Fixed steps i), ii), all 176 examples processed successfully, PSE cov…

…erage 58 elements, 5.9 billions ions in total, 77 projects from research of all major groups worldwide, next steps: iii) move to ifes, vi) nxdef refactor, v) eln, cfg parsing, RUN ALL and check proper annotation, styling, linting ruff

pynxtools/dataconverter/readers/apm/reader.py

@@ -119,8 +119,10 @@ def read(self,
                 print("No input-file defined for ranging definitions!")
                 return {}
 
+        """
         print("Create NeXus default plottable data...")
         apm_default_plot_generator(template, n_entries)
+        """
 
         # print("Reporting state of template before passing to HDF5 writing...")
         # for keyword in template.keys():

pynxtools/dataconverter/readers/apm/utils/apm_define_io_cases.py

@@ -59,11 +59,14 @@ def sort_files_by_file_name_suffix(self, file_paths: Tuple[str] = None):
                 if suffix not in [".h5", "range_.h5"]:
                     if (fpath.lower().endswith(suffix)) and (fpath not in self.case[suffix]):
                         self.case[suffix].append(fpath)
+                        break
                 else:
-                    if fpath.lower().endswith("range_.h5") is True:
+                    if fpath.lower().endswith("range_.h5") == True:
                         self.case["range_.h5"].append(fpath)
-                    elif fpath.lower().endswith(".h5") is True:
+                        break
+                    elif fpath.lower().endswith(".h5") == True:
                         self.case[".h5"].append(fpath)
+                        break
                     else:
                         continue
                 # HDF5 files need special treatment, this already shows that magic numbers
@@ -76,14 +79,20 @@ def check_validity_of_file_combinations(self):
         range_input = 0  # ranging definition file, e.g. RNG, RRNG, ENV, FIG.TXT
         other_input = 0  # generic ELN or OASIS-specific configurations
         for suffix, value in self.case.items():
-            if suffix in VALID_FILE_NAME_SUFFIX_RECON:
-                recon_input += len(value)
-            elif suffix in VALID_FILE_NAME_SUFFIX_RANGE:
-                range_input += len(value)
-            elif suffix in VALID_FILE_NAME_SUFFIX_CONFIG:
-                other_input += len(value)
+            if suffix not in [".h5", "range_.h5"]:
+                if suffix in VALID_FILE_NAME_SUFFIX_RECON:
+                    recon_input += len(value)
+                elif suffix in VALID_FILE_NAME_SUFFIX_RANGE:
+                    range_input += len(value)
+                elif suffix in VALID_FILE_NAME_SUFFIX_CONFIG:
+                    other_input += len(value)
+                else:
+                    continue
             else:
-                continue
+                if suffix == "range_.h5":
+                    range_input += len(value)
+                if suffix == ".h5":
+                    recon_input += len(value)
 
         if (recon_input == 1) and (range_input == 1):  # and (1 <= other_input <= 2):
             self.is_valid = True

pynxtools/dataconverter/readers/apm/utils/apm_load_ranging.py

@@ -39,6 +39,11 @@
 from pynxtools.dataconverter.readers.apm.utils.apm_define_io_cases \
     import VALID_FILE_NAME_SUFFIX_RANGE
 
+WARNING_TOO_MANY_DEFINITIONS \
+    = f"WARNING::Range file contains more than {MAX_NUMBER_OF_ION_SPECIES} " \
+      f"WARNING::definitions! This is often a signature of duplicates or " \
+      f"WARNING::contradicting definitions."
+
 
 def add_unknown_iontype(template: dict, entry_id: int) -> dict:
     """Add default unknown iontype."""
@@ -139,8 +144,7 @@ def extract_data_from_env_file(file_path: str, template: dict, entry_id: int) ->
     print(f"Extracting data from ENV file: {file_path}")
     rangefile = ReadEnvFileFormat(file_path)
     if len(rangefile.env["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
-        raise ValueError(f"Current implementation does not support "
-                         f"more than {MAX_NUMBER_OF_ION_SPECIES} ion types")
+        print(WARNING_TOO_MANY_DEFINITIONS)
 
     add_standardize_molecular_ions(
         rangefile.env["molecular_ions"], template, entry_id)
@@ -152,8 +156,7 @@ def extract_data_from_fig_txt_file(file_path: str, template: dict, entry_id: int
     print(f"Extracting data from FIG.TXT file: {file_path}")
     rangefile = ReadFigTxtFileFormat(file_path)
     if len(rangefile.fig["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
-        raise ValueError(f"Current implementation does not support "
-                         f"more than {MAX_NUMBER_OF_ION_SPECIES} ion types")
+        print(WARNING_TOO_MANY_DEFINITIONS)
 
     add_standardize_molecular_ions(
         rangefile.fig["molecular_ions"], template, entry_id)
@@ -165,8 +168,7 @@ def extract_data_from_pyccapt_file(file_path: str, template: dict, entry_id: int
     print(f"Extracting data from pyccapt/ranging HDF5 file: {file_path}")
     rangefile = ReadPyccaptRangingFileFormat(file_path)
     if len(rangefile.rng["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
-        raise ValueError(f"Current implementation does not support "
-                         f"more than {MAX_NUMBER_OF_ION_SPECIES} ion types")
+        print(WARNING_TOO_MANY_DEFINITIONS)
 
     add_standardize_molecular_ions(
         rangefile.rng["molecular_ions"], template, entry_id)
@@ -178,8 +180,7 @@ def extract_data_from_rng_file(file_path: str, template: dict, entry_id: int) ->
     print(f"Extracting data from RNG file: {file_path}")
     rangefile = ReadRngFileFormat(file_path)
     if len(rangefile.rng["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
-        raise ValueError(f"Current implementation does not support "
-                         f"more than {MAX_NUMBER_OF_ION_SPECIES} ion types")
+        print(WARNING_TOO_MANY_DEFINITIONS)
 
     add_standardize_molecular_ions(
         rangefile.rng["molecular_ions"], template, entry_id)
@@ -191,8 +192,7 @@ def extract_data_from_rrng_file(file_path: str, template: dict, entry_id) -> dic
     print(f"Extracting data from RRNG file: {file_path}")
     rangefile = ReadRrngFileFormat(file_path)
     if len(rangefile.rrng["molecular_ions"]) > np.iinfo(np.uint8).max + 1:
-        raise ValueError(f"Current implementation does not support more "
-                         f"than {MAX_NUMBER_OF_ION_SPECIES} ion types")
+        print(WARNING_TOO_MANY_DEFINITIONS)
 
     add_standardize_molecular_ions(
         rangefile.rrng["molecular_ions"], template, entry_id)
@@ -207,7 +207,7 @@ def __init__(self, file_path: str, entry_id: int):
                                      "file_path": file_path,
                                      "entry_id": entry_id}
         for suffix in VALID_FILE_NAME_SUFFIX_RANGE:
-            if file_path.lower().endswith(suffix) is True:
+            if file_path.lower().endswith(suffix) == True:
                 self.meta["file_format"] = suffix
                 break
         if self.meta["file_format"] is None:

pynxtools/dataconverter/readers/apm/utils/apm_load_reconstruction.py

@@ -224,7 +224,7 @@ def __init__(self, file_path: str, entry_id: int):
                                      "file_path": file_path,
                                      "entry_id": entry_id}
         for suffix in VALID_FILE_NAME_SUFFIX_RECON:
-            if file_path.lower().endswith(suffix) is True:
+            if file_path.lower().endswith(suffix) == True:
                 self.meta["file_format"] = suffix
                 break
         if self.meta["file_format"] is None: