ci/style: Ignore files that won't be type checked

Solution was to use `# mypy: ignore-errors` on individual files.

Adds the option `warn_unused_ignores = true` so that as individual type hints get corrected we can remove the specific
ignore statements that were added.

.pre-commit-config.yaml

@@ -89,7 +89,11 @@ repos:
     hooks:
       - id: mypy
         files: isoslam
-        args: []
+        args:
+          [
+            "--exclude='^all_introns_counts_and_info\\.py$'",
+            "--exclude='^pipeline_slam_3UIs\\.py$'",
+          ]
 
   # @ns-rse (2024-11-27) Currently fails due to `fastjsonschema` not covering `tool.ruff.lint` see
   # https://github.com/abravalheri/validate-pyproject/issues/180

isoslam/all_introns_counts_and_info.py

@@ -12,6 +12,8 @@
 about it's event assignment, number of conversions, coverage etc.
 """
 
+# mypy: ignore-errors
+
 from argparse import ArgumentParser
 import sys
 

isoslam/pipeline_slam_3UIs.py

@@ -4,12 +4,15 @@
 of 4sU-linked nucleotide conversions (T>C or A>G), exclusing SNPs.
 """
 
+# mypy: ignore-errors
+
 import os
 import sys
 
 import ruffus
 from cgatcore import pipeline as P
 
+
 # Read in pipeline.yml
 PARAMS = P.get_parameters(
     [

isoslam/pipeline_slam_3UIs/all_introns_counts_and_info.py

@@ -2,16 +2,18 @@
 all_introns_counts_and_info.py
 ====================
 Takes in the sorted and feature assigned `.bam` file from previous steps and passes them to a
-python script that uses pysam (python wrapper for htslib). This script iterates over the `.bam` 
+python script that uses pysam (python wrapper for htslib). This script iterates over the `.bam`
 file pair-by-pair (representing the sequencing insert), determines whether the read-pair shows
 evidence of intron splicing/retention and assigns these to specific events by referencing the
 `.gtf` and `.bed` files, and XT tag from featureCountsReadAssignments. Next, the script uses the
 XS tag from featureCountsReadAssignment to assign each read in the pair as the forward or reverse
 read, relative to the direction of transcription. Finally, it looks for T>C in FW read, A>G in RV
 read, checks these are not present in the SNP VCF file, and outputs metadata on each read-pair
-about it's event assignment, number of conversions, coverage etc. 
+about it's event assignment, number of conversions, coverage etc.
 """
 
+# mypy: ignore-errors
+
 import sys
 from collections import defaultdict
 
@@ -52,7 +54,7 @@ def main(argv=None):
         "--out",
         dest="outfile_tsv",
         type=str,
-        help="""Supply a path to the output file. This file will contain 
+        help="""Supply a path to the output file. This file will contain
                         conversions per pair, accounting for stranding""",
     )
 
@@ -108,7 +110,6 @@ def main(argv=None):
     conversion_dict = defaultdict(int)
 
     def fragment_iterator(read_iterator):
-
         read_list = list()
         last_read = None
 
@@ -137,7 +138,6 @@ def fragment_iterator(read_iterator):
         )
 
         for pair in fragment_iterator(bamfile.fetch(until_eof=True)):
-
             # if i_total_progress >= 2000000:
             ##    print("length break")
             #    break
@@ -461,7 +461,6 @@ def fragment_iterator(read_iterator):
                             converted_position.add(genome_pos)
 
                 for base in reverse_read.get_aligned_pairs(with_seq=True):
-
                     read_pos, genome_pos, genome_seq = base
                     if None in base:
                         continue

pyproject.toml

@@ -271,6 +271,7 @@ python_version = "3.10"
 strict = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
+warn_unused_ignores = true
 exclude = [
   '^all_introns_counts_and_info\.py$',
   '^pipeline_slam_3UIs\.py$',