diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml index 05ada96..e94f5b5 100644 --- a/.github/workflows/static-analysis.yml +++ b/.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 diff --git a/.gitignore b/.gitignore index b397a0b..7c660ca 100644 --- a/.gitignore +++ b/.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 diff --git a/.gitmodules b/.gitmodules index d32896a..a27cc5d 100644 --- a/.gitmodules +++ b/.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 diff --git a/.linkspector.yml b/.linkspector.yml index 9de8111..05471bf 100644 --- a/.linkspector.yml +++ b/.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: - . diff --git a/.reuse/templates/opentslm.jinja2 b/.reuse/templates/opentslm.jinja2 new file mode 100644 index 0000000..17928cd --- /dev/null +++ b/.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 %} \ No newline at end of file diff --git a/README.md b/README.md index ebabd3b..88abc42 100644 --- a/README.md +++ b/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 \ + . +``` +
Stanford Biodesign               ETH Centre for Digital Health Interventions diff --git a/REUSE.toml b/REUSE.toml index 699a366..9016f08 100644 --- a/REUSE.toml +++ b/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" diff --git a/__init__.py b/__init__.py index 7f7c8a3..266b136 100644 --- a/__init__.py +++ b/__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 -# \ No newline at end of file diff --git a/assets/ASL_Logo2.svg.license b/assets/ASL_Logo2.svg.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/ASLwhite.svg.license b/assets/ASLwhite.svg.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/CDHI_white.svg.license b/assets/CDHI_white.svg.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/cdhi_logo.png.license b/assets/cdhi_logo.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/ecg_rationale.png.license b/assets/ecg_rationale.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/eth_cdhi_logo.png.license b/assets/eth_cdhi_logo.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/eth_logo.png.license b/assets/eth_logo.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/har_rationale.png.license b/assets/har_rationale.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/m4_caption.png.license b/assets/m4_caption.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/schematic_overview_2.png.license b/assets/schematic_overview_2.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/schematic_overview_3.png.license b/assets/schematic_overview_3.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/sleep_rationale.png.license b/assets/sleep_rationale.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/assets/stanford_biodesign_logo.png.license b/assets/stanford_biodesign_logo.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/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 diff --git a/create_doctor_eval_dataset.py b/create_doctor_eval_dataset.py index 7c7216c..59473fa 100644 --- a/create_doctor_eval_dataset.py +++ b/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 diff --git a/curriculum_learning.py b/curriculum_learning.py index 1269414..a0d3b05 100644 --- a/curriculum_learning.py +++ b/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 diff --git a/data/.gitignore b/data/.gitignore index 8695fa1..2f75232 100644 --- a/data/.gitignore +++ b/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 diff --git a/demo/huggingface/.gitignore b/demo/huggingface/.gitignore index 6320cd2..935582c 100644 --- a/demo/huggingface/.gitignore +++ b/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 \ No newline at end of file diff --git a/demo/huggingface/01_test_hf_tsqa.py b/demo/huggingface/01_test_hf_tsqa.py index 23fcfeb..eab54d1 100755 --- a/demo/huggingface/01_test_hf_tsqa.py +++ b/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. diff --git a/demo/huggingface/02_test_hf_m4.py b/demo/huggingface/02_test_hf_m4.py index bf9a3f8..ab01030 100755 --- a/demo/huggingface/02_test_hf_m4.py +++ b/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. diff --git a/demo/huggingface/03_test_hf_har_cot.py b/demo/huggingface/03_test_hf_har_cot.py index d6d1ace..762c0d5 100755 --- a/demo/huggingface/03_test_hf_har_cot.py +++ b/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. diff --git a/demo/huggingface/04_test_hf_sleep_cot.py b/demo/huggingface/04_test_hf_sleep_cot.py index 2c5fa18..1e7498a 100755 --- a/demo/huggingface/04_test_hf_sleep_cot.py +++ b/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. diff --git a/demo/huggingface/05_test_hf_ecg_qa_cot.py b/demo/huggingface/05_test_hf_ecg_qa_cot.py index 153f6a9..c399b81 100755 --- a/demo/huggingface/05_test_hf_ecg_qa_cot.py +++ b/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. diff --git a/evaluation/.gitignore b/evaluation/.gitignore index 39646a4..b33036a 100644 --- a/evaluation/.gitignore +++ b/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 \ No newline at end of file diff --git a/evaluation/baseline/common_evaluator.py b/evaluation/baseline/common_evaluator.py index 9edbec4..56287d1 100644 --- a/evaluation/baseline/common_evaluator.py +++ b/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 diff --git a/evaluation/baseline/common_evaluator_plot.py b/evaluation/baseline/common_evaluator_plot.py index 886267c..fbe0c8f 100644 --- a/evaluation/baseline/common_evaluator_plot.py +++ b/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 diff --git a/evaluation/baseline/eval.sh b/evaluation/baseline/eval.sh index 5bd1c2a..eee8a90 100755 --- a/evaluation/baseline/eval.sh +++ b/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 diff --git a/evaluation/baseline/eval_remaining.sh b/evaluation/baseline/eval_remaining.sh index a143b4d..c8d6e2e 100644 --- a/evaluation/baseline/eval_remaining.sh +++ b/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" diff --git a/evaluation/baseline/evaluate_all.py b/evaluation/baseline/evaluate_all.py index 74a8fb2..6776ac4 100644 --- a/evaluation/baseline/evaluate_all.py +++ b/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 diff --git a/evaluation/baseline/evaluate_ecg_qa.py b/evaluation/baseline/evaluate_ecg_qa.py index 5c657d9..9b4c3c5 100644 --- a/evaluation/baseline/evaluate_ecg_qa.py +++ b/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 diff --git a/evaluation/baseline/evaluate_ecg_qa_plot.py b/evaluation/baseline/evaluate_ecg_qa_plot.py index 3975e01..305669e 100644 --- a/evaluation/baseline/evaluate_ecg_qa_plot.py +++ b/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 diff --git a/evaluation/baseline/evaluate_har.py b/evaluation/baseline/evaluate_har.py index c349a09..84dcf22 100644 --- a/evaluation/baseline/evaluate_har.py +++ b/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 diff --git a/evaluation/baseline/evaluate_har_plot.py b/evaluation/baseline/evaluate_har_plot.py index 05cecd1..73b2b51 100644 --- a/evaluation/baseline/evaluate_har_plot.py +++ b/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 diff --git a/evaluation/baseline/evaluate_pamap.py b/evaluation/baseline/evaluate_pamap.py index 32b8150..d966fa3 100644 --- a/evaluation/baseline/evaluate_pamap.py +++ b/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 diff --git a/evaluation/baseline/evaluate_sleep_cot.py b/evaluation/baseline/evaluate_sleep_cot.py index ba078c4..5d4058e 100644 --- a/evaluation/baseline/evaluate_sleep_cot.py +++ b/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 diff --git a/evaluation/baseline/evaluate_sleep_plot.py b/evaluation/baseline/evaluate_sleep_plot.py index ca71f0c..10029ba 100644 --- a/evaluation/baseline/evaluate_sleep_plot.py +++ b/evaluation/baseline/evaluate_sleep_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 diff --git a/evaluation/baseline/evaluate_tsqa.py b/evaluation/baseline/evaluate_tsqa.py index e08738f..96118bc 100644 --- a/evaluation/baseline/evaluate_tsqa.py +++ b/evaluation/baseline/evaluate_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 -# import re import sys diff --git a/evaluation/baseline/evaluate_tsqa_plot.py b/evaluation/baseline/evaluate_tsqa_plot.py index 3e8d03c..07ff325 100644 --- a/evaluation/baseline/evaluate_tsqa_plot.py +++ b/evaluation/baseline/evaluate_tsqa_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 diff --git a/evaluation/baseline/gruver_llmtime_tokenizer.py b/evaluation/baseline/gruver_llmtime_tokenizer.py index df2a14d..ad08cac 100644 --- a/evaluation/baseline/gruver_llmtime_tokenizer.py +++ b/evaluation/baseline/gruver_llmtime_tokenizer.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 numpy as np diff --git a/evaluation/baseline/openai_pipeline.py b/evaluation/baseline/openai_pipeline.py index 41fb555..e69588b 100644 --- a/evaluation/baseline/openai_pipeline.py +++ b/evaluation/baseline/openai_pipeline.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 from openai import OpenAI diff --git a/evaluation/baseline/parse_predictions_baseline.py b/evaluation/baseline/parse_predictions_baseline.py index 65e2711..a77e892 100644 --- a/evaluation/baseline/parse_predictions_baseline.py +++ b/evaluation/baseline/parse_predictions_baseline.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Parse baseline evaluation results and compute macro-F1 from detailed per-sample outputs. diff --git a/evaluation/baseline/parse_predictions_sleep_baseline.py b/evaluation/baseline/parse_predictions_sleep_baseline.py index 6352c8f..4e09091 100644 --- a/evaluation/baseline/parse_predictions_sleep_baseline.py +++ b/evaluation/baseline/parse_predictions_sleep_baseline.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Parse sleep baseline evaluation results from a structured JSON file and compute diff --git a/evaluation/baseline/parse_predictions_tsqa_baseline.py b/evaluation/baseline/parse_predictions_tsqa_baseline.py index 579527b..5db56c7 100644 --- a/evaluation/baseline/parse_predictions_tsqa_baseline.py +++ b/evaluation/baseline/parse_predictions_tsqa_baseline.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Parse sleep baseline evaluation results from a structured JSON file and compute diff --git a/evaluation/clinician_eval/create_doctor_eval_dataset.py b/evaluation/clinician_eval/create_doctor_eval_dataset.py index 8ebb3d9..7cc2fa5 100644 --- a/evaluation/clinician_eval/create_doctor_eval_dataset.py +++ b/evaluation/clinician_eval/create_doctor_eval_dataset.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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. diff --git a/evaluation/clinicianecg/.gitignore b/evaluation/clinicianecg/.gitignore index 4cd88ea..572e1fe 100644 --- a/evaluation/clinicianecg/.gitignore +++ b/evaluation/clinicianecg/.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 + .temp .venv venv diff --git a/evaluation/clinicianecg/pipeline/1_dataset_analyzer.py b/evaluation/clinicianecg/pipeline/1_dataset_analyzer.py index 5bf7f16..317d6dc 100644 --- a/evaluation/clinicianecg/pipeline/1_dataset_analyzer.py +++ b/evaluation/clinicianecg/pipeline/1_dataset_analyzer.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ ECG Dataset Analyzer and Review Assignment Generator diff --git a/evaluation/clinicianecg/pipeline/2.5_demo_responses.py b/evaluation/clinicianecg/pipeline/2.5_demo_responses.py index 6cd328c..d174fa0 100644 --- a/evaluation/clinicianecg/pipeline/2.5_demo_responses.py +++ b/evaluation/clinicianecg/pipeline/2.5_demo_responses.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 Response Generator for ECG Review System diff --git a/evaluation/clinicianecg/pipeline/2_excel_generator.py b/evaluation/clinicianecg/pipeline/2_excel_generator.py index 843f9f9..1dee6d3 100644 --- a/evaluation/clinicianecg/pipeline/2_excel_generator.py +++ b/evaluation/clinicianecg/pipeline/2_excel_generator.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ ECG Review Workbook Generator - Final Version diff --git a/evaluation/clinicianecg/pipeline/3_response_analyzer.py b/evaluation/clinicianecg/pipeline/3_response_analyzer.py index 18b52d6..024c80f 100644 --- a/evaluation/clinicianecg/pipeline/3_response_analyzer.py +++ b/evaluation/clinicianecg/pipeline/3_response_analyzer.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ ECG Review Response Analyzer diff --git a/evaluation/clinicianecg/pipeline/config.json.license b/evaluation/clinicianecg/pipeline/config.json.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/evaluation/clinicianecg/pipeline/config.json.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 diff --git a/evaluation/memory/get_memory_use.py b/evaluation/memory/get_memory_use.py index cb722a3..c7cf943 100644 --- a/evaluation/memory/get_memory_use.py +++ b/evaluation/memory/get_memory_use.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 argparse import csv diff --git a/evaluation/memory/plot_memory_scaling.py b/evaluation/memory/plot_memory_scaling.py index 4b4c1fd..93361a5 100644 --- a/evaluation/memory/plot_memory_scaling.py +++ b/evaluation/memory/plot_memory_scaling.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Paper-style plots: memory usage scaling with N for different lengths (L). diff --git a/evaluation/memory/plot_memory_simulation.py b/evaluation/memory/plot_memory_simulation.py index c71fc8f..c431da0 100644 --- a/evaluation/memory/plot_memory_simulation.py +++ b/evaluation/memory/plot_memory_simulation.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Plot memory usage on simulation datasets from memory_simulation.csv. diff --git a/evaluation/memory/plot_memory_simulation_per_length.py b/evaluation/memory/plot_memory_simulation_per_length.py index 045363e..cf3677a 100644 --- a/evaluation/memory/plot_memory_simulation_per_length.py +++ b/evaluation/memory/plot_memory_simulation_per_length.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Paper-style plots: memory usage scaling with N for different lengths (L). diff --git a/evaluation/memory/plot_memory_usage.py b/evaluation/memory/plot_memory_usage.py index c45d341..d676a68 100644 --- a/evaluation/memory/plot_memory_usage.py +++ b/evaluation/memory/plot_memory_usage.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Alternative visualization for memory usage. diff --git a/evaluation/memory/run_all_memory.sh b/evaluation/memory/run_all_memory.sh index bfa75d2..e743d1e 100644 --- a/evaluation/memory/run_all_memory.sh +++ b/evaluation/memory/run_all_memory.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 set -euo pipefail diff --git a/evaluation/opentslm/baseline_parse_predictions.py b/evaluation/opentslm/baseline_parse_predictions.py index 140004d..4b90f92 100644 --- a/evaluation/opentslm/baseline_parse_predictions.py +++ b/evaluation/opentslm/baseline_parse_predictions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """Parser for converting baseline JSON files to clean format.""" diff --git a/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py b/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py index c72223d..bff237c 100644 --- a/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py +++ b/evaluation/opentslm/ecg_qa_cot/parse_ecg_qa_cot_data.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """Parser for converting ECG-QA CoT JSONL files to clean format with per-template metrics.""" diff --git a/evaluation/opentslm/get_pamap_cot_predictions.py b/evaluation/opentslm/get_pamap_cot_predictions.py index cdc1c4d..8db1ad4 100644 --- a/evaluation/opentslm/get_pamap_cot_predictions.py +++ b/evaluation/opentslm/get_pamap_cot_predictions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 evaluate PAMAP2CoTQADataset with a trained OpenTSLMFlamingo model. diff --git a/evaluation/opentslm/parse_predictions.py b/evaluation/opentslm/parse_predictions.py index 8f1c67a..fa0314e 100644 --- a/evaluation/opentslm/parse_predictions.py +++ b/evaluation/opentslm/parse_predictions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """Parser for converting RTF-formatted JSONL files to clean format.""" diff --git a/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py b/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py index 816a9e0..118a487 100644 --- a/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py +++ b/evaluation/opentslm/sleep/baseline_parse_sleep_cot_data.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """Parser for converting baseline sleep COT JSON files to clean format.""" diff --git a/evaluation/opentslm/sleep/get_sleep_predictions.py b/evaluation/opentslm/sleep/get_sleep_predictions.py index ff826ec..d7a524d 100644 --- a/evaluation/opentslm/sleep/get_sleep_predictions.py +++ b/evaluation/opentslm/sleep/get_sleep_predictions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 evaluate SleepEDFCoTQADataset with a trained OpenTSLMSP model. diff --git a/evaluation/opentslm/sleep/parse_sleep_cot_data.py b/evaluation/opentslm/sleep/parse_sleep_cot_data.py index 1fb2086..4b4d6e4 100644 --- a/evaluation/opentslm/sleep/parse_sleep_cot_data.py +++ b/evaluation/opentslm/sleep/parse_sleep_cot_data.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """Parser for converting sleep COT JSONL files to clean format.""" diff --git a/evaluation/opentslm/sleep/plot_sleep_predictions.py b/evaluation/opentslm/sleep/plot_sleep_predictions.py index c613859..d0da465 100644 --- a/evaluation/opentslm/sleep/plot_sleep_predictions.py +++ b/evaluation/opentslm/sleep/plot_sleep_predictions.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Plot SleepEDF time series samples from sleep_cot_data.csv. diff --git a/evaluation/opentslm/tsqa/baseline_parse_predictions.py b/evaluation/opentslm/tsqa/baseline_parse_predictions.py index 8f907b4..3c5101e 100644 --- a/evaluation/opentslm/tsqa/baseline_parse_predictions.py +++ b/evaluation/opentslm/tsqa/baseline_parse_predictions.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 diff --git a/evaluation/opentslm/tsqa/parse_predictions.py b/evaluation/opentslm/tsqa/parse_predictions.py index ff024ec..cf2d9ec 100644 --- a/evaluation/opentslm/tsqa/parse_predictions.py +++ b/evaluation/opentslm/tsqa/parse_predictions.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 diff --git a/get_memory_use.py b/get_memory_use.py index f39f4e1..852423e 100644 --- a/get_memory_use.py +++ b/get_memory_use.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 argparse import csv diff --git a/hf_test.py b/hf_test.py index dba29e5..318d201 100644 --- a/hf_test.py +++ b/hf_test.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 src import OpenTSLM, TextPrompt, TextTimeSeriesPrompt, FullPrompt # Load model diff --git a/plot_memory_simulation.py b/plot_memory_simulation.py index 250a537..d033b66 100644 --- a/plot_memory_simulation.py +++ b/plot_memory_simulation.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 -# """ Plot memory usage on simulation datasets from memory_simulation.csv. diff --git a/plot_memory_simulation_per_length.py b/plot_memory_simulation_per_length.py index 3431a14..409028d 100644 --- a/plot_memory_simulation_per_length.py +++ b/plot_memory_simulation_per_length.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 -# """ Paper-style plots: memory usage scaling with N for different lengths (L). diff --git a/plot_memory_usage.py b/plot_memory_usage.py index 185c7e6..344cfb3 100644 --- a/plot_memory_usage.py +++ b/plot_memory_usage.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Alternative visualization for memory usage. diff --git a/requirements.txt b/requirements.txt index 52540d0..857847a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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 + numpy pandas torch diff --git a/run_all_memory.sh b/run_all_memory.sh index cf86bb3..e743d1e 100644 --- a/run_all_memory.sh +++ b/run_all_memory.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 diff --git a/run_all_memory_missing.sh b/run_all_memory_missing.sh index f109ea5..a6c50ff 100644 --- a/run_all_memory_missing.sh +++ b/run_all_memory_missing.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 diff --git a/src/data.py b/src/data.py index f6e2195..2045994 100644 --- a/src/data.py +++ b/src/data.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 ast from typing import Literal, Optional diff --git a/src/logger.py b/src/logger.py index 6fde4ad..669165f 100644 --- a/src/logger.py +++ b/src/logger.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 -# """ OpenTSLM Global Logger diff --git a/src/model/__init__.py b/src/model/__init__.py index 7566f7d..266b136 100644 --- a/src/model/__init__.py +++ b/src/model/__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 -# diff --git a/src/model/encoder/CNNTokenizer.py b/src/model/encoder/CNNTokenizer.py index bee3780..c622c0a 100644 --- a/src/model/encoder/CNNTokenizer.py +++ b/src/model/encoder/CNNTokenizer.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 torch import torch.nn as nn diff --git a/src/model/encoder/TimeSeriesEncoderBase.py b/src/model/encoder/TimeSeriesEncoderBase.py index fde57d6..e49a4c7 100644 --- a/src/model/encoder/TimeSeriesEncoderBase.py +++ b/src/model/encoder/TimeSeriesEncoderBase.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 abc import abstractmethod import torch diff --git a/src/model/encoder/TransformerCNNEncoder.py b/src/model/encoder/TransformerCNNEncoder.py index 5c96844..f22306c 100644 --- a/src/model/encoder/TransformerCNNEncoder.py +++ b/src/model/encoder/TransformerCNNEncoder.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 torch import torch.nn as nn diff --git a/src/model/encoder/TransformerMLPEncoder.py b/src/model/encoder/TransformerMLPEncoder.py index 6aa59e5..bccc57f 100644 --- a/src/model/encoder/TransformerMLPEncoder.py +++ b/src/model/encoder/TransformerMLPEncoder.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 torch import torch.nn as nn diff --git a/src/model/encoder/__init__.py b/src/model/encoder/__init__.py index 7566f7d..266b136 100644 --- a/src/model/encoder/__init__.py +++ b/src/model/encoder/__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 -# diff --git a/src/model/llm/OpenTSLM.py b/src/model/llm/OpenTSLM.py index d705e9b..1980625 100644 --- a/src/model/llm/OpenTSLM.py +++ b/src/model/llm/OpenTSLM.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 torch from typing import Optional, Union from enum import Enum diff --git a/src/model/llm/OpenTSLMFlamingo.py b/src/model/llm/OpenTSLMFlamingo.py index 58517c7..39e5101 100644 --- a/src/model/llm/OpenTSLMFlamingo.py +++ b/src/model/llm/OpenTSLMFlamingo.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 types import SimpleNamespace from model.encoder.CNNTokenizer import CNNTokenizer diff --git a/src/model/llm/OpenTSLMSP.py b/src/model/llm/OpenTSLMSP.py index d594433..59c290e 100644 --- a/src/model/llm/OpenTSLMSP.py +++ b/src/model/llm/OpenTSLMSP.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 torch import torch.nn as nn diff --git a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py b/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py index 9bebf84..5ca67eb 100644 --- a/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.py +++ b/src/model/llm/TimeSeriesFlamingoWithTrainableEncoder.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 torch from torch import nn diff --git a/src/model/llm/TimeSeriesLLM.py b/src/model/llm/TimeSeriesLLM.py index 987f52f..55af6d2 100644 --- a/src/model/llm/TimeSeriesLLM.py +++ b/src/model/llm/TimeSeriesLLM.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 torch import torch.nn as nn diff --git a/src/model/llm/__init__.py b/src/model/llm/__init__.py index 7566f7d..266b136 100644 --- a/src/model/llm/__init__.py +++ b/src/model/llm/__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 -# diff --git a/src/model/projector/LinearProjector.py b/src/model/projector/LinearProjector.py index 83e43a3..0e9c9e2 100644 --- a/src/model/projector/LinearProjector.py +++ b/src/model/projector/LinearProjector.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 torch.nn as nn diff --git a/src/model/projector/MLPProjector.py b/src/model/projector/MLPProjector.py index 2c47f41..af07ca9 100644 --- a/src/model/projector/MLPProjector.py +++ b/src/model/projector/MLPProjector.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 torch.nn as nn diff --git a/src/model/projector/__init__.py b/src/model/projector/__init__.py index 7566f7d..266b136 100644 --- a/src/model/projector/__init__.py +++ b/src/model/projector/__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 -# diff --git a/src/model_config.py b/src/model_config.py index 698b7f6..0412f6b 100644 --- a/src/model_config.py +++ b/src/model_config.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 -# # --------------------------- # Hyper‑parameters diff --git a/src/prompt/__init__.py b/src/prompt/__init__.py index a0e9941..6882dbc 100644 --- a/src/prompt/__init__.py +++ b/src/prompt/__init__.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 .prompt import Prompt # from .full_prompt import FullPrompt diff --git a/src/prompt/full_prompt.py b/src/prompt/full_prompt.py index 6d18239..501d61f 100644 --- a/src/prompt/full_prompt.py +++ b/src/prompt/full_prompt.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 List from prompt.text_prompt import TextPrompt diff --git a/src/prompt/prompt.py b/src/prompt/prompt.py index 59f237a..69b4fdd 100644 --- a/src/prompt/prompt.py +++ b/src/prompt/prompt.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 abc import ABC, abstractmethod diff --git a/src/prompt/prompt_with_answer.py b/src/prompt/prompt_with_answer.py index 21e2477..9df2d02 100644 --- a/src/prompt/prompt_with_answer.py +++ b/src/prompt/prompt_with_answer.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 List from prompt.text_prompt import TextPrompt diff --git a/src/prompt/text_prompt.py b/src/prompt/text_prompt.py index ebeff15..11c1945 100644 --- a/src/prompt/text_prompt.py +++ b/src/prompt/text_prompt.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 .prompt import Prompt diff --git a/src/prompt/text_time_series_prompt.py b/src/prompt/text_time_series_prompt.py index 8c8ab3a..d38da3c 100644 --- a/src/prompt/text_time_series_prompt.py +++ b/src/prompt/text_time_series_prompt.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 .prompt import Prompt import numpy as np diff --git a/src/time_series_datasets/QADataset.py b/src/time_series_datasets/QADataset.py index e8b492f..8375b9c 100644 --- a/src/time_series_datasets/QADataset.py +++ b/src/time_series_datasets/QADataset.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 abc import ABC, abstractmethod from functools import partial diff --git a/src/time_series_datasets/TSQADataset.py b/src/time_series_datasets/TSQADataset.py index dd826a0..9f1a4f3 100644 --- a/src/time_series_datasets/TSQADataset.py +++ b/src/time_series_datasets/TSQADataset.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 from typing import List, Tuple diff --git a/src/time_series_datasets/__init__.py b/src/time_series_datasets/__init__.py index 7f7c8a3..266b136 100644 --- a/src/time_series_datasets/__init__.py +++ b/src/time_series_datasets/__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 -# \ No newline at end of file diff --git a/src/time_series_datasets/constants.py b/src/time_series_datasets/constants.py index 3f5e8c3..9725661 100644 --- a/src/time_series_datasets/constants.py +++ b/src/time_series_datasets/constants.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 -# # constants.py diff --git a/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py b/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py index 03ad80b..1f15da9 100644 --- a/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.py +++ b/src/time_series_datasets/ecg_qa/ECGQACoTQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/ecg_qa/ECGQADataset.py b/src/time_series_datasets/ecg_qa/ECGQADataset.py index dacaffa..fc3c17b 100644 --- a/src/time_series_datasets/ecg_qa/ECGQADataset.py +++ b/src/time_series_datasets/ecg_qa/ECGQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/ecg_qa/__init__.py b/src/time_series_datasets/ecg_qa/__init__.py index 5c02d22..4ba0c41 100644 --- a/src/time_series_datasets/ecg_qa/__init__.py +++ b/src/time_series_datasets/ecg_qa/__init__.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 -# """ ECG-QA Dataset Module diff --git a/src/time_series_datasets/ecg_qa/dataset_distribution.png.license b/src/time_series_datasets/ecg_qa/dataset_distribution.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/src/time_series_datasets/ecg_qa/dataset_distribution.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 diff --git a/src/time_series_datasets/ecg_qa/ecg_example_real.png.license b/src/time_series_datasets/ecg_qa/ecg_example_real.png.license new file mode 100644 index 0000000..e83264a --- /dev/null +++ b/src/time_series_datasets/ecg_qa/ecg_example_real.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 diff --git a/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py b/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py index 868c125..b419d42 100644 --- a/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.py +++ b/src/time_series_datasets/ecg_qa/ecgqa_cot_loader.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 subprocess diff --git a/src/time_series_datasets/ecg_qa/ecgqa_loader.py b/src/time_series_datasets/ecg_qa/ecgqa_loader.py index 2b82dc7..5f112c9 100644 --- a/src/time_series_datasets/ecg_qa/ecgqa_loader.py +++ b/src/time_series_datasets/ecg_qa/ecgqa_loader.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 diff --git a/src/time_series_datasets/ecg_qa/plot_example.py b/src/time_series_datasets/ecg_qa/plot_example.py index 0dc4238..d04cfdc 100644 --- a/src/time_series_datasets/ecg_qa/plot_example.py +++ b/src/time_series_datasets/ecg_qa/plot_example.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ ECG-QA Example Plot Generator diff --git a/src/time_series_datasets/har_cot/HARAccQADataset.py b/src/time_series_datasets/har_cot/HARAccQADataset.py index 8250b03..7d0a71e 100644 --- a/src/time_series_datasets/har_cot/HARAccQADataset.py +++ b/src/time_series_datasets/har_cot/HARAccQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/har_cot/HARCoTQADataset.py b/src/time_series_datasets/har_cot/HARCoTQADataset.py index b23c6a4..914018c 100644 --- a/src/time_series_datasets/har_cot/HARCoTQADataset.py +++ b/src/time_series_datasets/har_cot/HARCoTQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/har_cot/__init__.py b/src/time_series_datasets/har_cot/__init__.py index 78a4fb7..266b136 100644 --- a/src/time_series_datasets/har_cot/__init__.py +++ b/src/time_series_datasets/har_cot/__init__.py @@ -1,9 +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 -# - - \ No newline at end of file diff --git a/src/time_series_datasets/har_cot/har_cot_loader.py b/src/time_series_datasets/har_cot/har_cot_loader.py index 89c9ff8..4b0721e 100644 --- a/src/time_series_datasets/har_cot/har_cot_loader.py +++ b/src/time_series_datasets/har_cot/har_cot_loader.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 pandas as pd diff --git a/src/time_series_datasets/m4/M4QADataset.py b/src/time_series_datasets/m4/M4QADataset.py index 518678c..1613c65 100644 --- a/src/time_series_datasets/m4/M4QADataset.py +++ b/src/time_series_datasets/m4/M4QADataset.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 -# """ M4QADataset.py diff --git a/src/time_series_datasets/m4/__init__.py b/src/time_series_datasets/m4/__init__.py index 4287c51..5fadb4e 100644 --- a/src/time_series_datasets/m4/__init__.py +++ b/src/time_series_datasets/m4/__init__.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 .m4_loader import load_m4_data, load_all_m4_data, create_combined_dataset from .M4QADataset import M4QADataset diff --git a/src/time_series_datasets/m4/m4_loader.py b/src/time_series_datasets/m4/m4_loader.py index 34c8974..df14427 100644 --- a/src/time_series_datasets/m4/m4_loader.py +++ b/src/time_series_datasets/m4/m4_loader.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 -# """ m4_loader.py diff --git a/src/time_series_datasets/monash/MonashDataset.py b/src/time_series_datasets/monash/MonashDataset.py index 30419aa..7d10e37 100644 --- a/src/time_series_datasets/monash/MonashDataset.py +++ b/src/time_series_datasets/monash/MonashDataset.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 logging import os diff --git a/src/time_series_datasets/monash/MonashSPO2QADataset.py b/src/time_series_datasets/monash/MonashSPO2QADataset.py index 87f2ead..2f22427 100644 --- a/src/time_series_datasets/monash/MonashSPO2QADataset.py +++ b/src/time_series_datasets/monash/MonashSPO2QADataset.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 List, Literal, Optional, Tuple from datasets import Dataset diff --git a/src/time_series_datasets/monash/__init__.py b/src/time_series_datasets/monash/__init__.py index c3b6620..266b136 100644 --- a/src/time_series_datasets/monash/__init__.py +++ b/src/time_series_datasets/monash/__init__.py @@ -1,8 +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 -# - diff --git a/src/time_series_datasets/monash/monash_utils.py b/src/time_series_datasets/monash/monash_utils.py index a5b2de5..f3d98e4 100644 --- a/src/time_series_datasets/monash/monash_utils.py +++ b/src/time_series_datasets/monash/monash_utils.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 numpy as np import pandas as pd diff --git a/src/time_series_datasets/pamap2/BalancedBatchSampler.py b/src/time_series_datasets/pamap2/BalancedBatchSampler.py index cd57d6f..47a795e 100644 --- a/src/time_series_datasets/pamap2/BalancedBatchSampler.py +++ b/src/time_series_datasets/pamap2/BalancedBatchSampler.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 numpy as np from torch.utils.data import Sampler diff --git a/src/time_series_datasets/pamap2/PAMAP2AccQADataset.py b/src/time_series_datasets/pamap2/PAMAP2AccQADataset.py index b57bf8e..dea805e 100644 --- a/src/time_series_datasets/pamap2/PAMAP2AccQADataset.py +++ b/src/time_series_datasets/pamap2/PAMAP2AccQADataset.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 datasets import Dataset from typing import List, Tuple diff --git a/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py b/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py index 4ec30d3..1b6c5a5 100644 --- a/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.py +++ b/src/time_series_datasets/pamap2/PAMAP2CoTQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/pamap2/PAMAP2Dataset.py b/src/time_series_datasets/pamap2/PAMAP2Dataset.py index ffe1bbe..bf485a9 100644 --- a/src/time_series_datasets/pamap2/PAMAP2Dataset.py +++ b/src/time_series_datasets/pamap2/PAMAP2Dataset.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 Tuple import pandas as pd diff --git a/src/time_series_datasets/pamap2/__init__.py b/src/time_series_datasets/pamap2/__init__.py index c3b6620..266b136 100644 --- a/src/time_series_datasets/pamap2/__init__.py +++ b/src/time_series_datasets/pamap2/__init__.py @@ -1,8 +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 -# - diff --git a/src/time_series_datasets/pamap2/pamap2_cot_loader.py b/src/time_series_datasets/pamap2/pamap2_cot_loader.py index 88a5c23..de38ec0 100644 --- a/src/time_series_datasets/pamap2/pamap2_cot_loader.py +++ b/src/time_series_datasets/pamap2/pamap2_cot_loader.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 pandas as pd diff --git a/src/time_series_datasets/pamap2/pamap2_loader.py b/src/time_series_datasets/pamap2/pamap2_loader.py index 0b3bb65..9f32ba0 100644 --- a/src/time_series_datasets/pamap2/pamap2_loader.py +++ b/src/time_series_datasets/pamap2/pamap2_loader.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 zipfile diff --git a/src/time_series_datasets/simulation/SimulationQADataset.py b/src/time_series_datasets/simulation/SimulationQADataset.py index ceedc22..fb1fdbf 100644 --- a/src/time_series_datasets/simulation/SimulationQADataset.py +++ b/src/time_series_datasets/simulation/SimulationQADataset.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 numpy as np import torch diff --git a/src/time_series_datasets/sleep/SleepEDFCoTQADataset.py b/src/time_series_datasets/sleep/SleepEDFCoTQADataset.py index a9b2241..09217b6 100644 --- a/src/time_series_datasets/sleep/SleepEDFCoTQADataset.py +++ b/src/time_series_datasets/sleep/SleepEDFCoTQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/sleep/SleepEDFQADataset.py b/src/time_series_datasets/sleep/SleepEDFQADataset.py index 24c7ead..bac0f4e 100644 --- a/src/time_series_datasets/sleep/SleepEDFQADataset.py +++ b/src/time_series_datasets/sleep/SleepEDFQADataset.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 datasets import Dataset from typing import List, Tuple, Literal diff --git a/src/time_series_datasets/sleep/__init__.py b/src/time_series_datasets/sleep/__init__.py index 78a4fb7..266b136 100644 --- a/src/time_series_datasets/sleep/__init__.py +++ b/src/time_series_datasets/sleep/__init__.py @@ -1,9 +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 -# - - \ No newline at end of file diff --git a/src/time_series_datasets/sleep/sleepedf_cot_loader.py b/src/time_series_datasets/sleep/sleepedf_cot_loader.py index 19d7ad3..c6f1db2 100644 --- a/src/time_series_datasets/sleep/sleepedf_cot_loader.py +++ b/src/time_series_datasets/sleep/sleepedf_cot_loader.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 pandas as pd diff --git a/src/time_series_datasets/tsqa.py b/src/time_series_datasets/tsqa.py index 58b2b2a..2657d4d 100644 --- a/src/time_series_datasets/tsqa.py +++ b/src/time_series_datasets/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 -# from typing import Literal, Optional diff --git a/src/time_series_datasets/ucr/__init__.py b/src/time_series_datasets/ucr/__init__.py index bdbed1f..29c6eab 100644 --- a/src/time_series_datasets/ucr/__init__.py +++ b/src/time_series_datasets/ucr/__init__.py @@ -1,9 +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 -# from .ucr_loader import get_ucr_loader, load_ucr_dataset, UCRDataset, collate_fn \ No newline at end of file diff --git a/src/time_series_datasets/ucr/ucr_loader.py b/src/time_series_datasets/ucr/ucr_loader.py index 381fc4b..285f883 100644 --- a/src/time_series_datasets/ucr/ucr_loader.py +++ b/src/time_series_datasets/ucr/ucr_loader.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 zipfile diff --git a/src/time_series_datasets/util.py b/src/time_series_datasets/util.py index 3649245..3afa617 100644 --- a/src/time_series_datasets/util.py +++ b/src/time_series_datasets/util.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 math from typing import List diff --git a/test/.gitignore b/test/.gitignore index 6320cd2..935582c 100644 --- a/test/.gitignore +++ b/test/.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 \ No newline at end of file diff --git a/test/__init__.py b/test/__init__.py index 7f7c8a3..266b136 100644 --- a/test/__init__.py +++ b/test/__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 -# \ No newline at end of file diff --git a/test/ecg_qa_cot_test.py b/test/ecg_qa_cot_test.py index a213551..f9a251d 100644 --- a/test/ecg_qa_cot_test.py +++ b/test/ecg_qa_cot_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the ECG-QA CoT loader and dataset. diff --git a/test/ecg_qa_test.py b/test/ecg_qa_test.py index 105f9cd..2451c4d 100644 --- a/test/ecg_qa_test.py +++ b/test/ecg_qa_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for ECG-QA dataset implementation. diff --git a/test/elastic_ddp.py b/test/elastic_ddp.py index fd557c9..41ccbb6 100644 --- a/test/elastic_ddp.py +++ b/test/elastic_ddp.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 torch import torch.distributed as dist diff --git a/test/eval_EmbedHealthFlamingo.py b/test/eval_EmbedHealthFlamingo.py index dce2c1b..c92e488 100644 --- a/test/eval_EmbedHealthFlamingo.py +++ b/test/eval_EmbedHealthFlamingo.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 from typing import List diff --git a/test/har_cot_test.py b/test/har_cot_test.py index 44226ee..08de573 100644 --- a/test/har_cot_test.py +++ b/test/har_cot_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the HAR CoT loader and dataset. diff --git a/test/m4_loader_test.py b/test/m4_loader_test.py index e80d808..1df4423 100644 --- a/test/m4_loader_test.py +++ b/test/m4_loader_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the M4QADataset with caption generation. diff --git a/test/pamap_cot_loader_test.py b/test/pamap_cot_loader_test.py index 99f3cd8..ab4f55b 100644 --- a/test/pamap_cot_loader_test.py +++ b/test/pamap_cot_loader_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the PAMAP2 CoT loader. diff --git a/test/sleepedf_cot_loader_test.py b/test/sleepedf_cot_loader_test.py index bfdbed7..babd393 100644 --- a/test/sleepedf_cot_loader_test.py +++ b/test/sleepedf_cot_loader_test.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the SleepEDF CoT loader. diff --git a/test/test_curriculum_trainer.py b/test/test_curriculum_trainer.py index da770b4..22cd4d0 100644 --- a/test/test_curriculum_trainer.py +++ b/test/test_curriculum_trainer.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script for the curriculum learning implementation. diff --git a/test/test_inference.py b/test/test_inference.py index 5d78afb..c6ff269 100644 --- a/test/test_inference.py +++ b/test/test_inference.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 torch import numpy as np diff --git a/test/test_medgemma_support.py b/test/test_medgemma_support.py index ba73af1..5abc390 100644 --- a/test/test_medgemma_support.py +++ b/test/test_medgemma_support.py @@ -1,11 +1,10 @@ #!/usr/bin/env python3 -# + # 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 -# """ Test script to verify MedGemma support in OpenTSLMFlamingo. diff --git a/test/test_train_EmbedHealthFlamingo.py b/test/test_train_EmbedHealthFlamingo.py index 4747463..90cd54f 100644 --- a/test/test_train_EmbedHealthFlamingo.py +++ b/test/test_train_EmbedHealthFlamingo.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 diff --git a/test/test_train_EmbedHealthSP.py b/test/test_train_EmbedHealthSP.py index e136004..1107739 100644 --- a/test/test_train_EmbedHealthSP.py +++ b/test/test_train_EmbedHealthSP.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