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Add mypy Pre-commit Hook and Fix tools folder Pt.1 #659

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11 changes: 10 additions & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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]
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4 changes: 4 additions & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -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"]
13 changes: 8 additions & 5 deletions tools/metadata_generation/metadata_generator.py
Original file line number Diff line number Diff line change
@@ -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.

Expand All @@ -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.
"""
Expand All @@ -27,15 +28,17 @@ 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.

Parameters
----------
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
Expand Down Expand Up @@ -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.

Expand Down
11 changes: 7 additions & 4 deletions tools/spice/spice_examples.py
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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.

Expand All @@ -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
Expand Down Expand Up @@ -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.

Expand Down
7 changes: 5 additions & 2 deletions tools/spice/spice_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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.

Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/ccsds_header_xtce_generator.py
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
64 changes: 41 additions & 23 deletions tools/xtce_generation/telemetry_generator.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import xml.etree.ElementTree as Et
from datetime import datetime
from typing import Optional

import pandas as pd

Expand Down Expand Up @@ -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
Expand All @@ -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.

Expand Down Expand Up @@ -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.

Expand Down Expand Up @@ -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.

Expand All @@ -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"
Expand All @@ -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"
Expand All @@ -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

Expand All @@ -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:
Expand All @@ -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.

Expand All @@ -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.
Expand All @@ -241,12 +260,11 @@ def create_container_set(

Returns
-------
telemetry_metadata
telemetry_metadata : Et.Element
The updated TelemetryMetaData element.
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"""
# 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"
Expand Down Expand Up @@ -288,20 +306,20 @@ 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.

These are based on DataFrame rows starting from SHCOARSE (also known as MET).

Parameters
----------
parameter_set : list todo check
parameter_set : Et.Element
The ParameterSet element where parameters will be added.

Returns
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-------
parameter_set
parameter_set : Et.Element
The updated ParameterSet element.
"""
# Process rows from SHCOARSE until the last available row in the DataFrame
Expand All @@ -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.

Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/xtce_generator_codice.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/xtce_generator_glows.py
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/xtce_generator_hi.py
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/xtce_generator_hit.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion tools/xtce_generation/xtce_generator_lo.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
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