From 2d65e476e4be571df67c76d8186b32fd42693999 Mon Sep 17 00:00:00 2001
From: Alexander Vowinkel <alexander.vowinkel@bayer.com>
Date: Fri, 17 Jan 2025 16:00:58 +0100
Subject: [PATCH] add ci pipeline

---
 .github/workflows/ci.yaml | 24 ++++++++++++++++++++++++
 README.md                 |  2 ++
 medconb_client.py         | 15 +++++++--------
 requirements-dev.txt      |  5 +++++
 4 files changed, 38 insertions(+), 8 deletions(-)
 create mode 100644 .github/workflows/ci.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..0a5351a
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,24 @@
+name: Lint and Build
+
+on: push
+
+jobs:
+  lint_and_build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository 🛎️
+        uses: actions/checkout@v4
+      - name: Install Python 3.10 🐍
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Set up runner 📦
+        run: pip install -r requirements.txt -r requirements-dev.txt
+      - name: "Black: Code Formatting 👮🏽‍♀️"
+        run: black --check medconb_client.py
+      - name: "Pylama: Linting 🧹"
+        run: ruff check medconb_client.py
+      - name: "Mypy: Type checking 👮🏽‍♀️"
+        run: mypy medconb_client.py
+      - name: Build 🏗️
+        run: python -m build
diff --git a/README.md b/README.md
index c77dfb8..732823f 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,9 @@
 # MedConB Client
 
 [![Documentation](https://img.shields.io/badge/Documentation-526CFE?logo=MaterialForMkDocs&logoColor=white)](https://bayer-group.github.io/medconb-client/)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Linting: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 This library provides a Python interface to the MedConB API. With this you can easily retrieve whole codelists from MedConB.
 
diff --git a/medconb_client.py b/medconb_client.py
index 30c4ff0..a5274ac 100644
--- a/medconb_client.py
+++ b/medconb_client.py
@@ -1,15 +1,13 @@
 import logging
-from dataclasses import dataclass
-from typing import Optional, overload, Callable
 from collections import UserList
-from uuid import UUID
+from dataclasses import dataclass
+from typing import Optional, overload
 
-from pydantic import BaseModel
 import pandas as pd
-from gql import Client as GQLClient, gql
-from gql.transport.requests import RequestsHTTPTransport
+from gql import Client as GQLClient
+from gql import gql
 from gql.transport.aiohttp import AIOHTTPTransport
-from msal import PublicClientApplication
+from pydantic import BaseModel
 
 
 class Workspace(BaseModel):
@@ -279,7 +277,8 @@ async def get_codelist_by_name(
             mode = "phenotype"
         else:
             raise ValueError(
-                "Invalid arguments: Specify either codelist_collection_name or phenotype_collection_name and phenotype_name"
+                "Invalid arguments: Specify either codelist_collection_name or"
+                " phenotype_collection_name and phenotype_name"
             )
 
         candidates = await self._search_codelist(codelist_name)
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 2507160..b39a136 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -6,3 +6,8 @@ mkdocs-gen-files
 mkdocs-literate-nav
 mkdocs-jupyter
 mkdocs-glightbox
+black
+ruff
+mypy
+pandas-stubs
+build