Merge branch 'bugfix/fix-cli' into develop

Makefile

@@ -48,36 +48,43 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 ./data/raw/processed_shorelines/orientations.mat: ./data/raw/processed_shorelines/profiles.mat
 	$(MATLAB_PATH) -nosplash -r "cd $(CURRENT_DIR); run('./src/data/beach_orientations.m'); quit"
 
+# # Produces a .csv of sites where our beach cross-sections are located
+# ./data/interim/sites.csv ./data/interim/profiles.csv: ./data/raw/processed_shorelines/profiles.mat
+# 	activate ./.venv && python ./src/data/parse_mat.py create-sites-and-profiles-csv \
+# 	--profiles-mat "./data/raw/processed_shorelines/profiles.mat" \
+# 	--profiles-output-file "./data/interim/profiles.csv" \
+# 	--sites-output-file "./data/interim/sites.csv"
+
 # Produces a .csv of sites where our beach cross-sections are located
 ./data/interim/sites.csv ./data/interim/profiles.csv: ./data/raw/processed_shorelines/profiles.mat
-	activate ./.venv && python ./src/data/parse_mat.py create-sites-and-profiles-csv \
+	activate ./.venv && python ./src/cli.py create-sites-and-profiles-csv \
 	--profiles-mat "./data/raw/processed_shorelines/profiles.mat" \
 	--profiles-output-file "./data/interim/profiles.csv" \
 	--sites-output-file "./data/interim/sites.csv"
 
 # Produces a .csv of waves for each site
 ./data/interim/waves.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/waves.mat
-	activate ./.venv && python ./src/data/parse_mat.py create-waves-csv \
+	activate ./.venv && python ./src/cli.py create-waves-csv \
 	--waves-mat "./data/raw/processed_shorelines/waves.mat" \
 	--sites-csv "./data/interim/sites.csv" \
 	--output-file "./data/interim/waves.csv"
 
 # Produces a .csv of tides for each site
 ./data/interim/tides.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/tides.mat
-	activate ./.venv && python ./src/data/parse_mat.py create-tides-csv \
+	activate ./.venv && python ./src/cli.py create-tides-csv \
 	--tides-mat "./data/raw/processed_shorelines/tides.mat" \
 	--sites-csv "./data/interim/sites.csv" \
 	--output-file "./data/interim/tides.csv"
 
 # Creates a .shp of our sites to load into QGis
 ./data/interim/sites.shp: ./data/interim/sites.csv
-	activate ./.venv && python ./src/data/csv_to_shp.py sites-csv-to-shp \
+	activate ./.venv && python ./src/cli.py sites-csv-to-shp \
 	--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
-	activate ./.venv && python ./src/data/profile_features.py create-profile-features \
+	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" \
@@ -86,7 +93,7 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 
 # 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
-	activate ./.venv && python ./src/analysis/forecast_twl.py create-twl-forecast \
+	activate ./.venv && python ./src/cli.py create-twl-forecast \
 	--waves-csv "./data/interim/waves.csv" \
 	--tides-csv "./data/interim/tides.csv" \
 	--profiles-csv "./data/interim/profiles.csv" \
@@ -96,7 +103,7 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 	--output-file "./data/interim/twl_foreshore_slope_sto06.csv"
 
 ./data/interim/twl_mean_slope_sto06.csv: ./data/interim/waves.csv ./data/interim/tides.csv ./data/interim/profiles.csv ./data/interim/sites.csv ./data/interim/profile_features.csv
-	activate ./.venv && python ./src/analysis/forecast_twl.py create-twl-forecast \
+	activate ./.venv && python ./src/cli.py create-twl-forecast \
 	--waves-csv "./data/interim/waves.csv" \
 	--tides-csv "./data/interim/tides.csv" \
 	--profiles-csv "./data/interim/profiles.csv" \
@@ -106,19 +113,19 @@ impacts: ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv ./data/inte
 	--output-file "./data/interim/twl_mean_slope_sto06.csv"
 
 ./data/interim/impacts_observed.csv: ./data/interim/profiles.csv ./data/interim/profile_features.csv
-	activate ./.venv && python ./src/analysis/observed_storm_impacts.py create-observed-impacts \
+	activate ./.venv && python ./src/cli.py create-observed-impacts \
 	--profiles-csv "./data/interim/profiles.csv" \
 	--profile-features-csv "./data/interim/profile_features.csv" \
 	--output-file "./data/interim/impacts_observed.csv"
 
 ./data/interim/impacts_forecasted_mean_slope_sto06.csv: ./data/interim/profile_features.csv ./data/interim/twl_mean_slope_sto06.csv
-	activate ./.venv && python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \
+	activate ./.venv && python ./src/cli.py create-forecasted-impacts \
 	--profile-features-csv "./data/interim/profile_features.csv" \
 	--forecasted-twl-csv "./data/interim/twl_mean_slope_sto06.csv" \
 	--output-file "./data/interim/impacts_forecasted_mean_slope_sto06.csv"
 
 ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv: ./data/interim/profile_features.csv ./data/interim/twl_foreshore_slope_sto06.csv
-	activate ./.venv && python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \
+	activate ./.venv && python ./src/cli.py create-forecasted-impacts \
 	--profile-features-csv "./data/interim/profile_features.csv" \
 	--forecasted-twl-csv "./data/interim/twl_foreshore_slope_sto06.csv" \
 	--output-file "./data/interim/impacts_forecasted_foreshore_slope_sto06.csv"

README.md

@@ -73,4 +73,5 @@ been corrected for systematic errors, so actual elevations should be taken from
 - [ ] Implement dune impact calculations as per Palmsten & Holman. Calculation should be done in a new dataframe.
 - [ ] Implement data/interim/*.csv file checking using py.test. Check for correct columns, number of nans etc. Testing of code is probably a lower priority than just checking the interim data files at the moment.
 - [ ] Investigate using [modin](https://github.com/modin-project/modin) to help speed up analysis.
-- [ ] Need to think about how relative imports are handled, see [here](https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html). Maybe the click CLI interface should be moved to the `./src/` folder and it can import all the other packages?
+- [ ] Need to think about how relative imports are handled, see [here](https://chrisyeh96.github.io/2017/08/08/definitive-guide-python-imports.html). Maybe the click CLI interface should be moved to the `./src/` folder and it can import all the other packages?
+- [ ] Simplify runup_models in Stockdon06 - we should really only have one function for each runup model. Need to make it work with individual values or entire dataframe. Use (np.maskedarray)[https://docs.scipy.org/doc/numpy-1.15.0/reference/maskedarray.generic.html]

src/analysis/analysis.py

@@ -1,15 +0,0 @@
-import pandas as pd
-import os
-
-
-def main():
-
-    data_folder = "./data/interim"
-    df_waves = pd.read_csv(os.path.join(data_folder, "waves.csv"), index_col=[0, 1])
-    df_tides = pd.read_csv(os.path.join(data_folder, "tides.csv"), index_col=[0, 1])
-    df_profiles = pd.read_csv(os.path.join(data_folder, "profiles.csv"), index_col=[0, 1, 2])
-    df_sites = pd.read_csv(os.path.join(data_folder, "sites.csv"), index_col=[0])
-
-
-if __name__ == "__main__":
-    main()

src/analysis/compare_impacts.py

@@ -2,13 +2,13 @@
 Compares forecasted and observed impacts, putting them into one data frame and exporting the results.
 """
 
-import logging.config
 import os
 
 import pandas as pd
 
-logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
-logger = logging.getLogger(__name__)
+from utils import setup_logging
+
+logger = setup_logging()
 
 
 def compare_impacts(df_forecasted, df_observed):

src/analysis/forecast_twl.py

@@ -1,16 +1,16 @@
-import logging.config
 import os
 from multiprocessing import Pool
+
 import click
 import numpy as np
 import numpy.ma as ma
 import pandas as pd
 from scipy import stats
 
-import runup_models
+from analysis import runup_models
+from utils import setup_logging
 
-logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
-logger = logging.getLogger(__name__)
+logger = setup_logging()
 
 MULTIPROCESS_THREADS = int(os.environ.get("MULTIPROCESS_THREADS", 4))
 
@@ -301,13 +301,3 @@ def create_twl_forecast(waves_csv, tides_csv, profiles_csv, profile_features_csv
     df_twl_foreshore_slope_sto06.to_csv(output_file)
     logger.info("Saved to %s", output_file)
     logger.info("Done!")
-
-
-@click.group()
-def cli():
-    pass
-
-
-if __name__ == "__main__":
-    cli.add_command(create_twl_forecast)
-    cli()

src/analysis/forecasted_storm_impacts.py

@@ -2,13 +2,12 @@
 Estimates the forecasted storm impacts based on the forecasted water level and dune crest/toe.
 """
 
-import logging.config
-import os
 import click
 import pandas as pd
 
-logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
-logger = logging.getLogger(__name__)
+from utils import setup_logging
+
+logger = setup_logging()
 
 
 def forecasted_impacts(df_profile_features, df_forecasted_twl):
@@ -72,7 +71,6 @@ def storm_regime(df_forecasted_impacts):
 @click.option("--forecasted-twl-csv", required=True, help="")
 @click.option("--output-file", required=True, help="")
 def create_forecasted_impacts(profile_features_csv, forecasted_twl_csv, output_file):
-
     logger.info("Creating observed wave impacts")
     logger.info("Importing existing data")
     df_profile_features = pd.read_csv(profile_features_csv, index_col=[0])
@@ -82,13 +80,3 @@ def create_forecasted_impacts(profile_features_csv, forecasted_twl_csv, output_f
     df_forecasted_impacts.to_csv(output_file)
     logger.info("Saved to %s", output_file)
     logger.info("Done!")
-
-
-@click.group()
-def cli():
-    pass
-
-
-if __name__ == "__main__":
-    cli.add_command(create_forecasted_impacts)
-    cli()

src/analysis/observed_storm_impacts.py

@@ -1,12 +1,11 @@
-import logging.config
-import os
 import click
 import numpy as np
 import pandas as pd
 from scipy.integrate import simps
 
-logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
-logger = logging.getLogger(__name__)
+from utils import setup_logging
+
+logger = setup_logging()
 
 
 def return_first_or_nan(l):
@@ -49,8 +48,8 @@ def volume_change(df_profiles, df_profile_features, zone):
             prestorm_dune_toe_x = prestorm_dune_crest_x
 
         # If no prestorm and poststorm profiles, skip site and continue
-        profile_lengths = [len(df_site.query("profile_type == '{}'".format(x))) for x in ['prestorm', 'poststorm']]
-        if any([length ==0 for length in profile_lengths]):
+        profile_lengths = [len(df_site.query("profile_type == '{}'".format(x))) for x in ["prestorm", "poststorm"]]
+        if any([length == 0 for length in profile_lengths]):
             continue
 
         # Find last x coordinate where we have both prestorm and poststorm measurements. If we don't do this,
@@ -182,13 +181,3 @@ def create_observed_impacts(profiles_csv, profile_features_csv, output_file):
 
     logger.info("Saved to %s", output_file)
     logger.info("Done!")
-
-
-@click.group()
-def cli():
-    pass
-
-
-if __name__ == "__main__":
-    cli.add_command(create_observed_impacts)
-    cli()

src/cli.py

@@ -0,0 +1,29 @@
+"""
+Entry point to run data processing and analysis commands.
+"""
+
+import click
+
+import data.parse_mat as parse_mat
+import data.profile_features as profile_features
+import data.csv_to_shp as csv_to_shp
+import analysis.forecast_twl as forecast_twl
+import analysis.forecasted_storm_impacts as forecasted_storm_impacts
+import analysis.observed_storm_impacts as observed_storm_impacts
+
+
+@click.group()
+def cli():
+    pass
+
+
+if __name__ == "__main__":
+    cli.add_command(parse_mat.create_waves_csv)
+    cli.add_command(parse_mat.create_sites_and_profiles_csv)
+    cli.add_command(parse_mat.create_tides_csv)
+    cli.add_command(profile_features.create_profile_features)
+    cli.add_command(csv_to_shp.sites_csv_to_shp)
+    cli.add_command(forecast_twl.create_twl_forecast)
+    cli.add_command(forecasted_storm_impacts.create_forecasted_impacts)
+    cli.add_command(observed_storm_impacts.create_observed_impacts)
+    cli()

src/data/csv_to_shp.py

@@ -1,12 +1,6 @@
 """
 Converts .csv files to .shape files
 """
-
-import os
-import sys
-
-sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-
 import click
 import fiona
 import pandas as pd
@@ -38,13 +32,3 @@ def sites_csv_to_shp(input_csv, output_shp):
             prop = {"beach": row["beach"], "site_id": index}
             output.write({"geometry": mapping(point), "properties": prop})
     logger.info("Done!")
-
-
-@click.group()
-def cli():
-    pass
-
-
-if __name__ == "__main__":
-    cli.add_command(sites_csv_to_shp)
-    cli()

src/data/parse_mat.py

@@ -2,14 +2,8 @@
 Converts raw .mat files into a flattened .csv structure which can be imported into python pandas.
 """
 
-import os
-import sys
-
-sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-
-from datetime import datetime, timedelta
 import math
-
+from datetime import datetime, timedelta
 
 import click
 import numpy as np
@@ -17,7 +11,7 @@ import pandas as pd
 from mat4py import loadmat
 from shapely.geometry import Point
 
-from profile_features import convert_coord_systems
+from data.profile_features import convert_coord_systems
 from utils import setup_logging
 
 logger = setup_logging()

src/data/profile_features.py

@@ -1,5 +1,5 @@
-import os
 from functools import partial
+
 import click
 import fiona
 import numpy as np
@@ -8,11 +8,10 @@ import pyproj
 from shapely.geometry import LineString, Point
 from shapely.geometry import shape
 from shapely.ops import transform
-import logging.config
 
+from utils import setup_logging
 
-logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
-logger = logging.getLogger(__name__)
+logger = setup_logging()
 
 
 def convert_coord_systems(g1, in_coord_system="EPSG:4326", out_coord_system="EPSG:28356"):
@@ -160,13 +159,3 @@ def create_profile_features(dune_crest_shp, dune_toe_shp, sites_csv, profiles_cs
     df_profile_features = parse_profile_features(df_sites, df_profiles, dune_crest_shp, dune_toe_shp)
     df_profile_features.to_csv(output_csv)
     logger.info("Done!")
-
-
-@click.group()
-def cli():
-    pass
-
-
-if __name__ == "__main__":
-    cli.add_command(create_profile_features)
-    cli()

src/logging.conf

@@ -1,32 +0,0 @@
-[loggers]
-keys=root, matplotlib, fiona
-
-[handlers]
-keys=consoleHandler
-
-[formatters]
-keys=simpleFormatter
-
-[logger_root]
-level=DEBUG
-handlers=consoleHandler
-
-[logger_matplotlib]
-level=WARNING
-handlers=consoleHandler
-qualname=matplotlib
-
-[logger_fiona]
-level=WARNING
-handlers=consoleHandler
-qualname=fiona
-
-[handler_consoleHandler]
-class=StreamHandler
-level=INFO
-formatter=simpleFormatter
-args=(sys.stdout,)
-
-[formatter_simpleFormatter]
-format=%(asctime)s %(name)-17s %(levelname)-8s %(message)s
-datefmt=%a, %d %b %Y %H:%M:%S