Add NLP metrics package and Unit Tests CI (#513)

* fix file mode of a non-executable text file

* add basic NLP scoring methods package, unit tests, and automation

* fix unit tests

* fix unit tests

* add test resources; fix tests

* add CI bulid status badge

Author: plandes

.github/workflows/run-unit-tests.yml

@@ -0,0 +1,36 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    paths-ignore:
+      - '**.md'
+      - 'doc/*'
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - name: Checkout reposistory
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      - name: Install dependent packages
+        run: 'make deps'
+
+      - name: Run tests
+        run: 'make test'

.github/workflows/test.yml

@@ -1,7 +1,7 @@
 .idea
 *DS_Store*
 *output*
-*resource*
+resource*
 
 debug_entry*
 playground.ipynb

.gitignore

@@ -39,6 +39,9 @@ Welcome to PyHealth!
    :target: https://www.youtube.com/playlist?list=PLR3CNIF8DDHJUl8RLhyOVpX_kT4bxulEV
    :alt: YouTube
 
+.. image:: https://github.com/sunlabuiuc/PyHealth/workflows/CI/badge.svg
+   :target: https://github.com/sunlabuiuc/PyHealth/actions
+   :alt: CI status
 
 
 .. -----

README.rst

@@ -0,0 +1,31 @@
+#@meta {author: "Paul Landes"}
+#@meta {desc: "PyHealth build automation", date: "2025-05-22"}
+
+
+## Build
+#
+# directory with the unit tests
+PY_TEST_DIR ?=		tests
+# test file glob pattern
+PY_TEST_GLOB ?=		test_metrics.py
+
+
+## Targets
+#
+# install dependencies
+.PHONY:			deps
+deps:
+			pip install -r requirements-nlp.txt
+
+# run the unit test cases
+.PHONY:			test
+test:
+			@echo "Running tests in $(PY_TEST_DIR)/$(PY_TEST_GLOB)"
+			python -m unittest discover \
+				-s $(PY_TEST_DIR) -p '$(PY_TEST_GLOB)' -v
+
+# clean derived objects
+.PHONY:			clean
+clean:
+			@echo "removing __pycache__"
+			@find . -type d -name __pycache__ -prune -exec rm -r {} \;