diff --git a/noxfile.py b/noxfile.py
index 234d783..e83ab39 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -61,7 +61,7 @@ def tests(session: nox.Session) -> None:
 
 
 if RUNNING_ON_RTD:
-    rtd_output_path = pathlib.Path(os.environ.get("READTHEDOCS_OUTPUT")) / "html"  # ty:ignore[invalid-argument-type]
+    rtd_output_path = pathlib.Path(os.environ.get("READTHEDOCS_OUTPUT")) / "html"  # ty: ignore[invalid-argument-type]
     rtd_output_path.mkdir(parents=True, exist_ok=True)
     doc_build_dir = str(rtd_output_path)
 else:
diff --git a/src/pyfaradaycup/pipeline/ccsds_reader_pipeline.py b/src/pyfaradaycup/pipeline/ccsds_reader_pipeline.py
index 59e213b..9fdc54e 100644
--- a/src/pyfaradaycup/pipeline/ccsds_reader_pipeline.py
+++ b/src/pyfaradaycup/pipeline/ccsds_reader_pipeline.py
@@ -5,6 +5,8 @@
 #  $LastChangedBy: acase $
 """  # ruff:ignore[D400]
 
+from __future__ import annotations
+
 __all__ = [
     "apid_obj",
     "choose_file",
@@ -38,11 +40,11 @@
 # import tkFileDialog
 
 
-def read_stdin(ptp=False, verbose=False):  # ruff:ignore[ANN001, ANN201, FBT002]
+def read_stdin(ptp: bool = False, verbose: bool = False) -> None:  # ruff:ignore[FBT001, FBT002]
     """Parse binary stream on stdin"""  # ruff:ignore[D400]
 
 
-def file2bytestr(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def file2bytestr(path: str = "", verbose: bool = False, gzip: bool = False) -> bytes:  # ruff:ignore[ARG001, FBT001, FBT002]
     """
     Read the entire contents of a file into a bytes object.
 
@@ -70,9 +72,9 @@ def file2bytestr(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN
     """
     try:
         if gzip:
-            import gzip  # ruff:ignore[PLC0415]
+            import gzip  # ruff:ignore[PLC0415]  # ty: ignore[invalid-assignment]
 
-            with gzip.open(path, "rb") as f:
+            with gzip.open(path, "rb") as f:  # ty: ignore[unresolved-attribute]
                 bytestr = f.read()
             return bytestr  # ruff:ignore[RET504]
         with open(path, "rb") as f:  # ruff:ignore[PTH123]
@@ -85,7 +87,7 @@ def file2bytestr(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN
         sys.exit()
 
 
-def choose_file(path="", ptp=False, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def choose_file(path: str = "", ptp: bool = False, verbose: bool = False) -> str:  # ruff:ignore[ARG001, FBT001, FBT002]
     # make sure file exists
     """
     Check that a file can be opened and return its path.
@@ -130,7 +132,12 @@ def choose_file(path="", ptp=False, verbose=False):  # ruff:ignore[ANN001, ANN20
     return path
 
 
-def wrapper_status(path="", verbose=False, gzip=False, spconly=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def wrapper_status(
+    path: str = "",
+    verbose: bool = False,  # ruff:ignore[ARG001, FBT001, FBT002]
+    gzip: bool = False,  # ruff:ignore[FBT001, FBT002]
+    spconly: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> dict[str, list[int]]:
     """
     Read CCSDS headers from SWEM wrapper packets and the packets inside them.
 
@@ -226,7 +233,11 @@ def wrapper_status(path="", verbose=False, gzip=False, spconly=False):  # ruff:i
     return data
 
 
-def read_file(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002]
+def read_file(  # ruff:ignore[C901]
+    path: str = "",
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+    gzip: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> dict[int, dict[str, list]]:
     """Read a CCSDS File and return data structure"""  # ruff:ignore[D400]
     # get a filename if not specified
     path = choose_file(path)
@@ -247,7 +258,7 @@ def read_file(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN201
         apidformat[apid] = get_layout(apid, verbose=verbose)
         if apidformat[apid]:
             data[apid] = {}
-            for name in apidformat[apid].names:
+            for name in apidformat[apid].names:  # ty: ignore[unresolved-attribute]
                 data[apid][name] = []
 
     # create a list of two dictionaries that can keep track of
@@ -317,7 +328,12 @@ def read_file(path="", verbose=False, gzip=False):  # ruff:ignore[ANN001, ANN201
     return data
 
 
-def read_file_sc(path="", verbose=False, ptp=False, gzip=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002, PLR0912, PLR0915]
+def read_file_sc(  # ruff:ignore[C901, PLR0912, PLR0915]
+    path: str = "",
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+    ptp: bool = False,  # ruff:ignore[FBT001, FBT002]
+    gzip: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> dict[int, dict[str, list]]:
     """Read a CCSDS File and return data structure"""  # ruff:ignore[D400]
     # get a filename if not specified
     path = choose_file(path)
@@ -409,7 +425,7 @@ def read_file_sc(path="", verbose=False, ptp=False, gzip=False):  # ruff:ignore[
             apid,
             verbose=verbose,
             filename=os.path.join("sc_hk_def", sc_hk_filename),  # ruff:ignore[PTH118]
-        )
+        )  # ty: ignore[not-iterable]
         if apidformat[apid]:
             data[apid] = {}
             for name in apidformat[apid].names:
@@ -511,7 +527,14 @@ def read_file_sc(path="", verbose=False, ptp=False, gzip=False):  # ruff:ignore[
     return data
 
 
-def read_bytestr(bytestr, pointer, data, apidformat, pktcnt, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002, PLR0912, PLR0913]
+def read_bytestr(  # ruff:ignore[C901, PLR0912, PLR0913]
+    bytestr: bytes,
+    pointer,  # ruff:ignore[ANN001]
+    data: dict[int, dict[str, list]],
+    apidformat,  # ruff:ignore[ANN001]
+    pktcnt: list[dict[int, int]],
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> tuple[()]:
     """Take a hex string and find packets"""  # ruff:ignore[D400]
     # Parse the CCSDS header
     try:
@@ -566,7 +589,7 @@ def read_bytestr(bytestr, pointer, data, apidformat, pktcnt, verbose=False):  #
     return ()
 
 
-def parse_ccsds_head(bytestr, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def parse_ccsds_head(bytestr: bytes, verbose: bool = False) -> dict[str, int]:  # ruff:ignore[ARG001, FBT001, FBT002]
     """
     Decode a 10-byte CCSDS packet header into its fields.
 
@@ -619,7 +642,14 @@ def parse_ccsds_head(bytestr, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG
     return head
 
 
-def parse_pkt(bytestr, data, apidformat, apid, ccsds_head, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, C901, FBT002, PLR0912, PLR0913]
+def parse_pkt(  # ruff:ignore[C901, PLR0912, PLR0913]
+    bytestr: bytes,
+    data: dict[int, dict[str, list]],
+    apidformat,  # ruff:ignore[ANN001]
+    apid: int,
+    ccsds_head: dict[str, int],  # ruff:ignore[ARG001]
+    verbose: bool = False,  # ruff:ignore[ARG001, FBT001, FBT002]
+) -> None:
     """Parse one CCSDS packet"""  # ruff:ignore[D400]
     # The format for this APIDs packet list
     form = apidformat[apid]
@@ -757,19 +787,22 @@ class apid_obj:  # ruff:ignore[N801]
     packets that have one.
     """
 
-    def __init__(self):  # ruff:ignore[ANN204]
-        self.names = []
-        self.bits = []
+    apid: int
+    sw_data_vars: list[str]
+
+    def __init__(self) -> None:
+        self.names: list[str] = []
+        self.bits: list[int] = []
         self.bytestart = []
         self.bitstart = []
         self.byteend = []
         self.bitend = []
-        self.data = {}
-        self.startbyte = []
-        self.startbit = []
+        self.data: dict[str, list] = {}
+        self.startbyte: list[int] = []
+        self.startbit: list[int] = []
 
 
-def get_layout(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002]
+def get_layout(apid: int, verbose: bool = False) -> apid_obj | None:  # ruff:ignore[C901, FBT001, FBT002]
     """
     Read the bit layout for one SWEAP APID from ``sweap_tlm.blk``.
 
@@ -818,7 +851,7 @@ def get_layout(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002
             if verbose:
                 print(f"APID {hex(apid)[2:]} Format Found".upper())  # ruff:ignore[FURB116, T201]
             thisapid = apid_obj()
-            thisapid.apid = apid  # ty: ignore[unresolved-attribute]
+            thisapid.apid = apid
             line = (  #  ruff:ignore[PLW2901]
                 ""  # so that the while loop will start out ok
             )
@@ -832,11 +865,11 @@ def get_layout(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002
                         thisapid.bits.append(int(pieces[3].strip()))
                         thisapid.data[pieces[0].strip()] = []
                         if hasattr(thisapid, "sw_data_vars"):
-                            thisapid.sw_data_vars.append(thisapid.names[-1])  # ty: ignore[unresolved-attribute]
+                            thisapid.sw_data_vars.append(thisapid.names[-1])
                     elif (line.strip()[0:9] == "( SW_DATA") | (
                         line.strip()[0:12] == "( SW_SPC_SCI"
                     ):
-                        thisapid.sw_data_vars = []  # ty: ignore[unresolved-attribute]
+                        thisapid.sw_data_vars = []
                 except IndexError:
                     break
                 except:  # ruff:ignore[E722]
@@ -862,7 +895,11 @@ def get_layout(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002
     return None
 
 
-def get_layout_sc(apid, verbose=False, filename=""):  # ruff:ignore[ANN001, ANN201, C901, FBT002]
+def get_layout_sc(  # ruff:ignore[C901]
+    apid: int,
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+    filename: str = "",
+) -> tuple[apid_obj, int] | None:
     """
     Read the bit layout for one spacecraft housekeeping APID.
 
@@ -906,7 +943,7 @@ def get_layout_sc(apid, verbose=False, filename=""):  # ruff:ignore[ANN001, ANN2
             if verbose:
                 print(f"APID {hex(apid)[2:]} Format Found".upper())  # ruff:ignore[FURB116, T201]
             thisapid = apid_obj()
-            thisapid.apid = apid  # ty: ignore[unresolved-attribute]
+            thisapid.apid = apid
 
             line = ""  # ruff:ignore[PLW2901]
             while line[0:4] != "SC_H":
diff --git a/src/pyfaradaycup/pipeline/swp_spc_l02l1.py b/src/pyfaradaycup/pipeline/swp_spc_l02l1.py
index 3672bf4..780d285 100644
--- a/src/pyfaradaycup/pipeline/swp_spc_l02l1.py
+++ b/src/pyfaradaycup/pipeline/swp_spc_l02l1.py
@@ -5,6 +5,8 @@
 #  $LastChangedBy: acase $
 """  # ruff:ignore[D400]
 
+from __future__ import annotations
+
 __all__ = [
     "cdf35e_35f",
     "cdf351_353_354",
@@ -24,6 +26,7 @@
 import os
 import pathlib
 import sys
+from typing import TextIO
 
 import numpy as np
 import spiceypy
@@ -33,6 +36,9 @@
 
 DATA_DIR = pathlib.Path(__file__).parent.parent / "data"
 
+# The log file, which is opened by main
+logfile: TextIO
+
 
 # Purpose: Convert binary "level-zero" or "ssr" files that come from the SWEM or Spacecraft
 #         into L0.5 or L1 CDF files
@@ -54,17 +60,17 @@
 # 				-	Added revision history
 
 
-def main(  # ruff:ignore[ANN201, C901, PLR0912, PLR0913, PLR0915, PLR0917]
-    l0file="",  # ruff:ignore[ANN001]
-    l1dir="",  # ruff:ignore[ANN001]
-    logdir="",  # ruff:ignore[ANN001]
-    spacecraft=False,  # ruff:ignore[ANN001, FBT002]
-    ptp=False,  # ruff:ignore[ANN001, FBT002]
-    gzip=False,  # ruff:ignore[ANN001, FBT002]
-    apidreq=0,  # ruff:ignore[ANN001]
-    overwrite=False,  # ruff:ignore[ANN001, FBT002]
-    verbose=False,  # ruff:ignore[ANN001, FBT002]
-):
+def main(  # ruff:ignore[C901, PLR0912, PLR0913, PLR0915, PLR0917]
+    l0file: str = "",
+    l1dir: str = "",
+    logdir: str = "",
+    spacecraft: bool = False,  # ruff:ignore[FBT001, FBT002]
+    ptp: bool = False,  # ruff:ignore[FBT001, FBT002]
+    gzip: bool = False,  # ruff:ignore[FBT001, FBT002]
+    apidreq: int = 0,
+    overwrite: bool = False,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> None:
     """
     Convert one SPC L0 file into L1 CDF files, one per APID.
 
@@ -138,7 +144,7 @@ def main(  # ruff:ignore[ANN201, C901, PLR0912, PLR0913, PLR0915, PLR0917]
         f"swp_spc_l02l1_{nowdt.year:04.0f}{nowdt.month:02.0f}{nowdt.day:02.0f}{nowdt.hour:02.0f}{nowdt.minute:02.0f}{nowdt.second:02.0f}.log",
     )
     try:
-        global logfile  # ruff:ignore[PLW0603]  # ty:ignore[unresolved-global]
+        global logfile  # ruff:ignore[PLW0603]
         logfile = open(logpath, "w")  # ruff:ignore[PTH123, SIM115]
     except:  # ruff:ignore[E722]
         print("\n***ERROR*** Could not open log file!\n")  # ruff:ignore[T201]
@@ -303,13 +309,13 @@ def main(  # ruff:ignore[ANN201, C901, PLR0912, PLR0913, PLR0915, PLR0917]
         # Create a new CDF file from the provided skeleton
         try:
             cdf = pycdf.CDF(l1path, skeleton_filename)
-        except "CDFError":  # ruff:ignore[B030]  # ty:ignore[invalid-exception-caught]
+        except "CDFError":  # ruff:ignore[B030]  # ty: ignore[invalid-exception-caught]
             statusmsg(
                 f"\n***ERROR*** [swp_spc_l02l1] Could not create new CDF (APID={apid})...continuing to next APID\n).",
                 screen=True,
                 verbose=verbose,
             )
-            statusmsg(sys.exc_info(), screen=True, verbose=verbose)
+            statusmsg(sys.exc_info(), screen=True, verbose=verbose)  # ty: ignore[invalid-argument-type]
             continue
 
         # Run a different procedure to put data into CDF file depending on APID
@@ -349,7 +355,7 @@ def main(  # ruff:ignore[ANN201, C901, PLR0912, PLR0913, PLR0915, PLR0917]
     logfile.close()
 
 
-def cdf35e_35f(cdf, dat, verbose=False) -> None:  # ruff:ignore[ANN001, C901, FBT002]
+def cdf35e_35f(cdf: pycdf.CDF, dat: dict[str, list], verbose: bool = False) -> None:  # ruff:ignore[C901, FBT001, FBT002]
     """
     Fill a CDF with housekeeping data, one row per packet.
 
@@ -446,7 +452,12 @@ def cdf35e_35f(cdf, dat, verbose=False) -> None:  # ruff:ignore[ANN001, C901, FB
             statusmsg(sys.exc_info())
 
 
-def cdf351_353_354(cdf, dat, nocdf=False, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002, PLR0912, PLR0915, RET503]
+def cdf351_353_354(  # ruff:ignore[C901, PLR0912, PLR0915, RET503]
+    cdf: pycdf.CDF,
+    dat: dict[str, list],
+    nocdf: bool = False,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> dict[str, list] | None:
     """
     Expand SPC science packets (APIDs 0x351, 0x353, 0x354) and write them to a CDF.
 
@@ -641,7 +652,12 @@ def cdf351_353_354(cdf, dat, nocdf=False, verbose=False):  # ruff:ignore[ANN001,
             raise RuntimeError  # ruff:ignore[B904]
 
 
-def cdf352(cdf, dat, nocdf=False, verbose=False):  # ruff:ignore[ANN001, ANN201, C901, FBT002, PLR0912, PLR0915]
+def cdf352(  # ruff:ignore[C901, PLR0912, PLR0915]
+    cdf: pycdf.CDF,
+    dat: dict[str, list],
+    nocdf: bool = False,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> dict[str, list] | tuple[()]:
     """
     Expand SPC time series (APID 0x352) packets into L1 data and write them to a CDF.
 
@@ -819,7 +835,12 @@ def cdf352(cdf, dat, nocdf=False, verbose=False):  # ruff:ignore[ANN001, ANN201,
     return ()
 
 
-def secsubsec2scet(sec, subsec, spacecraft=False, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def secsubsec2scet(
+    sec: list[int],
+    subsec: list[int],
+    spacecraft: bool = False,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[ARG001, FBT001, FBT002]
+) -> list[float]:
     """
     Convert MET seconds and subseconds to ephemeris time in nanoseconds.
 
@@ -873,7 +894,12 @@ def secsubsec2scet(sec, subsec, spacecraft=False, verbose=False):  # ruff:ignore
     return ephem_nanosec_j2000  # ruff:ignore[RET504]
 
 
-def statusmsg(string, screen=False, file=True, verbose=False):  # ruff:ignore[ANN001, ANN201, FBT002]
+def statusmsg(
+    string: str,
+    screen: bool = False,  # ruff:ignore[FBT001, FBT002]
+    file: bool = True,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[FBT001, FBT002]
+) -> None:
     """
     Write a timestamped status message to the log file and/or the screen.
 
@@ -907,7 +933,11 @@ def statusmsg(string, screen=False, file=True, verbose=False):  # ruff:ignore[AN
             print(string)  # ruff:ignore[T201]
 
 
-def get_newest_kernel(tls=False, sclk=False, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def get_newest_kernel(
+    tls: bool = False,  # ruff:ignore[FBT001, FBT002]
+    sclk: bool = False,  # ruff:ignore[FBT001, FBT002]
+    verbose: bool = False,  # ruff:ignore[ARG001, FBT001, FBT002]
+) -> str:
     """
     Find the newest NAIF leap second or PSP clock (SCLK) kernel file.
 
@@ -976,7 +1006,7 @@ def get_newest_kernel(tls=False, sclk=False, verbose=False):  # ruff:ignore[ANN0
     return path  # ruff:ignore[RET504]
 
 
-def get_newest_skeleton(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG001, FBT002]
+def get_newest_skeleton(apid: int, verbose: bool = False) -> str:  # ruff:ignore[ARG001, FBT001, FBT002]
     """
     Return the path to the skeleton CDF file for an APID.
 
@@ -1030,7 +1060,7 @@ def get_newest_skeleton(apid, verbose=False):  # ruff:ignore[ANN001, ANN201, ARG
     # return(path)
 
 
-def setup():  # ruff:ignore[ANN201]
+def setup() -> argparse.Namespace:
     """
     Read the command-line arguments for running this module as a script.
 
@@ -1170,13 +1200,13 @@ def setup():  # ruff:ignore[ANN201]
             statusmsg(
                 "***ERROR*** You must provide --l0file, if not using -b or -r",
                 screen=True,
-                verbose=verbose,  # ruff:ignore[F821]  # ty:ignore[unresolved-reference]
+                verbose=verbose,  # ruff:ignoreignore[F821]  # ty: ignore[unresolved-reference]
             )
     elif args.l0dir == "":
         statusmsg(
             "***ERROR*** You must provide --l0dir if using -b or -r",
             screen=True,
-            verbose=verbose,  # ruff:ignore[F821]  # ty:ignore[unresolved-reference]
+            verbose=verbose,  # ruff:ignore[F821]  # ty: ignore[unresolved-reference]
         )
 
     # Convert APID to an integer (it is read as a string from the command line)
@@ -1190,9 +1220,9 @@ def setup():  # ruff:ignore[ANN201]
         statusmsg(
             "Trouble parsing desired APID....exiting.",
             screen=True,
-            verbose=verbose,  # ruff:ignore[F821]  # ty:ignore[unresolved-reference]
+            verbose=verbose,  # ruff:ignore[F821]  # ty: ignore[unresolved-reference]
         )
-        statusmsg(sys.exc_info(), screen=True, verbose=verbose)  # ruff:ignore[F821]  # ty:ignore[unresolved-reference]
+        statusmsg(sys.exc_info(), screen=True, verbose=verbose)  # ruff:ignore[F821]  # ty: ignore[invalid-argument-type, unresolved-reference]
         sys.exit()
 
     # Make sure the environmental variable reference to the data directory is set and readable