From 0f0b2876a9aed86cbb96c5363ab166f4c6162e23 Mon Sep 17 00:00:00 2001
From: Andy Shapiro <shapiro.andy@epa.gov>
Date: Thu, 22 Aug 2024 10:18:49 -0400
Subject: [PATCH] switch to centos and update to python3.12 (#61)

* swtich to centos and update to python3.12

* add build notes and compose file for building

* commit content added for testing (remove in next commit)

* Revert "commit content added for testing (remove in next commit)"

This reverts commit a30febb7e3fcb9ba7310843394cab5e49ac18706.

* cleanup
---
 README.md              | 11 +++++++--
 compose/app/Dockerfile | 53 ++++++++++++++++++------------------------
 compose/app/test.py    |  9 -------
 compose/build.yml      | 25 ++++++++++++++++++++
 4 files changed, 56 insertions(+), 42 deletions(-)
 delete mode 100644 compose/app/test.py
 create mode 100644 compose/build.yml

diff --git a/README.md b/README.md
index 0f94bef1..16f2a597 100644
--- a/README.md
+++ b/README.md
@@ -5,14 +5,12 @@ BMDS UI is a user interface for running [pybmds](https://pypi.org/project/pybmds
 * It can deployed as a web application, such as [BMDS Online](https://bmdsonline.epa.gov)
 * It can be deployed locally as a desktop application, which we call **BMDS Desktop**.
 
-
 **BMDS Desktop application home screen:**
 ![](./docs/img/bmds-desktop.jpg)
 
 **An example of the the user interface for model results:**
 ![](./docs/img/bmds-output.jpg)
 
-
 ## BMDS Online vs. BMDS Desktop
 
 BMDS Desktop is designed to run locally on your desktop computer in fully offline mode; it does not interact with any resources on the internet after initial installation. BMDS Online can be deployed online publicly or internally at a company or organization. Key differences between the software are described below:
@@ -29,3 +27,12 @@ Database technology|Uses a sqlite database file (single file)|Uses a PostgreSQL
 
 The BMDS Desktop has a startup screen where you can select which database file you'd like to use in your application. You can have multiple databases on your computer, one per project for example:
 ![](./docs/img/desktop-startup.jpg)
+
+## Build Notes
+
+To build containers for deployment:
+
+```bash
+make build
+docker compose -f compose/build.yml --project-directory . build
+```
diff --git a/compose/app/Dockerfile b/compose/app/Dockerfile
index 13faa994..985a0f54 100644
--- a/compose/app/Dockerfile
+++ b/compose/app/Dockerfile
@@ -1,48 +1,39 @@
-FROM python:3.11-slim-bullseye
+FROM quay.io/centos/centos:stream9-minimal
 
-ENV BMDS_UI_VERSION=24.1a4
-ENV BMDS_VERSION=24.1a4
-ENV EXTRA_BMDS_BUILD_ARGS=
+ENV PYTHON_VERSION=3.12 \
+    PYTHONBUFFERED=1 \
+    PYTHONIOENCODING=UTF-8 \
+    PYTHONFAULTHANDLER=1 \
+    PIP_NO_CACHE=off \
+    LANG=C.UTF-8
 
 RUN groupadd -g 555 -r app && \
-    useradd -u 555 -r -g app app
-
-# dependencies wait-for: netcat
-# dependencies bmds: libgslcblas0 libgsl-dev
-RUN apt-get update -y && \
-    apt-get install -y netcat libgslcblas0 libgsl-dev
+    useradd -u 555 -r -g app app && \
+    \
+    INSTALL_PKGS="python${PYTHON_VERSION} nc" && \
+    VERIFY_PKGS="python${PYTHON_VERSION}" && \
+    microdnf -y --setopt=tsflags=nodocs install $INSTALL_PKGS && \
+    rpm -V $VERIFY_PKGS && \
+    microdnf -y clean all --enablerepo='*' && \
+    ln -s /usr/bin/"python${PYTHON_VERSION}" /usr/local/bin/python
 
 COPY ./compose/app/wait-for.sh /app/bin/wait-for.sh
 COPY ./compose/app/sync.sh /app/bin/sync.sh
 COPY ./compose/app/web.sh /app/bin/web.sh
 COPY ./compose/app/workers.sh /app/bin/workers.sh
 COPY ./compose/app/cron.sh /app/bin/cron.sh
-COPY ./compose/app/test.py /app/test.py
-
-# used in some dev/staging environments
 COPY ./tests/data/db.yaml /app/test-db-fixture.yaml
-
-# 1) install start-scripts
-# 2) install fonts
-# 3) create logs path
-RUN mkdir -p /app/logs && \
-    mkdir -p /app/public/media
-
 COPY ./dist /dist
 
-RUN pip install -U pip && \
-    pip install "${EXTRA_BMDS_BUILD_ARGS} pybmds==${BMDS_VERSION}" --no-cache-dir && \
-    pip install "dist/bmds_ui-${BMDS_UI_VERSION}-py3-none-any.whl[pg,prod]" --no-cache-dir && \
+RUN python -m ensurepip --upgrade && \
+    python -m pip install -U pip && \
+    \
+    for file in dist/bmds_ui-*.whl; do python -m pip install "$file[pg,prod]" --no-cache-dir ; done && \
     \
     rm -rf /dist && \
-    pip uninstall -y pip
+    python -m pip uninstall -y pip && \
+    \
+    chown -R app:app /app
 
 WORKDIR /app
-
-RUN chown -R app:app /app
 USER app
-
-ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-
-RUN ldd /usr/local/lib/python3.11/site-packages/pybmds/bmdscore.cpython-*-x86_64-linux-gnu.so && \
-    python /app/test.py
diff --git a/compose/app/test.py b/compose/app/test.py
deleted file mode 100644
index ddfe49c8..00000000
--- a/compose/app/test.py
+++ /dev/null
@@ -1,9 +0,0 @@
-import pybmds
-from pybmds.models.dichotomous import Logistic
-
-dataset = pybmds.DichotomousDataset(
-    doses=[0, 50, 100, 150, 200], ns=[100, 100, 100, 100, 100], incidences=[0, 5, 30, 65, 90]
-)
-model = Logistic(dataset=dataset)
-result = model.execute()
-print(result.model_dump())  # noqa: T201
diff --git a/compose/build.yml b/compose/build.yml
new file mode 100644
index 00000000..13c71d48
--- /dev/null
+++ b/compose/build.yml
@@ -0,0 +1,25 @@
+version: '3'
+
+services:
+
+  postgres:
+    build: ./compose/postgres
+    platform: linux/x86_64
+    ports:
+      - "0.0.0.0:5432:5432"
+
+  redis:
+    build: ./compose/redis
+    platform: linux/x86_64
+    ports:
+      - "0.0.0.0:6379:6379"
+
+  app:
+    build:
+      context: .
+      dockerfile: ./compose/app/Dockerfile
+    platform: linux/x86_64
+
+  nginx:
+    build: ./compose/nginx
+    platform: linux/x86_64