diff --git a/.github/workflows/black.yml b/.github/workflows/lint.yml
similarity index 56%
rename from .github/workflows/black.yml
rename to .github/workflows/lint.yml
index 1856598d..47eadabf 100644
--- a/.github/workflows/black.yml
+++ b/.github/workflows/lint.yml
@@ -11,18 +11,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Setup Python 3
+      - name: Setup Python 3.10
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"
 
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
       - name: Run black
         uses: psf/black@stable
 
-      - name: Check for debugging print statements
+      - name: Lint with Ruff
         run: |
-          if grep -rq "print(" mokapot; then
-              echo "Found the following print statements:"
-              grep -r "print(" mokapot
-              exit 1
-          fi
+          ruff check . --format=github
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d3e5aceb..753caf42 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,19 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0 # Replace by any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.6+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: detect-private-key
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.261
+  hooks:
+    - id: ruff
+      args: ['--fix']
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+      language_version: python3.10
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 90fff412..2a81e5f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,17 @@
-# Changelog for mokapot  
+# Changelog for mokapot
 
 ## [Unreleased]
 ### Breaking changes
-- Mokapot now uses `numpy.random.Generator` instead of the deprecated `numpy.random.RandomState` API. 
+- Mokapot now uses `numpy.random.Generator` instead of the deprecated `numpy.random.RandomState` API.
   New `rng` arguments have been added to functions and classes that rely on randomness in lieu of setting a global random seed with `np.random.seed()`. Thanks @sjust-seerbio!
 
+### Changed
+- Added linting with Ruff to tests and pre-commit hooks (along with others)!
+
+### Fixed
+- The PepXML reader, which broke due to a Pandas update.
+- Potential bug if lowercase peptide sequences were used and protein-level confidence estimates were enabled
+
 ## [0.9.1] - 2022-12-14
 ### Changed
 - Cross-validation classes are now detected by looking for inheritance from the `sklearn.model_selection._search.BaseSearchCV` class.
@@ -30,8 +37,8 @@
 
 ## [0.8.2] - 2022-07-18
 ### Added
-- `mokapot.Model()` objects now recored the CV fold that they were fit on.
-  This means that they can be provided to `mokapot.brew()` in any order 
+- `mokapot.Model()` objects now recorded the CV fold that they were fit on.
+  This means that they can be provided to `mokapot.brew()` in any order
   and still maintain proper cross-validation bins.
 
 ### Fixed
@@ -41,7 +48,7 @@
 ## [0.8.1] - 2022-06-24
 
 ### Added
-- Support for previously trained models in the `brew()` function and the CLI 
+- Support for previously trained models in the `brew()` function and the CLI
   using the `--load_models` argument. Thanks @sambenfredj!
 
 ### Fixed
@@ -51,18 +58,18 @@
 
 ## [0.8.0] - 2022-03-11
 
-Thanks to @sambenfredj, @gessulat, @tkschmidt, and @MatthewThe for 
+Thanks to @sambenfredj, @gessulat, @tkschmidt, and @MatthewThe for
 PR #44, which made these things happen!
 
 ### Added
 - A new command line argument, `--max_workers`. This allows the
   cross-validation folds to be computed in parallel.
-- The `PercolatorModel` class now has an `n_jobs` parameter, which 
+- The `PercolatorModel` class now has an `n_jobs` parameter, which
   controls parallelization of the grid search.
 
 ### Changes
 - Improved speed by using multiple jobs for grid search by default.
-- Parallelization within `mokapot.brew()` now uses `joblib` 
+- Parallelization within `mokapot.brew()` now uses `joblib`
   instead of `concurrent.futures`.
 
 ## [0.7.4] - 2021-09-03
@@ -75,37 +82,37 @@ PR #44, which made these things happen!
 - Fixed bug where the `--keep_decoys` did not work with `--aggregate`. Also,
   added tests to cover this. Thanks @jspaezp!
 
-## [0.7.2] - 2021-07-16  
-### Added  
+## [0.7.2] - 2021-07-16
+### Added
 - `--keep_decoys` option to the command line interface. Thanks @jspaezp!
 - Notes about setting a random seed to the Python API documentation. (Issue #30)
-- Added more information about peptides that couldn't be mapped to proteins. (Issue #29) 
+- Added more information about peptides that couldn't be mapped to proteins. (Issue #29)
 
-### Fixed  
+### Fixed
 - Loading a saved model with `mokapot.load_model()` would fail because of an
-  update to Pandas that introduced a new exception. We've updated mokapot 
+  update to Pandas that introduced a new exception. We've updated mokapot
   accordingly.
 
-### Changed  
+### Changed
 - Updates to unit tests. Warnings are now treated as errors for system tests.
 
-## [0.7.1] - 2021-03-22  
-### Changed  
+## [0.7.1] - 2021-03-22
+### Changed
 - Updated the build to align with
   [PEP517](https://www.python.org/dev/peps/pep-0517/)
 
-## [0.7.0] - 2021-03-19  
-### Added  
+## [0.7.0] - 2021-03-19
+### Added
 - Support for downstream peptide and protein quantitation with
   [FlashLFQ](https://github.com/smith-chem-wisc/FlashLFQ). This is accomplished
   through the `mokapot.to_flashlfq()` function or the `to_flashlfq()` method of
   `LinearConfidence` objects. Note that to support the FlashLFQ format, you'll
   need to specify additional columns in `read_pin()` or use a PepXML input file
-  (`read_pepxml()`). 
+  (`read_pepxml()`).
 - Added a top-level function for exporting confident PSMs, peptides, and
   proteins from one or more `LinearConfidence` objects as a tab-delimited file:
   `mokapot.to_txt()`.
-- Added a top-level function for reading FASTA files for protein-level 
+- Added a top-level function for reading FASTA files for protein-level
   confidence estimates: `mokapot.read_fasta()`.
 - Tests accompanying the support for the features above.
 - Added a "mokapot cookbook" to the documentation with helpful code snippets.
@@ -120,39 +127,39 @@ PR #44, which made these things happen!
   `importlib.metadata` to the standard library, saving a few hundred
   milliseconds.
 
-## [0.6.2] - 2021-03-12  
+## [0.6.2] - 2021-03-12
 ### Added
 - Now checks to verify there are no debugging print statements in the code
   base when linting.
 
-### Fixed  
+### Fixed
 - Removed debugging print statements.
 
 ## [0.6.1] - 2021-03-11
 ### Fixed
 - Parsing Percolator tab-delimited files with a "DefaultDirection" line.
-- `Label` column is now converted to boolean during PIN file parsing. 
+- `Label` column is now converted to boolean during PIN file parsing.
   Previously, problems occurred if the `Label` column was of dtype `object`.
 - Parsing modifications from pepXML files were indexed incorrectly on the
   peptide string.
 
-## [0.6.0] - 2021-03-03  
-### Added  
+## [0.6.0] - 2021-03-03
+### Added
 - Support for parsing PSMs from PepXML input files.
 - This changelog.
 
-### Fixed  
-- Parsing a FASTA file previously failed if an entry was not followed by a 
-  sequence. Now, missing sequences are tolerated and a warning is given instead.  
+### Fixed
+- Parsing a FASTA file previously failed if an entry was not followed by a
+  sequence. Now, missing sequences are tolerated and a warning is given instead.
 - When the learned model was worse than the best feature and the lower scores
-  were better for the best feature, assigning confidence would fail.  
+  were better for the best feature, assigning confidence would fail.
 - Easy access to grouped confidence estimates in the Python API were not working
-  due to a typo.  
-- Deprecation warnings from Pandas about the `regex` argument.  
+  due to a typo.
+- Deprecation warnings from Pandas about the `regex` argument.
 - Sometimes peptides were removed as shared incorrectly when part of a protein
-  group.  
+  group.
 
-### Changed  
+### Changed
 - Refactored and added many new unit and system tests.
 - New pull-requests must now improve or maintain test coverage.
 - Improved error messages.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 2025e114..245e9c03 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -27,7 +27,7 @@
 copyright = "2022, William E. Fondrie"
 author = "William E. Fondrie"
 
-import mokapot
+import mokapot  # noqa: E402
 
 version = str(mokapot.__version__)
 release = version
diff --git a/mokapot/confidence.py b/mokapot/confidence.py
index a8578ef8..dec56614 100644
--- a/mokapot/confidence.py
+++ b/mokapot/confidence.py
@@ -17,9 +17,7 @@
 """
 import copy
 import logging
-from pathlib import Path
 
-import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
 from triqler import qvality
@@ -651,7 +649,7 @@ def plot_qvalues(qvalues, threshold=0.1, ax=None, **kwargs):
 
     ax.set_xlim(0 - xmargin, threshold + xmargin)
     ax.set_xlabel("q-value")
-    ax.set_ylabel(f"Discoveries")
+    ax.set_ylabel("Discoveries")
 
     ax.step(qvals["qvalue"].values, qvals.num.values, where="post", **kwargs)
 
diff --git a/mokapot/config.py b/mokapot/config.py
index cff445f0..e32819b8 100644
--- a/mokapot/config.py
+++ b/mokapot/config.py
@@ -12,8 +12,8 @@ class MokapotHelpFormatter(argparse.HelpFormatter):
     """Format help text to keep newlines and whitespace"""
 
     def _fill_text(self, text, width, indent):
-        text_list = text.splitlines(keepends=True)
-        return "\n".join(_process_line(l, width, indent) for l in text_list)
+        lines = text.splitlines(keepends=True)
+        return "\n".join(_process_line(txt, width, indent) for txt in lines)
 
 
 class Config:
diff --git a/mokapot/model.py b/mokapot/model.py
index 06484fbc..da50812a 100644
--- a/mokapot/model.py
+++ b/mokapot/model.py
@@ -16,7 +16,6 @@
 import copy
 import logging
 import pickle
-import warnings
 
 import numpy as np
 import pandas as pd
diff --git a/mokapot/mokapot.py b/mokapot/mokapot.py
index e4dd5291..760db931 100644
--- a/mokapot/mokapot.py
+++ b/mokapot/mokapot.py
@@ -123,7 +123,7 @@ def main():
             model = list(plugin_models.values())[0]
 
     if model is None:
-        logging.debug(f"Loading Percolator model.")
+        logging.debug("Loading Percolator model.")
         model = PercolatorModel(
             train_fdr=config.train_fdr,
             max_iter=config.max_iter,
diff --git a/mokapot/parsers/pepxml.py b/mokapot/parsers/pepxml.py
index 4dfbee5f..6dfe4b28 100644
--- a/mokapot/parsers/pepxml.py
+++ b/mokapot/parsers/pepxml.py
@@ -332,6 +332,8 @@ def _log_features(col, features):
     """
     if col.name not in features:
         return col
+    elif col.dtype == "bool":
+        return col.astype(float)
 
     col = col.astype(str).str.lower()
 
diff --git a/mokapot/parsers/pin.py b/mokapot/parsers/pin.py
index 8f988507..719f842d 100644
--- a/mokapot/parsers/pin.py
+++ b/mokapot/parsers/pin.py
@@ -4,7 +4,6 @@
 import gzip
 import logging
 
-import numpy as np
 import pandas as pd
 
 from .. import utils
@@ -234,7 +233,7 @@ def _parse_in_chunks(file_obj, columns, chunk_size=int(1e8)):
         if not psms:
             break
 
-        psms = [l.rstrip().split("\t", len(columns) - 1) for l in psms]
+        psms = [p.rstrip().split("\t", len(columns) - 1) for p in psms]
         psms = pd.DataFrame.from_records(psms, columns=columns)
         yield psms.apply(pd.to_numeric, errors="ignore")
 
diff --git a/mokapot/peptides.py b/mokapot/peptides.py
index 09c7904e..eb9d5fd3 100644
--- a/mokapot/peptides.py
+++ b/mokapot/peptides.py
@@ -3,10 +3,6 @@
 """
 from collections import defaultdict
 
-import numpy as np
-import pandas as pd
-import numba as nb
-
 
 def match_decoy(decoys, targets, ignore_mods=True):
     """Find a corresponding target for each decoy.
diff --git a/mokapot/picked_protein.py b/mokapot/picked_protein.py
index ab2f7d59..9c97db80 100644
--- a/mokapot/picked_protein.py
+++ b/mokapot/picked_protein.py
@@ -3,7 +3,6 @@
 confidence estimates.
 """
 import logging
-import numpy as np
 import pandas as pd
 
 from .peptides import match_decoy
@@ -42,21 +41,7 @@ def picked_protein(
         columns={peptide_column: "best peptide"}
     )
 
-    # Strip modifications and flanking AA's from peptide sequences.
-    prots["stripped sequence"] = (
-        prots["best peptide"]
-        .str.replace(r"[\[\(].*?[\]\)]", "", regex=True)
-        .str.replace(r"^.*?\.", "", regex=True)
-        .str.replace(r"\..*?$", "", regex=True)
-    )
-
-    # Sometimes folks use lowercase letters for the termini or mods:
-    if all(prots["stripped sequence"].str.islower()):
-        seqs = prots["stripped sequence"].upper()
-    else:
-        seqs = prots["stripped sequence"].str.replace(r"[a-z]", "", regex=True)
-
-    prots["stripped sequence"] = seqs
+    prots["stripped sequence"] = strip_peptides(prots["best peptide"])
 
     # There are two cases we need to deal with:
     # 1. The fasta contained both targets and decoys (ideal)
@@ -131,6 +116,42 @@ def picked_protein(
     return prots.loc[prot_idx, final_cols]
 
 
+def strip_peptides(sequences):
+    """Strip modifications and flanking AA's from peptide sequences.
+
+    Parameters
+    ----------
+    sequences : pandas.Series
+        The peptide sequences.
+
+    Returns
+    -------
+    pandas.Series
+        The stripped peptide sequences.
+
+    Example
+    -------
+    >>> pep = pd.Series(["A.LES[+79.]LIEK.A"])
+    >>> srip_peptides(pep)
+    0    LESLIEK
+    dtype: object
+    """
+    # Strip modifications and flanking AA's from peptide sequences.
+    sequences = (
+        sequences.str.replace(r"[\[\(].*?[\]\)]", "", regex=True)
+        .str.replace(r"^.*?\.", "", regex=True)
+        .str.replace(r"\..*?$", "", regex=True)
+    )
+
+    # Sometimes folks use lowercase letters for the termini or mods:
+    if all(sequences.str.islower()):
+        sequences = sequences.str.upper()
+    else:
+        sequences = sequences.str.replace(r"[a-z]", "", regex=True)
+
+    return sequences
+
+
 def group_with_decoys(peptides, proteins):
     """Retrieve the protein group in the case where the FASTA has decoys.
 
diff --git a/mokapot/qvalues.py b/mokapot/qvalues.py
index ad41a72c..a0e0066e 100644
--- a/mokapot/qvalues.py
+++ b/mokapot/qvalues.py
@@ -2,7 +2,6 @@
 This module estimates q-values.
 """
 import numpy as np
-import pandas as pd
 import numba as nb
 
 
diff --git a/pyproject.toml b/pyproject.toml
index bb197a50..add3baf0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,9 +62,17 @@ find = {namespaces = false}
 
 [tool.setuptools_scm]
 
+[tool.ruff]
+select = ["E", "F", "T20"]  # T20 is for print() statements.
+extend-exclude = ["docs/source/conf.py"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
+"test_parser_pepxml.py" = ["E501"]
+
 [tool.black]
 line-length = 79
-target-version = ['py37']
+target-version = ['py310']
 include = '\.pyi?$'
 exclude = '''
 
diff --git a/tests/system_tests/test_system.py b/tests/system_tests/test_system.py
index 9bc34d81..087cdd5f 100644
--- a/tests/system_tests/test_system.py
+++ b/tests/system_tests/test_system.py
@@ -24,10 +24,10 @@ def test_compare_to_percolator():
     dat.add_proteins(os.path.join("data", "human_sp_td.fasta"))
     res, _ = mokapot.brew(dat)
 
-    perc_path = os.path.join("data", "percolator.{l}.txt")
+    perc_path = os.path.join("data", "percolator.{p}.txt")
     perc_res = {
-        l: mokapot.read_percolator(perc_path.format(l=l))
-        for l in ["psms", "peptides", "proteins"]
+        p: mokapot.read_percolator(perc_path.format(p=p))
+        for p in ["psms", "peptides", "proteins"]
     }
 
     for level in ["psms", "peptides", "proteins"]:
diff --git a/tests/unit_tests/test_brew.py b/tests/unit_tests/test_brew.py
index 5c9b0aa3..319626b1 100644
--- a/tests/unit_tests/test_brew.py
+++ b/tests/unit_tests/test_brew.py
@@ -111,7 +111,9 @@ def test_brew_trained_models(psms, svm):
 
 
 def test_brew_using_few_models_error(psms, svm):
-    """Test that if the number of trained models less than the number of folds we get the expected error message"""
+    """Test that if the number of trained models less than the number of
+    folds we get the expected error message.
+    """
     with pytest.raises(ValueError) as err:
         mokapot.brew(psms, [svm, svm], test_fdr=0.05)
     assert (
diff --git a/tests/unit_tests/test_confidence.py b/tests/unit_tests/test_confidence.py
index 63a6fc56..34994f07 100644
--- a/tests/unit_tests/test_confidence.py
+++ b/tests/unit_tests/test_confidence.py
@@ -1,7 +1,6 @@
 """Test that Confidence classes are working correctly"""
 import pickle
 
-import pytest
 import numpy as np
 import pandas as pd
 from mokapot import LinearPsmDataset
diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py
index b90b43b3..252396ed 100644
--- a/tests/unit_tests/test_model.py
+++ b/tests/unit_tests/test_model.py
@@ -39,8 +39,6 @@ def test_model_init():
     model = mokapot.Model(LogisticRegression())
     assert isinstance(model.scaler, StandardScaler)
 
-    print(model)
-
 
 def test_perc_init():
     """Test the initialization of a PercolatorModel"""
diff --git a/tests/unit_tests/test_parser_pepxml.py b/tests/unit_tests/test_parser_pepxml.py
index 368b26cc..454412aa 100644
--- a/tests/unit_tests/test_parser_pepxml.py
+++ b/tests/unit_tests/test_parser_pepxml.py
@@ -2,7 +2,6 @@
 import pytest
 import mokapot
 import numpy as np
-from lxml import etree
 
 
 @pytest.fixture
@@ -36,8 +35,6 @@ def test_pepxml_success(small_pepxml):
 def test_pepxml2df(small_pepxml):
     """Test that we can create a dataframe"""
     single = mokapot.read_pepxml(small_pepxml, decoy_prefix="rev_", to_df=True)
-
-    print(single)
     assert len(single) == 4
     assert len(single["scan"].unique()) == 2
     np.testing.assert_array_equal(single["charge_2"], np.array([1, 1, 1, 0]))
diff --git a/tests/unit_tests/test_parser_pin.py b/tests/unit_tests/test_parser_pin.py
index bae0fd31..c8010bcd 100644
--- a/tests/unit_tests/test_parser_pin.py
+++ b/tests/unit_tests/test_parser_pin.py
@@ -34,4 +34,4 @@ def test_pin_parsing(std_pin):
 
 def test_pin_wo_dir():
     """Test a PIN file without a DefaultDirection line"""
-    dat = mokapot.read_pin("data/scope2_FP97AA.pin")
+    mokapot.read_pin("data/scope2_FP97AA.pin")
diff --git a/tests/unit_tests/test_picked_protein.py b/tests/unit_tests/test_picked_protein.py
index e69de29b..f761a4dc 100644
--- a/tests/unit_tests/test_picked_protein.py
+++ b/tests/unit_tests/test_picked_protein.py
@@ -0,0 +1,17 @@
+"""Test the picked protein approach functions"""
+import pandas as pd
+
+from mokapot.picked_protein import strip_peptides
+
+
+def test_strip_peptides():
+    """Test removing modifications from a peptide sequence"""
+    in_df = pd.Series(["A.B.C", "nABCc", "BL[+mod]AH", "A.B[1.1].C"])
+    expected = pd.Series(["B", "ABC", "BLAH", "B"])
+    out_df = strip_peptides(in_df)
+    pd.testing.assert_series_equal(out_df, expected)
+
+    in_df = pd.Series(["abc"])
+    expected = pd.Series(["ABC"])
+    out_df = strip_peptides(in_df)
+    pd.testing.assert_series_equal(out_df, expected)
diff --git a/tests/unit_tests/test_writer_flashlfq.py b/tests/unit_tests/test_writer_flashlfq.py
index 968b4f2e..9aba9d70 100644
--- a/tests/unit_tests/test_writer_flashlfq.py
+++ b/tests/unit_tests/test_writer_flashlfq.py
@@ -1,5 +1,4 @@
 """Test that FlashLFQ export is working"""
-import copy
 
 import pytest
 import mokapot
@@ -11,7 +10,7 @@ def test_sanity(psms, tmp_path):
     """Run simple sanity checks"""
     conf = psms.assign_confidence()
     test1 = conf.to_flashlfq(tmp_path / "test1.txt")
-    test2 = mokapot.to_flashlfq(conf, tmp_path / "test2.txt")
+    mokapot.to_flashlfq(conf, tmp_path / "test2.txt")
     test3 = mokapot.to_flashlfq([conf, conf], tmp_path / "test3.txt")
     with pytest.raises(ValueError):
         mokapot.to_flashlfq("blah", tmp_path / "test4.txt")
diff --git a/tests/unit_tests/test_writer_txt.py b/tests/unit_tests/test_writer_txt.py
index 14068f84..fea7f19a 100644
--- a/tests/unit_tests/test_writer_txt.py
+++ b/tests/unit_tests/test_writer_txt.py
@@ -3,7 +3,6 @@
 
 import pytest
 import mokapot
-import numpy as np
 import pandas as pd
 
 
@@ -11,7 +10,7 @@ def test_sanity(psms, tmp_path):
     """Run simple sanity checks"""
     conf = psms.assign_confidence()
     test1 = conf.to_txt(dest_dir=tmp_path, file_root="test1")
-    test2 = mokapot.to_txt(conf, dest_dir=tmp_path, file_root="test2")
+    mokapot.to_txt(conf, dest_dir=tmp_path, file_root="test2")
     test3 = mokapot.to_txt([conf, conf], dest_dir=tmp_path, file_root="test3")
     with pytest.raises(ValueError):
         mokapot.to_txt("blah", dest_dir=tmp_path)