From 16976f9220906cb385f5b51f13fcd0b35c6e7035 Mon Sep 17 00:00:00 2001
From: Jeremy Fee <jmfee@usgs.gov>
Date: Mon, 1 Feb 2021 14:01:55 -0700
Subject: [PATCH] Change how docker python dependencies are installed (into
system environment)
---
Dockerfile | 26 ++++++++++++--------------
Pipfile | 1 +
Pipfile.lock | 10 +++++++++-
docker-entrypoint.sh | 6 ++----
docs/install_docker.md | 5 -----
5 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index d78f30c1c..17ee426a6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,24 +13,22 @@ ENV GIT_BRANCH_NAME=${GIT_BRANCH_NAME} \
WEBSERVICE=${WEBSERVICE}
-RUN useradd \
- -c 'Docker image user' \
- -m \
- -r \
- -s /sbin/nologin \
- geomag_user \
- && mkdir -p /data \
- && chown -R geomag_user:geomag_user /data
+# install packages into system python, when Pipfile changes
+COPY Pipfile Pipfile.lock /geomag-algorithms/
+RUN cd /geomag-algorithms \
+ && pipenv install --dev --pre --system
-USER geomag_user
+# install rest of library as editable
+COPY . /geomag-algorithms
+RUN cd /geomag-algorithms \
+ && pip install -e . \
+ # add data directory owned by usgs-user
+ && mkdir -p /data \
+ && chown -R usgs-user:usgs-user /data
-# install dependencies via pipenv
+USER usgs-user
WORKDIR /data
-COPY Pipfile /data/
-RUN pipenv --site-packages install --dev --skip-lock
-# copy library (ignores set in .dockerignore)
-COPY . /geomag-algorithms
# entrypoint needs double quotes
ENTRYPOINT [ "/geomag-algorithms/docker-entrypoint.sh" ]
diff --git a/Pipfile b/Pipfile
index 074a95e9e..c3750f0e9 100644
--- a/Pipfile
+++ b/Pipfile
@@ -29,6 +29,7 @@ openpyxl = "*"
pydantic = "*"
sqlalchemy = "*"
sqlalchemy-utc = "*"
+typer = "*"
typing = "*"
typing-extensions = "*"
uvicorn = {extras=["standard"], version="*"}
diff --git a/Pipfile.lock b/Pipfile.lock
index ecc8b256a..365431ebc 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
- "sha256": "b6b3f6007a0217e08bc3edc72ea081fac5139bbe48974af84faac7d7993b2ef5"
+ "sha256": "65a11d9d155cdecca0ed4d14ceead8df52ac6adff775f439b151f6ff7a1063ee"
},
"pipfile-spec": 6,
"requires": {},
@@ -727,6 +727,14 @@
"markers": "python_version >= '3.6'",
"version": "==0.13.6"
},
+ "typer": {
+ "hashes": [
+ "sha256:5455d750122cff96745b0dec87368f56d023725a7ebc9d2e54dd23dc86816303",
+ "sha256:ba58b920ce851b12a2d790143009fa00ac1d05b3ff3257061ff69dbdfc3d161b"
+ ],
+ "index": "pypi",
+ "version": "==0.3.2"
+ },
"typing": {
"hashes": [
"sha256:1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9",
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 665e82ecd..7c05ad6ed 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -1,18 +1,16 @@
#! /bin/bash
+
# Environment variable to determine whether to start webservice
export WEBSERVICE=${WEBSERVICE:-false}
-# add geomagio to notebook path
-export PYTHONPATH=/geomag-algorithms
-
if [ "${WEBSERVICE}" = "false" ]; then
# run arguments as command, or bash prompt if no arguments
exec "${@:-/bin/bash}"
else
# run gunicorn server for web service
- exec pipenv run gunicorn \
+ exec gunicorn \
--access-logfile - \
--bind 0.0.0.0:8000 \
--threads 2 \
diff --git a/docs/install_docker.md b/docs/install_docker.md
index 02beede91..f87b9193f 100644
--- a/docs/install_docker.md
+++ b/docs/install_docker.md
@@ -25,13 +25,8 @@ The following command creates and starts a container in the background.
- Run an interactive python prompt
-
docker exec -it geomagio python
-- Use the Jupyter Notebook server
-
- Check the output for a URL like this, that can be opened in a web browser: `http://127.0.0.1:8000/?token=...`
-
- Use the `geomag.py` command line interface
docker exec -it geomagio geomag.py \
--
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