requires-Dist: mkdocs-click; extra == "docs"
 Provides-Extra: dev
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: ruff==0.3.4; extra == "dev"
@@ -245,7 +247,7 @@ Requires-Dist: structlog; extra == "dev"
 Requires-Dist: types-pyyaml; extra == "dev"
 Requires-Dist: types-pytz; extra == "dev"
 Requires-Dist: types-requests; extra == "dev"
-Requires-Dist: pip-tools; extra == "dev"
+Requires-Dist: uv; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: convert
 Requires-Dist: pynxtools[apm,ellips,em,mpes,stm,xps,xrd]; extra == "convert"
@@ -303,7 +305,7 @@ making experimental data searchable and publishable.
 NOMAD is developed by the FAIRMAT consortium, as a part of the German National Research Data Infrastructure
 (NFDI).
 
-The software tools are located inside [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools) and they are
+The software tools are located inside [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/src/pynxtools) and they are
 shipped with unit tests located in [`tests`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/tests).
 Some examples with real datasets are provided in [`examples`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/examples).
 It guides you through the process of converting instrument raw
@@ -311,9 +313,9 @@ data into the NeXus standard and visualising the files content.
 
 # Command line tools
 
-- [**dataconverter**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/dataconverter/README.md): Creates compliant instances of NeXus/HDF5 files to [NeXus schemas](https://nexusformat.org).
-- [**read_nexus**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/nexus/README.md): Outputs a debug log for a given NeXus file.
-- [**generate_eln**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/eln_mapper/README.md): Outputs ELN files that can be used to add metadata to the dataconverter routine.
+- [**dataconverter**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/dataconverter/README.md): Creates compliant instances of NeXus/HDF5 files to [NeXus schemas](https://nexusformat.org).
+- [**read_nexus**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/nexus/README.md): Outputs a debug log for a given NeXus file.
+- [**generate_eln**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/eln_mapper/README.md): Outputs ELN files that can be used to add metadata to the dataconverter routine.
 
 # Documentation
 Documentation for the different tools can be found [here](https://fairmat-nfdi.github.io/pynxtools/).

{pynxtools-0.3.2 → pynxtools-0.3.3}/README.md

@@ -37,7 +37,7 @@ making experimental data searchable and publishable.
 NOMAD is developed by the FAIRMAT consortium, as a part of the German National Research Data Infrastructure
 (NFDI).
 
-The software tools are located inside [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools) and they are
+The software tools are located inside [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/src/pynxtools) and they are
 shipped with unit tests located in [`tests`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/tests).
 Some examples with real datasets are provided in [`examples`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/examples).
 It guides you through the process of converting instrument raw
@@ -45,9 +45,9 @@ data into the NeXus standard and visualising the files content.
 
 # Command line tools
 
-- [**dataconverter**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/dataconverter/README.md): Creates compliant instances of NeXus/HDF5 files to [NeXus schemas](https://nexusformat.org).
-- [**read_nexus**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/nexus/README.md): Outputs a debug log for a given NeXus file.
-- [**generate_eln**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/pynxtools/eln_mapper/README.md): Outputs ELN files that can be used to add metadata to the dataconverter routine.
+- [**dataconverter**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/dataconverter/README.md): Creates compliant instances of NeXus/HDF5 files to [NeXus schemas](https://nexusformat.org).
+- [**read_nexus**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/nexus/README.md): Outputs a debug log for a given NeXus file.
+- [**generate_eln**](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/eln_mapper/README.md): Outputs ELN files that can be used to add metadata to the dataconverter routine.
 
 # Documentation
 Documentation for the different tools can be found [here](https://fairmat-nfdi.github.io/pynxtools/).

{pynxtools-0.3.2 → pynxtools-0.3.3}/dev-requirements.txt

@@ -1,17 +1,11 @@
-#
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
-#
-#    pip-compile --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
 anytree==2.12.1
     # via pynxtools (pyproject.toml)
 ase==3.22.1
     # via pynxtools (pyproject.toml)
 babel==2.14.0
     # via mkdocs-material
-build==1.1.1
-    # via pip-tools
 certifi==2024.2.2
     # via requests
 cfgv==3.4.0
@@ -20,17 +14,21 @@ charset-normalizer==3.3.2
     # via requests
 click==8.1.7
     # via
+    #   pynxtools (pyproject.toml)
     #   click-default-group
     #   mkdocs
-    #   pip-tools
-    #   pynxtools (pyproject.toml)
+    #   mkdocs-click
 click-default-group==1.2.4
     # via pynxtools (pyproject.toml)
 colorama==0.4.6
-    # via mkdocs-material
+    # via
+    #   click
+    #   mkdocs
+    #   mkdocs-material
+    #   pytest
 contourpy==1.2.0
     # via matplotlib
-coverage[toml]==7.4.4
+coverage==7.4.4
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
@@ -66,6 +64,7 @@ lxml==5.1.0
 markdown==3.6
     # via
     #   mkdocs
+    #   mkdocs-click
     #   mkdocs-material
     #   pymdown-extensions
 markupsafe==2.1.5
@@ -76,21 +75,23 @@ matplotlib==3.8.3
     # via ase
 mergedeep==1.3.4
     # via
-    #   mkdocs
     #   pynxtools (pyproject.toml)
+    #   mkdocs
 mkdocs==1.5.3
     # via
+    #   pynxtools (pyproject.toml)
     #   mkdocs-macros-plugin
     #   mkdocs-material
-    #   pynxtools (pyproject.toml)
+mkdocs-click==0.8.1
+    # via pynxtools (pyproject.toml)
 mkdocs-macros-plugin==1.0.5
     # via pynxtools (pyproject.toml)
 mkdocs-material==9.5.15
     # via pynxtools (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
-    #   mkdocs-material
     #   pynxtools (pyproject.toml)
+    #   mkdocs-material
 mypy==1.9.0
     # via pynxtools (pyproject.toml)
 mypy-extensions==1.0.0
@@ -99,17 +100,16 @@ nodeenv==1.8.0
     # via pre-commit
 numpy==1.26.4
     # via
+    #   pynxtools (pyproject.toml)
     #   ase
     #   contourpy
     #   h5py
     #   matplotlib
     #   pandas
-    #   pynxtools (pyproject.toml)
     #   scipy
     #   xarray
 packaging==24.0
     # via
-    #   build
     #   matplotlib
     #   mkdocs
     #   pytest
@@ -124,8 +124,6 @@ pathspec==0.12.1
     # via mkdocs
 pillow==10.2.0
     # via matplotlib
-pip-tools==7.4.1
-    # via pynxtools (pyproject.toml)
 platformdirs==4.2.0
     # via
     #   mkdocs
@@ -140,10 +138,6 @@ pymdown-extensions==10.7.1
     # via mkdocs-material
 pyparsing==3.1.2
     # via matplotlib
-pyproject-hooks==1.0.0
-    # via
-    #   build
-    #   pip-tools
 pytest==8.1.1
     # via
     #   pynxtools (pyproject.toml)
@@ -163,11 +157,11 @@ pytz==2024.1
     # via pandas
 pyyaml==6.0.1
     # via
+    #   pynxtools (pyproject.toml)
     #   mkdocs
     #   mkdocs-macros-plugin
     #   pre-commit
     #   pymdown-extensions
-    #   pynxtools (pyproject.toml)
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
@@ -179,6 +173,8 @@ ruff==0.3.4
     # via pynxtools (pyproject.toml)
 scipy==1.12.0
     # via ase
+setuptools==70.0.0
+    # via nodeenv
 six==1.16.0
     # via
     #   anytree
@@ -189,11 +185,8 @@ termcolor==2.4.0
     # via mkdocs-macros-plugin
 tomli==2.0.1
     # via
-    #   build
     #   coverage
     #   mypy
-    #   pip-tools
-    #   pyproject-hooks
     #   pytest
 types-pytz==2024.1.0.20240203
     # via pynxtools (pyproject.toml)
@@ -209,17 +202,13 @@ urllib3==2.2.1
     # via
     #   requests
     #   types-requests
+uv==0.2.9
+    # via pynxtools (pyproject.toml)
 virtualenv==20.25.1
     # via pre-commit
 watchdog==4.0.0
     # via mkdocs
-wheel==0.43.0
-    # via pip-tools
 xarray==2024.2.0
     # via pynxtools (pyproject.toml)
 zipp==3.18.1
     # via importlib-metadata
-
-# The following packages are considered to be unsafe in a requirements file:
-# pip
-# setuptools

{pynxtools-0.3.2 → pynxtools-0.3.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 requires = ["setuptools>=64.0.1", "setuptools-scm[toml]>=6.2"]
-backend-path = ["pynxtools"]
+backend-path = ["src/pynxtools"]
 build-backend = "_build_wrapper"
 
 [project]
@@ -28,13 +28,14 @@ dependencies = [
     "h5py>=3.6.0",
     "xarray>=0.20.2",
     "PyYAML>=6.0",
-    "numpy>=1.21.2",
+    "numpy>=1.21.2,<2.0.0",
     "pandas>=1.3.2",
     "ase>=3.19.0",
     "mergedeep",
     "importlib-metadata",
     "lxml>=4.9.1",
     "anytree",
+    "setuptools>=64.0.1"
 ]
 
 [project.urls]
@@ -47,6 +48,7 @@ docs = [
     "mkdocs-material",
     "mkdocs-material-extensions",
     "mkdocs-macros-plugin",
+    "mkdocs-click",
 ]
 dev = [
     "mypy",
@@ -58,7 +60,7 @@ dev = [
     "types-pyyaml",
     "types-pytz",
     "types-requests",
-    "pip-tools",
+    "uv",
     "pre-commit",
 ]
 convert = [
@@ -93,20 +95,22 @@ generate_eln = "pynxtools.eln_mapper.eln_mapper:get_eln"
 
 [tool.setuptools.package-data]
 pynxtools = ["definitions/**/*.xml", "definitions/**/*.xsd"]
-"pynxtools.dataconverter.readers.xps" = ["*.json"]
 "pynxtools.dataconverter.readers.hall" = ["enum_map.json"]
 "pynxtools.dataconverter.readers.rii_database.formula_parser" = ["dispersion_function_grammar.lark"]
 
 [tool.setuptools.packages.find]
-exclude = ["pynxtools/definitions*"]
+where = [
+    "src",
+]
+exclude = ["src/pynxtools/definitions*"]
 
 [tool.setuptools_scm]
 version_scheme = "no-guess-dev"
 local_scheme = "node-and-date"
 
 [tool.ruff]
-include = ["pynxtools/*.py", "tests/*.py"]
-exclude = ["pynxtools/definitions"]
+include = ["src/*.py", "tests/*.py"]
+exclude = ["src/pynxtools/definitions"]
 line-length = 88
 indent-width = 4
 
@@ -145,4 +149,4 @@ ignore_missing_imports = true
 follow_imports = "silent"
 no_strict_optional = true
 disable_error_code = "import, annotation-unchecked"
-exclude = ["pynxtools/definitions/*"]
+exclude = ["src/pynxtools/definitions/*"]

pynxtools-0.3.3/src/pynxtools/data/NXtest.nxdl.xml

@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
+<definition xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd"
+    xmlns="http://definition.nexusformat.org/nxdl/3.1"
+ name="NXtest"
+ extends="NXobject"
+ type="group"
+ category="application"
+>
+    <doc>This is a dummy NXDL to test out the dataconverter.</doc>
+    <group type="NXentry">
+        <field name="program_name"/>
+        <field name="definition">
+            <doc>This is a dummy NXDL to test out the dataconverter.</doc>
+            <attribute name="version"/>
+            <enumeration>
+                <item value="NXTEST"/>
+                <item value="NXtest"/>
+            </enumeration>
+        </field>
+        <group type="NXdata" name="OPTIONAL_group" optional="true">
+            <field name="required_field" required="true" type="NX_INT">
+                <doc>A dummy entry to test optional parent check for a required child.</doc>
+            </field>
+            <field name="optional_field" optional="true" type="NX_INT">
+                <doc>A dummy entry to test optional parent check for an optional child.</doc>
+            </field>
+        </group>
+        <group type="NXdata" name="NXODD_name">
+            <field name="float_value" type="NX_FLOAT" optional="true" units="NX_ENERGY">
+                <doc>A dummy entry for a float value.</doc>
+            </field>
+            <field name="bool_value" type="NX_BOOLEAN" required="true" units="NX_UNITLESS">
+                <doc>A dummy entry for a bool value.</doc>
+            </field>
+            <field name="int_value" type="NX_INT" units="NX_LENGTH">
+                <doc>A dummy entry for an int value.</doc>
+            </field>
+            <field name="posint_value" type="NX_POSINT" units="NX_LENGTH">
+                <doc>A dummy entry for a positive int value.</doc>
+            </field>
+            <field name="char_value" type="NX_CHAR" units="NX_UNITLESS">
+                <doc>A dummy entry for a char value.</doc>
+            </field>
+            <field name="date_value" type="NX_DATE_TIME" units="NX_UNITLESS">
+                <doc>A dummy entry for a date value.</doc>
+            </field>
+            <field name="type">
+                <enumeration>
+                    <item value="1st type" />
+                    <item value="2nd type" />
+                    <item value="3rd type" />
+                    <item value="4th type" />
+                </enumeration>
+            </field>
+        </group>
+        <group type="NXnote" name="required_group">
+            <doc>This is a required yet empty group.</doc>
+        </group>
+        <group type="NXnote" name="required_group2">
+            <doc>This is a second required yet empty group.</doc>
+        </group>
+        <group type="NXdata" name="optional_parent" optional="true">
+            <field name="required_child" required="true" type="NX_INT">
+                <doc>A dummy entry to test optional parent check for required child.</doc>
+            </field>
+            <field name="optional_child" optional="true" type="NX_INT">
+                <doc>A dummy entry to test optional parent check for required child.</doc>
+            </field>
+            <group type="NXdata" name="req_group_in_opt_group">
+                <doc>This is a required group in an optional group.</doc>
+            </group>
+        </group>
+    </group>
+</definition>

pynxtools-0.3.3/src/pynxtools/data/NXtest_extended.nxdl.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl" ?>
+<definition xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd"
+    xmlns="http://definition.nexusformat.org/nxdl/3.1"
+ name="NXtest_extended"
+ extends="NXtest"
+ type="group"
+ category="application"
+>
+    <doc>This is a dummy NXDL to test an extended application definition.</doc>
+    <group type="NXentry">
+        <field name="definition">
+            <doc>This is a dummy NXDL to test out the dataconverter.</doc>
+            <enumeration>
+                <item value="NXtest_extended"/>
+            </enumeration>
+        </field>
+        <field name="extended_field" type="NX_FLOAT" units="NX_ENERGY">
+            <doc>A dummy entry for an extended field.</doc>
+        </field>
+    </group>
+</definition>

{pynxtools-0.3.2 → pynxtools-0.3.3/src}/pynxtools/dataconverter/helpers.py

@@ -193,6 +193,75 @@ def get_nxdl_name_from_elem(xml_element) -> str:
     return name_to_add
 
 
+def get_nxdl_name_for(xml_elem: ET._Element) -> Optional[str]:
+    """
+    Get the name of the element from the NXDL element.
+    For an entity having a name this is just the name.
+    For groups it is the uppercase type without NX, e.g. "ENTRY" for "NXentry".
+
+    Args:
+        xml_elem (ET._Element): The xml element to get the name for.
+
+    Returns:
+        Optional[str]:
+            The name of the element.
+            None if the xml element has no name or type attribute.
+    """
+    """"""
+    if "name" in xml_elem.attrib:
+        return xml_elem.attrib["name"]
+    if "type" in xml_elem.attrib:
+        return convert_nexus_to_caps(xml_elem.attrib["type"])
+    return None
+
+
+def get_appdef_root(xml_elem: ET._Element) -> ET._Element:
+    """
+    Get the root element of the tree of xml_elem
+
+    Args:
+        xml_elem (ET._Element): The element for which to get the root element.
+
+    Returns:
+        ET._Element: The root element of the tree.
+    """
+    return xml_elem.getroottree().getroot()
+
+
+def is_appdef(xml_elem: ET._Element) -> bool:
+    """
+    Check whether the xml element is part of an application definition.
+
+    Args:
+        xml_elem (ET._Element): The xml_elem whose tree to check.
+
+    Returns:
+        bool: True if the xml_elem is part of an application definition.
+    """
+    return get_appdef_root(xml_elem).attrib.get("category") == "application"
+
+
+def get_all_parents_for(xml_elem: ET._Element) -> List[ET._Element]:
+    """
+    Get all parents from the nxdl (via extends keyword)
+
+    Args:
+        xml_elem (ET._Element): The element to get the parents for.
+
+    Returns:
+        List[ET._Element]: The list of parents xml nodes.
+    """
+    root = get_appdef_root(xml_elem)
+    inheritance_chain = []
+    extends = root.get("extends")
+    while extends is not None and extends != "NXobject":
+        parent_xml_root, _ = get_nxdl_root_and_path(extends)
+        extends = parent_xml_root.get("extends")
+        inheritance_chain.append(parent_xml_root)
+
+    return inheritance_chain
+
+
 def get_nxdl_root_and_path(nxdl: str):
     """Get xml root element and file path from nxdl name e.g. NXapm.
 
@@ -213,18 +282,20 @@ def get_nxdl_root_and_path(nxdl: str):
     FileNotFoundError
         Error if no file with the given nxdl name is found.
     """
+
     # Reading in the NXDL and generating a template
     definitions_path = nexus.get_nexus_definitions_path()
-    if nxdl == "NXtest":
-        nxdl_f_path = os.path.join(
-            f"{os.path.abspath(os.path.dirname(__file__))}/../../",
-            "tests",
-            "data",
-            "dataconverter",
-            "NXtest.nxdl.xml",
-        )
-    elif nxdl == "NXroot":
-        nxdl_f_path = os.path.join(definitions_path, "base_classes", "NXroot.nxdl.xml")
+    data_path = os.path.join(
+        f"{os.path.abspath(os.path.dirname(__file__))}/../",
+        "data",
+    )
+    special_names = {
+        "NXtest": os.path.join(data_path, "NXtest.nxdl.xml"),
+        "NXtest_extended": os.path.join(data_path, "NXtest_extended.nxdl.xml"),
+    }
+
+    if nxdl in special_names:
+        nxdl_f_path = special_names[nxdl]
     else:
         nxdl_f_path = os.path.join(
             definitions_path, "contributed_definitions", f"{nxdl}.nxdl.xml"
@@ -813,6 +884,12 @@ def write_nexus_def_to_entry(data, entry_name: str, nxdl_def: str):
         get_nexus_version(),
         overwrite=False,
     )
+    update_and_warn(
+        f"/ENTRY[{entry_name}]/definition/@URL",
+        "https://github.com/FAIRmat-NFDI/nexus_definitions/"
+        f"blob/{get_nexus_version_hash()}",
+        overwrite=False,
+    )
 
 
 def extract_atom_types(formula, mode="hill"):