add pre-commit; pre-commit fixes

.gitattributes

@@ -10,4 +10,3 @@
 *.json text eol=lf
 *.yml text eol=lf
 *.csv text eol=lf
-

.github/actions/pre-commit/action.yaml

@@ -0,0 +1,16 @@
+name: pre-commit
+description: run pre-commit
+inputs:
+  extra_args:
+    description: options to pass to pre-commit run
+    required: false
+    default: '--all-files'
+runs:
+  using: composite
+  steps:
+  - run: python -m pip install pre-commit
+    shell: bash
+  - run: python -m pip freeze --local
+    shell: bash
+  - run: pre-commit run --show-diff-on-failure --color=always ${{ inputs.extra_args }}
+    shell: bash

.github/workflows/pre-commit.yaml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: ./.github/actions/pre-commit

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+repos:
+################################################################################
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=10000']
+    -   id: check-yaml
+        args: [--allow-multiple-documents]
+    -   id: check-toml
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+    -   id: trailing-whitespace
+################################################################################
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
+    hooks:
+    -   id: black-jupyter
+        args: ['--line-length', '79']
+        language_version: python3
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: ['--profile', 'black',
+               '--line-length', '79']
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.7
+    hooks:
+      - id: ruff
+        args: ['--ignore=E741', '--ignore=E731', '--fix']
+################################################################################
+-   repo: https://github.com/rhysd/actionlint
+    rev: v1.7.1
+    hooks:
+    -   id: actionlint
+################################################################################
+-   repo: https://github.com/crate-ci/typos
+    rev: v1.21.0
+    hooks:
+    -   id: typos
+        args: ["--force-exclude"]
+################################################################################

.vscode/settings.json

@@ -5,4 +5,4 @@
         "ISSO",
         "cybersecurity"
     ]
-}
+}

README.md

@@ -2,7 +2,7 @@
 
 **Template for clearance: This project serves as a template to aid projects in starting up and moving through clearance procedures. To start, create a new repository and implement the required [open practices](open_practices.md), train on and agree to adhere to the organization's [rules of behavior](rules_of_behavior.md), and [send a request through the create repo form](https://forms.office.com/Pages/ResponsePage.aspx?id=aQjnnNtg_USr6NJ2cHf8j44WSiOI6uNOvdWse4I-C2NUNk43NzMwODJTRzA4NFpCUk1RRU83RTFNVi4u) using language from this template as a Guide.**
 
-**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. 
+**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
 
 ## Access Request, Repo Creation Request
 
@@ -20,7 +20,7 @@
 ## Overview
 
 Describe the purpose of your project. Add additional sections as necessary to help collaborators and potential collaborators understand and use your project.
-  
+
 ## Public Domain Standard Notice
 This repository constitutes a work of the United States Government and is not
 subject to domestic copyright protection under 17 USC § 105. This repository is in

rules_of_behavior.md

@@ -48,7 +48,7 @@ Examples of information which has been deemed not sensitive and may be posted on
 * Process flows
 * Program pain points
 * Software Service Descriptions
- 
+
 Sensitive information, which should not be posted, includes (but is not limited to) the following.
 
 * Information directly attributed to an individual in a sensitive manner
@@ -59,7 +59,7 @@ Sensitive information, which should not be posted, includes (but is not limited
 * Non-public Links to CDC SharePoint or other internal references
 * Non-public Details on CDC internal infrastructure
 
-If there’s any question on whether information may be sensitive (such as detailed interview notes or specific references provided during a program interview), further guidance should be sought from the security steward prior to posting the information on any GitHub. 
+If there’s any question on whether information may be sensitive (such as detailed interview notes or specific references provided during a program interview), further guidance should be sought from the security steward prior to posting the information on any GitHub.
 
 ## Enforcement