Updates to use Pathlib rather than str or os.path (#41)

* Updates to use Pathlib rather than str or os.path

* formatting

* Updates to use Pathlib rather than str or os.path

* Update hermes_eea/calibration/calibration.py

Co-authored-by: Damian Barrous Dume <damianbarrous@gmail.com>

* More Updates for Pathlib

* Remove Unused Import

---------

Co-authored-by: Damian Barrous Dume <damianbarrous@gmail.com>

hermes_eea/__init__.py

@@ -1,6 +1,5 @@
 # Licensed under Apache License v2 - see LICENSE.rst
-import os.path
-import sys
+from pathlib import Path
 
 from hermes_core import log
 from hermes_eea.io.file_tools import read_file
@@ -20,9 +19,9 @@
 INST_TO_SHORTNAME = {INST_NAME: INST_SHORTNAME}
 INST_TO_TARGETNAME = {INST_NAME: INST_TARGETNAME}
 
-_package_directory = os.path.dirname(os.path.abspath(__file__))
-_data_directory = os.path.abspath(os.path.join(_package_directory, "data"))
-_calibration_directory = os.path.abspath(os.path.join(_data_directory, "calibration"))
+_package_directory = Path(__file__).parent
+_data_directory = _package_directory / "data"
+_calibration_directory = _data_directory / "calibration"
 
 
 log.info(f"hermes_eea version: {__version__}")

hermes_eea/calibration/calibration.py

@@ -2,9 +2,6 @@
 A module for all things calibration.
 """
 
-from datetime import datetime, timezone, timedelta
-import random
-import os.path
 from pathlib import Path
 import sys
 import ccsdspy
@@ -36,33 +33,37 @@
 def process_file(data_filename: Path) -> list:
     """
     This is the entry point for the pipeline processing.
-    It runs all of the various processing steps required
-    to create a L1A Hermes CDF File
+    It runs all of the various processing steps required to create a L1A Hermes CDF File.
     calls:
-        calibrate_file()
-           parse_science
-           CCSDSPY (parse_L0_sci_packets())
-           l0_sci_data_to_cdf()
-                SkymapFactory()
-                Use HermesData to populate CDF output file
-                Write the File
-        A Custom EEA SkymapFactory
-        HermesData
+
+    .. code-block:: python
+
+        calibrate_file(...)
+            parse_science_filename(...)
+            parse_l0_sci_packets(...)
+            l0_sci_data_to_cdf(...)
+                SkymapFactory(...)
+                # Use HermesData to populate CDF output file
+                Hermes_EEA_Data_Processor(...).build_HermesData()
+                # Write the File
+                hermes_eea_data.save(...)
+        # A Custom EEA SkymapFactory
+        # HermesData
+
 
     Parameters
     ----------
-    data_filename: str
+    data_filename: `pathlib.Path`
         Fully specificied filename of an input file.
-        The file contents:
-            Traditional binary packets in CCSDS format
+        The file contents: Traditional binary packets in CCSDS format
 
 
     Returns
     -------
-    output_filenames: list
-        Fully specificied filenames for the output files.
-    The file contents:
-        CDF formatted file with n packets iincluding time and [41,4,32] skymap.
+    output_files: `list[pathlib.Path]`
+        Fully specificied filenames for the output CDF files.
+        The file contains CDF formatted file with n packets iincluding time and [41,4,32] skymap.
+
     """
     log.info(f"Processing file {data_filename}.")
     output_files = []
@@ -82,19 +83,21 @@ def process_file(data_filename: Path) -> list:
     return output_files
 
 
-def calibrate_file(data_filename: Path, destination_dir) -> Path:
+def calibrate_file(data_filename: Path, destination_dir: Path) -> Path:
     """
     Given an input data file, raise it to the next level
     (e.g. level 0 to level 1, level 1 to quicklook) it and return a new file.
 
     Parameters
     ----------
-    data_filename: Path
+    data_filename: `pathlib.Path`
         Fully specificied filename of the input data file.
+    destination_dir: `pathlib.Path`
+        Fully specificied directory where the output file will be written.
 
     Returns
     -------
-    output_filename: Path
+    output_filename: `pathlib.Path`
         Fully specificied filename of the output file.
 
     """
@@ -156,7 +159,7 @@ def parse_l0_sci_packets(data_filename: Path) -> dict:
 
     Parameters
     ----------
-    data_filename: str
+    data_filename: `pathlib.Path`
         Fully specificied filename
 
     Returns
@@ -173,7 +176,7 @@ def parse_l0_sci_packets(data_filename: Path) -> dict:
     log.info(f"Parsing packets from file:{data_filename}.")
 
     pkt = ccsdspy.FixedLength.from_file(
-        os.path.join(hermes_eea._data_directory, "hermes_EEA_sci_packet_def.csv")
+        Path(hermes_eea._data_directory) / "hermes_EEA_sci_packet_def.csv"
     )
     data = pkt.load(data_filename)
     return data
@@ -189,12 +192,14 @@ def l0_sci_data_to_cdf(
     ----------
     data: dict
         A dictionary of arrays which includes the ccsds header fields
-    original_filename: Path
+    original_filename: `pathlib.Path`
         The Path to the originating file.
+    destination_dir: `pathlib.Path`
+        The directory where the output file will be written.
 
     Returns
     -------
-    output_filename: Path
+    output_filename: `pathlib.Path`
         Fully specificied filename of cdf file
 
     Examples
@@ -243,7 +248,7 @@ def l0_sci_data_to_cdf(
         try:
             # this writes out the data to CDF file format
             cdf_path = hermes_eea_factory.hermes_eea_data.save(
-                str(destination_dir), True
+                output_path=destination_dir, overwrite=True
             )
         except Exception as e:
             log.error(e)
@@ -257,19 +262,19 @@ def get_calibration_file(data_filename: Path, time=None) -> Path:
     Given a time, return the appropriate calibration file.
     Parameters
     ----------
-    data_filename: str
+    data_filename: `pathlib.Path`
         Fully specificied filename of the non-calibrated file (data level < 2)
     time: ~astropy.time.Time
 
     Returns
     -------
-    calib_filename: str
+    calib_filename: `pathlib.Path`
         Fully specificied filename for the appropriate calibration file.
 
     Examples
     --------
     """
-    return os.path.join(hermes_eea._calibration_directory, data_filename)
+    return Path(hermes_eea._calibration_directory) / data_filename
 
 
 def read_calibration_file(calib_filename: Path):
@@ -278,18 +283,18 @@ def read_calibration_file(calib_filename: Path):
 
     Parameters
     ----------
-    calib_filename: str
+    calib_filename: `pathlib.Path`
         Fully specificied filename of the non-calibrated file (data level < 2)
 
     Returns
     -------
-    output_filename: str
+    output_filename: `pathlib.Path`
         Fully specificied filename of the appropriate calibration file.
 
     Examples
     --------
     """
-    lines = read_file(os.path.join(calib_filename))
+    lines = read_file(calib_filename)
     calib.energies = []
     calib.deflections = []
     for line in lines:

hermes_eea/io/file_tools.py

@@ -1,6 +1,6 @@
+from pathlib import Path
 from ccsdspy import FixedLength
 import numpy as np
-import os
 
 """
 This module provides a generic file reader.
@@ -9,13 +9,13 @@
 __all__ = ["read_file", "read_ccsds"]
 
 
-def read_file(data_filename):
+def read_file(data_filename: Path):
     """
     Read a file.
 
     Parameters
     ----------
-    data_filename: str
+    data_filename: `pathlib.Path`
         A file to read.
 
     Returns
@@ -29,16 +29,16 @@ def read_file(data_filename):
         with open(data_filename) as fh:
             return fh.readlines()
     except Exception:
-        raise Exception("Could not find: " + os.path.abspath(data_filename))
+        raise Exception("Could not find: " + data_filename)
 
 
-def read_ccsds(filename: str, pkt_def: FixedLength):
+def read_ccsds(filename: Path, pkt_def: FixedLength):
     """
     Read a ccsds packet file.
 
     Parameters
     ----------
-    filename: str
+    filename: `pathlib.Path`
         A file to read.
 
     pkt_def: `ccsdspy.FixedLength`

hermes_eea/tests/go_plotly.py

@@ -1,5 +1,5 @@
-import os
 import sys
+from pathlib import Path
 import numpy as np
 import math
 
@@ -40,7 +40,7 @@ def read_data(file):
         print("file len:", length)
         return cdffile
     except Exception:
-        if not os.path.exists(file):
+        if not Path(file).exists():
             print(file + " does not exist")
             return None
 

hermes_eea/tests/test_calibration.py

@@ -1,5 +1,4 @@
 import pytest
-import os.path
 from pathlib import Path
 import shutil
 import tempfile
@@ -16,7 +15,7 @@
 
 @pytest.fixture(scope="session")  # this is a pytest fixture
 def small_level0_file(tmp_path_factory):
-    fn = Path(os.path.join(_data_directory, "hermes_EEA_l0_2023042-000000_v0.bin"))
+    fn = Path(_data_directory) / "hermes_EEA_l0_2023042-000000_v0.bin"
     return fn
 
 
@@ -32,7 +31,7 @@ def test_read_ccsdspy(small_level0_file):
 
     """
     pkt = ccsdspy.FixedLength.from_file(
-        os.path.join(hermes_eea._data_directory, "hermes_EEA_sci_packet_def.csv")
+        Path(hermes_eea._data_directory) / "hermes_EEA_sci_packet_def.csv"
     )
     result = read_ccsds(small_level0_file, pkt)
     assert len(result["ACCUM"]) == 3051
@@ -54,10 +53,12 @@ def test_process_file(small_level0_file):
             # Process the File
             output_files = calib.process_file(temp_test_file_path)
 
-            assert os.path.getsize(output_files[0]) > 0
+            for f in output_files:
+                assert isinstance(f, Path)
+            assert output_files[0].stat().st_size > 0
 
             # Ensure the file is closed before attempting to delete it
-            with pycdf.CDF(output_files[0]) as cdf:
+            with pycdf.CDF(str(output_files[0])) as cdf:
                 assert len(cdf["Epoch"][:]) == 18
 
     # Ensure the temporary directory is cleaned up even if an exception is raised (needed for Windows)

hermes_eea/tests/test_file_tools.py

@@ -1,5 +1,8 @@
+from pathlib import Path
 from hermes_eea.io.file_tools import read_file
 
 
 def test_read_file():
-    assert read_file("./hermes_eea/data/calibration/flight_stepper.txt") is not None
+    assert (
+        read_file(Path("./hermes_eea/data/calibration/flight_stepper.txt")) is not None
+    )