Merge branch 'main' into fix-missing-schema-json-file

Author: bendhouseart

Makefile

@@ -26,7 +26,6 @@ add:
 
 # copies metadata to path included in pypet2bids project to enable packaging of those files w/ poetry
 buildpackage:
-	@cp -R metadata/ pypet2bids/pypet2bids/metadata
 	@cp pypet2bids/pyproject.toml pypet2bids/pypet2bids/pyproject.toml
 	@rm -rf pypet2bids/dist
 	@cd pypet2bids && poetry lock && poetry build

pypet2bids/poetry.lock

@@ -588,7 +588,7 @@ def run_dcm2niix(self):
                             created_path,
                             check_for_missing,
                             dicom_header,
-                            dicom2bids_json=metadata_dictionaries["dicom2bids.json"],
+                            dicom2bids_json=metadata_dictionaries["dicom2bids"],
                             **self.additional_arguments,
                         )
 

pypet2bids/pypet2bids/dcm2niix4pet.py

@@ -39,6 +39,12 @@
 import argparse
 from typing import Union
 from platform import system
+import importlib
+
+try:
+    import metadata
+except ImportError:
+    from pypet2bids import metadata
 
 parent_dir = pathlib.Path(__file__).parent.resolve()
 project_dir = parent_dir.parent.parent
@@ -55,14 +61,12 @@
 )
 
 # load bids schema
-bids_schema_path = os.path.join(metadata_dir, "schema.json")
-schema = json.load(open(bids_schema_path, "r"))
+schema = metadata.schema
 
 # putting these paths here as they are reused in dcm2niix4pet.py, update_json_pet_file.py, and ecat.py
 module_folder = Path(__file__).parent.resolve()
 python_folder = module_folder.parent
 pet2bids_folder = python_folder.parent
-metadata_folder = os.path.join(pet2bids_folder, "metadata")
 
 loggers = {}
 
@@ -316,27 +320,37 @@ def load_vars_from_config(
 
 def get_version():
     """
-    Gets the version of this software from the toml file
-    :return: version number from pyproject.toml
+    Gets the version of this software
+    :return: version number
     """
     # this scripts directory path
     scripts_dir = pathlib.Path(os.path.dirname(__file__))
 
-    try:
-        # if this is bundled as a package look next to this file for the pyproject.toml
-        toml_path = os.path.join(scripts_dir, "pyproject.toml")
-        with open(toml_path, "r") as infile:
-            tomlfile = toml.load(infile)
-    except FileNotFoundError:
-        # when in development the toml file with the version is 2 directories above (e.g. where it should actually live)
-        toml_dir = scripts_dir.parent
-        toml_path = os.path.join(toml_dir, "pyproject.toml")
-        with open(toml_path, "r") as infile:
-            tomlfile = toml.load(infile)
-
-    attrs = tomlfile.get("tool", {})
-    poetry = attrs.get("poetry", {})
-    version = poetry.get("version", "")
+    # first try using importlib.metadata.version to determine version
+
+    version = importlib.metadata.version("pypet2bids")
+
+    if not version:
+        tomlfile = {}
+
+        try:
+            # if this is bundled as a package look next to this file for the pyproject.toml
+            toml_path = os.path.join(scripts_dir, "pyproject.toml")
+            with open(toml_path, "r") as infile:
+                tomlfile = toml.load(infile)
+        except FileNotFoundError:
+            # when in development the toml file with the version is 2 directories above (e.g. where it should actually live)
+            try:
+                toml_dir = scripts_dir.parent
+                toml_path = os.path.join(toml_dir, "pyproject.toml")
+                with open(toml_path, "r") as infile:
+                    tomlfile = toml.load(infile)
+            except FileNotFoundError:
+                pass
+
+        attrs = tomlfile.get("tool", {})
+        poetry = attrs.get("poetry", {})
+        version = poetry.get("version", "")
 
     return version
 
@@ -820,9 +834,7 @@ def get_recon_method(ReconstructionMethodString: str) -> dict:
         dimension = re.search(search_criteria, ReconMethodName)[0]
 
     # doing some more manipulation of the recon method name to expand it from not so helpful acronyms
-    possible_names = load_pet_bids_requirements_json(pet_reconstruction_metadata_json)[
-        "reconstruction_names"
-    ]
+    possible_names =  metadata.PET_reconstruction_methods.get("reconstruction_names", [])
 
     # we want to sort the possible names by longest first that we don't break up an acronym prematurely
     sorted_df = pandas.DataFrame(possible_names).sort_values(