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reinitializing commit to accomodate large files
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‎.dockerignore

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.git

‎.gitattributes

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data/biodiversity filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly filter=lfs diff=lfs merge=lfs -text
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data/local filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02 filter=lfs diff=lfs merge=lfs -text
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data/biodiversity/comments.csv filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02/comments.csv filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02/participants-votes.csv filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02/stats-history.csv filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly/stats-history.csv filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly/votes.csv filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02/summary.csv filter=lfs diff=lfs merge=lfs -text
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data/biodiversity/summary.csv filter=lfs diff=lfs merge=lfs -text
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data/biodiversity/participants-votes.csv filter=lfs diff=lfs merge=lfs -text
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data/biodiversity/stats-history.csv filter=lfs diff=lfs merge=lfs -text
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data/biodiversity/votes.csv filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly/comments.csv filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly/participants-votes.csv filter=lfs diff=lfs merge=lfs -text
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data/bowling-green.american-assembly/summary.csv filter=lfs diff=lfs merge=lfs -text
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data/vtaiwan-uber-conv.ts-2015-08-28.exported-2020-07-02/votes.csv filter=lfs diff=lfs merge=lfs -text

‎.gitignore

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target
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.ipynb_checkpoints
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notebooks/jupyter/.ipynb_checkpoints
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data/local
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notebooks/oz/local/
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notebooks/jupyter/local
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notebooks/build/local
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clojupyter-standalone.jar

‎.nrepl.edn

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{:bind "0.0.0.0" :port 3850}

‎Dockerfile

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FROM clojure:openjdk-11-tools-deps
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EXPOSE 3850
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EXPOSE 3860
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EXPOSE 3870
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EXPOSE 3880
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RUN echo "deb http://fr.archive.ubuntu.com/ubuntu bionic main" >> /etc/apt/sources.list &&\
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apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3B4FE6ACC0B21F32 &&\
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apt-get update &&\
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apt-get install libpython3.6-dev python3-pip -y --allow-unauthenticated
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# This should make tech.ml stuff fast for things like pca/svd
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RUN apt-get install -y libblas-dev
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# Preinstall these packages, so later requirements.txt install will be faster
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RUN pip3 install seaborn &&\
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pip3 install matplotlib &&\
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pip3 install sklearn &&\
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pip3 install numpy &&\
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pip3 install umap-learn &&\
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pip3 install trimap &&\
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pip3 install altair &&\
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pip3 install jupyter
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RUN clojure -Sdeps '{:deps {org.clojure/clojure {:mvn/version "1.10.0"} \
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techascent/tech.ml.dataset {:mvn/version "3.01" \
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:exclusions [org.slf4j/slf4j-api]} \
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semantic-csv {:mvn/version "0.2.1-alpha1"} \
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net.mikera/core.matrix {:mvn/version "0.62.0"} \
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clj-python/libpython-clj {:mvn/version "1.45"} \
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org.clojure/tools.deps.alpha {:mvn/version "0.6.496" \
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:exclusions [org.slf4j/slf4j-nop]} \
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cider/cider-nrepl {:mvn/version "0.21.1"} \
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metasoarous/oz {:mvn/version "1.6.0-alpha11"} \
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clojupyter {:mvn/version "0.3.2"}}}' \
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-e "(clojure.core/println :deps-downloaded)"
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# Installing node
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ENV NODE_VERSION=14.5.0
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RUN apt-get install -y curl
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RUN curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash
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ENV NVM_DIR=/root/.nvm
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RUN . "$NVM_DIR/nvm.sh" && nvm install ${NODE_VERSION}
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RUN . "$NVM_DIR/nvm.sh" && nvm use v${NODE_VERSION}
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RUN . "$NVM_DIR/nvm.sh" && nvm alias default v${NODE_VERSION}
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ENV PATH="/root/.nvm/versions/node/v${NODE_VERSION}/bin/:${PATH}"
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RUN node --version
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RUN npm --version
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# Install vega-cli for exporting
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RUN apt-get install -y build-essential libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev g++
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RUN apt-get install -y zlibc zlib1g-dev zlib1g
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RUN npm install -g node-gyp
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RUN npm install -g --unsafe-perm canvas
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RUN npm install -g --unsafe-perm vega vega-lite vega-cli
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# Pandoc for fun and profit
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RUN apt-get -y install pandoc
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# Everything after this will get rerun even if the commands haven't changed, since data could change
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WORKDIR /app
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COPY . .
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# Make sure deps are pre-installed
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RUN pip3 install -r requirements.txt
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RUN clojure -e "(clojure.core/println :deps-downloaded)"
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# Build a uberjar target for clojupyter kernel
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RUN clojure -Spom
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RUN clojure -A:depstar -m hf.depstar.uberjar clojupyter-standalone.jar -C -m polis.main
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RUN clojure -m clojupyter.cmdline install --ident polis-clojupyter-kernel --jarfile clojupyter-standalone.jar
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# Systems go
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CMD bin/run.sh
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‎Makefile

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# Makefile adapted from
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# from https://tech.davis-hansson.com/p/make/
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# Use bash as the shell
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SHELL := bash
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# Exit on any shell error
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.SHELLFLAGS := -eu -o pipefail -c
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# Delete target file if script fails
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.DELETE_ON_ERROR:
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# Warn when a Make variable is not defined
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MAKEFLAGS += --warn-undefined-variables
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# Do not use standard rules for C builds
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MAKEFLAGS += --no-builtin-rules
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# No default target
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.PHONY: all
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all:
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# Working tree state:
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ALLOW_DIRTY=false
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.PHONY: dirty
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dirty:
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$(eval ALLOW_DIRTY=true)
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@echo "WARNING: Deploys will be allowed from a dirty working tree."
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# Make sure there aren't uncommitted changes
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.PHONY: check-clean-tree
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check-clean-tree:
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@if [[ "$(ALLOW_DIRTY)" != "true" && -n "$$(git status --porcelain)" ]]; then \
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echo "ERROR: Working directory not clean."; \
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exit 97; \
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fi
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.PHONY: build
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build:
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docker build . -f Dockerfile -t polis-analysis-docker
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.PHONY: clean
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clean:
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ifeq ($(strip $(shell docker ps -aq)),)
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echo "No running processes"
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else
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docker rm -fv $(shell docker ps -aq)
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endif
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nrepl_port ?=3850
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oz_port ?=3860
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jupyter_port ?=3870
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.PHONY: run
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run: clean
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docker run -p $(nrepl_port):3850 -p $(oz_port):3860 -p $(jupyter_port):3870 -v ${PWD}:/app -e CHOKIDAR_USEPOLLING=true polis-analysis-docker
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‎README.md

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## Setup
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First install Docker, however you'd like to do that for your system.
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For Ubuntu-like Linux,
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```
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sudo apt-get install docker.io
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sudo systemctl start docker
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sudo systemctl enable docker
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```
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See https://phoenixnap.com/kb/how-to-install-docker-on-ubuntu-18-04
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If you don't want to have to run Docker with sudo, see:
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```
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https://docs.docker.com/engine/install/linux-postinstall/
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```
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The rest of these instructions assume this has been run.
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## Building docker image
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Clone the code, cd in, then
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```
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make build
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```
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## Running docker image
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Once you've built the image (see above), you can run
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```
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make run
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```
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‎bin/run.sh

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jupyter notebook --allow-root --ip 0.0.0.0 --port=3870 &
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clojure -R:nREPL -m nrepl.cmdline --middleware "[cider.nrepl/cider-middleware]" --port 3850
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#jupyter notebook --port=3870 &
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#P1=$!
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#clojure -R:nREPL -m nrepl.cmdline --middleware "[cider.nrepl/cider-middleware]" --port 3850 &
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#P2=$!
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#wait $P1 $P2
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#(trap 'kill 0' SIGINT; clojure -R:nREPL -m nrepl.cmdline --middleware "[cider.nrepl/cider-middleware]" &\
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#jupyter notebook --port=8890)
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‎data/biodiversity/comments.csv

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version https://git-lfs.github.com/spec/v1
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oid sha256:de84b8c9d9b4b70d4929ee0603aa242ba60f53cc456dbf03a62719f1abc16165
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size 52444

‎data/biodiversity/participants-votes.csv

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version https://git-lfs.github.com/spec/v1
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oid sha256:58aaff458ef8dc5679e683e990c8aab3c56bcca82a7929b06b1559d4a04f29e0
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size 213160

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