Fix environment

Makefile

@@ -14,11 +14,14 @@ CURRENT_DIR = $(shell pwd)
 . PHONY: venv_init
 
 venv-init: ##@environment Setup virtual environment
-	conda create -f environment.yml --prefix=.venv python=3.7
+	conda env create -f environment.yml --prefix=.venv python=3.7
 
 venv-activate: ##@environment Activates the virtual environment
 	activate $(CURRENT_DIR)/.venv
 
+venv-update: ##@environment Updates to latest packages
+	conda update ipykernel && conda update --prefix .venv --all
+
 venv-requirements-install: ##@environment Ensures environment.yml packages are installed
 	conda env update
 
@@ -82,14 +85,22 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 	--input-csv "./data/interim/sites.csv" \
 	--output-shp "./data/interim/sites.shp"
 
-# Creates a .csv of our dune toe and crest profile features
-./data/interim/profile_features.csv: ./data/raw/profile_features/dune_crests.shp ./data/raw/profile_features/dune_toes.shp ./data/interim/sites.csv ./data/interim/profiles.csv
+# # Creates a .csv of our dune toe and crest profile features from .shp file
+# ./data/interim/profile_features.csv: ./data/raw/profile_features/dune_crests.shp ./data/raw/profile_features/dune_toes.shp ./data/interim/sites.csv ./data/interim/profiles.csv
+# 	activate ./.venv && python ./src/cli.py create-profile-features \
+# 	--dune-crest-shp "./data/raw/profile_features/dune_crests.shp" \
+# 	--dune-toe-shp "./data/raw/profile_features/dune_toes.shp" \
+# 	--sites-csv "./data/interim/sites.csv" \
+# 	--profiles-csv "./data/interim/profiles.csv" \
+# 	--output-csv "./data/interim/profile_features.csv"
+
+# Create a .csv of our dune toe and crest profile features from Tom Beuzen's .mat file
+./data/interim/profile_features.csv: ./data/raw/profile_features_tom_beuzen/*.mat ./data/interim/sites.csv
 	activate ./.venv && python ./src/cli.py create-profile-features \
-	--dune-crest-shp "./data/raw/profile_features/dune_crests.shp" \
-	--dune-toe-shp "./data/raw/profile_features/dune_toes.shp" \
+	--crest-mat "./data/raw/profile_features_tom_beuzen/J16_DuneCrest.mat" \
+	--toe-mat "./data/raw/profile_features_tom_beuzen/J16_DuneToe.mat" \
 	--sites-csv "./data/interim/sites.csv" \
-	--profiles-csv "./data/interim/profiles.csv" \
-	--output-csv "./data/interim/profile_features.csv"
+	--output-file "./data/interim/profile_features.csv"
 
 # Creates a forecast of twl using sto06 and prestorm time varying prestorm foreshore slope
 ./data/interim/twl_foreshore_slope_sto06.csv: ./data/interim/waves.csv ./data/interim/tides.csv ./data/interim/profiles.csv ./data/interim/sites.csv ./data/interim/profile_features.csv
@@ -168,5 +179,3 @@ HELP_FUN = \
 
 help: ##@other Show this help.
 	@perl -e '$(HELP_FUN)' $(MAKEFILE_LIST)
-
-