improved some docs

ml/Makefile

-.PHONY: clean data test lint requirements sync_data_to_s3 sync_data_from_s3
-
-#################################################################################
-# GLOBALS                                                                       #
-#################################################################################
-
-PROJECT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
-BUCKET = [OPTIONAL] your-bucket-for-syncing-data (do not include 's3://')
-PROFILE = default
-PROJECT_NAME = air
-PYTHON_INTERPRETER = python3
-
-ifeq (,$(shell which conda))
-HAS_CONDA=False
-else
-HAS_CONDA=True
-endif
-
-#################################################################################
-# COMMANDS                                                                      #
-#################################################################################
-
-## Install Python Dependencies
-requirements: test_environment
-	$(PYTHON_INTERPRETER) -m pip install -U pip setuptools wheel
-	$(PYTHON_INTERPRETER) -m pip install -r requirements.txt
-
-## Make Dataset
-data: requirements
-	$(PYTHON_INTERPRETER) src/data/make_dataset.py data/raw data/processed
-
-## Delete all compiled Python files
-clean:
-	find . -type f -name "*.py[co]" -delete
-	find . -type d -name "__pycache__" -delete
-
-## Lint using flake8
-lint:
-	flake8 src
-
-test:
-	PYTHONPATH=. pytest
-
-## Upload Data to S3
-sync_data_to_s3:
-ifeq (default,$(PROFILE))
-	aws s3 sync data/ s3://$(BUCKET)/data/
-else
-	aws s3 sync data/ s3://$(BUCKET)/data/ --profile $(PROFILE)
-endif
-
-## Download Data from S3
-sync_data_from_s3:
-ifeq (default,$(PROFILE))
-	aws s3 sync s3://$(BUCKET)/data/ data/
-else
-	aws s3 sync s3://$(BUCKET)/data/ data/ --profile $(PROFILE)
-endif
-
-## Set up python interpreter environment
-create_environment:
-ifeq (True,$(HAS_CONDA))
-		@echo ">>> Detected conda, creating conda environment."
-ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER)))
-	conda create --name $(PROJECT_NAME) python=3
-else
-	conda create --name $(PROJECT_NAME) python=2.7
-endif
-		@echo ">>> New conda env created. Activate with:\nsource activate $(PROJECT_NAME)"
-else
-	$(PYTHON_INTERPRETER) -m pip install -q virtualenv virtualenvwrapper
-	@echo ">>> Installing virtualenvwrapper if not already installed.\nMake sure the following lines are in shell startup file\n\
-	export WORKON_HOME=$$HOME/.virtualenvs\nexport PROJECT_HOME=$$HOME/Devel\nsource /usr/local/bin/virtualenvwrapper.sh\n"
-	@bash -c "source `which virtualenvwrapper.sh`;mkvirtualenv $(PROJECT_NAME) --python=$(PYTHON_INTERPRETER)"
-	@echo ">>> New virtualenv created. Activate with:\nworkon $(PROJECT_NAME)"
-endif
-
-## Test python environment is setup correctly
-test_environment:
-	$(PYTHON_INTERPRETER) test_environment.py
-
-#################################################################################
-# PROJECT RULES                                                                 #
-#################################################################################
-
-
-
-#################################################################################
-# Self Documenting Commands                                                     #
-#################################################################################
-
-.DEFAULT_GOAL := help
-
-# Inspired by <http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html>
-# sed script explained:
-# /^##/:
-# 	* save line in hold space
-# 	* purge line
-# 	* Loop:
-# 		* append newline + line to hold space
-# 		* go to next line
-# 		* if line starts with doc comment, strip comment character off and loop
-# 	* remove target prerequisites
-# 	* append hold space (+ newline) to line
-# 	* replace newline plus comments by `---`
-# 	* print line
-# Separate expressions are necessary because labels cannot be delimited by
-# semicolon; see <http://stackoverflow.com/a/11799865/1968>
-.PHONY: help
-help:
-	@echo "$$(tput bold)Available rules:$$(tput sgr0)"
-	@echo
-	@sed -n -e "/^## / { \
-		h; \
-		s/.*//; \
-		:doc" \
-		-e "H; \
-		n; \
-		s/^## //; \
-		t doc" \
-		-e "s/:.*//; \
-		G; \
-		s/\\n## /---/; \
-		s/\\n/ /g; \
-		p; \
-	}" ${MAKEFILE_LIST} \
-	| LC_ALL='C' sort --ignore-case \
-	| awk -F '---' \
-		-v ncol=$$(tput cols) \
-		-v indent=19 \
-		-v col_on="$$(tput setaf 6)" \
-		-v col_off="$$(tput sgr0)" \
-	'{ \
-		printf "%s%*s%s ", col_on, -indent, $$1, col_off; \
-		n = split($$2, words, " "); \
-		line_length = ncol - indent; \
-		for (i = 1; i <= n; i++) { \
-			line_length -= length(words[i]) + 1; \
-			if (line_length <= 0) { \
-				line_length = ncol - indent - length(words[i]) - 1; \
-				printf "\n%*s ", -indent, " "; \
-			} \
-			printf "%s ", words[i]; \
-		} \
-		printf "\n"; \
-	}' \
-	| more $(shell test $(shell uname) = Darwin && echo '--no-init --raw-control-chars')

ml/README.md

@@ -26,7 +26,7 @@ Project Organization
     ├── references         <- Data dictionaries, manuals, and all other explanatory materials.
     │
     ├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
-    │ 
+    │
     ├── requirements.txt   <- The requirements file for reproducing the analysis environment, e.g.
     │                         generated with `pip freeze > requirements.txt`
     │

ml/conf.py

-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
-# -- Project information -----------------------------------------------------
-
-project = 'air'
-copyright = '2021, Christian Marius Lillelund'
-author = 'Christian Marius Lillelund, Christian Fischer Pedersen'
-
-# The full version, including alpha/beta/rc tags
-release = '0.0.1'
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
\ No newline at end of file

ml/setup.py

@@ -6,7 +6,7 @@ setup(
     packages=find_packages(where='src'),
 	setup_requires=["pytest-runner"],
 	tests_require=["pytest"],
-    version='0.0.1',
+    version='1.0.0',
     description='AIR is an open-source machine learning project to improve rehabilitation.',
     author='Christian Marius Lillelund',
     author_email='cl@ece.au.dk',

ml/src/data/make_alarm_data.py

 """
 make_survival_data.py
 ====================================
-Script to make dataset for Alarm case
+Script to make dataset for Alarm case.
 """
 
 from tools import  preprocessor

ml/src/data/make_dataset_full.py

@@ -2,7 +2,7 @@
 make_dataset_full.py
 ====================================
 Script to make a dataset for Complete, Compliance, Fall and Risk
-case based on the screenings
+case based on the screenings.
 """
 
 import paths as pt

ml/src/data/make_dataset_ohe.py

@@ -2,7 +2,7 @@
 make_dataset_ohe.py
 ====================================
 Script to make a dataset for Complete, Compliance, Fall and Risk
-case using one hot encoding of categorial features
+case using one hot encoding of categorial features.
 """
 
 import paths as pt

ml/src/data/make_dataset_ordinal.py

@@ -2,7 +2,7 @@
 make_dataset_ordinal.py
 ====================================
 Script to make a dataset for Complete, Compliance, Fall and Risk
-using ordinal encoding of categorial features
+using ordinal encoding of categorial features.
 """
 
 import paths as pt

ml/src/data/make_screening_data.py

 """
 make_screening_data.py
 ====================================
-Script to make dataset of screenings to be used for cases
+Script to make dataset of screenings to be used for cases.
 """
 
 import numpy as np

ml/src/utility/data.py

@@ -56,4 +56,4 @@ class Data:
     ss: pd.DataFrame
     td: pd.DataFrame
     tc: pd.DataFrame
-    ats: pd.DataFrame
\ No newline at end of file
+    ats: pd.DataFrame

ml/src/utility/embedder.py

@@ -253,4 +253,4 @@ def check_epochs(epochs: int) -> None:
 
 def check_batch_size(batch_size: int) -> None:
     if batch_size <= 0:
-        raise ValueError("You should provide a batch size greater than zero")
\ No newline at end of file
+        raise ValueError("You should provide a batch size greater than zero")

ml/src/utility/metrics.py

@@ -9,7 +9,6 @@ import pandas as pd
 import xgboost
 from typing import List, Tuple
 from sklearn.metrics import confusion_matrix
-import matplotlib
 
 def compute_mean(values: List):
     return round(np.mean(values)*100, 3)
@@ -39,15 +38,15 @@ def eval_gini(y_true: np.array, y_prob: np.array) -> float:
 
 def get_cm_by_protected_variable(df, protected_col_name, y_target_name, y_pred_name):
     confusion_df = pd.DataFrame(columns=[protected_col_name, "FPR", "FNR"])
-    
+
     for name in list(df[protected_col_name].unique()):
         a=df[df[protected_col_name]==name][y_target_name]
         b=df[df[protected_col_name]==name][y_pred_name]
 
         TN, FP, FN, TP = confusion_matrix(list(a), list(b),labels=[0, 1]).ravel()
-        
+
         TPR = TP/(TP+FN)
-        TNR = TN/(TN+FP) 
+        TNR = TN/(TN+FP)
         PPV = TP/(TP+FP)
         NPV = TN/(TN+FN)
         FPR = FP/(FP+TN)
@@ -59,8 +58,8 @@ def get_cm_by_protected_variable(df, protected_col_name, y_target_name, y_pred_n
         F1=2*(PPV*TPR)/(PPV+TPR)
 
         confusion_df = confusion_df.append({protected_col_name:name, "TPR":TPR, "TNR":TNR, "FPR":FPR,
-                                          "FNR":FNR, "PPV":PPV, "NPV":NPV, "FDR":FDR, "ACC":ACC,
-                                          "F1":F1, "LRplus":LRplus, "LRminus":LRminus, "TN":TN,
-                                          "FP":FP, "FN":FN, "TP":TP}, ignore_index=True)
-        
-    return confusion_df
\ No newline at end of file
+                                            "FNR":FNR, "PPV":PPV, "NPV":NPV, "FDR":FDR, "ACC":ACC,
+                                            "F1":F1, "LRplus":LRplus, "LRminus":LRminus, "TN":TN,
+                                            "FP":FP, "FN":FN, "TP":TP}, ignore_index=True)
+
+    return confusion_df

ml/src/utility/settings.py

@@ -5,10 +5,9 @@ Utility settings functions.
 """
 
 from pathlib import Path
-import paths as pt
 import yaml
 
 def load_settings(file_path, file_name):
     with open(Path.joinpath(file_path, file_name), 'r') as stream:
         settings = yaml.safe_load(stream)
-    return settings
\ No newline at end of file
+    return settings

ml/src/utility/time.py

@@ -13,4 +13,4 @@ def assert_datetime(entry: str) -> bool:
     :param entry: entry to check
     :return: boolean value whether conversion successful
     """
-    return pd.to_datetime(entry, format='%d-%m-%Y', errors='coerce') is not pd.NaT
\ No newline at end of file
+    return pd.to_datetime(entry, format='%d-%m-%Y', errors='coerce') is not pd.NaT