Reapply "Initial commit"

This reverts commit 0bca1c7.

Author: dlobuecmi

.gitignore

@@ -164,3 +164,16 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+
+
+# Ignore data folders
+data/**/*
+
+#Dont ignore the data folders
+!data/**/.gitkeep
+
+
+# Ignore Environments
+venv/
+.venv/
+env/

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-ENTER_YOUR_EMAIL_ADDRESS.
+david.lobue@childmind.org.
 
 All complaints will be reviewed and investigated promptly and fairly.
 

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# template-python-repository pull request guidelines
+# anonymize-pii pull request guidelines
 
-Pull requests are always welcome, and we appreciate any help you give. Note that a code of conduct applies to all spaces managed by the template-python-repository project, including issues and pull requests. Please see the [Code of Conduct](CODE_OF_CONDUCT.md) for details.
+Pull requests are always welcome, and we appreciate any help you give. Note that a code of conduct applies to all spaces managed by the anonymize-pii project, including issues and pull requests. Please see the [Code of Conduct](CODE_OF_CONDUCT.md) for details.
 
 When submitting a pull request, we ask you to check the following:
 

LICENSE

@@ -4,7 +4,7 @@
 
 Welcome to the CMI-DAIR Template Python Repository! This template is designed to streamline your project setup and ensure a consistent structure. To get started, follow these steps:
 
-- [ ] Run `setup_template.py` to initialize the repository.
+- [x] Run `setup_template.py` to initialize the repository.
 - [ ] Replace the content of this `README.md` with details specific to your project.
 - [ ] Install the `pre-commit` hooks to ensure code quality on each commit.
 - [ ] Revise SECURITY.md to reflect supported versions or remove it if not applicable.
@@ -15,12 +15,11 @@ Welcome to the CMI-DAIR Template Python Repository! This template is designed to
 
 # Project name
 
-[![Build](https://github.com/childmindresearch/template-python-repository/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/template-python-repository/actions/workflows/test.yaml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/childmindresearch/template-python-repository/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/template-python-repository)
+[![Build](https://github.com/childmindresearch/anonymize-pii/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/anonymize-pii/actions/workflows/test.yaml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/childmindresearch/anonymize-pii/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/anonymize-pii)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![stability-stable](https://img.shields.io/badge/stability-stable-green.svg)
-[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/childmindresearch/template-python-repository/blob/main/LICENSE)
-[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/template-python-repository)
+[![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/anonymize-pii)
 
 What problem does this tool solve?
 
@@ -41,7 +40,7 @@ pip install APP_NAME
 Or get the newest development version via:
 
 ```sh
-pip install git+https://github.com/childmindresearch/template-python-repository
+pip install git+https://github.com/childmindresearch/anonymize-pii
 ```
 
 ## Quick start

README.md

@@ -15,6 +15,6 @@ Note which version(s) will receive security updates. For example:
 
 ## Reporting Vulnerabilities
 
-To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at ENTER_YOUR_EMAIL_ADDRESS. Please refrain from using other communication channels.
+To report security vulnerabilities, please do NOT use our issues page. Instead, kindly email us at david.lobue@childmind.org. Please refrain from using other communication channels.
 
 For non-security-related issues, we welcome your input and feedback on our issues page. Feel free to share your ideas and suggestions to help us improve our services.

SECURITY.md

@@ -1,51 +1,21 @@
+[build-system]
+requires = ["setuptools>=65.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
 [project]
-name = "app-name"
+name = "anonymize-pii"
 version = "0.1.0"
-description = "A beautiful description."
+description = "A PII anonymizer for text data that includes sensitive information."
 authors = [
   {name = "CMI DAIR", email = "dair@childmind.org"}
 ]
-license = "LGPL-2.1-only"
 readme = "README.md"
 requires-python = ">=3.12"
-dependencies = []
-
-[dependency-groups]
-dev = [
-  "pytest>=8.3.4",
-  "mypy>=1.13.0",
-  "pre-commit>=4.0.1",
-  "pytest-cov>=6.0.0",
-  "ruff>=0.8.1",
-  "deptry>=0.23.0"
-]
-docs = ["pdoc>=15.0.0"]
 
-[tool.pytest.ini_options]
-pythonpath = ["src"]
-testpaths = ["tests"]
 
-[tool.mypy]
-ignore_missing_imports = true
+[tool.setuptools]
+package-dir = {"" = "src"}
 
-[tool.ruff]
-line-length = 88
-indent-width = 4
-src = ["src"]
-target-version = "py312"
-
-[tool.ruff.lint]
-select = ["ANN", "D", "E", "F", "I"]
-ignore = []
-fixable = ["ALL"]
-unfixable = []
-
-[tool.ruff.lint.pydocstyle]
-convention = "google"
-
-[tool.ruff.lint.per-file-ignores]
-"tests/**/*.py" = []
-
-[build-system]
-requires = ["uv_build>=0.9.3,<0.10.0"]
-build-backend = "uv_build"
+[tool.setuptools.packages.find]
+where = ["src"]

pyproject.toml

@@ -0,0 +1,65 @@
+annotated-types==0.7.0
+blis==1.3.3
+catalogue==2.0.10
+certifi==2025.11.12
+cffi==2.0.0
+charset-normalizer==3.4.4
+click==8.3.1
+cloudpathlib==0.23.0
+coloredlogs==15.0.1
+confection==0.1.5
+cryptography==44.0.3
+cymem==2.0.13
+emoji==2.15.0
+en_core_web_lg @ https://github.com/explosion/spacy-models/releases/download/en_core_web_lg-3.8.0/en_core_web_lg-3.8.0-py3-none-any.whl#sha256=293e9547a655b25499198ab15a525b05b9407a75f10255e405e8c3854329ab63
+en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.8.0/en_core_web_sm-3.8.0-py3-none-any.whl#sha256=1932429db727d4bff3deed6b34cfc05df17794f4a52eeb26cf8928f7c1a0fb85
+filelock==3.20.1
+flatbuffers==25.12.19
+fsspec==2025.12.0
+gliner==0.2.24
+hf-xet==1.2.0
+huggingface-hub==0.36.0
+humanfriendly==10.0
+idna==3.11
+Jinja2==3.1.6
+MarkupSafe==3.0.3
+mpmath==1.3.0
+murmurhash==1.0.15
+networkx==3.6.1
+numpy==2.4.0
+onnxruntime==1.23.2
+packaging==25.0
+phonenumbers==9.0.21
+preshed==3.0.12
+presidio_analyzer==2.2.360
+presidio_anonymizer==2.2.360
+protobuf==6.33.2
+pycparser==2.23
+pydantic==2.12.5
+pydantic_core==2.41.5
+PyYAML==6.0.3
+regex==2025.11.3
+requests==2.32.5
+requests-file==3.0.1
+safetensors==0.7.0
+sentencepiece==0.2.1
+smart_open==7.5.0
+spacy==3.8.11
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+srsly==2.5.2
+stanza==1.11.0
+sympy==1.14.0
+thinc==8.3.10
+tldextract==5.3.0
+tokenizers==0.22.1
+torch==2.9.1
+tqdm==4.67.1
+transformers==4.57.3
+typer-slim==0.21.0
+typing-inspection==0.4.2
+typing_extensions==4.15.0
+urllib3==2.6.2
+wasabi==1.1.3
+weasel==0.4.3
+wrapt==2.0.1

requirements.txt

@@ -0,0 +1,6 @@
+""" Setup file """
+
+from setuptools import setup
+
+# Configuration is pyproject.toml
+setup()