Merge branch 'develop' into hackdna/citation

onnela-lab · Dec 16, 2024 · f6296e2 · f6296e2
2 parents 4a2a2a1 + 6a07c48
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -36,7 +36,5 @@ jobs:
         run: flake8
       - name: Run static type checking
         run: mypy -p forest
-      - name: Run legacy tests
-        run: python -m unittest tests/imports.py
-      - name: Run pytest suite
+      - name: Run the test suite
         run: pytest
diff --git a/.gitignore b/.gitignore
@@ -1,14 +1,15 @@
 __pycache__/
 dist/
-/forest_analysis.egg-info
+forest_analysis.egg-info/
 
 .vagrant/
 .venv/
+venv/
 .DS_Store
 
 # IntelliJ, VsCode project files
-.idea
-.vscode
+.idea/
+.vscode/
 
 #We don't want to add data to github
 /tutorials/data/

diff --git a/README.md b/README.md
@@ -156,5 +156,9 @@ log_stats_main(path_to_synthetic_log_data, path_to_log_summary, tz_str, option,
 * [Onnela lab](https://www.hsph.harvard.edu/onnela-lab/)
 
 ## Publications
-* Straczkiewicz, M., Huang, E.J., and Onnela, JP. A “one-size-fits-most” walking recognition method for smartphones, smartwatches, and wearable accelerometers. _npj Digit. Med._ **6**, 29 (2023). https://doi.org/10.1038/s41746-022-00745-z Open Access: https://rdcu.be/c6dGV
-* Onnela JP, Dixon C, Griffin K, Jaenicke T, Minowada L, Esterkin S, Siu A, Zagorsky J, and Jones E. Beiwe: A data collection platform for high-throughput digital phenotyping. Journal of Open Source Software, 6(68), 3417 (2021). [![DOI](https://joss.theoj.org/papers/10.21105/joss.03417/status.svg)](https://doi.org/10.21105/joss.03417)
+* Straczkiewicz, M., Huang, E.J., and Onnela, JP. A “one-size-fits-most” walking recognition method for smartphones, smartwatches, and wearable accelerometers. _npj Digit. Med._ **6**, 29 (2023) [![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41746--022--00745--z-blue)](https://doi.org/10.1038/s41746-022-00745-z) [Open Access](https://rdcu.be/c6dGV)
+* Huang E, Yan K, and Onnela JP. Smartphone-Based Activity Recognition Using Multistream Movelets Combining Accelerometer and Gyroscope Data. Sensors 22 (7), 2618 (2022) [![DOI](https://img.shields.io/badge/DOI-10.3390%2Fs22072618-blue)](https://doi.org/10.3390/s22072618)
+* Onnela JP, Dixon C, Griffin K, Jaenicke T, Minowada L, Esterkin S, Siu A, Zagorsky J, and Jones E. Beiwe: A data collection platform for high-throughput digital phenotyping. Journal of Open Source Software, 6(68), 3417 (2021) [![DOI](https://joss.theoj.org/papers/10.21105/joss.03417/status.svg)](https://doi.org/10.21105/joss.03417)
+* Liu G and Onnela JP. Bidirectional imputation of spatial GPS trajectories with missingness using sparse online Gaussian Process. Journal of the American Medical Informatics Association 28(8), 1777 (2021) [![DOI](https://img.shields.io/badge/DOI-10.1093%2Fjamia%2Focab069-blue)](https://doi.org/10.1093/jamia/ocab069)
+* Barnett I and Onnela JP. Inferring mobility measures from GPS with missing data. Biostatistics 21:2, e98, 2020 [![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbiostatistics%2Fkxy059-blue)](https://doi.org/10.1093/biostatistics/kxy059) [Open Access](https://academic.oup.com/biostatistics/article/21/2/e98/5145908?guestAccessKey=0e3baa8c-2a80-405e-a7b4-1444099f48a2)
+* Huang E and Onnela JP. Augmented movelet method for activity classification using smartphone gyroscope and accelerometer data. Sensors 20(13), 3706, 2020 [![DOI](https://img.shields.io/badge/DOI-10.3390%2Fs20133706-blue)](https://doi.org/10.3390/s20133706) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3925679.svg)](https://doi.org/10.5281/zenodo.3925679)
diff --git a/docs/source/development.md b/docs/source/development.md
@@ -6,7 +6,7 @@ Information for contributors
 * Change current directory to the top level of your local Forest repository
 * Install Forest in editable mode along with development tools: `pip install -e ".[dev]"`
 * Run code style checks: `flake8`
-* Run type hint checks: `mypy -p forest`
+* Run type hint checks: `mypy`
 * Run test suite: `pytest`
 
 ### Documentation
@@ -52,6 +52,9 @@ Open `docs/_build/html/index.html` in a web browser to check the results
 * [Register an account](https://test.pypi.org/account/register/)
 * [Create an API token](https://test.pypi.org/manage/account/#api-tokens) (setting the "Scope" to "Entire account")
 * [Add API token](https://packaging.python.org/en/latest/specifications/pypirc/#using-a-pypi-token) to your `$HOME/.pypirc` file
+* Increment the project version in `pyproject.toml`
+* Commit and push all local changes to GitHub
+* Clear the build directory: `rm -r dist`
 * Generate distribution archives: `python -m build`
 * Check the results: `twine check dist/*`
 * Upload distribution archives:

diff --git a/docs/source/jasmine.md b/docs/source/jasmine.md
@@ -163,3 +163,7 @@ A flight is defined to be a longest straight-line trip of a particle from one lo
 
 - Definition of a place  
 A place is defined as a location where a person has paused for at least 15 minutes.
+
+### Common Errors
+- "GPS data are not collected or the data quality is too low"
+This error gets triggered when the subject either has no data, or when less than a given proportion of their generated data files have at least 60 seconds of data. The default proportion of files required to avoid this error is 5%, but this can be toggled using the `parameters` argument in `jasmine.traj2stats.gps_stats_main`.
diff --git a/forest/poplar/raw/__init__.py b/forest/poplar/raw/__init__.py
diff --git a/forest/willow/__init__.py b/forest/willow/__init__.py
diff --git a/mypy.ini b/mypy.ini
@@ -1,4 +1,6 @@
 [mypy]
+mypy_path = src
+packages = forest
 python_version = 3.11
 
 [mypy-holidays]

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "forest-analysis"
-version = "1.0.dev2"
+version = "1.0.dev4"
 description = "Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data"
 authors = [
     { name = "Onnela Lab", email = "[email protected]" }
@@ -67,8 +67,5 @@ dev = [
     "types-setuptools",
 ]
 
-[tool.setuptools.packages.find]
-include = ["forest*"]
-
 [tool.setuptools.package-data]
 "forest.poplar.raw" = ["noncode/*.csv", "noncode/*.json"]
diff --git a/pytest.ini b/pytest.ini
@@ -1,4 +1,6 @@
 [pytest]
+addopts = --import-mode=importlib
+testpaths = tests
 filterwarnings =
     error
     # Ignore specific DeprecationWarnings from librosa.core.intervals

diff --git a/forest/__init__.py → src/forest/__init__.py b/forest/__init__.py → src/forest/__init__.py
diff --git a/forest/bonsai/__init__.py → src/forest/bonsai/__init__.py b/forest/bonsai/__init__.py → src/forest/bonsai/__init__.py
diff --git a/forest/bonsai/simulate_gps_data.py → src/forest/bonsai/simulate_gps_data.py b/forest/bonsai/simulate_gps_data.py → src/forest/bonsai/simulate_gps_data.py
diff --git a/forest/bonsai/simulate_log_data.py → src/forest/bonsai/simulate_log_data.py b/forest/bonsai/simulate_log_data.py → src/forest/bonsai/simulate_log_data.py
diff --git a/forest/constants.py → src/forest/constants.py b/forest/constants.py → src/forest/constants.py
diff --git a/forest/bonsai/tests/__init__.py → src/forest/jasmine/__init__.py b/forest/bonsai/tests/__init__.py → src/forest/jasmine/__init__.py
diff --git a/forest/jasmine/data2mobmat.py → src/forest/jasmine/data2mobmat.py b/forest/jasmine/data2mobmat.py → src/forest/jasmine/data2mobmat.py
diff --git a/forest/jasmine/mobmat2traj.py → src/forest/jasmine/mobmat2traj.py b/forest/jasmine/mobmat2traj.py → src/forest/jasmine/mobmat2traj.py
diff --git a/forest/jasmine/sogp_gps.py → src/forest/jasmine/sogp_gps.py b/forest/jasmine/sogp_gps.py → src/forest/jasmine/sogp_gps.py
diff --git a/forest/jasmine/traj2stats.py → src/forest/jasmine/traj2stats.py b/forest/jasmine/traj2stats.py → src/forest/jasmine/traj2stats.py
diff --git a/forest/jasmine/__init__.py → src/forest/oak/__init__.py b/forest/jasmine/__init__.py → src/forest/oak/__init__.py
diff --git a/forest/oak/base.py → src/forest/oak/base.py b/forest/oak/base.py → src/forest/oak/base.py
diff --git a/forest/jasmine/tests/__init__.py → src/forest/poplar/__init__.py b/forest/jasmine/tests/__init__.py → src/forest/poplar/__init__.py
diff --git a/forest/oak/__init__.py → src/forest/poplar/classes/__init__.py b/forest/oak/__init__.py → src/forest/poplar/classes/__init__.py
diff --git a/forest/poplar/classes/history.py → src/forest/poplar/classes/history.py b/forest/poplar/classes/history.py → src/forest/poplar/classes/history.py
diff --git a/forest/poplar/classes/registry.py → src/forest/poplar/classes/registry.py b/forest/poplar/classes/registry.py → src/forest/poplar/classes/registry.py
diff --git a/forest/poplar/classes/template.py → src/forest/poplar/classes/template.py b/forest/poplar/classes/template.py → src/forest/poplar/classes/template.py
diff --git a/forest/poplar/classes/trackers.py → src/forest/poplar/classes/trackers.py b/forest/poplar/classes/trackers.py → src/forest/poplar/classes/trackers.py
diff --git a/forest/poplar/__init__.py → src/forest/poplar/constants/__init__.py b/forest/poplar/__init__.py → src/forest/poplar/constants/__init__.py
diff --git a/forest/poplar/constants/misc.py → src/forest/poplar/constants/misc.py b/forest/poplar/constants/misc.py → src/forest/poplar/constants/misc.py
diff --git a/forest/poplar/constants/time.py → src/forest/poplar/constants/time.py b/forest/poplar/constants/time.py → src/forest/poplar/constants/time.py
diff --git a/forest/poplar/classes/__init__.py → src/forest/poplar/functions/__init__.py b/forest/poplar/classes/__init__.py → src/forest/poplar/functions/__init__.py
diff --git a/forest/poplar/functions/helpers.py → src/forest/poplar/functions/helpers.py b/forest/poplar/functions/helpers.py → src/forest/poplar/functions/helpers.py
diff --git a/forest/poplar/functions/holidays.py → src/forest/poplar/functions/holidays.py b/forest/poplar/functions/holidays.py → src/forest/poplar/functions/holidays.py
diff --git a/forest/poplar/functions/io.py → src/forest/poplar/functions/io.py b/forest/poplar/functions/io.py → src/forest/poplar/functions/io.py
diff --git a/forest/poplar/functions/log.py → src/forest/poplar/functions/log.py b/forest/poplar/functions/log.py → src/forest/poplar/functions/log.py
diff --git a/forest/poplar/functions/time.py → src/forest/poplar/functions/time.py b/forest/poplar/functions/time.py → src/forest/poplar/functions/time.py
diff --git a/forest/poplar/functions/timezone.py → src/forest/poplar/functions/timezone.py b/forest/poplar/functions/timezone.py → src/forest/poplar/functions/timezone.py
diff --git a/forest/poplar/constants/__init__.py → src/forest/poplar/legacy/__init__.py b/forest/poplar/constants/__init__.py → src/forest/poplar/legacy/__init__.py
diff --git a/forest/poplar/legacy/common_funcs.py → src/forest/poplar/legacy/common_funcs.py b/forest/poplar/legacy/common_funcs.py → src/forest/poplar/legacy/common_funcs.py
diff --git a/forest/poplar/functions/__init__.py → src/forest/poplar/raw/__init__.py b/forest/poplar/functions/__init__.py → src/forest/poplar/raw/__init__.py
diff --git a/forest/poplar/raw/doc.py → src/forest/poplar/raw/doc.py b/forest/poplar/raw/doc.py → src/forest/poplar/raw/doc.py
diff --git a/forest/poplar/raw/noncode/data_streams.csv → ...orest/poplar/raw/noncode/data_streams.csv b/forest/poplar/raw/noncode/data_streams.csv → ...orest/poplar/raw/noncode/data_streams.csv
diff --git a/forest/poplar/raw/noncode/headers.json → src/forest/poplar/raw/noncode/headers.json b/forest/poplar/raw/noncode/headers.json → src/forest/poplar/raw/noncode/headers.json
diff --git a/forest/poplar/raw/noncode/power_events.csv → ...orest/poplar/raw/noncode/power_events.csv b/forest/poplar/raw/noncode/power_events.csv → ...orest/poplar/raw/noncode/power_events.csv
diff --git a/...plar/raw/noncode/question_type_names.json → ...plar/raw/noncode/question_type_names.json b/...plar/raw/noncode/question_type_names.json → ...plar/raw/noncode/question_type_names.json
diff --git a/forest/poplar/raw/readers.py → src/forest/poplar/raw/readers.py b/forest/poplar/raw/readers.py → src/forest/poplar/raw/readers.py
diff --git a/forest/sycamore/__init__.py → src/forest/sycamore/__init__.py b/forest/sycamore/__init__.py → src/forest/sycamore/__init__.py
diff --git a/forest/sycamore/__main__.py → src/forest/sycamore/__main__.py b/forest/sycamore/__main__.py → src/forest/sycamore/__main__.py
diff --git a/forest/sycamore/base.py → src/forest/sycamore/base.py b/forest/sycamore/base.py → src/forest/sycamore/base.py
diff --git a/forest/sycamore/common.py → src/forest/sycamore/common.py b/forest/sycamore/common.py → src/forest/sycamore/common.py
diff --git a/forest/sycamore/constants.py → src/forest/sycamore/constants.py b/forest/sycamore/constants.py → src/forest/sycamore/constants.py
diff --git a/forest/sycamore/read_audio.py → src/forest/sycamore/read_audio.py b/forest/sycamore/read_audio.py → src/forest/sycamore/read_audio.py
diff --git a/forest/sycamore/responses.py → src/forest/sycamore/responses.py b/forest/sycamore/responses.py → src/forest/sycamore/responses.py
diff --git a/forest/sycamore/submits.py → src/forest/sycamore/submits.py b/forest/sycamore/submits.py → src/forest/sycamore/submits.py
diff --git a/forest/sycamore/utils.py → src/forest/sycamore/utils.py b/forest/sycamore/utils.py → src/forest/sycamore/utils.py
diff --git a/forest/utils.py → src/forest/utils.py b/forest/utils.py → src/forest/utils.py
diff --git a/forest/poplar/legacy/__init__.py → src/forest/willow/__init__.py b/forest/poplar/legacy/__init__.py → src/forest/willow/__init__.py
diff --git a/forest/willow/log_stats.py → src/forest/willow/log_stats.py b/forest/willow/log_stats.py → src/forest/willow/log_stats.py
diff --git a/tests/__init__.py b/tests/__init__.py
diff --git a/...st/bonsai/tests/test_simulate_gps_data.py → tests/bonsai/test_simulate_gps_data.py b/...st/bonsai/tests/test_simulate_gps_data.py → tests/bonsai/test_simulate_gps_data.py
diff --git a/tests/imports.py b/tests/imports.py
diff --git a/forest/jasmine/tests/test_traj2stats.py → tests/jasmine/test_traj2stats.py b/forest/jasmine/tests/test_traj2stats.py → tests/jasmine/test_traj2stats.py
diff --git a/forest/oak/tests/conftest.py → tests/oak/conftest.py b/forest/oak/tests/conftest.py → tests/oak/conftest.py
diff --git a/forest/oak/tests/test_adjust_bout.py → tests/oak/test_adjust_bout.py b/forest/oak/tests/test_adjust_bout.py → tests/oak/test_adjust_bout.py
diff --git a/...oak/tests/test_compute_interpolate_cwt.py → tests/oak/test_compute_interpolate_cwt.py b/...oak/tests/test_compute_interpolate_cwt.py → tests/oak/test_compute_interpolate_cwt.py
diff --git a/forest/oak/tests/test_data_bout.csv → tests/oak/test_data_bout.csv b/forest/oak/tests/test_data_bout.csv → tests/oak/test_data_bout.csv
diff --git a/...ts/test_find_continuous_dominant_peaks.py → ...ak/test_find_continuous_dominant_peaks.py b/...ts/test_find_continuous_dominant_peaks.py → ...ak/test_find_continuous_dominant_peaks.py
diff --git a/forest/oak/tests/test_find_walking.py → tests/oak/test_find_walking.py b/forest/oak/tests/test_find_walking.py → tests/oak/test_find_walking.py
diff --git a/forest/oak/tests/test_get_pp.py → tests/oak/test_get_pp.py b/forest/oak/tests/test_get_pp.py → tests/oak/test_get_pp.py
diff --git a/...t/oak/tests/test_identify_peaks_in_cwt.py → tests/oak/test_identify_peaks_in_cwt.py b/...t/oak/tests/test_identify_peaks_in_cwt.py → tests/oak/test_identify_peaks_in_cwt.py
diff --git a/forest/oak/tests/test_preprocess_bout.py → tests/oak/test_preprocess_bout.py b/forest/oak/tests/test_preprocess_bout.py → tests/oak/test_preprocess_bout.py
diff --git a/forest/oak/tests/test_preprocess_dates.py → tests/oak/test_preprocess_dates.py b/forest/oak/tests/test_preprocess_dates.py → tests/oak/test_preprocess_dates.py
diff --git a/forest/oak/tests/test_run_hourly.py → tests/oak/test_run_hourly.py b/forest/oak/tests/test_run_hourly.py → tests/oak/test_run_hourly.py
diff --git a/...dr8gqdh/gps/2021-12-15 01_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-15 01_00_00+00_00.csv b/...dr8gqdh/gps/2021-12-15 01_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-15 01_00_00+00_00.csv
diff --git a/...dr8gqdh/gps/2021-12-16 21_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-16 21_00_00+00_00.csv b/...dr8gqdh/gps/2021-12-16 21_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-16 21_00_00+00_00.csv
diff --git a/...dr8gqdh/gps/2021-12-17 00_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-17 00_00_00+00_00.csv b/...dr8gqdh/gps/2021-12-17 00_00_00+00_00.csv → ...dr8gqdh/gps/2021-12-17 00_00_00+00_00.csv
diff --git a/forest/poplar/tests/test_poplar_functions.py → tests/poplar/test_poplar_functions.py b/forest/poplar/tests/test_poplar_functions.py → tests/poplar/test_poplar_functions.py
diff --git a/...t/sycamore/tests/audio_survey_config.json → tests/sycamore/audio_survey_config.json b/...t/sycamore/tests/audio_survey_config.json → tests/sycamore/audio_survey_config.json
diff --git a/.../sycamore/tests/audio_survey_history.json → tests/sycamore/audio_survey_history.json b/.../sycamore/tests/audio_survey_history.json → tests/sycamore/audio_survey_history.json
diff --git a/...camore/tests/config_file_for_submits.json → tests/sycamore/config_file_for_submits.json b/...camore/tests/config_file_for_submits.json → tests/sycamore/config_file_for_submits.json
diff --git a/...nfig_file_with_commas_and_semicolons.json → ...nfig_file_with_commas_and_semicolons.json b/...nfig_file_with_commas_and_semicolons.json → ...nfig_file_with_commas_and_semicolons.json
diff --git a/...jR3MBb4fwIG/2022-06-03 04_44_17+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_17+00_00.csv b/...jR3MBb4fwIG/2022-06-03 04_44_17+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_17+00_00.csv
diff --git a/...jR3MBb4fwIG/2022-06-03 04_44_33+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_33+00_00.csv b/...jR3MBb4fwIG/2022-06-03 04_44_33+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_33+00_00.csv
diff --git a/...jR3MBb4fwIG/2022-06-03 04_44_44+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_44+00_00.csv b/...jR3MBb4fwIG/2022-06-03 04_44_44+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_44_44+00_00.csv
diff --git a/...jR3MBb4fwIG/2022-06-03 04_49_00+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_49_00+00_00.csv b/...jR3MBb4fwIG/2022-06-03 04_49_00+00_00.csv → ...jR3MBb4fwIG/2022-06-03 04_49_00+00_00.csv
diff --git a/...jR3MBb4fwIG/2022-06-04 04_00_00+00_00.csv → ...jR3MBb4fwIG/2022-06-04 04_00_00+00_00.csv b/...jR3MBb4fwIG/2022-06-04 04_00_00+00_00.csv → ...jR3MBb4fwIG/2022-06-04 04_00_00+00_00.csv
diff --git a/forest/sycamore/tests/empty_dir/registry → tests/sycamore/empty_dir/registry b/forest/sycamore/tests/empty_dir/registry → tests/sycamore/empty_dir/registry
diff --git a/...camore/tests/empty_intervention_data.json → tests/sycamore/empty_intervention_data.json b/...camore/tests/empty_intervention_data.json → tests/sycamore/empty_intervention_data.json
diff --git a/...t/sycamore/tests/far_relative_survey.json → tests/sycamore/far_relative_survey.json b/...t/sycamore/tests/far_relative_survey.json → tests/sycamore/far_relative_survey.json
diff --git a/...tory_file_with_commas_and_semicolons.json → ...tory_file_with_commas_and_semicolons.json b/...tory_file_with_commas_and_semicolons.json → ...tory_file_with_commas_and_semicolons.json
diff --git a/forest/sycamore/tests/one_weekly_survey.json → tests/sycamore/one_weekly_survey.json b/forest/sycamore/tests/one_weekly_survey.json → tests/sycamore/one_weekly_survey.json
diff --git a/...NyVMQDiWWEP/2022-03-10 13_58_51+00_00.csv → ...NyVMQDiWWEP/2022-03-10 13_58_51+00_00.csv b/...NyVMQDiWWEP/2022-03-10 13_58_51+00_00.csv → ...NyVMQDiWWEP/2022-03-10 13_58_51+00_00.csv
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diff --git a/...amore/tests/sample_intervention_data.json → tests/sycamore/sample_intervention_data.json b/...amore/tests/sample_intervention_data.json → tests/sycamore/sample_intervention_data.json
diff --git a/...ts/sample_study_surveys_and_settings.json → ...re/sample_study_surveys_and_settings.json b/...ts/sample_study_surveys_and_settings.json → ...re/sample_study_surveys_and_settings.json
diff --git a/forest/sycamore/tests/test_functions.py → tests/sycamore/test_functions.py b/forest/sycamore/tests/test_functions.py → tests/sycamore/test_functions.py
diff --git a/forest/willow/tests/test_log_stats.py → tests/willow/test_log_stats.py b/forest/willow/tests/test_log_stats.py → tests/willow/test_log_stats.py