Add Automated REUSE Setup

.github/workflows/static-analysis.yml

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 name: Static Analysis
 

.gitignore

@@ -1,3 +1,9 @@
+# This source file is part of the OpenTSLM open-source project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+
 venv
 __pycache__
 .DS_STORE

.gitmodules

@@ -1,3 +1,9 @@
+# This source file is part of the OpenTSLM open-source project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+
 [submodule "open_flamingo"]
 	path = open_flamingo
 	url = https://github.com/mlfoundations/open_flamingo.git

.linkspector.yml

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 dirs:
   - .

.reuse/templates/opentslm.jinja2

@@ -0,0 +1,9 @@
+This source file is part of the OpenTSLM open-source project
+
+{% for line in copyright_lines %}
+{{ line }}
+{% endfor %}
+
+{% for expr in spdx_expressions %}
+SPDX-License-Identifier: {{ expr }}
+{% endfor %}

README.md

@@ -335,6 +335,19 @@ For researchers and project partners interested in collaboration opportunities,
 
 This project is licensed under the MIT License.
 
+We use the [REUSE specification](https://reuse.software/spec/) to ensure consistent and machine-readable licensing across the repository.
+
+To add or update license headers, run:
+
+```bash
+reuse annotate --recursive \
+  --template opentslm \
+  --copyright "Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)" \
+  --license MIT \
+  --skip-unrecognised \
+  .
+```
+
 <div align="left">
   <img src="assets/stanford_biodesign_logo.png" alt="Stanford Biodesign" height="90">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
   <img src="assets/CDHI_white.svg" alt="ETH Centre for Digital Health Interventions" height="90">

REUSE.toml

@@ -1,6 +1,6 @@
 version = 1
 
 [[annotations]]
-path = ["assets/**", "data/**", "**/*.png", "**/*.jpg", "**/*.jpeg", "**/*.gif", "**/*.svg", "**/*.ico", "**/*.pt", "**/*.jsonl", "**/*.json", ".gitignore", ".gitmodules", "**/.gitignore", "LICENSE.md", "requirements.txt"]
+path = ["data/**"]
 SPDX-FileCopyrightText = "2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)"
 SPDX-License-Identifier = "MIT"

__init__.py

@@ -1,7 +1,5 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#

assets/ASL_Logo2.svg.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/ASLwhite.svg.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/CDHI_white.svg.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/cdhi_logo.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/ecg_rationale.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/eth_cdhi_logo.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/eth_logo.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/har_rationale.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/m4_caption.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/schematic_overview_2.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/schematic_overview_3.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/sleep_rationale.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

assets/stanford_biodesign_logo.png.license

@@ -0,0 +1,5 @@
+This source file is part of the OpenTSLM open-source project
+
+SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+
+SPDX-License-Identifier: MIT

create_doctor_eval_dataset.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Script to create doctor evaluation dataset with correct model predictions.
 This script extracts ECG-QA templates with correct model outputs from llama3b_flamingo_predictions.jsonl

curriculum_learning.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import sys
 import os

data/.gitignore

@@ -1,3 +1,9 @@
+# This source file is part of the OpenTSLM open-source project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+
 *.csv
 *.json
 *.jsonl

demo/huggingface/.gitignore

@@ -1 +1,7 @@
+# This source file is part of the OpenTSLM open-source project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+
 data

demo/huggingface/01_test_hf_tsqa.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Demo script for testing TSQA (Time Series Question Answering) model from HuggingFace.
 

demo/huggingface/02_test_hf_m4.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Demo script for testing M4 (Time Series Captioning) model from HuggingFace.
 

demo/huggingface/03_test_hf_har_cot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Demo script for testing HAR CoT (Human Activity Recognition Chain-of-Thought) model from HuggingFace.
 

demo/huggingface/04_test_hf_sleep_cot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Demo script for testing Sleep CoT (Sleep Stage Classification Chain-of-Thought) model from HuggingFace.
 

demo/huggingface/05_test_hf_ecg_qa_cot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 """
 Demo script for testing ECG QA CoT (ECG Question Answering Chain-of-Thought) model from HuggingFace.
 

evaluation/.gitignore

@@ -1 +1,7 @@
+# This source file is part of the OpenTSLM open-source project
+#
+# SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+
 *.jsonl

evaluation/baseline/common_evaluator.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import json
 import os

evaluation/baseline/common_evaluator_plot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import os
 import io

evaluation/baseline/eval.sh

@@ -1,11 +1,10 @@
 #!/usr/bin/env bash
-#
+
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 set -euo pipefail
 

evaluation/baseline/eval_remaining.sh

@@ -1,5 +1,9 @@
 #!/usr/bin/env bash
+
+# This source file is part of the OpenTSLM open-source project
+#
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+#
 # SPDX-License-Identifier: MIT
 
 python evaluate_tsqa.py "google/gemma-3-270m"

evaluation/baseline/evaluate_all.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 from typing import Dict, Any, Callable
 from common_evaluator import CommonEvaluator

evaluation/baseline/evaluate_ecg_qa.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys

evaluation/baseline/evaluate_ecg_qa_plot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys

evaluation/baseline/evaluate_har.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys

evaluation/baseline/evaluate_har_plot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys

evaluation/baseline/evaluate_pamap.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys

evaluation/baseline/evaluate_sleep_cot.py

@@ -1,10 +1,8 @@
-#
 # This source file is part of the OpenTSLM open-source project
 #
 # SPDX-FileCopyrightText: 2025 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
 #
 # SPDX-License-Identifier: MIT
-#
 
 import re
 import sys