fix(depds): Move from ngboost to ngboost-release (#171)

Author: xmnlab

.github/workflows/build.yml

@@ -53,7 +53,7 @@ jobs:
       run: |
         make docker-compose-build
         make docker-compose-start
-        sleep 30
+        make docker-compose-wait SERVICE=postgres
 
     - name: Run tests
       run: make test ARGS="--disable-warnings"

Makefile

@@ -1,12 +1,16 @@
 #* Variables
 SHELL:=/usr/bin/env bash
 ARGS:=
+CONSOLE:=bash
 
 #* Docker variables
 DOCKER=docker-compose --file docker/compose.yaml --env-file docker/.env
 DOCKER_IMAGE:=epigraphhub_py
 DOCKER_VERSION:=latest
 DOCKER_SERVICES:=
+DOCKER_SERVICE:=
+TIMEOUT:=90
+
 
 #* Formatters
 .PHONY: linter
@@ -56,6 +60,11 @@ docker-compose-build:
 docker-compose-start:
 	$(DOCKER) up -d ${DOCKER_SERVICES}
 
+.PHONY: docker-compose-run-console
+docker-compose-run-console:
+	$(DOCKER) run ${DOCKER_SERVICE} ${CONSOLE}
+
+
 .PHONY: docker-compose-start-no-detatched
 docker-compose-start-no-detatched:  # useful for debugging
 	$(DOCKER) up ${DOCKER_SERVICES}
@@ -75,6 +84,10 @@ docker-compose-logs:
 .PHONY: docker-compose-restart
 docker-compose-restart: docker-compose-stop docker-compose-stop
 
+.PHONY: docker-compose-wait
+docker-compose-wait:
+	timeout ${TIMEOUT} ./docker/healthcheck.sh ${SERVICE}
+
 
 #* Config
 .PHONY:

docker/healthcheck.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# shellcheck disable=all
+
+PROJECT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd ../ && pwd )"
+
+if [ -f ${PROJECT_DIR}/.env ]; then
+    # Load Environment Variables
+    export $(cat ${PROJECT_DIR}/.env | grep -v '#' | sed 's/\r$//' | awk '/=/ {print $1}' )
+fi
+
+export CONTAINER_NAME=${1:-"superset"}
+export CONTAINER_NAME="docker_${CONTAINER_NAME}_1"
+
+echo "[II] Checking ${CONTAINER_NAME} ..."
+
+while [ "`docker inspect -f {{.State.Health.Status}} ${CONTAINER_NAME}`" != "healthy" ];
+do
+    echo "[II] Waiting for ${CONTAINER_NAME} ..."
+    sleep 5;
+done
+
+echo "[II] ${CONTAINER_NAME} is healthy."

docker/postgresql/Dockerfile

@@ -1,11 +1,27 @@
-FROM postgis/postgis:14-3.2
+# from https://github.com/postgis/docker-postgis/blob/969ef8a9e4a22e1556ca99cab4178f6e60c1483d/14-3.2/Dockerfile
+FROM postgres:14-bullseye
+
+LABEL maintainer="PostGIS Project - https://postgis.net"
+
+ENV POSTGIS_MAJOR 3
+
+RUN apt-get update \
+      && apt-cache showpkg postgresql-$PG_MAJOR-postgis-$POSTGIS_MAJOR \
+      && apt-get install -y --no-install-recommends \
+           postgresql-$PG_MAJOR-postgis-$POSTGIS_MAJOR \
+           postgresql-$PG_MAJOR-postgis-$POSTGIS_MAJOR-scripts \
+      && rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p /docker-entrypoint-initdb.d
+COPY ./docker/postgresql/initdb-postgis.sh /docker-entrypoint-initdb.d/10_postgis.sh
+COPY ./docker/postgresql/update-postgis.sh /usr/local/bin
+
 
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get -qq update --yes \
   && apt-get -qq install --yes --no-install-recommends \
   build-essential ca-certificates \
-  postgresql-14-plr \
-  postgresql-14-postgis-3-scripts \
-  postgresql-plpython3-14 \
+  postgresql-$PG_MAJOR-plr \
+  postgresql-plpython3-$PG_MAJOR \
   postgresql-contrib \
   && rm -rf /var/lib/apt/lists/*

docker/postgresql/initdb-postgis.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+# shellcheck disable=all
+
+# ref: https://github.com/postgis/docker-postgis/blob/a6a9f021e243c0b6f908cf8ad8d0ae5460dcb1b1/14-3.2/initdb-postgis.sh
+
+set -e
+
+# Perform all actions as $POSTGRES_USER
+export PGUSER="$POSTGRES_USER"
+
+# Create the 'template_postgis' template db
+"${psql[@]}" <<- 'EOSQL'
+CREATE DATABASE template_postgis IS_TEMPLATE true;
+EOSQL
+
+# Load PostGIS into both template_database and $POSTGRES_DB
+for DB in template_postgis "$POSTGRES_DB"; do
+	echo "Loading PostGIS extensions into $DB"
+	"${psql[@]}" --dbname="$DB" <<-'EOSQL'
+		CREATE EXTENSION IF NOT EXISTS postgis;
+		CREATE EXTENSION IF NOT EXISTS postgis_topology;
+		-- Reconnect to update pg_setting.resetval
+		-- See https://github.com/postgis/docker-postgis/issues/288
+		\c
+		CREATE EXTENSION IF NOT EXISTS fuzzystrmatch;
+		CREATE EXTENSION IF NOT EXISTS postgis_tiger_geocoder;
+EOSQL
+done

docker/postgresql/update-postgis.sh

@@ -0,0 +1,31 @@
+#!/bin/sh
+# shellcheck disable=all
+
+# ref: https://github.com/postgis/docker-postgis/blob/a6a9f021e243c0b6f908cf8ad8d0ae5460dcb1b1/14-3.2/update-postgis.sh
+
+set -e
+
+# Perform all actions as $POSTGRES_USER
+export PGUSER="$POSTGRES_USER"
+
+POSTGIS_VERSION="${POSTGIS_VERSION%%+*}"
+
+# Load PostGIS into both template_database and $POSTGRES_DB
+for DB in template_postgis "$POSTGRES_DB" "${@}"; do
+    echo "Updating PostGIS extensions '$DB' to $POSTGIS_VERSION"
+    psql --dbname="$DB" -c "
+        -- Upgrade PostGIS (includes raster)
+        CREATE EXTENSION IF NOT EXISTS postgis VERSION '$POSTGIS_VERSION';
+        ALTER EXTENSION postgis  UPDATE TO '$POSTGIS_VERSION';
+
+        -- Upgrade Topology
+        CREATE EXTENSION IF NOT EXISTS postgis_topology VERSION '$POSTGIS_VERSION';
+        ALTER EXTENSION postgis_topology UPDATE TO '$POSTGIS_VERSION';
+
+        -- Install Tiger dependencies in case not already installed
+        CREATE EXTENSION IF NOT EXISTS fuzzystrmatch;
+        -- Upgrade US Tiger Geocoder
+        CREATE EXTENSION IF NOT EXISTS postgis_tiger_geocoder VERSION '$POSTGIS_VERSION';
+        ALTER EXTENSION postgis_tiger_geocoder UPDATE TO '$POSTGIS_VERSION';
+    "
+done

poetry.lock

@@ -55,14 +55,14 @@ jupyter = "^1.0.0"
 joblib = "^1.1.0"
 tensorflow = "^2.5.0"
 scikit-learn = "^1.0.2"
-ngboost = {git = "https://github.com/stanfordmlgroup/ngboost", rev = "v0.3.12"}
 rioxarray = "^0.10.2"
 wget = "^3.2"
 requests = "^2.27.1"
 tabulate = "^0.8.9"
 click = "^8.1.0"
 wbgapi = "1.0.7"
 PyYAML = "^6.0"
+ngboost-release = "0.3.12-2"
 
 [tool.poetry.dev-dependencies]
 bandit = "^1.7.2"