diff --git a/.gitignore b/.gitignore index 0d7d75ec..e42cf1d3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ __pycache__/ dist/ -/forest_analysis.egg-info/ +forest_analysis.egg-info/ .vagrant/ .venv/ diff --git a/docs/source/development.md b/docs/source/development.md index f9aec7e6..1fb52ea8 100644 --- 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 diff --git a/mypy.ini b/mypy.ini index d06e36b7..99811965 100644 --- 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 index 9381dd2f..95035f2d 100644 --- 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.dev3" description = "Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data" authors = [ { name = "Onnela Lab", email = "onnela.lab@gmail.com" } @@ -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/forest/__init__.py b/src/forest/__init__.py similarity index 100% rename from forest/__init__.py rename to src/forest/__init__.py diff --git a/forest/bonsai/__init__.py b/src/forest/bonsai/__init__.py similarity index 100% rename from forest/bonsai/__init__.py rename to src/forest/bonsai/__init__.py diff --git a/forest/bonsai/simulate_gps_data.py b/src/forest/bonsai/simulate_gps_data.py similarity index 100% rename from forest/bonsai/simulate_gps_data.py rename to src/forest/bonsai/simulate_gps_data.py diff --git a/forest/bonsai/simulate_log_data.py b/src/forest/bonsai/simulate_log_data.py similarity index 100% rename from forest/bonsai/simulate_log_data.py rename to src/forest/bonsai/simulate_log_data.py diff --git a/forest/constants.py b/src/forest/constants.py similarity index 100% rename from forest/constants.py rename to src/forest/constants.py diff --git a/forest/jasmine/__init__.py b/src/forest/jasmine/__init__.py similarity index 100% rename from forest/jasmine/__init__.py rename to src/forest/jasmine/__init__.py diff --git a/forest/jasmine/data2mobmat.py b/src/forest/jasmine/data2mobmat.py similarity index 100% rename from forest/jasmine/data2mobmat.py rename to src/forest/jasmine/data2mobmat.py diff --git a/forest/jasmine/mobmat2traj.py b/src/forest/jasmine/mobmat2traj.py similarity index 100% rename from forest/jasmine/mobmat2traj.py rename to src/forest/jasmine/mobmat2traj.py diff --git a/forest/jasmine/sogp_gps.py b/src/forest/jasmine/sogp_gps.py similarity index 100% rename from forest/jasmine/sogp_gps.py rename to src/forest/jasmine/sogp_gps.py diff --git a/forest/jasmine/traj2stats.py b/src/forest/jasmine/traj2stats.py similarity index 100% rename from forest/jasmine/traj2stats.py rename to src/forest/jasmine/traj2stats.py diff --git a/forest/oak/__init__.py b/src/forest/oak/__init__.py similarity index 100% rename from forest/oak/__init__.py rename to src/forest/oak/__init__.py diff --git a/forest/oak/base.py b/src/forest/oak/base.py similarity index 100% rename from forest/oak/base.py rename to src/forest/oak/base.py diff --git a/forest/poplar/__init__.py b/src/forest/poplar/__init__.py similarity index 100% rename from forest/poplar/__init__.py rename to src/forest/poplar/__init__.py diff --git a/forest/poplar/classes/__init__.py b/src/forest/poplar/classes/__init__.py similarity index 100% rename from forest/poplar/classes/__init__.py rename to src/forest/poplar/classes/__init__.py diff --git a/forest/poplar/classes/history.py b/src/forest/poplar/classes/history.py similarity index 100% rename from forest/poplar/classes/history.py rename to src/forest/poplar/classes/history.py diff --git a/forest/poplar/classes/registry.py b/src/forest/poplar/classes/registry.py similarity index 100% rename from forest/poplar/classes/registry.py rename to src/forest/poplar/classes/registry.py diff --git a/forest/poplar/classes/template.py b/src/forest/poplar/classes/template.py similarity index 100% rename from forest/poplar/classes/template.py rename to src/forest/poplar/classes/template.py diff --git a/forest/poplar/classes/trackers.py b/src/forest/poplar/classes/trackers.py similarity index 100% rename from forest/poplar/classes/trackers.py rename to src/forest/poplar/classes/trackers.py diff --git a/forest/poplar/constants/__init__.py b/src/forest/poplar/constants/__init__.py similarity index 100% rename from forest/poplar/constants/__init__.py rename to src/forest/poplar/constants/__init__.py diff --git a/forest/poplar/constants/misc.py b/src/forest/poplar/constants/misc.py similarity index 100% rename from forest/poplar/constants/misc.py rename to src/forest/poplar/constants/misc.py diff --git a/forest/poplar/constants/time.py b/src/forest/poplar/constants/time.py similarity index 100% rename from forest/poplar/constants/time.py rename to src/forest/poplar/constants/time.py diff --git a/forest/poplar/functions/__init__.py b/src/forest/poplar/functions/__init__.py similarity index 100% rename from forest/poplar/functions/__init__.py rename to src/forest/poplar/functions/__init__.py diff --git a/forest/poplar/functions/helpers.py b/src/forest/poplar/functions/helpers.py similarity index 100% rename from forest/poplar/functions/helpers.py rename to src/forest/poplar/functions/helpers.py diff --git a/forest/poplar/functions/holidays.py b/src/forest/poplar/functions/holidays.py similarity index 100% rename from forest/poplar/functions/holidays.py rename to src/forest/poplar/functions/holidays.py diff --git a/forest/poplar/functions/io.py b/src/forest/poplar/functions/io.py similarity index 100% rename from forest/poplar/functions/io.py rename to src/forest/poplar/functions/io.py diff --git a/forest/poplar/functions/log.py b/src/forest/poplar/functions/log.py similarity index 100% rename from forest/poplar/functions/log.py rename to src/forest/poplar/functions/log.py diff --git a/forest/poplar/functions/time.py b/src/forest/poplar/functions/time.py similarity index 100% rename from forest/poplar/functions/time.py rename to src/forest/poplar/functions/time.py diff --git a/forest/poplar/functions/timezone.py b/src/forest/poplar/functions/timezone.py similarity index 100% rename from forest/poplar/functions/timezone.py rename to src/forest/poplar/functions/timezone.py diff --git a/forest/poplar/legacy/__init__.py b/src/forest/poplar/legacy/__init__.py similarity index 100% rename from forest/poplar/legacy/__init__.py rename to src/forest/poplar/legacy/__init__.py diff --git a/forest/poplar/legacy/common_funcs.py b/src/forest/poplar/legacy/common_funcs.py similarity index 100% rename from forest/poplar/legacy/common_funcs.py rename to src/forest/poplar/legacy/common_funcs.py diff --git a/forest/poplar/raw/__init__.py b/src/forest/poplar/raw/__init__.py similarity index 100% rename from forest/poplar/raw/__init__.py rename to src/forest/poplar/raw/__init__.py diff --git a/forest/poplar/raw/doc.py b/src/forest/poplar/raw/doc.py similarity index 100% rename from forest/poplar/raw/doc.py rename to src/forest/poplar/raw/doc.py diff --git a/forest/poplar/raw/noncode/data_streams.csv b/src/forest/poplar/raw/noncode/data_streams.csv similarity index 100% rename from forest/poplar/raw/noncode/data_streams.csv rename to src/forest/poplar/raw/noncode/data_streams.csv diff --git a/forest/poplar/raw/noncode/headers.json b/src/forest/poplar/raw/noncode/headers.json similarity index 100% rename from forest/poplar/raw/noncode/headers.json rename to src/forest/poplar/raw/noncode/headers.json diff --git a/forest/poplar/raw/noncode/power_events.csv b/src/forest/poplar/raw/noncode/power_events.csv similarity index 100% rename from forest/poplar/raw/noncode/power_events.csv rename to src/forest/poplar/raw/noncode/power_events.csv diff --git a/forest/poplar/raw/noncode/question_type_names.json b/src/forest/poplar/raw/noncode/question_type_names.json similarity index 100% rename from forest/poplar/raw/noncode/question_type_names.json rename to src/forest/poplar/raw/noncode/question_type_names.json diff --git a/forest/poplar/raw/readers.py b/src/forest/poplar/raw/readers.py similarity index 100% rename from forest/poplar/raw/readers.py rename to src/forest/poplar/raw/readers.py diff --git a/forest/sycamore/__init__.py b/src/forest/sycamore/__init__.py similarity index 100% rename from forest/sycamore/__init__.py rename to src/forest/sycamore/__init__.py diff --git a/forest/sycamore/__main__.py b/src/forest/sycamore/__main__.py similarity index 100% rename from forest/sycamore/__main__.py rename to src/forest/sycamore/__main__.py diff --git a/forest/sycamore/base.py b/src/forest/sycamore/base.py similarity index 100% rename from forest/sycamore/base.py rename to src/forest/sycamore/base.py diff --git a/forest/sycamore/common.py b/src/forest/sycamore/common.py similarity index 100% rename from forest/sycamore/common.py rename to src/forest/sycamore/common.py diff --git a/forest/sycamore/constants.py b/src/forest/sycamore/constants.py similarity index 100% rename from forest/sycamore/constants.py rename to src/forest/sycamore/constants.py diff --git a/forest/sycamore/read_audio.py b/src/forest/sycamore/read_audio.py similarity index 100% rename from forest/sycamore/read_audio.py rename to src/forest/sycamore/read_audio.py diff --git a/forest/sycamore/responses.py b/src/forest/sycamore/responses.py similarity index 100% rename from forest/sycamore/responses.py rename to src/forest/sycamore/responses.py diff --git a/forest/sycamore/submits.py b/src/forest/sycamore/submits.py similarity index 100% rename from forest/sycamore/submits.py rename to src/forest/sycamore/submits.py diff --git a/forest/sycamore/utils.py b/src/forest/sycamore/utils.py similarity index 100% rename from forest/sycamore/utils.py rename to src/forest/sycamore/utils.py diff --git a/forest/utils.py b/src/forest/utils.py similarity index 100% rename from forest/utils.py rename to src/forest/utils.py diff --git a/forest/willow/__init__.py b/src/forest/willow/__init__.py similarity index 100% rename from forest/willow/__init__.py rename to src/forest/willow/__init__.py diff --git a/forest/willow/log_stats.py b/src/forest/willow/log_stats.py similarity index 100% rename from forest/willow/log_stats.py rename to src/forest/willow/log_stats.py