pynxtools 0.3.1__tar.gz → 0.3.2__tar.gz

{pynxtools-0.3.1 → pynxtools-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynxtools
-Version: 0.3.1
+Version: 0.3.2
 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: 
@@ -249,16 +249,16 @@ Requires-Dist: pip-tools; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: convert
 Requires-Dist: pynxtools[apm,ellips,em,mpes,stm,xps,xrd]; extra == "convert"
+Provides-Extra: mpes
+Requires-Dist: pynxtools-mpes; extra == "mpes"
 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
-Requires-Dist: pynxtools-xps; extra == "xps"
 Provides-Extra: stm
 Requires-Dist: pynxtools-stm; extra == "stm"
+Provides-Extra: xps
+Requires-Dist: pynxtools-xps; extra == "xps"
 Provides-Extra: xrd
 Requires-Dist: pynxtools-xrd; extra == "xrd"
 Provides-Extra: ellips

pynxtools-0.3.2/pynxtools/testing/nexus_conversion.py

@@ -0,0 +1,134 @@
+"""Generic test for reader plugins."""
+
+from typing import Literal
+
+import logging
+import os
+from glob import glob
+
+from pynxtools.dataconverter.helpers import get_nxdl_root_and_path
+from pynxtools.dataconverter.convert import get_reader, transfer_data_into_template
+from pynxtools.dataconverter.validation import validate_dict_against
+from pynxtools.dataconverter.writer import Writer
+from pynxtools.nexus import nexus
+
+
+def get_log_file(nxs_file, log_file, tmp_path):
+    """Get log file for the nexus file with read_nexus tools."""
+    logger = logging.getLogger(__name__)
+    logger.handlers.clear()
+    logger.setLevel(logging.DEBUG)
+    log_file = os.path.join(tmp_path, log_file)
+    handler = logging.FileHandler(log_file, "w")
+    formatter = logging.Formatter("%(levelname)s - %(message)s")
+    handler.setLevel(logging.DEBUG)
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+    nexus_helper = nexus.HandleNexus(logger, nxs_file, None, None)
+    nexus_helper.process_nexus_master_file(None)
+    return log_file
+
+
+class ReaderTest:
+    """Generic test for reader plugins."""
+
+    def __init__(self, nxdl, reader_name, files_or_dir, tmp_path, caplog) -> None:
+        """Initialize the test object.
+
+        Parameters
+        ----------
+        nxdl : str
+            Name of the NXDL application definition that is to be tested by this reader plugin (e.g. NXsts, NXmpes, etc).
+        reader_name : str
+            The name of the reader class (e.g. stm, mpes, xps, ...) to be tested.
+        files_or_dir : str
+            List of input files or full path string to the example data directory that contains all the files
+            required for running the data conversion through the reader.
+        ref_nexus_file : str
+            Full path string to the reference NeXus file generated from the same
+            set of input files.
+        tmp_path : pathlib.PosixPath
+            Pytest fixture variable, used to clean up the files generated during the test.
+        caplog : _pytest.logging.LogCaptureFixture
+            Pytest fixture variable, used to capture the log messages during the test.
+        """
+
+        self.nxdl = nxdl
+        self.reader_name = reader_name
+        self.reader = get_reader(self.reader_name)
+        self.files_or_dir = files_or_dir
+        self.ref_nexus_file = ""
+        self.tmp_path = tmp_path
+        self.caplog = caplog
+        self.created_nexus = f"{tmp_path}/{os.sep}/output.nxs"
+
+    def convert_to_nexus(
+        self,
+        caplog_level: Literal["ERROR", "WARNING"] = "ERROR",
+        ignore_undocumented: bool = False,
+    ):
+        """
+        Test the example data for the reader plugin.
+        """
+        assert hasattr(
+            self.reader, "supported_nxdls"
+        ), f"Reader{self.reader} must have supported_nxdls attribute"
+        assert callable(self.reader.read), f"Reader{self.reader} must have read method"
+
+        if isinstance(self.files_or_dir, (list, tuple)):
+            example_files = self.files_or_dir
+        else:
+            example_files = sorted(glob(os.path.join(self.files_or_dir, "*")))
+        self.ref_nexus_file = [file for file in example_files if file.endswith(".nxs")][
+            0
+        ]
+        input_files = [file for file in example_files if not file.endswith(".nxs")]
+        assert self.ref_nexus_file, "Reference nexus (.nxs) file not found"
+        assert (
+            self.nxdl in self.reader.supported_nxdls
+        ), f"Reader does not support {self.nxdl} NXDL."
+
+        nxdl_root, nxdl_file = get_nxdl_root_and_path(self.nxdl)
+        assert os.path.exists(nxdl_file), f"NXDL file {nxdl_file} not found"
+
+        read_data = transfer_data_into_template(
+            input_file=input_files,
+            reader=self.reader_name,
+            nxdl_name=self.nxdl,
+            nxdl_root=nxdl_root,
+            skip_verify=True,
+        )
+
+        # Clear the log of `transfer_data_into_template`
+        self.caplog.clear()
+
+        with self.caplog.at_level(caplog_level):
+            _ = validate_dict_against(
+                self.nxdl, read_data, ignore_undocumented=ignore_undocumented
+            )
+        assert self.caplog.text == ""
+
+        Writer(read_data, nxdl_file, self.created_nexus).write()
+
+    def check_reproducibility_of_nexus(self):
+        """Reproducibility test for the generated nexus file."""
+        ref_log = get_log_file(self.ref_nexus_file, "ref_nexus.log", self.tmp_path)
+        gen_log = get_log_file(self.created_nexus, "gen_nexus.log", self.tmp_path)
+        with open(gen_log, "r", encoding="utf-8") as gen, open(
+            ref_log, "r", encoding="utf-8"
+        ) as ref:
+            gen_lines = gen.readlines()
+            ref_lines = ref.readlines()
+        if len(gen_lines) != len(ref_lines):
+            assert False, "Log files are different"
+        for ind, (gen_l, ref_l) in enumerate(zip(gen_lines, ref_lines)):
+            if gen_l != ref_l:
+                # skip version conflicts
+                if gen_l.startswith("DEBUG - value: v") and ref_l.startswith(
+                    "DEBUG - value: v"
+                ):
+                    continue
+                assert False, (
+                    f"Log files are different at line {ind}"
+                    f" generated: {gen_l} \n referenced : {ref_l}"
+                )

{pynxtools-0.3.1 → pynxtools-0.3.2}/pynxtools.egg-info/SOURCES.txt

@@ -402,4 +402,6 @@ pynxtools/eln_mapper/eln.py
 pynxtools/eln_mapper/eln_mapper.py
 pynxtools/eln_mapper/scheme_eln.py
 pynxtools/nexus/__init__.py
-pynxtools/nexus/nexus.py
+pynxtools/nexus/nexus.py
+pynxtools/testing/__init__.py
+pynxtools/testing/nexus_conversion.py