Switch to src layout

onnela-lab · Dec 13, 2024 · 45fb410 · 45fb410
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Showing 53 changed files with 5 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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.dev3"
 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/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/jasmine/__init__.py → src/forest/jasmine/__init__.py b/forest/jasmine/__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/oak/__init__.py → src/forest/oak/__init__.py b/forest/oak/__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/poplar/__init__.py → src/forest/poplar/__init__.py b/forest/poplar/__init__.py → src/forest/poplar/__init__.py
diff --git a/forest/poplar/classes/__init__.py → src/forest/poplar/classes/__init__.py b/forest/poplar/classes/__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/constants/__init__.py → src/forest/poplar/constants/__init__.py b/forest/poplar/constants/__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/functions/__init__.py → src/forest/poplar/functions/__init__.py b/forest/poplar/functions/__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/legacy/__init__.py → src/forest/poplar/legacy/__init__.py b/forest/poplar/legacy/__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/raw/__init__.py → src/forest/poplar/raw/__init__.py b/forest/poplar/raw/__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/willow/__init__.py → src/forest/willow/__init__.py b/forest/willow/__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