From abaeec53046b5dba3daa576efcd30f05296e598a Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Fri, 29 Nov 2024 15:20:31 +0000
Subject: [PATCH 1/3] chore: Ruff ignore more files that won't ever be linted

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 0e5e0c1..f44688f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -174,6 +174,9 @@ exclude = [
   "dist",
   "docs/source/conf.py",
   "isoslam/all_introns_counts_and_info.py",
+  "isoslam/pipeline_slam_3UIs.py",
+  "isoslam/pipeline_slam_3UIs/*.py",
+  "tests/__init__.py"
 ]
 # per-file-ignores = []
 line-length = 120

From 4dbfda1fe54a1fe615fb3a07acba19bc36c9c795 Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Fri, 29 Nov 2024 15:42:41 +0000
Subject: [PATCH 2/3] chore: Exclude old files numpydoc-validation and
 codespell

---
 .gitignore     |  3 +++
 pyproject.toml | 18 ++++++++++--------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.gitignore b/.gitignore
index efd1441..ba6b857 100644
--- a/.gitignore
+++ b/.gitignore
@@ -174,3 +174,6 @@ cython_debug/
 \#*
 *~
 .dir-locals.el
+
+# pytest-testmon
+.testmon*
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index f44688f..d9f13c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -236,7 +236,7 @@ convention = "numpy"
 fixture-parentheses = true
 
 [tool.codespell]
-skip = '*.bed*,*.gtf,*.fasta,*.fas,*.fa,*.fna,*.ffn,*.faa,*.mpfa,*.frn'
+skip = '*.bed*,*.gtf,*.fasta,*.fas,*.fa,*.fna,*.ffn,*.faa,*.mpfa,*.frn,*pipeline_slam_3UIs.py,*all_introns_counts_and_info.py'
 count = ''
 quiet-level = 3
 
@@ -248,13 +248,15 @@ checks = [
   "PR10", # Conflicts with black formatting
   "SA01",
 ]
-exclude = [  # don't report on objects that match any of these regex
-    "\\.undocumented_method$",
-    "\\.__repr__$",
-    "^test_",
-    "^conftest",
-    "^conf$",
-    "isoslam/all_introns_counts_and_info.py",
+exclude = [  # don't report on objects that match any of these regex (use single quotes for regex in toml)
+    '\\.undocumented_method$',
+    '\\.__repr__$',
+    '^test_',
+    '^conftest',
+    '^conf$',
+    '^__init__',
+    '^all_introns_counts_and_info',
+    '^pipeline_slam_3UIs',
 ]
 override_SS05 = [  # override SS05 to allow docstrings starting with these words
     "^Process ",

From 8add7ae4c9d3b103d7f3501a5f436d8a5b7ae63c Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Fri, 29 Nov 2024 15:42:41 +0000
Subject: [PATCH 3/3] chore: Exclude old files numpydoc-validation and
 codespell

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d9f13c0..1bf5778 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -274,7 +274,8 @@ strict = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
 exclude = [
-  "isoslam/all_introns_counts_and_info.py",
+  '^all_introns_counts_and_info\.py$',
+  '^pipeline_slam_3UIs\.py$',
 ]
 
 [[tool.mypy.overrides]]