diff --git a/.git_archival.txt b/.git_archival.txt
index b1a286b..8fb235d 100644
--- a/.git_archival.txt
+++ b/.git_archival.txt
@@ -1,4 +1,4 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$
\ No newline at end of file
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
index 343a755..f0e3f77 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -21,4 +21,4 @@
 # png image files
 # *.png	filter=lfs diff=lfs merge=lfs -text
 
-.git_archival.txt export-subst
\ No newline at end of file
+.git_archival.txt export-subst
diff --git a/.github/workflows/smoke-test.yml b/.github/workflows/smoke-test.yml
index 946b205..a1468eb 100644
--- a/.github/workflows/smoke-test.yml
+++ b/.github/workflows/smoke-test.yml
@@ -10,7 +10,7 @@ on:
   # Runs this workflow automatically
   schedule:
     - cron: 45 6 * * *
-    
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ac6fbbb..b14b692 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 
 repos:
     # Compare the local template version to the latest remote template version
-    # This hook should always pass. It will print a message if the local version 
+    # This hook should always pass. It will print a message if the local version
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
     rev: 439dda8bd784f4aa721851ecec03877df286f6b5
@@ -21,9 +21,14 @@ repos:
         stages: [pre-commit]
         language: system
         entry: jupyter nbconvert --clear-output
-    # Prevents committing directly branches named 'main' and 'master'.
+    # Run a series of standard precommit checks, including:
+    #  - no commits to branches named 'main' and 'master'.
+    #  - No large files (>= 500kb)
+    #  - All YAML and TOML files are valid.
+    #  - No whitespace at the end of lines and a single newline at end of file.
+    #  - No outstanding merge conflict markers in the codebase.
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c
+    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c  # v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent main branch commits
@@ -32,6 +37,18 @@ repos:
         name: Check for large files
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
+      - id: trailing-whitespace
+        exclude: \.(rst|md|txt|html)$  # Skip rst, md, txt, and html files
+        name: Fix trailing whitespace
+      - id: end-of-file-fixer
+        name: Files end with a newline
+      - id: check-toml
+        name: Validate TOML files
+      - id: check-yaml
+        args: [--allow-multiple-documents]  # Allow multiple document format
+        name: Validate YAML files
+      - id: check-merge-conflict
+        name: Check for merge conflicts
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: 17e12779811926f000bdfa1795f9e3735dd71ac3
@@ -79,7 +96,9 @@ repos:
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.11
+        # This currently uses the default language version. Uncomment
+        # the following line to use the max version.
+        # language_version: python{{ py.max(python_versions) }}
     # Run unit tests, verify that they pass. Note that coverage is run against
     # the ./src directory here because that is what will be committed. In the
     # github workflow script, the coverage is run against the installed package
diff --git a/docs/practices/issue_pr_templating.rst b/docs/practices/issue_pr_templating.rst
index f76e57c..d4fd3bc 100644
--- a/docs/practices/issue_pr_templating.rst
+++ b/docs/practices/issue_pr_templating.rst
@@ -60,4 +60,4 @@ provides generic fields for:
 
 As well as a set of additional project and issue-specific fields. This template
 only serves as an initial framework, and you should feel free to modify this as
-you see fit by directly modifying the template file.
\ No newline at end of file
+you see fit by directly modifying the template file.
diff --git a/docs/source/update_project.rst b/docs/source/update_project.rst
index 7a688fd..7cefd7d 100644
--- a/docs/source/update_project.rst
+++ b/docs/source/update_project.rst
@@ -141,4 +141,4 @@ For all the details about updating with Copier checkout the
 Still have questions?
 -------------------------------------
 
-:doc:`/source/contact`
\ No newline at end of file
+:doc:`/source/contact`
diff --git a/python-project-template/.git_archival.txt b/python-project-template/.git_archival.txt
index b1a286b..8fb235d 100644
--- a/python-project-template/.git_archival.txt
+++ b/python-project-template/.git_archival.txt
@@ -1,4 +1,4 @@
 node: $Format:%H$
 node-date: $Format:%cI$
 describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
-ref-names: $Format:%D$
\ No newline at end of file
+ref-names: $Format:%D$
diff --git a/python-project-template/.gitattributes b/python-project-template/.gitattributes
index 343a755..f0e3f77 100644
--- a/python-project-template/.gitattributes
+++ b/python-project-template/.gitattributes
@@ -21,4 +21,4 @@
 # png image files
 # *.png	filter=lfs diff=lfs merge=lfs -text
 
-.git_archival.txt export-subst
\ No newline at end of file
+.git_archival.txt export-subst
diff --git a/python-project-template/.github/workflows/README.md b/python-project-template/.github/workflows/README.md
index e34a71f..231bf1e 100644
--- a/python-project-template/.github/workflows/README.md
+++ b/python-project-template/.github/workflows/README.md
@@ -6,4 +6,4 @@ or when you create a new PR.
 
 For more information about CI and workflows, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci.html
 
-Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html
\ No newline at end of file
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html
diff --git a/python-project-template/.github/workflows/pre-commit-ci.yml.jinja b/python-project-template/.github/workflows/pre-commit-ci.yml.jinja
index 47e522f..9f40a11 100644
--- a/python-project-template/.github/workflows/pre-commit-ci.yml.jinja
+++ b/python-project-template/.github/workflows/pre-commit-ci.yml.jinja
@@ -39,4 +39,4 @@ jobs:
       env:
         SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
     - uses: pre-commit-ci/lite-action@062bca0919bc9d6e66755cc05074b70c77e111fc  # v1.2.0
-      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false
\ No newline at end of file
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false
diff --git a/python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja
index cc82270..1a25aa5 100644
--- a/python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if contains_code %}smoke-test.yml{% endif %}.jinja	
@@ -122,4 +122,4 @@ jobs:
             ]
           }
     {%- endraw %}
-{%- endif %}
\ No newline at end of file
+{%- endif %}
diff --git a/python-project-template/.github/workflows/{% if contains_code %}testing-and-coverage.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if contains_code %}testing-and-coverage.yml{% endif %}.jinja
index f620030..5972f33 100644
--- a/python-project-template/.github/workflows/{% if contains_code %}testing-and-coverage.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if contains_code %}testing-and-coverage.yml{% endif %}.jinja	
@@ -83,4 +83,4 @@ jobs:
       run: |
         source venv/bin/activate
         python -m pytest
-{%- endif %}
\ No newline at end of file
+{%- endif %}
diff --git a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-main.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-main.yml{% endif %}.jinja
index 2eb356d..5aaa2e9 100644
--- a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-main.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-main.yml{% endif %}.jinja	
@@ -73,4 +73,5 @@ jobs:
       with:
         branch: gh-pages
         folder: ${{env.WORKING_DIR}}/_html
-{%- endraw -%}
\ No newline at end of file
+
+{%- endraw -%}
diff --git a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-nightly.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-nightly.yml{% endif %}.jinja
index 745b136..3459efc 100644
--- a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-nightly.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-nightly.yml{% endif %}.jinja	
@@ -79,4 +79,5 @@ jobs:
       with:
         path: ${{env.WORKING_DIR}}
         key: nightly-results-${{steps.nightly-dates.outputs.today}}
-{%- endraw -%}
\ No newline at end of file
+
+{%- endraw -%}
diff --git a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-pr.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-pr.yml{% endif %}.jinja
index 511785a..5440bea 100644
--- a/python-project-template/.github/workflows/{% if include_benchmarks %}asv-pr.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if include_benchmarks %}asv-pr.yml{% endif %}.jinja	
@@ -78,4 +78,5 @@ jobs:
       with:
         name: benchmark-artifacts
         path: ${{env.ARTIFACTS_DIR}}
-{%- endraw -%}
\ No newline at end of file
+
+{%- endraw -%}
diff --git a/python-project-template/.github/workflows/{% if include_benchmarks %}publish-benchmarks-pr.yml{% endif %}.jinja b/python-project-template/.github/workflows/{% if include_benchmarks %}publish-benchmarks-pr.yml{% endif %}.jinja
index f1aa290..70c53fa 100644
--- a/python-project-template/.github/workflows/{% if include_benchmarks %}publish-benchmarks-pr.yml{% endif %}.jinja	
+++ b/python-project-template/.github/workflows/{% if include_benchmarks %}publish-benchmarks-pr.yml{% endif %}.jinja	
@@ -55,4 +55,5 @@ jobs:
         issue-number: ${{ steps.pr-info.outputs.pr }}
         body-path: output
         edit-mode: replace
+
 {%- endraw -%}
diff --git a/python-project-template/.pre-commit-config.yaml.jinja b/python-project-template/.pre-commit-config.yaml.jinja
index c0401e0..837e9de 100644
--- a/python-project-template/.pre-commit-config.yaml.jinja
+++ b/python-project-template/.pre-commit-config.yaml.jinja
@@ -21,7 +21,12 @@ repos:
         stages: [pre-commit]
         language: system
         entry: jupyter nbconvert --clear-output
-    # Prevents committing directly branches named 'main' and 'master'.
+    # Run a series of standard precommit checks, including:
+    #  - no commits to branches named 'main' and 'master'.
+    #  - No large files (>= 500kb)
+    #  - All YAML and TOML files are valid.
+    #  - No whitespace at the end of lines and a single newline at end of file.
+    #  - No outstanding merge conflict markers in the codebase.
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c  # v6.0.0
     hooks:
@@ -32,6 +37,18 @@ repos:
         name: Check for large files
         description: Prevent the user from committing very large files.
         args: ['--maxkb=500']
+      - id: trailing-whitespace
+        exclude: \.(rst|md|txt|html)$  # Skip rst, md, txt, and html files
+        name: Fix trailing whitespace
+      - id: end-of-file-fixer
+        name: Files end with a newline
+      - id: check-toml
+        name: Validate TOML files
+      - id: check-yaml
+        args: [--allow-multiple-documents]  # Allow multiple document format
+        name: Validate YAML files
+      - id: check-merge-conflict
+        name: Check for merge conflicts
     # Verify that pyproject.toml is well formed
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: 17e12779811926f000bdfa1795f9e3735dd71ac3  # v0.26
diff --git a/python-project-template/README.md.jinja b/python-project-template/README.md.jinja
index 2913a20..777dee0 100644
--- a/python-project-template/README.md.jinja
+++ b/python-project-template/README.md.jinja
@@ -15,13 +15,13 @@
 [![Benchmarks](https://img.shields.io/github/actions/workflow/status/{{project_organization}}/{{project_name}}/asv-main.yml?label=benchmarks)](https://{{project_organization}}.github.io/{{project_name}}/)
 {%- endif %}
 
-This project was automatically generated using the LINCC-Frameworks 
+This project was automatically generated using the LINCC-Frameworks
 [python-project-template](https://github.com/lincc-frameworks/python-project-template).
 
 A repository badge was added to show that this project uses the python-project-template, however it's up to
 you whether or not you'd like to display it!
 
-For more information about the project template see the 
+For more information about the project template see the
 [documentation](https://lincc-ppt.readthedocs.io/en/latest/).
 
 ## Dev Guide - Getting Started
@@ -47,7 +47,7 @@ development using the following commands:
 Notes:
 1. `./.setup_dev.sh` will initialize pre-commit for this local repository, so
    that a set of tests will be run prior to completing a local commit. For more
-   information, see the Python Project Template documentation on 
+   information, see the Python Project Template documentation on
    [pre-commit](https://lincc-ppt.readthedocs.io/en/latest/practices/precommit.html)
 {%- if include_notebooks %}
 2. Install `pandoc` allows you to verify that automatic rendering of Jupyter notebooks
diff --git a/python-project-template/{% if include_dev_guide %}DEVELOPMENT_GUIDE.md{% endif %}.jinja b/python-project-template/{% if include_dev_guide %}DEVELOPMENT_GUIDE.md{% endif %}.jinja
index da6d001..dc1b89d 100644
--- a/python-project-template/{% if include_dev_guide %}DEVELOPMENT_GUIDE.md{% endif %}.jinja	
+++ b/python-project-template/{% if include_dev_guide %}DEVELOPMENT_GUIDE.md{% endif %}.jinja	
@@ -65,4 +65,3 @@ benchmarks/                       ASV performance benchmarks
 - **File naming:** `tests/{{package_name}}/<SUBDIR>/test_<name>.py`, mirroring the `src/{{package_name}}/` layout.
 - **Fixtures:** defined in `tests/conftest.py`. Use existing fixtures, do not duplicate test data.
 - Default test run: `python -m pytest`
-
diff --git a/python-project-template/{% if project_license == 'GPL3' %}LICENSE{% endif%}.jinja b/python-project-template/{% if project_license == 'GPL3' %}LICENSE{% endif%}.jinja
index e72bfdd..f288702 100644
--- a/python-project-template/{% if project_license == 'GPL3' %}LICENSE{% endif%}.jinja	
+++ b/python-project-template/{% if project_license == 'GPL3' %}LICENSE{% endif%}.jinja	
@@ -671,4 +671,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
\ No newline at end of file
+<https://www.gnu.org/licenses/why-not-lgpl.html>.