From fc55f8caca8e184e3ea028bd289ea82027e1caed Mon Sep 17 00:00:00 2001
From: Vicky Bikia <vickybikia@gmail.com>
Date: Wed, 12 Feb 2025 12:34:02 -0800
Subject: [PATCH 1/2] Add workflows .yml files for markdown link check and
 pylinting

---
 .github/workflows/build-and-test.yml | 45 ++++++++++++++++++++++++++++
 .github/workflows/pull_request.yml   | 37 +++++++++++++++++++++++
 .reuse/dep5.txt                      |  6 ++++
 3 files changed, 88 insertions(+)
 create mode 100644 .github/workflows/build-and-test.yml
 create mode 100644 .github/workflows/pull_request.yml
 create mode 100644 .reuse/dep5.txt

diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
new file mode 100644
index 0000000..23d3d99
--- /dev/null
+++ b/.github/workflows/build-and-test.yml
@@ -0,0 +1,45 @@
+#
+# This source file is part of the  Daneshjou Lab projects
+#
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Build and Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  pylint:
+    name: PyLint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install Infrastructure
+        run: |
+          pip install -r requirements.txt
+          pip install pylint
+      - name: Analysing the code with pylint
+        run: |
+          pylint $(git ls-files '*.py')
+  black_lint:
+    name: Black Code Formatter Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install Black
+        run: pip install black[jupyter]
+      - name: Check code formatting with Black
+        run: black . --exclude '\.ipynb$'
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
new file mode 100644
index 0000000..9026caa
--- /dev/null
+++ b/.github/workflows/pull_request.yml
@@ -0,0 +1,37 @@
+#
+# This source file is part of the Daneshjou Lab projects
+#
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+name: Pull Request
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  reuse_action:
+    name: REUSE Compliance Check
+    uses: PathReportParsing_MRA_DeepDerm/.github/.github/workflows/reuse.yml@v2
+  markdown_link_check:
+    name: Markdown Link Check
+    uses: DaneshjouLab/.github/.github/workflows/markdown-link-check.yml@v2
+  yamllint:
+    name: YAML Lint Check
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+
+      - name: Install yamllint
+        run: pip install yamllint
+
+      - name: Run yamllint with custom config
+        run: yamllint -c .yamllint .github/workflows/*.yml
diff --git a/.reuse/dep5.txt b/.reuse/dep5.txt
new file mode 100644
index 0000000..9d6c7d7
--- /dev/null
+++ b/.reuse/dep5.txt
@@ -0,0 +1,6 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+
+Files: tests/*
+Copyright: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+License: MIT
+Comment: All files are part of the Daneshjou Lab projects.

From ab534329c1e2cb5f6b1c0fe713ca1cdf1d412e3b Mon Sep 17 00:00:00 2001
From: Vicky Bikia <vickybikia@gmail.com>
Date: Thu, 13 Feb 2025 19:24:47 -0800
Subject: [PATCH 2/2] Integrate REUSE Compliance check workflow

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 9026caa..c74fa09 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -15,10 +15,10 @@ on:
 jobs:
   reuse_action:
     name: REUSE Compliance Check
-    uses: PathReportParsing_MRA_DeepDerm/.github/.github/workflows/reuse.yml@v2
+    uses: DaneshjouLab/.github/.github/workflows/reuse.yml@main
   markdown_link_check:
     name: Markdown Link Check
-    uses: DaneshjouLab/.github/.github/workflows/markdown-link-check.yml@v2
+    uses: DaneshjouLab/.github/.github/workflows/markdown-link-check.yml@main
   yamllint:
     name: YAML Lint Check
     runs-on: ubuntu-latest