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nsw-2016-storm-impact
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Switch to conda rather than pipenv to manage environment

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Chris Leaman 6 years ago
parent f141b85745
commit db59978895
6 changed files with 206 additions and 835 deletions
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6
.env
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@ -10,10 +10,10 @@ MATLAB_PATH="C:/Program Files/MATLAB/R2016b/bin/win64/MATLAB.exe"
# total water level. # total water level.
MULTIPROCESS_THREADS=2 MULTIPROCESS_THREADS=2
# The settings below should be left as is unless you know what you're doing. # GDAL_DATA="C://Users//z5189959//Desktop//nsw-2016-storm-impact//.venv//Library//share//gdal"
# We want to create the pipenv virtualenv in the current folder # The settings below should be left as is unless you know what you're doing.
PIPENV_VENV_IN_PROJECT=1
# Need to set pythonpath so that relative imports can be properly used in with pipenv # Need to set pythonpath so that relative imports can be properly used in with pipenv
# Refer to https://stackoverflow.com/q/52986500 and https://stackoverflow.com/a/49797761 # Refer to https://stackoverflow.com/q/52986500 and https://stackoverflow.com/a/49797761

64
Makefile
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@ -1,3 +1,5 @@
SHELL=cmd
############################### ###############################
# Load environment variables # Load environment variables
@ -12,13 +14,21 @@ CURRENT_DIR = $(shell pwd)
. PHONY: venv_init . PHONY: venv_init
venv-init: ##@environment Setup virtual environment venv-init: ##@environment Setup virtual environment
pip install pipenv conda create -f environment.yml --prefix=.venv python=3.7
pipenv --python 3.7
pipenv install venv-activate: ##@environment Activates the virtual environment
activate $(CURRENT_DIR)/.venv
venv-requirements-install: ##@enviornment Ensures environment.yml packages are installed
conda env update
venv-requirements-export: ##@environment Exports current environment to environment.yml
conda env export --file environment.yml
############################### ###############################
# Get data from network drive # Get data from network drive
.PHONY: push-data pull-data
push-data: ##@data Copies data from ./data/ to data backup directory push-data: ##@data Copies data from ./data/ to data backup directory
rclone copy ./data/ $(DATA_BACKUP_DIR) --exclude "*.las" --progress rclone copy ./data/ $(DATA_BACKUP_DIR) --exclude "*.las" --progress
@ -39,44 +49,35 @@ process-mat: ./data/interim/sites.csv ./data/interim/waves.csv ./data/interim/pr
$(MATLAB_PATH) -nosplash -r "cd $(CURRENT_DIR); run('./src/data/beach_orientations.m'); quit" $(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 # Produces a .csv of sites where our beach cross-sections are located
./data/interim/sites.csv: ./data/raw/processed_shorelines/*.mat ./data/interim/sites.csv ./data/interim/profiles.csv: ./data/raw/processed_shorelines/profiles.mat
pipenv run python ./src/data/parse_mat.py create-sites-csv \ activate ./.venv && python ./src/data/parse_mat.py create-sites-and-profiles-csv \
--waves-mat "./data/raw/processed_shorelines/waves.mat" \
--tides-mat "./data/raw/processed_shorelines/tides.mat" \
--profiles-mat "./data/raw/processed_shorelines/profiles.mat" \ --profiles-mat "./data/raw/processed_shorelines/profiles.mat" \
--orientations-mat "./data/raw/processed_shorelines/orientations.mat" \ --profiles-output-file "./data/interim/profiles.csv" \
--output-file "./data/interim/sites.csv" --sites-output-file "./data/interim/sites.csv"
# Produces a .csv of waves for each site # Produces a .csv of waves for each site
./data/interim/waves.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/waves.mat ./data/interim/waves.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/waves.mat
pipenv run python ./src/data/parse_mat.py create-waves-csv \ activate ./.venv && python ./src/data/parse_mat.py create-waves-csv \
--waves-mat "./data/raw/processed_shorelines/waves.mat" \ --waves-mat "./data/raw/processed_shorelines/waves.mat" \
--sites-csv "./data/interim/sites.csv" \ --sites-csv "./data/interim/sites.csv" \
--output-file "./data/interim/waves.csv" --output-file "./data/interim/waves.csv"
# Produces a .csv of profiles for each site
./data/interim/profiles.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/profiles.mat
pipenv run python ./src/data/parse_mat.py create-profiles-csv \
--profiles-mat "./data/raw/processed_shorelines/profiles.mat" \
--sites-csv "./data/interim/sites.csv" \
--output-file "./data/interim/profiles.csv"
# Produces a .csv of tides for each site # Produces a .csv of tides for each site
./data/interim/tides.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/tides.mat ./data/interim/tides.csv: ./data/interim/sites.csv ./data/raw/processed_shorelines/tides.mat
pipenv run python ./src/data/parse_mat.py create-tides-csv \ activate ./.venv && python ./src/data/parse_mat.py create-tides-csv \
--tides-mat "./data/raw/processed_shorelines/tides.mat" \ --tides-mat "./data/raw/processed_shorelines/tides.mat" \
--sites-csv "./data/interim/sites.csv" \ --sites-csv "./data/interim/sites.csv" \
--output-file "./data/interim/tides.csv" --output-file "./data/interim/tides.csv"
# Creates a .shp of our sites to load into QGis # Creates a .shp of our sites to load into QGis
./data/interim/sites.shp: ./data/interim/sites.csv ./data/interim/sites.shp: ./data/interim/sites.csv
pipenv run python ./src/data/csv_to_shp.py sites-csv-to-shp \ activate ./.venv && python ./src/data/csv_to_shp.py sites-csv-to-shp \
--input-csv "./data/interim/sites.csv" \ --input-csv "./data/interim/sites.csv" \
--output-shp "./data/interim/sites.shp" --output-shp "./data/interim/sites.shp"
# Creates a .csv of our dune toe and crest profile features # 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 ./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
pipenv run python ./src/data/profile_features.py create-profile-features \ activate ./.venv && python ./src/data/profile_features.py create-profile-features \
--dune-crest-shp "./data/raw/profile_features/dune_crests.shp" \ --dune-crest-shp "./data/raw/profile_features/dune_crests.shp" \
--dune-toe-shp "./data/raw/profile_features/dune_toes.shp" \ --dune-toe-shp "./data/raw/profile_features/dune_toes.shp" \
--sites-csv "./data/interim/sites.csv" \ --sites-csv "./data/interim/sites.csv" \
@ -85,7 +86,7 @@ process-mat: ./data/interim/sites.csv ./data/interim/waves.csv ./data/interim/pr
# Creates a forecast of twl using sto06 and prestorm time varying prestorm foreshore slope # 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 ./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
pipenv run python ./src/analysis/forecast_twl.py create-twl-forecast \ activate ./.venv && python ./src/analysis/forecast_twl.py create-twl-forecast \
--waves-csv "./data/interim/waves.csv" \ --waves-csv "./data/interim/waves.csv" \
--tides-csv "./data/interim/tides.csv" \ --tides-csv "./data/interim/tides.csv" \
--profiles-csv "./data/interim/profiles.csv" \ --profiles-csv "./data/interim/profiles.csv" \
@ -96,7 +97,7 @@ process-mat: ./data/interim/sites.csv ./data/interim/waves.csv ./data/interim/pr
# Creates a forecast of twl using sto06 and prestorm mean foreshore slope # Creates a forecast of twl using sto06 and prestorm mean foreshore slope
./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 ./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
pipenv run python ./src/analysis/forecast_twl.py create-twl-forecast \ activate ./.venv && python ./src/analysis/forecast_twl.py create-twl-forecast \
--waves-csv "./data/interim/waves.csv" \ --waves-csv "./data/interim/waves.csv" \
--tides-csv "./data/interim/tides.csv" \ --tides-csv "./data/interim/tides.csv" \
--profiles-csv "./data/interim/profiles.csv" \ --profiles-csv "./data/interim/profiles.csv" \
@ -106,37 +107,24 @@ process-mat: ./data/interim/sites.csv ./data/interim/waves.csv ./data/interim/pr
--output-file "./data/interim/twl_mean_slope_sto06.csv" --output-file "./data/interim/twl_mean_slope_sto06.csv"
./data/interim/impacts_observed.csv: ./data/interim/profiles.csv ./data/interim/profile_features.csv ./data/interim/impacts_observed.csv: ./data/interim/profiles.csv ./data/interim/profile_features.csv
pipenv run python ./src/analysis/observed_storm_impacts.py create-observed-impacts \ activate ./.venv && python ./src/analysis/observed_storm_impacts.py create-observed-impacts \
--profiles-csv "./data/interim/profiles.csv" \ --profiles-csv "./data/interim/profiles.csv" \
--profile-features-csv "./data/interim/profile_features.csv" \ --profile-features-csv "./data/interim/profile_features.csv" \
--output-file "./data/interim/impacts_observed.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 ./data/interim/impacts_forecasted_mean_slope_sto06.csv: ./data/interim/profile_features.csv ./data/interim/twl_mean_slope_sto06.csv
pipenv run python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \ activate ./.venv && python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \
--profile-features-csv "./data/interim/profile_features.csv" \ --profile-features-csv "./data/interim/profile_features.csv" \
--forecasted-twl-csv "./data/interim/twl_mean_slope_sto06.csv" \ --forecasted-twl-csv "./data/interim/twl_mean_slope_sto06.csv" \
--output-file "./data/interim/impacts_forecasted_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 ./data/interim/impacts_forecasted_foreshore_slope_sto06.csv: ./data/interim/profile_features.csv ./data/interim/twl_foreshore_slope_sto06.csv
pipenv run python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \ activate ./.venv && python ./src/analysis/forecasted_storm_impacts.py create-forecasted-impacts \
--profile-features-csv "./data/interim/profile_features.csv" \ --profile-features-csv "./data/interim/profile_features.csv" \
--forecasted-twl-csv "./data/interim/twl_foreshore_slope_sto06.csv" \ --forecasted-twl-csv "./data/interim/twl_foreshore_slope_sto06.csv" \
--output-file "./data/interim/impacts_forecasted_foreshore_slope_sto06.csv" --output-file "./data/interim/impacts_forecasted_foreshore_slope_sto06.csv"
#################################################################################
# PROJECT RULES #
#################################################################################
.PHONY: push-data parse_mat sites-csv-to-shp
mat-to-csv: ##@data Converts raw .mat files to .csv for python
cd ./src/data/ && python parse_mat.py
sites-csv-to-shp: ##@data Create the sites.shp from sites.csv
cd ./src/data && python csv_to_shp.py sites_csv_to_shp "..\..\data\interim\sites.csv" "..\..\data\interim\sites.shp"
############################### ###############################
# Misc commands # Misc commands
format: ./src/*.py ##@misc Check python file formatting format: ./src/*.py ##@misc Check python file formatting

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Pipfile
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@ -1,31 +0,0 @@
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[dev-packages]
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jupyter = "*"
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jupyter-contrib-nbextensions = "*"
jupyter-nbextensions-configurator = "*"
[requires]
python_version = "3.7"
[pipenv]
allow_prereleases = true

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36
README.md
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@ -7,19 +7,36 @@ structure where possible. The analysis is done in python (look at the `/src/` fo
Development is conducted using a [gitflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow) approach. The `master` branch stores the officialrelease history and the `develop` branch serves as an integration branch for features. Other `hotfix` and `feature` branches should be created and merged as necessary. Development is conducted using a [gitflow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow) approach. The `master` branch stores the officialrelease history and the `develop` branch serves as an integration branch for features. Other `hotfix` and `feature` branches should be created and merged as necessary.
## Where to start? ## How to start?
Check .env
Uses pipenv ### # Getting software requirements
1. Clone this repository.
2. Pull data from WRL coastal J drive with `make pull-data`
3. Check out jupyter notebook `./notebooks/01_exploration.ipynb` which has an example of how to import the data and some interactive widgets.
## Requirements
The following requirements are needed to run various bits: The following requirements are needed to run various bits:
- [Python 3.6+](https://conda.io/docs/user-guide/install/windows.html): Used for processing and analysing data. Jupyter notebooks are used for exploratory analyis and communication. - [Anacond](https://www.anaconda.com/download/): Used for processing and analysing data. The Anaconda distribution is used for managing environments and is available for Windows, Mac and Linux. Jupyter notebooks are used for exploratory analyis and communication.
- [QGIS](https://www.qgis.org/en/site/forusers/download): Used for looking at raw LIDAR pre/post storm surveys and extracting dune crests/toes - [QGIS](https://www.qgis.org/en/site/forusers/download): Used for looking at raw LIDAR pre/post storm surveys and extracting dune crests/toes
- [rclone](https://rclone.org/downloads/): Data is not tracked by this repository, but is backed up to a remote Chris Leaman working directory located on the WRL coastal drive. Rclone is used to sync local and remote copies. Ensure rclone.exe is located on your `PATH` environment. - [rclone](https://rclone.org/downloads/): Data is not tracked by this repository, but is backed up to a remote Chris Leaman working directory located on the WRL coastal drive. Rclone is used to sync local and remote copies. Ensure rclone.exe is located on your `PATH` environment.
- [gnuMake](http://gnuwin32.sourceforge.net/packages/make.htm): A list of commands for processing data is provided in the `./Makefile`. Use gnuMake to launch these commands. Ensure make.exe is located on your `PATH` environment. - [gnuMake](http://gnuwin32.sourceforge.net/packages/make.htm): A list of commands for processing data is provided in the `./Makefile`. Use gnuMake to launch these commands. Ensure make.exe is located on your `PATH` environment.
- git
#### Getting the repository
Clone the repository:
```
git clone http://git.wrl.unsw.edu.au:3000/chrisl/nsw-2016-storm-impact.git
cd nsw-2016-storm-impact
```
#### Getting the python environment set up
Commands for setting up the python environment are provided in the `Makefile`. Simply run the following commands in the repo root directory:
```
make venv-init
make venv-activate
make venv-requirements-install
```
You can see what these commands are actually running by inspecting the `Makefile`.
#### Pull data
#### View notebooks
## Available data ## Available data
Raw, interim and processed data used in this analysis is kept in the `/data/` folder. Data is not tracked in the repository due to size constraints, but stored locally. A mirror is kept of the coastal folder J drive which you can Raw, interim and processed data used in this analysis is kept in the `/data/` folder. Data is not tracked in the repository due to size constraints, but stored locally. A mirror is kept of the coastal folder J drive which you can
@ -45,3 +62,4 @@ 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 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. - [ ] 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. - [ ] 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?

149
environment.yml
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@ -0,0 +1,149 @@
name: C:\Users\z5189959\Desktop\nsw-2016-storm-impact\.venv
channels:
- defaults
- conda-forge
dependencies:
- appdirs=1.4.3=py_1
- attrs=18.2.0=py_0
- backcall=0.1.0=py_0
- black=18.9b0=py_0
- bleach=3.0.2=py_0
- boost=1.66.0=py36_vc14_1
- boost-cpp=1.66.0=vc14_1
- ca-certificates=2018.10.15=ha4d7672_0
- certifi=2018.10.15=py36_1000
- colorama=0.4.0=py_0
- colorlover=0.2.1=py_0
- curl=7.60.0=vc14_0
- entrypoints=0.2.3=py36_1002
- expat=2.2.5=vc14_0
- freetype=2.8.1=vc14_0
- freexl=1.0.2=vc14_2
- geotiff=1.4.2=vc14_1
- hdf4=4.2.13=vc14_0
- hdf5=1.10.1=vc14_2
- icu=58.2=vc14_0
- ipykernel=5.1.0=py36h39e3cac_1001
- ipython=7.1.1=py36h39e3cac_1000
- jedi=0.13.1=py36_1000
- jinja2=2.10=py_1
- jpeg=9b=vc14_2
- jupyter_client=5.2.3=py_1
- jupyter_contrib_core=0.3.3=py_2
- jupyter_contrib_nbextensions=0.5.0=py36_1000
- jupyter_highlight_selected_word=0.2.0=py36_1000
- jupyter_latex_envs=1.4.4=py36_1000
- jupyter_nbextensions_configurator=0.4.0=py36_1000
- kealib=1.4.7=vc14_4
- krb5=1.14.6=vc14_0
- libgdal=2.2.4=vc14_5
- libiconv=1.14=vc14_4
- libnetcdf=4.6.1=vc14_2
- libpng=1.6.34=vc14_0
- libpq=9.6.3=vc14_0
- libsodium=1.0.16=vc14_0
- libspatialite=4.3.0a=vc14_19
- libtiff=4.0.9=vc14_0
- libxml2=2.9.5=vc14_1
- libxslt=1.1.32=vc14_0
- lxml=4.2.3=py36heafd4d3_0
- markupsafe=1.1.0=py36hfa6e2cd_1000
- matplotlib=2.2.2=py36_1
- mistune=0.8.4=py36hfa6e2cd_1000
- nbconvert=5.3.1=py_1
- notebook=5.7.2=py36_1000
- openjpeg=2.3.0=vc14_2
- openssl=1.0.2p=hfa6e2cd_1001
- pandoc=2.4=0
- pandocfilters=1.4.2=py_1
- parso=0.3.1=py_0
- pickleshare=0.7.5=py36_1000
- proj4=4.9.3=vc14_5
- prometheus_client=0.4.2=py_0
- prompt_toolkit=2.0.7=py_0
- pygments=2.2.0=py_1
- python=3.6.6=he025d50_0
- pywinpty=0.5.4=py36_1002
- pyzmq=17.1.2=py36hf576995_1001
- qt=5.6.2=vc14_1
- send2trash=1.5.0=py_0
- sqlite=3.20.1=vc14_2
- terminado=0.8.1=py36_1001
- testpath=0.4.2=py36_1000
- tk=8.6.8=vc14_0
- toml=0.10.0=py_0
- vc=14=0
- wcwidth=0.1.7=py_1
- webencodings=0.5.1=py_1
- winpty=0.4.3=4
- xerces-c=3.2.0=vc14_0
- yaml=0.1.7=vc14_0
- zeromq=4.2.5=vc14_2
- zlib=1.2.11=vc14_0
- asn1crypto=0.24.0=py36_0
- blas=1.0=mkl
- cffi=1.11.5=py36h74b6da3_1
- chardet=3.0.4=py36_1
- click=7.0=py36_0
- click-plugins=1.0.4=py36_0
- cligj=0.5.0=py36_0
- cryptography=2.3.1=py36h74b6da3_0
- cycler=0.10.0=py36h009560c_0
- decorator=4.3.0=py36_0
- fiona=1.7.10=py36h5bf8d1d_0
- gdal=2.2.2=py36hcebd033_1
- geos=3.6.2=h9ef7328_2
- icc_rt=2017.0.4=h97af966_0
- idna=2.7=py36_0
- intel-openmp=2019.1=144
- ipython_genutils=0.2.0=py36h3c5d0ee_0
- jsonschema=2.6.0=py36h7636477_0
- jupyter_core=4.4.0=py36_0
- kiwisolver=1.0.1=py36h6538335_0
- libboost=1.67.0=hd9e427e_4
- libcurl=7.61.1=h7602738_0
- libkml=1.3.0=he5f2a48_4
- libssh2=1.8.0=hd619d38_4
- m2w64-gcc-libgfortran=5.3.0=6
- m2w64-gcc-libs=5.3.0=7
- m2w64-gcc-libs-core=5.3.0=7
- m2w64-gmp=6.1.0=2
- m2w64-libwinpthread-git=5.0.0.4634.697f757=2
- mkl=2018.0.3=1
- mkl_fft=1.0.6=py36hdbbee80_0
- mkl_random=1.0.1=py36h77b88f5_1
- msys2-conda-epoch=20160418=1
- munch=2.3.2=py36_0
- nbformat=4.4.0=py36h3a5bc1b_0
- numpy=1.15.4=py36ha559c80_0
- numpy-base=1.15.4=py36h8128ebf_0
- pandas=0.23.4=py36h830ac7b_0
- pip=18.1=py36_0
- plotly=3.4.1=py36h28b3542_0
- pycparser=2.19=py36_0
- pyopenssl=18.0.0=py36_0
- pyparsing=2.3.0=py36_0
- pyproj=1.9.5.1=py36_0
- pyqt=5.6.0=py36_2
- pysocks=1.6.8=py36_0
- python-dateutil=2.7.5=py36_0
- pytz=2018.7=py36_0
- pyyaml=3.13=py36hfa6e2cd_0
- requests=2.20.1=py36_0
- retrying=1.3.3=py36_2
- scipy=1.1.0=py36h4f6bf74_1
- setuptools=40.6.2=py36_0
- shapely=1.6.4=py36hc90234e_0
- sip=4.19.8=py36h6538335_0
- six=1.11.0=py36_1
- tornado=5.1.1=py36hfa6e2cd_0
- traitlets=4.3.2=py36h096827d_0
- urllib3=1.23=py36_0
- vs2015_runtime=14.15.26706=h3a45250_0
- wheel=0.32.3=py36_0
- win_inet_pton=1.0.1=py36_1
- wincertstore=0.2=py36h7fe50ca_0
- xz=5.2.4=h2fa13f4_4
- pip:
- mat4py==0.4.1
prefix: C:\Users\z5189959\Desktop\nsw-2016-storm-impact\.venv
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