diff --git a/.github/workflows/init.yml b/.github/workflows/init.yml
deleted file mode 100644
index 0336013..0000000
--- a/.github/workflows/init.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-# Workflow runs only once when the template is first used.
-# File can be safely deleted after repo is initialized.
-name: Initialize repository
-on:
-  push:
-    branches:
-      - main
-
-jobs:
-  initialize-package:
-    name: Initialize the package
-    if: ${{github.event.repository.name != 'aind-library-template'}}
-    runs-on: ubuntu-latest
-    env:
-      REPO_NAME: ${{ github.event.repository.name }}
-      GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v3
-    - name: Rename package
-      run: |
-        pkg_name=$(echo "${REPO_NAME}" | tr - _)
-        current_description='description = "Prints messages to stdout. Simple boilerplate for libraries."'
-        new_description='description = "Generated from aind-library-template"'
-        readme_description='Template for a minimal, basic repository for an AIND library.'
-        new_readme_description='Generated from aind-library-template'
-        echo "Package Name ${pkg_name}"
-        mkdir src/${pkg_name}
-        touch src/${pkg_name}/__init__.py
-        echo '"""Init package"""' >> src/${pkg_name}/__init__.py
-        echo '__version__ = "0.0.0"' >> src/${pkg_name}/__init__.py
-        sed -i "s/aind_library_template/${pkg_name}/" pyproject.toml
-        sed -i "s/aind-library-template/${REPO_NAME}/" pyproject.toml
-        sed -i "s/aind_library_template/${pkg_name}/" doc_template/source/conf.py
-        sed -i "s/${current_description}/${new_description}/" pyproject.toml
-        sed -i "/pandas/d" pyproject.toml
-        sed -i "s/aind-library-template/${REPO_NAME}/" README.md
-        sed -i "s/${readme_description}/${new_readme_description}/" README.md
-    - name: Commit changes
-      uses: EndBug/add-and-commit@v9
-      with:
-        default_author: github_actions
-        message: "ci: version bump [skip actions]"
-        add: '["pyproject.toml", "README.md", "src/*", "doc_template/source/conf.py"]'
-        remove: '["-r src/aind_library_template", "tests/test_message_handler.py"]'
-    - name: Add first tag
-      run: |
-        git tag v0.0.0
-        git push origin v0.0.0
-    - name: Disable workflow
-      run: |
-        gh workflow disable -R $GITHUB_REPOSITORY "${{ github.workflow }}"
diff --git a/doc_template/source/conf.py b/doc_template/source/conf.py
index 9f9c46c..d602401 100644
--- a/doc_template/source/conf.py
+++ b/doc_template/source/conf.py
@@ -1,12 +1,15 @@
 """Configuration file for the Sphinx documentation builder."""
+
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+from datetime import date
+
 # -- Path Setup --------------------------------------------------------------
-from os.path import dirname, abspath
+from os.path import abspath, dirname
 from pathlib import Path
-from datetime import date
+
 from aind_smartspim_data_transformation import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"
diff --git a/src/aind_smartspim_data_transformation/compress/__init__.py b/src/aind_smartspim_data_transformation/compress/__init__.py
index f8926e0..a3c9cb6 100644
--- a/src/aind_smartspim_data_transformation/compress/__init__.py
+++ b/src/aind_smartspim_data_transformation/compress/__init__.py
@@ -1,3 +1,3 @@
 """
-Init internal package
+Init SmartSPIM data transformation package
 """
diff --git a/src/aind_smartspim_data_transformation/compress/dask_utils.py b/src/aind_smartspim_data_transformation/compress/dask_utils.py
index 764b5a7..6f70187 100644
--- a/src/aind_smartspim_data_transformation/compress/dask_utils.py
+++ b/src/aind_smartspim_data_transformation/compress/dask_utils.py
@@ -39,9 +39,9 @@ def log_dashboard_address(
         client: the Client instance
         login_node_address: the address of the cluster login node
     """
-    host = client.run_on_scheduler(socket.gethostname)
-    port = client.scheduler_info()["services"]["dashboard"]
-    user = os.getenv("USER")
+    host = client.run_on_scheduler(socket.gethostname)  # noqa: F841
+    port = client.scheduler_info()["services"]["dashboard"]  # noqa: F841
+    user = os.getenv("USER")  # noqa: F841
     LOGGER.info(
         f"To access the dashboard, run the following in "
         "a terminal: ssh -L {port}:{host}:{port} {user}@"
diff --git a/src/aind_smartspim_data_transformation/compress/png_to_zarr.py b/src/aind_smartspim_data_transformation/compress/png_to_zarr.py
index 602bfa1..5758d76 100644
--- a/src/aind_smartspim_data_transformation/compress/png_to_zarr.py
+++ b/src/aind_smartspim_data_transformation/compress/png_to_zarr.py
@@ -15,8 +15,6 @@
 
 import dask
 import dask.array as da
-
-# import matplotlib.pyplot as plt
 import numpy as np
 import pims
 import xarray_multiscale
@@ -33,7 +31,11 @@
 from ome_zarr.writer import write_multiscales_metadata
 from skimage.io import imread as sk_imread
 
-from aind_smartspim_data_transformation.compress.zarr_utilities import *
+from aind_smartspim_data_transformation.compress.zarr_utilities import (
+    ArrayLike,
+    PathLike,
+    pad_array_n_d,
+)
 from aind_smartspim_data_transformation.compress.zarr_writer import (
     BlockedArrayWriter,
 )
@@ -144,16 +146,20 @@ def _compute_scales(
     data_shape: Tuple[int, int, int, int, int],
     translation: Optional[List[float]] = None,
 ) -> Tuple[List, List]:
-    """Generate the list of coordinate transformations and associated chunk options.
+    """
+    Generate the list of coordinate transformations
+    and associated chunk options.
 
     Parameters
     ----------
     scale_num_levels: the number of downsampling levels
     scale_factor: a tuple of scale factors in each spatial dimension (Z, Y, X)
     pixelsizes: a list of pixel sizes in each spatial dimension (Z, Y, X)
-    chunks: a 5D tuple of integers with size of each chunk dimension (T, C, Z, Y, X)
+    chunks: a 5D tuple of integers with size of each
+    chunk dimension (T, C, Z, Y, X)
     data_shape: a 5D tuple of the full resolution image's shape
-    translation: a 5 element list specifying the offset in physical units in each dimension
+    translation: a 5 element list specifying the offset
+    in physical units in each dimension
 
     Returns
     -------
@@ -364,7 +370,7 @@ def _get_pyramid_metadata():
     """
     return {
         "metadata": {
-            "description": "Downscaling implementation based on the windowed mean of the original array",
+            "description": "Downscaling using the windowed mean",
             "method": "xarray_multiscale.reducers.windowed_mean",
             "version": str(xarray_multiscale.__version__),
             "args": "[false]",
@@ -438,7 +444,8 @@ def wavelength_to_hex(wavelength: int) -> int:
     """
     # Each wavelength key is the upper bound to a wavelgnth band.
     # Wavelengths range from 380-750nm.
-    # Color map wavelength/hex pairs are generated by sampling along a CIE diagram arc.
+    # Color map wavelength/hex pairs are generated
+    # by sampling along a CIE diagram arc.
     color_map = {
         460: 0x690AFE,  # Purple
         470: 0x3F2EFE,  # Blue-Purple
@@ -657,6 +664,7 @@ def smartspim_channel_zarr_writer(
         # Formatting to 5D block shape
         block_shape = ([1] * (5 - len(block_shape))) + block_shape
         written_pyramid = []
+        pyramid_group = None
 
         # Writing multiple levels
         for level in range(n_lvls):
diff --git a/src/aind_smartspim_data_transformation/io/_io.py b/src/aind_smartspim_data_transformation/io/_io.py
index 20a9f81..6effab0 100644
--- a/src/aind_smartspim_data_transformation/io/_io.py
+++ b/src/aind_smartspim_data_transformation/io/_io.py
@@ -262,7 +262,8 @@ def metadata(self) -> Dict:
 
         zattrs_metadata = ""
         zarray_metadata = ""
-        # Checking inside and outside of folder due to dimension separator "." or "/"
+        # Checking inside and outside of folder
+        # due to dimension separator "." or "/"
         for path in [data_path, data_path.parent]:
             if path.joinpath(".zattrs").exists():
                 zattrs_metadata = path.joinpath(".zattrs")