feat: pixi init + gitignore

.gitattributes

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+# SPDX-License-Identifier: Apache-2.0
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/build-and-test.yml

@@ -1,9 +1,8 @@
-#
 # 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: Apache
+# SPDX-License-Identifier: Apache-2.0
 #
 
 name: Build and Test

.github/workflows/pull_request.yml

@@ -1,9 +1,8 @@
-#
 # 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: Apache
+# SPDX-License-Identifier: Apache-2.0
 #
 
 name: Pull Request

.gitignore

@@ -1 +1,19 @@
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+# SPDX-License-Identifier: Apache-2.0
+
 .vscode
+
+# pixi environments
+.pixi
+*.egg-info
+
+# python
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+*.pyw
+
+# environments
+.pyenv
+.env

.reuse/dep5.txt

@@ -2,10 +2,10 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 
 Files: DataSet/**
 Copyright: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
-License: Apache
+License: Apache-2.0
 Comment: All files are part of the Daneshjou Lab projects.
 
 Files: Config/**
 Copyright: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
-License: Apache
+License: Apache-2.0
 Comment: All files are part of the Daneshjou Lab projects.

.yamllint

@@ -0,0 +1,16 @@
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+# SPDX-License-Identifier: Apache-2.0
+---
+extends: default
+
+rules:
+  truthy:
+    level: warning
+    allowed-values: ["false", "true", "on", "off"]
+  document-start:
+    level: warning 
+  line-length:
+    max: 180
+    level: warning
+  document-start:
+    present: false

README.MD

@@ -1,3 +1,6 @@
+<!-- SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md) -->
+<!-- SPDX-License-Identifier: Apache-2.0 -->
+
 ![Build and Test](https://github.com/DaneshjouLab/AutoGKB/actions/workflows/build-and-test.yml/badge.svg)
 
 

pixi.toml

@@ -0,0 +1,16 @@
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+# SPDX-License-Identifier: Apache-2.0
+
+[project]
+authors = [
+    "Aaron Fanous <aron7628@stanford.edu>",
+    "Shlok Natarajan <shlok.natarajan@gmail.com>"
+]
+channels = ["conda-forge"]
+name = "AutoGKB"
+platforms = ["osx-arm64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]

requirements.txt

@@ -0,0 +1,2 @@
+# SPDX-FileCopyrightText: 22025 Stanford University and the project authors (see CONTRIBUTORS.md)
+# SPDX-License-Identifier: Apache-2.0

src/__init__.py

@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2025 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: Apache-2.0