diff --git a/.flake8 b/.flake8
index 138a4973..e7169d49 100644
--- a/.flake8
+++ b/.flake8
@@ -1,7 +1,8 @@
 [flake8]
-ignore = E203, E266, E501, W503
+extend-ignore = E203, E266, E501, W503, E721, F722, E731
 max-line-length = 79
-max-complexity = 10
-select = E9, F63, F7, F82
+max-complexity = 25
+extend-select = E9, F63, F7, F82
 show-source = true
 statistics = true
+exclude = ./sae_training/geom_median/
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 748aaef8..7316b376 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -47,11 +47,7 @@ jobs:
       - name: Install dependencies
         run: poetry install --no-interaction
       - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        run: poetry run flake8 .
       - name: black code formatting
         run: poetry run black . --check
       - name: isort linting
diff --git a/sae_analysis/dashboard_runner.py b/sae_analysis/dashboard_runner.py
index 815c6b14..4a3815ab 100644
--- a/sae_analysis/dashboard_runner.py
+++ b/sae_analysis/dashboard_runner.py
@@ -1,3 +1,6 @@
+# flake8: noqa: E402
+# TODO: are these sys.path.append calls really necessary?
+
 import sys
 
 sys.path.append("..")
diff --git a/sae_analysis/visualizer/data_fns.py b/sae_analysis/visualizer/data_fns.py
index effe6f3f..7deb5d94 100644
--- a/sae_analysis/visualizer/data_fns.py
+++ b/sae_analysis/visualizer/data_fns.py
@@ -20,8 +20,6 @@
 from transformer_lens import HookedTransformer, utils
 from transformer_lens.hook_points import HookPoint
 
-Arr = np.ndarray
-
 from sae_analysis.visualizer.html_fns import (
     CSS,
     HTML_HOVERTEXT_SCRIPT,
@@ -39,6 +37,8 @@
     to_str_tokens,
 )
 
+Arr = np.ndarray
+
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
 
@@ -497,7 +497,7 @@ def __init__(self):
         self.x2_sum = 0
         self.y2_sum = 0
 
-    def update(self, x: Float[Tensor, "X N"], y: Float[Tensor, "Y N"]):  # noqa
+    def update(self, x: Float[Tensor, "X N"], y: Float[Tensor, "Y N"]):
         assert x.ndim == 2 and y.ndim == 2, "Both x and y should be 2D"
         assert (
             x.shape[-1] == y.shape[-1]
@@ -510,7 +510,7 @@ def update(self, x: Float[Tensor, "X N"], y: Float[Tensor, "Y N"]):  # noqa
         self.x2_sum += einops.reduce(x**2, "X N -> X", "sum")
         self.y2_sum += einops.reduce(y**2, "Y N -> Y", "sum")
 
-    def corrcoef(self) -> Tuple[Float[Tensor, "X Y"], Float[Tensor, "X Y"]]:  # noqa
+    def corrcoef(self) -> Tuple[Float[Tensor, "X Y"], Float[Tensor, "X Y"]]:
         cossim_numer = self.xy_sum
         cossim_denom = torch.sqrt(torch.outer(self.x2_sum, self.y2_sum)) + 1e-6
         cossim = cossim_numer / cossim_denom
@@ -549,7 +549,7 @@ def get_feature_data(
     hook_point: str,
     hook_point_layer: int,
     hook_point_head_index: Optional[int],
-    tokens: Int[Tensor, "batch seq"],  # noqa
+    tokens: Int[Tensor, "batch seq"],
     feature_idx: Union[int, List[int]],
     max_batch_size: Optional[int] = None,
     left_hand_k: int = 3,
@@ -624,10 +624,8 @@ def get_feature_data(
 
     # ! Define hook function to perform feature ablation
 
-    def hook_fn_act_post(
-        act_post: Float[Tensor, "batch seq d_mlp"], hook: HookPoint  # noqa
-    ):  # noqa
-        """
+    def hook_fn_act_post(act_post: Float[Tensor, "batch seq d_mlp"], hook: HookPoint):
+        r"""
         Encoder has learned x^j \approx b + \sum_i f_i(x^j)d_i where:
             - f_i are the feature activations
             - d_i are the feature output directions
@@ -663,10 +661,9 @@ def hook_fn_act_post(
         # )
 
     def hook_fn_query(
-        hook_q: Float[Tensor, "batch seq n_head d_head"], hook: HookPoint  # noqa
+        hook_q: Float[Tensor, "batch seq n_head d_head"], hook: HookPoint
     ):
-        """
-
+        r"""
         Replace act_post with projection of query onto the resid by W_k^T.
         Encoder has learned x^j \approx b + \sum_i f_i(x^j)d_i where:
             - f_i are the feature activations
@@ -698,7 +695,7 @@ def hook_fn_query(
         )
 
     def hook_fn_resid_post(
-        resid_post: Float[Tensor, "batch seq d_model"], hook: HookPoint  # noqa
+        resid_post: Float[Tensor, "batch seq d_model"], hook: HookPoint
     ):
         """
         This hook function stores the residual activations, which we'll need later on to calculate the effect of feature ablation.
@@ -1020,7 +1017,8 @@ def hook_fn_resid_post(
                     save_obj, filename=filename, save_type=save_type
                 )
                 t1 = time.time()
-                loaded_obj = FeatureData.load_batch(
+                # TODO: is this doing anything? the result isn't read
+                FeatureData.load_batch(
                     filename, save_type=save_type, vocab_dict=vocab_dict
                 )
                 t2 = time.time()
diff --git a/sae_analysis/visualizer/html_fns.py b/sae_analysis/visualizer/html_fns.py
index 9b0e546d..2b524dcc 100644
--- a/sae_analysis/visualizer/html_fns.py
+++ b/sae_analysis/visualizer/html_fns.py
@@ -82,20 +82,20 @@ def generate_tok_html(
 
     # Make all the substitutions
     html_output = re.sub(
-        "pos_str_(\d)",
+        r"pos_str_(\d)",
         lambda m: pos_str[int(m.group(1))].replace(" ", " "),
         html_output,
     )
     html_output = re.sub(
-        "neg_str_(\d)",
+        r"neg_str_(\d)",
         lambda m: neg_str[int(m.group(1))].replace(" ", " "),
         html_output,
     )
     html_output = re.sub(
-        "pos_val_(\d)", lambda m: f"{pos_val[int(m.group(1))]:+.3f}", html_output
+        r"pos_val_(\d)", lambda m: f"{pos_val[int(m.group(1))]:+.3f}", html_output
     )
     html_output = re.sub(
-        "neg_val_(\d)", lambda m: f"{neg_val[int(m.group(1))]:+.3f}", html_output
+        r"neg_val_(\d)", lambda m: f"{neg_val[int(m.group(1))]:+.3f}", html_output
     )
 
     # If the effect on loss is nothing (because feature isn't active), replace the HTML output with smth saying this
@@ -235,7 +235,7 @@ def generate_tables_html(
             if myformat is None
             else format(mylist[int(m.group(1))], myformat)
         )
-        html_output = re.sub(letter + "(\d)", fn, html_output, count=3)
+        html_output = re.sub(letter + r"(\d)", fn, html_output, count=3)
 
     html_output_2 = HTML_LOGIT_TABLES
 
@@ -258,7 +258,7 @@ def generate_tables_html(
             fn = lambda m: format(mylist[int(m.group(1))], "+.2f")
         elif letter == "C":
             fn = lambda m: str(mylist[int(m.group(1))])
-        html_output_2 = re.sub(letter + "(\d)", fn, html_output_2, count=10)
+        html_output_2 = re.sub(letter + r"(\d)", fn, html_output_2, count=10)
 
     return (html_output, html_output_2)
 
diff --git a/sae_analysis/visualizer/model_fns.py b/sae_analysis/visualizer/model_fns.py
index 3a4d6879..ebf4b570 100644
--- a/sae_analysis/visualizer/model_fns.py
+++ b/sae_analysis/visualizer/model_fns.py
@@ -4,7 +4,6 @@
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
-import tqdm.notebook as tqdm
 from transformer_lens import utils
 
 DTYPES = {"fp32": torch.float32, "fp16": torch.float16, "bf16": torch.bfloat16}
diff --git a/sae_analysis/visualizer/utils_fns.py b/sae_analysis/visualizer/utils_fns.py
index 51ab8980..7b0c59b6 100644
--- a/sae_analysis/visualizer/utils_fns.py
+++ b/sae_analysis/visualizer/utils_fns.py
@@ -1,23 +1,20 @@
 import re
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Dict, Optional, Tuple, Union
 
-import einops
 import numpy as np
 import torch
-from eindex import eindex
 from jaxtyping import Float, Int
 from torch import Tensor
-from transformer_lens import HookedTransformer
 
 Arr = np.ndarray
 
 
 def k_largest_indices(
-    x: Float[Tensor, "rows cols"],  # noqa
+    x: Float[Tensor, "rows cols"],
     k: int,
     largest: bool = True,
     buffer: Tuple[int, int] = (5, 5),
-) -> Int[Tensor, "k 2"]:  # noqa
+) -> Int[Tensor, "k 2"]:
     """w
     Given a 2D array, returns the indices of the top or bottom `k` elements.
 
@@ -40,11 +37,11 @@ def sample_unique_indices(large_number, small_number):
 
 
 def random_range_indices(
-    x: Float[Tensor, "batch seq"],  # noqa
+    x: Float[Tensor, "batch seq"],
     bounds: Tuple[float, float],
     k: int,
     buffer: Tuple[int, int] = (5, 5),
-) -> Int[Tensor, "k 2"]:  # noqa
+) -> Int[Tensor, "k 2"]:
     """
     Given a 2D array, returns the indices of `k` elements whose values are in the range `bounds`.
     Will return fewer than `k` values if there aren't enough values in the range.
diff --git a/sae_training/activations_store.py b/sae_training/activations_store.py
index 9bae6824..103aae19 100644
--- a/sae_training/activations_store.py
+++ b/sae_training/activations_store.py
@@ -3,7 +3,6 @@
 import torch
 from datasets import load_dataset
 from torch.utils.data import DataLoader
-from tqdm import tqdm
 from transformer_lens import HookedTransformer
 
 
diff --git a/sae_training/lm_runner.py b/sae_training/lm_runner.py
index ec038de8..9b51e960 100644
--- a/sae_training/lm_runner.py
+++ b/sae_training/lm_runner.py
@@ -1,6 +1,3 @@
-import os
-
-import torch
 import wandb
 
 # from sae_training.activation_store import ActivationStore
diff --git a/sae_training/sparse_autoencoder.py b/sae_training/sparse_autoencoder.py
index 23abbf05..7d5c3bf3 100644
--- a/sae_training/sparse_autoencoder.py
+++ b/sae_training/sparse_autoencoder.py
@@ -5,15 +5,10 @@
 import gzip
 import os
 import pickle
-from functools import partial
 
 import einops
 import torch
-import torch.nn.functional as F
-from jaxtyping import Float
-from torch import Tensor, nn
-from torch.distributions.categorical import Categorical
-from tqdm import tqdm
+from torch import nn
 from transformer_lens.hook_points import HookedRootModule, HookPoint
 
 from sae_training.geom_median.src.geom_median.torch import compute_geometric_median
diff --git a/sae_training/toy_model_runner.py b/sae_training/toy_model_runner.py
index 7726a24f..67aa267a 100644
--- a/sae_training/toy_model_runner.py
+++ b/sae_training/toy_model_runner.py
@@ -3,7 +3,6 @@
 import einops
 import torch
 import wandb
-from transformer_lens import HookedTransformer
 
 from sae_training.sparse_autoencoder import SparseAutoencoder
 from sae_training.toy_models import Config as ToyConfig
diff --git a/sae_training/toy_models.py b/sae_training/toy_models.py
index 32671de4..384954f7 100644
--- a/sae_training/toy_models.py
+++ b/sae_training/toy_models.py
@@ -10,15 +10,12 @@
 
 import einops
 import numpy as np
-import plotly.express as px
-import plotly.graph_objects as go
 import torch as t
 from IPython.display import clear_output
-from jaxtyping import Float, Int
+from jaxtyping import Float
 from matplotlib import pyplot as plt
 from matplotlib.animation import FuncAnimation
 from matplotlib.widgets import Slider  # , Button
-from plotly.subplots import make_subplots
 from torch import Tensor, nn
 from torch.nn import functional as F
 from tqdm import tqdm
@@ -51,8 +48,8 @@ class Config:
 
 
 class Model(nn.Module):
-    W: Float[Tensor, "n_instances n_hidden n_features"]  # noqa
-    b_final: Float[Tensor, "n_instances n_features"]  # noqa
+    W: Float[Tensor, "n_instances n_hidden n_features"]
+    b_final: Float[Tensor, "n_instances n_features"]
     # Our linear map is x -> ReLU(W.T @ W @ x + b_final)
 
     def __init__(
@@ -89,8 +86,8 @@ def __init__(
         self.to(device)
 
     def forward(
-        self, features: Float[Tensor, "... instances features"]  # noqa
-    ) -> Float[Tensor, "... instances features"]:  # noqa
+        self, features: Float[Tensor, "... instances features"]
+    ) -> Float[Tensor, "... instances features"]:
         hidden = einops.einsum(
             features,
             self.W,
@@ -119,7 +116,7 @@ def forward(
 
     def generate_correlated_features(
         self, batch_size, n_correlated_pairs
-    ) -> Float[Tensor, "batch_size instances features"]:  # noqa
+    ) -> Float[Tensor, "batch_size instances features"]:
         """
         Generates a batch of correlated features.
         Each output[i, j, 2k] and output[i, j, 2k + 1] are correlated, i.e. one is present iff the other is present.
@@ -141,7 +138,7 @@ def generate_correlated_features(
 
     def generate_anticorrelated_features(
         self, batch_size, n_anticorrelated_pairs
-    ) -> Float[Tensor, "batch_size instances features"]:  # noqa
+    ) -> Float[Tensor, "batch_size instances features"]:
         """
         Generates a batch of anti-correlated features.
         Each output[i, j, 2k] and output[i, j, 2k + 1] are anti-correlated, i.e. one is present iff the other is absent.
@@ -178,7 +175,7 @@ def generate_anticorrelated_features(
 
     def generate_uncorrelated_features(
         self, batch_size, n_uncorrelated
-    ) -> Float[Tensor, "batch_size instances features"]:  # noqa
+    ) -> Float[Tensor, "batch_size instances features"]:
         """
         Generates a batch of uncorrelated features.
         """
@@ -193,7 +190,7 @@ def generate_uncorrelated_features(
 
     def generate_batch(
         self, batch_size
-    ) -> Float[Tensor, "batch_size instances features"]:  # noqa
+    ) -> Float[Tensor, "batch_size instances features"]:
         """
         Generates a batch of data, with optional correlated & anticorrelated features.
         """
@@ -222,9 +219,9 @@ def generate_batch(
 
     def calculate_loss(
         self,
-        out: Float[Tensor, "batch instances features"],  # noqa
-        batch: Float[Tensor, "batch instances features"],  # noqa
-    ) -> Float[Tensor, ""]:  # noqa
+        out: Float[Tensor, "batch instances features"],
+        batch: Float[Tensor, "batch instances features"],
+    ) -> Float[Tensor, ""]:
         """
         Calculates the loss for a given batch, using this loss described in the Toy Models paper:
 
@@ -278,7 +275,7 @@ def optimize(
 
 
 def plot_features_in_2d(
-    values: Float[Tensor, "timesteps instances d_hidden feats"],  # noqa
+    values: Float[Tensor, "timesteps instances d_hidden feats"],
     colors=None,  # shape [timesteps instances feats]
     title: Optional[str] = None,
     subplot_titles: Optional[List[str]] = None,
@@ -431,7 +428,7 @@ def play(event):
 
 
 def parse_colors_for_superposition_plot(
-    colors: Optional[Union[Tuple[int, int], Float[Tensor, "instances feats"]]],  # noqa
+    colors: Optional[Union[Tuple[int, int], Float[Tensor, "instances feats"]]],
     n_instances: int,
     n_feats: int,
 ) -> List[List[str]]:
diff --git a/sae_training/train_sae_on_toy_model.py b/sae_training/train_sae_on_toy_model.py
index 5554d4db..c43b75c4 100644
--- a/sae_training/train_sae_on_toy_model.py
+++ b/sae_training/train_sae_on_toy_model.py
@@ -1,11 +1,9 @@
-import einops
 import torch
 import wandb
 from torch.utils.data import DataLoader
 from tqdm import tqdm
 
 from sae_training.sparse_autoencoder import SparseAutoencoder
-from sae_training.toy_models import Model as ToyModel
 
 
 def train_toy_sae(
@@ -65,7 +63,6 @@ def train_toy_sae(
                 )
 
             l0 = (feature_acts > 0).float().sum(-1).mean()
-            current_learning_rate = optimizer.param_groups[0]["lr"]
             l2_norm = torch.norm(feature_acts, dim=1).mean()
 
             l2_norm_in = torch.norm(batch, dim=-1)
diff --git a/scripts/generate_dashboards.py b/scripts/generate_dashboards.py
index 7da5dc02..bbfa0af7 100644
--- a/scripts/generate_dashboards.py
+++ b/scripts/generate_dashboards.py
@@ -1,3 +1,5 @@
+# flake8: noqa: E402
+# TODO: are these sys.path.append calls really necessary?
 import sys
 
 sys.path.append("..")
diff --git a/tests/benchmark/test_toy_model_sae_runner.py b/tests/benchmark/test_toy_model_sae_runner.py
index 811ac9c4..ed904d9f 100644
--- a/tests/benchmark/test_toy_model_sae_runner.py
+++ b/tests/benchmark/test_toy_model_sae_runner.py
@@ -1,4 +1,3 @@
-import pytest
 import torch
 
 from sae_training.toy_model_runner import SAEToyModelRunnerConfig, toy_model_sae_runner
diff --git a/tests/unit/test_sparse_autoencoder.py b/tests/unit/test_sparse_autoencoder.py
index 63422b09..e30b2103 100644
--- a/tests/unit/test_sparse_autoencoder.py
+++ b/tests/unit/test_sparse_autoencoder.py
@@ -92,7 +92,7 @@ def test_sparse_autoencoder_init(cfg):
 def test_save_model(cfg):
     with tempfile.TemporaryDirectory() as tmpdirname:
         # assert file does not exist
-        assert os.path.exists(tmpdirname + "/test.pt") == False
+        assert not os.path.exists(tmpdirname + "/test.pt")
 
         sparse_autoencoder = SparseAutoencoder(cfg)
         sparse_autoencoder.save_model(tmpdirname + "/test.pt")
@@ -120,7 +120,7 @@ def test_save_model(cfg):
 def test_load_from_pretrained_pt(cfg):
     with tempfile.TemporaryDirectory() as tmpdirname:
         # assert file does not exist
-        assert os.path.exists(tmpdirname + "/test.pt") == False
+        assert not os.path.exists(tmpdirname + "/test.pt")
 
         sparse_autoencoder = SparseAutoencoder(cfg)
         sparse_autoencoder_state_dict = sparse_autoencoder.state_dict()
@@ -152,7 +152,7 @@ def test_load_from_pretrained_pt(cfg):
 def test_load_from_pretrained_pkl_gz(cfg):
     with tempfile.TemporaryDirectory() as tmpdirname:
         # assert file does not exist
-        assert os.path.exists(tmpdirname + "/test.pkl.gz") == False
+        assert not os.path.exists(tmpdirname + "/test.pkl.gz")
 
         sparse_autoencoder = SparseAutoencoder(cfg)
         sparse_autoencoder_state_dict = sparse_autoencoder.state_dict()