From d617c2a5a43bd0dce417173771a7d8e1455ca964 Mon Sep 17 00:00:00 2001
From: Daralynn Rhode <143308810+daralynnrhode@users.noreply.github.com>
Date: Thu, 4 Jul 2024 09:05:06 -0600
Subject: [PATCH] Add mypy Pre-commit Hook and Fix tools folder Pt.1 (#659)

* mypy for tools folder

* mypy check for tools folder

* xtce generation mypy update

* reworking the usage

* some mypy changes

* exclude type-arg check for list and dict

* mypy update for tools folder, completed

* small change

* updates for Et.Element

* merge conflict changes
---
 .pre-commit-config.yaml                       | 11 +++-
 pyproject.toml                                |  4 ++
 .../metadata_generation/metadata_generator.py | 13 ++--
 tools/spice/spice_examples.py                 | 11 ++--
 tools/spice/spice_utils.py                    |  7 +-
 .../ccsds_header_xtce_generator.py            |  2 +-
 tools/xtce_generation/telemetry_generator.py  | 64 ++++++++++++-------
 .../xtce_generation/xtce_generator_codice.py  |  2 +-
 tools/xtce_generation/xtce_generator_glows.py |  2 +-
 tools/xtce_generation/xtce_generator_hi.py    |  2 +-
 tools/xtce_generation/xtce_generator_hit.py   |  2 +-
 tools/xtce_generation/xtce_generator_lo.py    |  2 +-
 tools/xtce_generation/xtce_generator_mag.py   |  6 +-
 tools/xtce_generation/xtce_generator_swapi.py |  2 +-
 tools/xtce_generation/xtce_generator_swe.py   |  2 +-
 .../xtce_generator_template.py                | 10 +--
 16 files changed, 93 insertions(+), 49 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8d90509e4..ead9bd442 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -37,4 +37,13 @@ repos:
     hooks:
       - id: numpydoc-validation
         exclude: '^imap_processing/tests/|.*test.*'
-
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.10.0'
+    hooks:
+      - id: mypy
+        pass_filenames: false
+        args: [., --strict, --explicit-package-bases,
+                --disable-error-code, import-untyped,
+                --disable-error-code, import-not-found,
+                --disable-error-code, no-untyped-call,
+                --disable-error-code, type-arg]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 7dfa204ea..1203e73ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -116,3 +116,7 @@ checks = ["all", #report on all checks, except the following
     "ES01", # Ignore No extended summary found
     "RT02" ] # Ignore The first line of the Returns section
 exclude = ['__init__' ] # don't report on objects that match any of these regex
+
+[tool.mypy]
+follow_imports = 'skip'
+exclude = ["tests", "docs", "imap_processing"]
diff --git a/tools/metadata_generation/metadata_generator.py b/tools/metadata_generation/metadata_generator.py
index 9e4f305ac..9dab2c454 100644
--- a/tools/metadata_generation/metadata_generator.py
+++ b/tools/metadata_generation/metadata_generator.py
@@ -1,12 +1,13 @@
 """SWAPI metadata generator."""
 
 from pathlib import Path
+from typing import Optional, Union
 
 import pandas as pd
 import yaml
 
 
-def get_global_attributes(sheet):
+def get_global_attributes(sheet: pd.DataFrame) -> pd.DataFrame:
     """
     Get the global attributes from a metadata spreadsheet.
 
@@ -17,7 +18,7 @@ def get_global_attributes(sheet):
 
     Returns
     -------
-    dict
+    pd.DataFrame
         A dictionary of the global attributes, where the keys are the attribute names
         and the values are the attribute descriptions.
     """
@@ -27,7 +28,9 @@ def get_global_attributes(sheet):
     return sheet.to_dict()["CATDESC"]
 
 
-def get_dataset_attributes(sheet, global_attrs=None):
+def get_dataset_attributes(
+    sheet: pd.DataFrame, global_attrs: Optional[dict] = None
+) -> dict:
     """
     Get the dataset attributes from a metadata spreadsheet.
 
@@ -35,7 +38,7 @@ def get_dataset_attributes(sheet, global_attrs=None):
     ----------
     sheet : pandas.DataFrame
         A sheet/tab from an Excel file represented as a pandas DataFrame.
-    global_attrs : list todo check
+    global_attrs : dict or None
         List of global attributes.
 
     Returns
@@ -64,7 +67,7 @@ def get_dataset_attributes(sheet, global_attrs=None):
 
 
 # Load all sheets
-def process_file(excel_path, output_folder):
+def process_file(excel_path: Union[str, Path], output_folder: Path) -> None:
     """
     Will process the metadata file and output the metadata to a JSON file.
 
diff --git a/tools/spice/spice_examples.py b/tools/spice/spice_examples.py
index 2906d56e4..8bf7b6d4e 100644
--- a/tools/spice/spice_examples.py
+++ b/tools/spice/spice_examples.py
@@ -8,13 +8,14 @@
 
 import logging
 
+import numpy as np
 import spiceypy as spice
 
 # Logger setup
 logger = logging.getLogger(__name__)
 
 
-def get_attitude_timerange(ck_kernel, id):
+def get_attitude_timerange(ck_kernel: str, id: int) -> tuple:
     """
     Get attitude timerange using the ck kernel.
 
@@ -65,7 +66,9 @@ def get_attitude_timerange(ck_kernel, id):
     return start, end
 
 
-def _get_particle_velocity(direct_events):
+def _get_particle_velocity(
+    direct_events: dict,
+) -> np.ndarray:
     """
     Get the particle velocity in the heliosphere frame.
 
@@ -76,7 +79,7 @@ def _get_particle_velocity(direct_events):
 
     Returns
     -------
-    vultra_heliosphere_frame : np.ndarray
+    vultra_heliosphere_frame : numpy.ndarray
         Particle velocity in the heliosphere frame.
 
     Notes
@@ -108,7 +111,7 @@ def _get_particle_velocity(direct_events):
     return ultra_velocity_heliosphere_frame
 
 
-def build_annotated_events(direct_events, kernels):
+def build_annotated_events(direct_events: dict, kernels: list) -> None:
     """
     Build annotated events.
 
diff --git a/tools/spice/spice_utils.py b/tools/spice/spice_utils.py
index 5f939c5fd..00e928931 100644
--- a/tools/spice/spice_utils.py
+++ b/tools/spice/spice_utils.py
@@ -2,13 +2,16 @@
 
 import logging
 import os
+from typing import Optional
 
 import spiceypy as spice
 
 logger = logging.getLogger(__name__)
 
 
-def list_files_with_extensions(directory: str, extensions=None) -> list[str]:
+def list_files_with_extensions(
+    directory: str, extensions: Optional[list[str]] = None
+) -> list[str]:
     """
     List all files in a given directory that have the specified extensions.
 
@@ -41,7 +44,7 @@ def list_files_with_extensions(directory: str, extensions=None) -> list[str]:
     return matching_files
 
 
-def list_loaded_kernels(extensions=None) -> list:
+def list_loaded_kernels(extensions: Optional[list[str]] = None) -> list:
     """
     List furnished spice kernels, optionally filtered by specific extensions.
 
diff --git a/tools/xtce_generation/ccsds_header_xtce_generator.py b/tools/xtce_generation/ccsds_header_xtce_generator.py
index 83e540c52..4de32474e 100644
--- a/tools/xtce_generation/ccsds_header_xtce_generator.py
+++ b/tools/xtce_generation/ccsds_header_xtce_generator.py
@@ -9,7 +9,7 @@
 class CCSDSParameters:
     """The defined class for CCSDS parameters. Contains the object itself."""
 
-    def __init__(self):
+    def __init__(self) -> None:
         self.parameters = [
             {
                 "name": "VERSION",
diff --git a/tools/xtce_generation/telemetry_generator.py b/tools/xtce_generation/telemetry_generator.py
index b710e9b29..2d7560598 100644
--- a/tools/xtce_generation/telemetry_generator.py
+++ b/tools/xtce_generation/telemetry_generator.py
@@ -2,6 +2,7 @@
 
 import xml.etree.ElementTree as Et
 from datetime import datetime
+from typing import Optional
 
 import pandas as pd
 
@@ -39,7 +40,13 @@ class TelemetryGenerator:
         Default set to None.
     """
 
-    def __init__(self, packet_name, path_to_excel_file, apid, pkt=None):
+    def __init__(
+        self,
+        packet_name: str,
+        path_to_excel_file: str,
+        apid: int,
+        pkt: Optional[str] = None,
+    ) -> None:
         """Initialize TelemetryGenerator."""
         self.packet_name = packet_name
         self.apid = apid
@@ -52,7 +59,7 @@ def __init__(self, packet_name, path_to_excel_file, apid, pkt=None):
         else:
             self.pkt = pkt
 
-    def create_telemetry_xml(self):
+    def create_telemetry_xml(self) -> tuple:
         """
         Create an XML representation of telemetry data based on input parameters.
 
@@ -97,7 +104,7 @@ def create_telemetry_xml(self):
 
         return root, parameter_type_set, parameter_set, telemetry_metadata
 
-    def get_unique_bits_length(self):
+    def get_unique_bits_length(self) -> dict:
         """
         Create dictionary.
 
@@ -135,7 +142,11 @@ def get_unique_bits_length(self):
         unique_lengths = dict(sorted(unique_lengths.items(), key=lambda item: item[1]))
         return unique_lengths
 
-    def create_parameter_types(self, parameter_type_set, unique_lengths):
+    def create_parameter_types(
+        self,
+        parameter_type_set: Et.Element,
+        unique_lengths: dict,
+    ) -> Et.Element:
         """
         Create parameter types based on 'dataType' for the unique 'lengthInBits' values.
 
@@ -144,20 +155,21 @@ def create_parameter_types(self, parameter_type_set, unique_lengths):
 
         Parameters
         ----------
-        parameter_type_set : list TODO Double Check
+        parameter_type_set : Et.Element
             The ParameterTypeSet element where parameter types are.
-        unique_lengths : list TODO Double Check
+        unique_lengths : dict
             Unique values from the 'lengthInBits' column.
 
         Returns
         -------
-        parameter_type_set
+        parameter_type_set : Et.Element
             The updated ParameterTypeSet element.
         """
         for parameter_type_ref_name, size in unique_lengths.items():
             if "UINT" in parameter_type_ref_name:
                 parameter_type = Et.SubElement(
-                    parameter_type_set, "xtce:IntegerParameterType"
+                    parameter_type_set,
+                    "xtce:IntegerParameterType",
                 )
                 parameter_type.attrib["name"] = parameter_type_ref_name
                 parameter_type.attrib["signed"] = "false"
@@ -168,7 +180,8 @@ def create_parameter_types(self, parameter_type_set, unique_lengths):
 
             elif any(x in parameter_type_ref_name for x in ["SINT", "INT"]):
                 parameter_type = Et.SubElement(
-                    parameter_type_set, "xtce:IntegerParameterType"
+                    parameter_type_set,
+                    "xtce:IntegerParameterType",
                 )
                 parameter_type.attrib["name"] = parameter_type_ref_name
                 parameter_type.attrib["signed"] = "true"
@@ -178,7 +191,8 @@ def create_parameter_types(self, parameter_type_set, unique_lengths):
 
             elif "BYTE" in parameter_type_ref_name:
                 binary_parameter_type = Et.SubElement(
-                    parameter_type_set, "xtce:BinaryParameterType"
+                    parameter_type_set,
+                    "xtce:BinaryParameterType",
                 )
                 binary_parameter_type.attrib["name"] = parameter_type_ref_name
 
@@ -195,20 +209,22 @@ def create_parameter_types(self, parameter_type_set, unique_lengths):
 
         return parameter_type_set
 
-    def create_ccsds_packet_parameters(self, parameter_set, ccsds_parameters):
+    def create_ccsds_packet_parameters(
+        self, parameter_set: Et.Element, ccsds_parameters: list
+    ) -> Et.Element:
         """
         Create XML elements to define CCSDS packet parameters based on the given data.
 
         Parameters
         ----------
-        parameter_set : list
+        parameter_set : Et.Element
             The ParameterSet element where parameters will be added.
-        ccsds_parameters : dict
+        ccsds_parameters : list
             A list of dictionaries containing CCSDS parameter data.
 
         Returns
         -------
-        parameter_set
+        parameter_set : Et.Element
             The updated ParameterSet element.
         """
         for parameter_data in ccsds_parameters:
@@ -222,8 +238,11 @@ def create_ccsds_packet_parameters(self, parameter_set, ccsds_parameters):
         return parameter_set
 
     def create_container_set(
-        self, telemetry_metadata, ccsds_parameters, container_name
-    ):
+        self,
+        telemetry_metadata: Et.Element,
+        ccsds_parameters: list,
+        container_name: str,
+    ) -> Et.Element:
         """
         Create XML elements.
 
@@ -232,7 +251,7 @@ def create_container_set(
 
         Parameters
         ----------
-        telemetry_metadata : dict todo check
+        telemetry_metadata : Et.Element
             The TelemetryMetaData element where containers are.
         ccsds_parameters : list
             A list of dictionaries containing CCSDS parameter data.
@@ -241,12 +260,11 @@ def create_container_set(
 
         Returns
         -------
-        telemetry_metadata
+        telemetry_metadata : Et.Element
             The updated TelemetryMetaData element.
         """
         # Create ContainerSet element
         container_set = Et.SubElement(telemetry_metadata, "xtce:ContainerSet")
-
         # Create CCSDSPacket SequenceContainer
         ccsds_packet_container = Et.SubElement(container_set, "xtce:SequenceContainer")
         ccsds_packet_container.attrib["name"] = "CCSDSPacket"
@@ -288,7 +306,7 @@ def create_container_set(
 
         return telemetry_metadata
 
-    def create_remaining_parameters(self, parameter_set):
+    def create_remaining_parameters(self, parameter_set: Et.Element) -> Et.Element:
         """
         Create XML elements for parameters.
 
@@ -296,12 +314,12 @@ def create_remaining_parameters(self, parameter_set):
 
         Parameters
         ----------
-        parameter_set : list todo check
+        parameter_set : Et.Element
             The ParameterSet element where parameters will be added.
 
         Returns
         -------
-        parameter_set
+        parameter_set : Et.Element
             The updated ParameterSet element.
         """
         # Process rows from SHCOARSE until the last available row in the DataFrame
@@ -326,7 +344,7 @@ def create_remaining_parameters(self, parameter_set):
 
         return parameter_set
 
-    def generate_telemetry_xml(self, output_xml_path, container_name):
+    def generate_telemetry_xml(self, output_xml_path: str, container_name: str) -> None:
         """
         Create and output an XTCE file based on the data within the class.
 
diff --git a/tools/xtce_generation/xtce_generator_codice.py b/tools/xtce_generation/xtce_generator_codice.py
index 0c9420675..76d8fc6ad 100644
--- a/tools/xtce_generation/xtce_generator_codice.py
+++ b/tools/xtce_generation/xtce_generator_codice.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """Function used by instrument to generate XTCE."""
     instrument_name = "codice"
     current_directory = Path(__file__).parent
diff --git a/tools/xtce_generation/xtce_generator_glows.py b/tools/xtce_generation/xtce_generator_glows.py
index 96dda5a71..31a9a9669 100644
--- a/tools/xtce_generation/xtce_generator_glows.py
+++ b/tools/xtce_generation/xtce_generator_glows.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """
     Function is used to generate the GLOWS XTCE files for packet processing.
 
diff --git a/tools/xtce_generation/xtce_generator_hi.py b/tools/xtce_generation/xtce_generator_hi.py
index 7717bf435..4a74000a4 100644
--- a/tools/xtce_generation/xtce_generator_hi.py
+++ b/tools/xtce_generation/xtce_generator_hi.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """Function used by hi to generate XTCE."""
 
     instrument_name = "hi"
diff --git a/tools/xtce_generation/xtce_generator_hit.py b/tools/xtce_generation/xtce_generator_hit.py
index 4206da406..a8428804f 100644
--- a/tools/xtce_generation/xtce_generator_hit.py
+++ b/tools/xtce_generation/xtce_generator_hit.py
@@ -13,7 +13,7 @@
 from imap_processing import imap_module_directory
 
 
-def main():
+def main() -> None:
     """Function used by hit to generate XTCE."""
     instrument_name = "hit"
     current_directory = Path(__file__).parent
diff --git a/tools/xtce_generation/xtce_generator_lo.py b/tools/xtce_generation/xtce_generator_lo.py
index 670704d1d..536d14107 100644
--- a/tools/xtce_generation/xtce_generator_lo.py
+++ b/tools/xtce_generation/xtce_generator_lo.py
@@ -18,7 +18,7 @@
 # P_ILO_SCI_DE
 
 
-def main():
+def main() -> None:
     """Function used by lo to generate XTCE."""
     instrument_name = "lo"
     current_directory = Path(__file__).parent
diff --git a/tools/xtce_generation/xtce_generator_mag.py b/tools/xtce_generation/xtce_generator_mag.py
index a44adf161..b70b04176 100644
--- a/tools/xtce_generation/xtce_generator_mag.py
+++ b/tools/xtce_generation/xtce_generator_mag.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """Function used by mag to generate XTCE."""
 
     instrument_name = "mag"
@@ -36,7 +36,9 @@ def main():
     for packet_name, app_id in packets.items():
         print(packet_name)
         telemetry_generator = TelemetryGenerator(
-            packet_name=packet_name, path_to_excel_file=path_to_excel_file, apid=app_id
+            packet_name=packet_name,
+            path_to_excel_file=path_to_excel_file,
+            apid=int(app_id),
         )
         telemetry_generator.generate_telemetry_xml(
             f"{packet_definition_path}/{packet_name}.xml", packet_name
diff --git a/tools/xtce_generation/xtce_generator_swapi.py b/tools/xtce_generation/xtce_generator_swapi.py
index c847d8902..80fd26e62 100644
--- a/tools/xtce_generation/xtce_generator_swapi.py
+++ b/tools/xtce_generation/xtce_generator_swapi.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """Function used by swapi to generate XTCE."""
 
     instrument_name = "swapi"
diff --git a/tools/xtce_generation/xtce_generator_swe.py b/tools/xtce_generation/xtce_generator_swe.py
index 5d737dc73..dab0d89b0 100644
--- a/tools/xtce_generation/xtce_generator_swe.py
+++ b/tools/xtce_generation/xtce_generator_swe.py
@@ -11,7 +11,7 @@
 from tools.xtce_generation.telemetry_generator import TelemetryGenerator
 
 
-def main():
+def main() -> None:
     """Function used by swe to generate XTCE."""
 
     instrument_name = "swe"
diff --git a/tools/xtce_generation/xtce_generator_template.py b/tools/xtce_generation/xtce_generator_template.py
index 596ac30db..352075bfb 100644
--- a/tools/xtce_generation/xtce_generator_template.py
+++ b/tools/xtce_generation/xtce_generator_template.py
@@ -10,7 +10,7 @@
 
 
 # Function to parse command line arguments
-def _parse_args():
+def _parse_args() -> argparse.Namespace:
     """
     Parse the command line arguments.
 
@@ -56,7 +56,7 @@ def _parse_args():
     return args
 
 
-def _validate_args(args):
+def _validate_args(args: argparse.Namespace) -> None:
     """
     Ensure that the instrument is valid.
 
@@ -76,7 +76,7 @@ def _validate_args(args):
         raise FileNotFoundError(f"{args.file_path} not found, and may not exist.")
 
 
-def main():
+def main() -> None:
     """
     Generate xtce file from CLI information given.
 
@@ -99,7 +99,9 @@ def main():
     for packet_name, app_id in packets.items():
         print(packet_name)
         telemetry_generator = TelemetryGenerator(
-            packet_name=packet_name, path_to_excel_file=path_to_excel_file, apid=app_id
+            packet_name=packet_name,
+            path_to_excel_file=path_to_excel_file,
+            apid=int(app_id),
         )
         telemetry_generator.generate_telemetry_xml(
             packet_definition_path / f"{packet_name}.xml", packet_name