pynxtools 0.7.0__tar.gz → 0.7.2__tar.gz

{pynxtools-0.7.0 → pynxtools-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynxtools
-Version: 0.7.0
+Version: 0.7.2
 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: 
@@ -223,7 +223,7 @@ 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,>=1.22.4
 Requires-Dist: pandas>=1.3.2
 Requires-Dist: ase>=3.19.0
 Requires-Dist: mergedeep

{pynxtools-0.7.0 → pynxtools-0.7.2}/dev-requirements.txt

@@ -4,9 +4,9 @@ anytree==2.12.1
     # via pynxtools (pyproject.toml)
 ase==3.23.0
     # via pynxtools (pyproject.toml)
-babel==2.15.0
+babel==2.16.0
     # via mkdocs-material
-certifi==2024.7.4
+certifi==2024.8.30
     # via requests
 cfgv==3.4.0
     # via pre-commit
@@ -22,17 +22,15 @@ click-default-group==1.2.4
     # via pynxtools (pyproject.toml)
 colorama==0.4.6
     # via mkdocs-material
-contourpy==1.2.1
+contourpy==1.3.0
     # via matplotlib
-coverage==7.5.4
+coverage==7.6.1
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
 distlib==0.3.8
     # via virtualenv
-exceptiongroup==1.2.1
-    # via pytest
-filelock==3.15.4
+filelock==3.16.0
     # via virtualenv
 fonttools==4.53.1
     # via matplotlib
@@ -40,11 +38,11 @@ ghp-import==2.1.0
     # via mkdocs
 h5py==3.11.0
     # via pynxtools (pyproject.toml)
-identify==2.5.36
+identify==2.6.0
     # via pre-commit
-idna==3.7
+idna==3.8
     # via requests
-importlib-metadata==8.0.0
+importlib-metadata==8.5.0
     # via pynxtools (pyproject.toml)
 iniconfig==2.0.0
     # via pytest
@@ -53,28 +51,31 @@ jinja2==3.1.4
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
-kiwisolver==1.4.5
+kiwisolver==1.4.7
     # via matplotlib
-lxml==5.2.2
+lxml==5.3.0
     # via pynxtools (pyproject.toml)
-markdown==3.6
+markdown==3.7
     # via
+    #   markdown-include
     #   mkdocs
     #   mkdocs-click
     #   mkdocs-material
     #   pymdown-extensions
+markdown-include==0.8.1
+    # via pynxtools (pyproject.toml)
 markupsafe==2.1.5
     # via
     #   jinja2
     #   mkdocs
-matplotlib==3.9.1
+matplotlib==3.9.2
     # via ase
 mergedeep==1.3.4
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs
     #   mkdocs-get-deps
-mkdocs==1.6.0
+mkdocs==1.6.1
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs-macros-plugin
@@ -85,19 +86,19 @@ mkdocs-get-deps==0.2.0
     # via mkdocs
 mkdocs-macros-plugin==1.0.5
     # via pynxtools (pyproject.toml)
-mkdocs-material==9.5.28
+mkdocs-material==9.5.34
     # via pynxtools (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs-material
-mypy==1.10.1
+mypy==1.11.2
     # via pynxtools (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
 nodeenv==1.9.1
     # via pre-commit
-numpy==2.0.0
+numpy==1.26.4
     # via
     #   pynxtools (pyproject.toml)
     #   ase
@@ -113,7 +114,7 @@ packaging==24.1
     #   mkdocs
     #   pytest
     #   xarray
-paginate==0.5.6
+paginate==0.5.7
     # via mkdocs-material
 pandas==2.2.2
     # via
@@ -123,21 +124,21 @@ pathspec==0.12.1
     # via mkdocs
 pillow==10.4.0
     # via matplotlib
-platformdirs==4.2.2
+platformdirs==4.3.2
     # via
     #   mkdocs-get-deps
     #   virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==3.7.1
+pre-commit==3.8.0
     # via pynxtools (pyproject.toml)
 pygments==2.18.0
     # via mkdocs-material
-pymdown-extensions==10.8.1
+pymdown-extensions==10.9
     # via mkdocs-material
-pyparsing==3.1.2
+pyparsing==3.1.4
     # via matplotlib
-pytest==8.2.2
+pytest==8.3.3
     # via
     #   pynxtools (pyproject.toml)
     #   pytest-cov
@@ -152,9 +153,9 @@ python-dateutil==2.9.0.post0
     #   matplotlib
     #   mkdocs-macros-plugin
     #   pandas
-pytz==2024.1
+pytz==2024.2
     # via pandas
-pyyaml==6.0.1
+pyyaml==6.0.2
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs
@@ -165,48 +166,43 @@ pyyaml==6.0.1
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-regex==2024.5.15
+regex==2024.9.11
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.4.8
+ruff==0.5.5
     # via pynxtools (pyproject.toml)
-scipy==1.14.0
+scipy==1.14.1
     # via ase
 six==1.16.0
     # via
     #   anytree
     #   python-dateutil
-structlog==24.2.0
+structlog==24.4.0
     # via pynxtools (pyproject.toml)
 termcolor==2.4.0
     # via mkdocs-macros-plugin
-tomli==2.0.1
-    # via
-    #   coverage
-    #   mypy
-    #   pytest
-types-pytz==2024.1.0.20240417
+types-pytz==2024.2.0.20240913
     # via pynxtools (pyproject.toml)
-types-pyyaml==6.0.12.20240311
+types-pyyaml==6.0.12.20240808
     # via pynxtools (pyproject.toml)
-types-requests==2.32.0.20240622
+types-requests==2.32.0.20240907
     # via pynxtools (pyproject.toml)
 typing-extensions==4.12.2
     # via mypy
 tzdata==2024.1
     # via pandas
-urllib3==2.2.2
+urllib3==2.2.3
     # via
     #   requests
     #   types-requests
-uv==0.2.21
+uv==0.4.9
     # via pynxtools (pyproject.toml)
-virtualenv==20.26.3
+virtualenv==20.26.4
     # via pre-commit
-watchdog==4.0.1
+watchdog==5.0.2
     # via mkdocs
-xarray==2024.6.0
+xarray==2024.9.0
     # via pynxtools (pyproject.toml)
-zipp==3.19.2
+zipp==3.20.1
     # via importlib-metadata

{pynxtools-0.7.0 → pynxtools-0.7.2}/pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "h5py>=3.6.0",
     "xarray>=0.20.2",
     "PyYAML>=6.0",
-    "numpy>=1.21.2",
+    'numpy>=1.22.4,<2.0.0',
     "pandas>=1.3.2",
     "ase>=3.19.0",
     "mergedeep",

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/__init__.py

@@ -105,3 +105,10 @@ def get_nexus_version_hash() -> str:
         return MAIN_BRANCH_NAME
 
     return version.group(1)
+
+
+def get_definitions_url() -> str:
+    """Get the URL of the NeXus definitions that are submoduled in pynxtools."""
+    url_file = os.path.join(os.path.dirname(__file__), "remote_definitions_url.txt")
+    with open(url_file, encoding="utf-8") as file:
+        return file.read().strip()

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/_build_wrapper.py

@@ -56,13 +56,61 @@ def _write_version_to_metadata():
         file.write(version)
 
 
+def get_definitions_submodule_url():
+    """
+    The URL of the definitions submodule in pynxtools.
+    """
+    submodule_path = "src/pynxtools/definitions"
+
+    try:
+        # Define the command to run
+        url_line = run(
+            [
+                "git",
+                "config",
+                "--file",
+                ".git/config",
+                "--get-regexp",
+                f"^submodule\\.{submodule_path}\\.url",
+            ],
+            text=True,
+            capture_output=True,
+            check=True,
+        ).stdout.strip()
+
+        if url_line:
+            url = url_line.split(" ")[1]
+            return url
+        else:
+            return None
+
+    except (FileNotFoundError, CalledProcessError):
+        return None
+
+
+def _write_definitions_remote_url():
+    """Write the URL of the definitions remote to file."""
+    remote_repo_url = get_definitions_submodule_url()
+    if remote_repo_url is None or not remote_repo_url:
+        return
+
+    with open(
+        os.path.join(os.path.dirname(__file__), "remote_definitions_url.txt"),
+        "w+",
+        encoding="utf-8",
+    ) as file:
+        file.write(remote_repo_url)
+
+
 # pylint: disable=function-redefined
 def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
     """
     PEP 517 compliant build wheel hook.
-    This is a wrapper for setuptools and adds a nexus version file.
+    This is a wrapper for setuptools and adds a nexus version file and a
+    file with the remote of the definitions submodule.
     """
     _write_version_to_metadata()
+    _write_definitions_remote_url()
     return _orig.build_wheel(wheel_directory, config_settings, metadata_directory)
 
 
@@ -70,7 +118,9 @@ def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
 def build_sdist(sdist_directory, config_settings=None):
     """
     PEP 517 compliant build sdist hook.
-    This is a wrapper for setuptools and adds a nexus version file.
+    This is a wrapper for setuptools and adds a nexus version file and a
+    file with the remote of the definitions submodule.
     """
     _write_version_to_metadata()
+    _write_definitions_remote_url()
     return _orig.build_sdist(sdist_directory, config_settings)

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/dataconverter/helpers.py

@@ -577,23 +577,47 @@ def is_value_valid_element_of_enum(value, elist) -> Tuple[bool, list]:
 NUMPY_FLOAT_TYPES = (np.half, np.float16, np.single, np.double, np.longdouble)
 NUMPY_INT_TYPES = (np.short, np.intc, np.int_)
 NUMPY_UINT_TYPES = (np.ushort, np.uintc, np.uint)
-
+# np int for np version 1.26.0
+np_int = (
+    np.intc,
+    np.int_,
+    np.intp,
+    np.int8,
+    np.int16,
+    np.int32,
+    np.int64,
+    np.uint8,
+    np.uint16,
+    np.uint32,
+    np.uint64,
+    np.unsignedinteger,
+    np.signedinteger,
+)
+np_float = (np.float16, np.float32, np.float64, np.floating)
+np_bytes = (np.bytes_, np.byte, np.ubyte)
+np_char = (np.str_, np.char.chararray, *np_bytes)
+np_bool = (np.bool_,)
+np_complex = (np.complex64, np.complex128, np.cdouble, np.csingle)
 NEXUS_TO_PYTHON_DATA_TYPES = {
     "ISO8601": (str,),
-    "NX_BINARY": (bytes, bytearray, np.byte, np.ubyte, np.ndarray),
-    "NX_BOOLEAN": (bool, np.ndarray, np.bool_),
-    "NX_CHAR": (str, np.ndarray, np.chararray),
+    "NX_BINARY": (
+        bytes,
+        bytearray,
+        np.ndarray,
+        *np_bytes,
+    ),
+    "NX_BOOLEAN": (bool, np.ndarray, *np_bool),
+    "NX_CHAR": (str, np.ndarray, *np_char),
     "NX_DATE_TIME": (str,),
-    "NX_FLOAT": (float, np.ndarray, np.floating),
-    "NX_INT": (int, np.ndarray, np.signedinteger),
+    "NX_FLOAT": (float, np.ndarray, *np_float),
+    "NX_INT": (int, np.ndarray, *np_int),
     "NX_UINT": (np.ndarray, np.unsignedinteger),
     "NX_NUMBER": (
         int,
         float,
         np.ndarray,
-        np.signedinteger,
-        np.unsignedinteger,
-        np.floating,
+        *np_int,
+        *np_float,
         dict,
     ),
     "NX_POSINT": (
@@ -601,8 +625,18 @@ NEXUS_TO_PYTHON_DATA_TYPES = {
         np.ndarray,
         np.signedinteger,
     ),  # > 0 is checked in is_valid_data_field()
-    "NX_COMPLEX": (complex, np.ndarray, np.cdouble, np.csingle),
+    "NX_COMPLEX": (complex, np.ndarray, *np_complex),
     "NXDL_TYPE_UNAVAILABLE": (str,),  # Defaults to a string if a type is not provided.
+    "NX_CHAR_OR_NUMBER": (
+        str,
+        int,
+        float,
+        np.ndarray,
+        *np_char,
+        *np_int,
+        *np_float,
+        dict,
+    ),
 }
 
 
@@ -647,7 +681,9 @@ def convert_str_to_bool_safe(value):
     return None
 
 
-def is_valid_data_field(value, nxdl_type, path) -> bool:
+def is_valid_data_field(value, nxdl_type, path):
+    # todo: Check this funciton and wtire test for it. It seems the funciton is not
+    # working as expected.
     """Checks whether a given value is valid according to what is defined in the NXDL.
 
     This function will also try to convert typical types, for example int to float,

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/dataconverter/readers/example/reader.py

@@ -15,7 +15,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-#
 """An example reader implementation for the DataConverter."""
 
 import json

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/definitions/base_classes/NXbeam.nxdl.xml

@@ -202,7 +202,7 @@
     <field name="extent" type="NX_FLOAT" units="NX_LENGTH">
         <doc>
              Size of the beam entering this component. Note this represents
-             a rectangular beam aperture, and values represent FWHM. 
+             a rectangular beam aperture, and values represent FWHM.
              If applicable, the first dimension shall be the horizontal extent
              and the second dimension shall be the vertical extent.
         </doc>
@@ -362,6 +362,16 @@
              FWHM duration of the pulses at the diagnostic point
         </doc>
     </field>
+    <field name="pulse_delay" type="NX_FLOAT" units="NX_TIME">
+        <doc>
+             Delay time between two pulses of a pulsed beam.
+        </doc>
+        <attribute name="reference_beam" type="NX_CHAR">
+            <doc>
+                 A reference to the beam in relation to which the delay is.
+            </doc>
+        </attribute>
+    </field>
     <field name="frog_trace" type="NX_FLOAT">
         <doc>
              FROG trace of the pulse.

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/definitions/dev_tools/tests/test_nxdl_utils.py

@@ -194,3 +194,41 @@ def test_namefitting_precedence(better_fit, better_ref, worse_fit, worse_ref):
     assert nexus.get_nx_namefit(better_fit, better_ref) > nexus.get_nx_namefit(
         worse_fit, worse_ref
     )
+
+
+@pytest.mark.parametrize(
+    "string_obj, decode, expected",
+    [
+        # Test with lists of bytes and strings
+        ([b"bytes", "string"], True, ["bytes", "string"]),
+        ([b"bytes", "string"], False, [b"bytes", "string"]),
+        ([b"bytes", b"more_bytes", "string"], True, ["bytes", "more_bytes", "string"]),
+        (
+            [b"bytes", b"more_bytes", "string"],
+            False,
+            [b"bytes", b"more_bytes", "string"],
+        ),
+        ([b"fixed", b"length", b"strings"], True, ["fixed", "length", "strings"]),
+        ([b"fixed", b"length", b"strings"], False, [b"fixed", b"length", b"strings"]),
+        # Test with nested lists
+        ([[b"nested1"], [b"nested2"]], True, [["nested1"], ["nested2"]]),
+        ([[b"nested1"], [b"nested2"]], False, [[b"nested1"], [b"nested2"]]),
+        # Test with bytes
+        (b"single", True, "single"),
+        (b"single", False, b"single"),
+        # Test with str
+        ("single", True, "single"),
+        ("single", False, "single"),
+        # Test with int
+        (123, True, 123),
+        (123, False, 123),
+    ],
+)
+def test_decode_or_not(string_obj, decode, expected):
+    # Handle normal cases
+    result = nexus.decode_or_not(elem=string_obj, decode=decode)
+    if isinstance(expected, list):
+        assert isinstance(result, list), f"Expected list, but got {type(result)}"
+    # Handle all other cases
+    else:
+        assert result == expected, f"Failed for {string_obj} with decode={decode}"

{pynxtools-0.7.0 → pynxtools-0.7.2}/src/pynxtools/definitions/dev_tools/utils/nxdl_utils.py

@@ -14,10 +14,40 @@ import lxml.etree as ET
 from lxml.etree import ParseError as xmlER
 
 
-def decode_or_not(elem):
-    """Decodes a byte array to string if necessary"""
+def decode_or_not(elem, encoding: str = "utf-8", decode: bool = True):
+    """
+    Decodes a byte array to a string if necessary. All other types are returned untouched.
+    If `decode` is False, the initial value is returned without decoding, including for byte arrays.
+
+    Args:
+        elem: Any Python object that may need decoding.
+        encoding: The encoding scheme to use. Default is "utf-8".
+        decode: A boolean flag indicating whether to perform decoding.
+
+    Returns:
+        A decoded string (in case of a byte string) or the initial value.
+        If `decode` is False, always returns the initial value.
+
+    Raises:
+        ValueError: If a byte string cannot be decoded using the provided encoding.
+    """
+    if not decode:
+        return elem
+
+    # Handle lists of bytes or strings
+    elif isinstance(elem, list):
+        if not elem:
+            return elem  # Return an empty list unchanged
+
+        decoded_list = [decode_or_not(x, encoding, decode) for x in elem]
+        return decoded_list
+
     if isinstance(elem, bytes):
-        elem = elem.decode("UTF-8")
+        try:
+            return elem.decode(encoding)
+        except UnicodeDecodeError as e:
+            raise ValueError(f"Error decoding bytes: {e}")
+
     return elem