add --version option to the programs

ChangeLog.md

@@ -2,6 +2,8 @@
 
 2024-03
 
+- added `--version` option to the programs
+- minor code reorg
 - enabled poetry
     - now packaging and publishing to PyPI 
     - TODO ongoing: README/justfile adjustments, etc. 

pbp/__init__.py

@@ -1,49 +1,14 @@
-import os
-
-import xarray as xr
-
-from pbp.logging_helper import PbpLogger
-
-
-def save_dataset_to_netcdf(logger: PbpLogger, ds: xr.Dataset, filename: str) -> bool:
-    logger.info(f"  - saving dataset to: {filename}")
-    try:
-        ds.to_netcdf(
-            filename,
-            engine="h5netcdf",
-            encoding={
-                "effort": {"_FillValue": None},
-                "frequency": {"_FillValue": None},
-                "sensitivity": {"_FillValue": None},
-            },
-        )
-        return True
-    except Exception as e:  # pylint: disable=broad-exception-caught
-        error = f"Unable to save {filename}: {e}"
-        logger.error(error)
-        print(error)
-        return False
-
-
-def save_dataset_to_csv(logger: PbpLogger, ds: xr.Dataset, filename: str):
-    logger.info(f"  - saving dataset to: {filename}")
+def get_pbp_version() -> str:
     try:
-        ds.to_pandas().to_csv(filename, float_format="%.1f")
-    except Exception as e:  # pylint: disable=broad-exception-caught
-        logger.error(f"Unable to save {filename}: {e}")
-
-
-def get_cpus_to_use(num_cpus: int) -> int:
-    cpu_count: int = os.cpu_count() or 1
-    if num_cpus <= 0 or num_cpus > cpu_count:
-        num_cpus = cpu_count
-    return num_cpus
-
-
-class PBPException(Exception):
-    """
-    Placeholder for a more specific exception.
-    """
-
-    def __init__(self, msg: str):
-        super().__init__(f"PBPException({msg})")
+        import importlib.metadata
+
+        return importlib.metadata.version("mbari-pbp")
+    except Exception:  # pylint: disable=broad-exception-caught
+        try:
+            from poetry.core.factory import Factory
+
+            factory = Factory()
+            poetry = factory.create_poetry()
+            return poetry.package.version.text
+        except Exception:  # pylint: disable=broad-exception-caught
+            return "version not found"

pbp/json_generator/corrector.py

@@ -12,7 +12,7 @@
 import tempfile
 import json
 
-from pbp import PbpLogger
+from pbp.logging_helper import PbpLogger
 
 
 class MetadataCorrector:

pbp/json_generator/gen_iclisten.py

@@ -13,7 +13,7 @@
 import pbp.json_generator.utils as utils
 from pbp.json_generator.corrector import MetadataCorrector
 from pbp.json_generator.metadata_extractor import IcListenWavFile
-from pbp import PbpLogger
+from pbp.logging_helper import PbpLogger
 from pbp.json_generator.gen_abstract import MetadataGeneratorAbstract
 
 

pbp/json_generator/gen_nrs.py

@@ -12,7 +12,7 @@
 from progressbar import progressbar
 from pbp.json_generator.corrector import MetadataCorrector
 from pbp.json_generator.metadata_extractor import FlacFile
-from pbp import PbpLogger
+from pbp.logging_helper import PbpLogger
 from pbp.json_generator.gen_abstract import MetadataGeneratorAbstract
 from pbp.json_generator.utils import parse_s3_or_gcp_url
 

pbp/json_generator/gen_soundtrap.py

@@ -13,7 +13,7 @@
 from pathlib import Path
 from progressbar import progressbar
 
-from pbp import PbpLogger
+from pbp.logging_helper import PbpLogger
 from pbp.json_generator.gen_abstract import MetadataGeneratorAbstract
 from pbp.json_generator.metadata_extractor import SoundTrapWavFile
 from pbp.json_generator.corrector import MetadataCorrector

pbp/main_args.py

@@ -1,6 +1,9 @@
 from argparse import ArgumentParser, RawTextHelpFormatter
 
 
+from pbp import get_pbp_version
+
+
 def parse_arguments():
     description = "PyPAM based processing of Pacific Sound data."
     example = """
@@ -15,6 +18,12 @@ def parse_arguments():
         description=description, epilog=example, formatter_class=RawTextHelpFormatter
     )
 
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=get_pbp_version(),
+    )
+
     parser.add_argument(
         "--json-base-dir",
         type=str,

pbp/main_json_generator_args.py

@@ -1,5 +1,7 @@
 from argparse import ArgumentParser, RawTextHelpFormatter
 
+from pbp import get_pbp_version
+
 
 def parse_arguments():
     description = (
@@ -22,6 +24,12 @@ def parse_arguments():
         description=description, epilog=example, formatter_class=RawTextHelpFormatter
     )
 
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=get_pbp_version(),
+    )
+
     class InstrumentType:
         NRS = "NRS"
         ICLISTEN = "ICLISTEN"

pbp/plot.py

@@ -7,13 +7,20 @@
     DEFAULT_YLIM,
     DEFAULT_CMLIM,
 )
+from pbp import get_pbp_version
 
 
 def parse_arguments():
     description = "Generate summary plots for given netcdf files."
 
     parser = ArgumentParser(description=description, formatter_class=RawTextHelpFormatter)
 
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=get_pbp_version(),
+    )
+
     parser.add_argument(
         "--latlon",
         type=float,

pbp/process_helper.py

@@ -7,8 +7,6 @@
 import numpy as np
 import xarray as xr
 
-from pbp import save_dataset_to_csv, save_dataset_to_netcdf
-
 from pbp.file_helper import FileHelper
 from pbp.logging_helper import PbpLogger
 from pbp.metadata import MetadataHelper, parse_attributes, replace_snippets
@@ -312,3 +310,31 @@ def _get_global_attributes(self, year: int, month: int, day: int):
         for k, v in global_attrs.items():
             snippets["{{" + k + "}}"] = v
         return replace_snippets(global_attrs, snippets)
+
+
+def save_dataset_to_netcdf(logger: PbpLogger, ds: xr.Dataset, filename: str) -> bool:
+    logger.info(f"  - saving dataset to: {filename}")
+    try:
+        ds.to_netcdf(
+            filename,
+            engine="h5netcdf",
+            encoding={
+                "effort": {"_FillValue": None},
+                "frequency": {"_FillValue": None},
+                "sensitivity": {"_FillValue": None},
+            },
+        )
+        return True
+    except Exception as e:  # pylint: disable=broad-exception-caught
+        error = f"Unable to save {filename}: {e}"
+        logger.error(error)
+        print(error)
+        return False
+
+
+def save_dataset_to_csv(logger: PbpLogger, ds: xr.Dataset, filename: str):
+    logger.info(f"  - saving dataset to: {filename}")
+    try:
+        ds.to_pandas().to_csv(filename, float_format="%.1f")
+    except Exception as e:  # pylint: disable=broad-exception-caught
+        logger.error(f"Unable to save {filename}: {e}")