From 7046db9044573602e8d235af79b32ebc2099df6c Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Tue, 5 Sep 2023 11:17:35 +0100
Subject: [PATCH 1/2] Revert #66 build libvips twice

---
 Dockerfile | 57 ++----------------------------------------------------
 1 file changed, 2 insertions(+), 55 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 546afc0..4dbfb67 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,61 +5,7 @@ RUN apt-get update
 RUN apt-get -q update --fix-missing
 RUN apt-get -q install -y python3-pip openslide-tools python3-openslide vim openssl
 RUN apt-get -q install -y openssl libcurl4-openssl-dev libssl-dev
-
-### Install libvips
-
-# Tony has a future use case where we may adapt caMic to GIS visualization
-# install libvips-dev for pyvips. No need for libvips.
-RUN apt-get -q install -y libvips-dev
-
-# But, build libvips instead of using libvips-dev from apt
-# Build without OpenSlide to open images with rather ImageMagick to handle
-# images without pyramids. Otherwise opens e.g. DICOM with OpenSlide so conversion
-# of files OpenSlide cannot open does not help at all.
-# So, we'll have two copies on openslide on the system.
-# By changing LD_LIBRARY_PATH before we launch python
-# we can choose which openslide to run
-# TODO: use libjpeg-turbo8-dev instead of libjpeg-dev if current apt repo has it; for performance
-RUN apt-get -q install -y meson libjpeg-turbo8-dev libexif-dev libgsf-1-dev libtiff-dev libfftw3-dev liblcms2-dev libpng-dev libmagickcore-dev libmagickwand-dev liborc-0.4-dev libopenjp2-7 libgirepository1.0-dev
-WORKDIR /root/src
-RUN git clone https://github.com/libvips/libvips.git --depth=1 --branch=8.14
-RUN mkdir /root/src/libvips/build
-WORKDIR /root/src/libvips
-RUN mkdir /usr/local/vips-no-openslide/
-# normally --prefix=/usr/local/ --libdir=lib build
-RUN meson setup -Dopenslide=disabled --buildtype=release --prefix=/usr/local/vips-no-openslide/ --libdir=lib build
-RUN meson compile -C build
-RUN meson test -C build
-RUN meson install -C build
-
-RUN pip install pyvips --break-system-packages
-
-# verify pyvips can call libvips
-RUN python3 -c "import pyvips"
-
-# verify that the apt libvips has openslide
-ADD test_imgs/CMU-1-Small-Region.svs .
-RUN python3 -c "import pyvips; pyvips.Image.openslideload(('CMU-1-Small-Region.svs'))"
-
-# back up previous ld_library_path
-ENV LD_LIBRARY_PATH_ORIG="${LD_LIBRARY_PATH}"
-
-# now, prioritize openslideless libvips
-# the path shown in output lines of "meson install" where .so.42 are installed
-# normally /usr/local/lib/:
-ENV LD_LIBRARY_PATH="/usr/local/vips-no-openslide/lib/:${LD_LIBRARY_PATH}"
-
-# verify that this libvips has no openslide
-RUN ! python3 -c "import pyvips; pyvips.Image.openslideload(('CMU-1-Small-Region.svs'))"
-
-# ok, so to recap,
-# there are two libvips are installed and which one pyvips connects to
-# is chosen when "import pyvips" is run.
-# at this point in this dockerfile,
-# ld_library_path is set so that no-openslide version is run
-# but if you do LD_LIBRARY_PATH="${LD_LIBRARY_PATH_ORIG}" python a.py
-# or likewise using docker ENV command or os.environ in python before
-# importing, this will remove the no-openslide libvips from path.
+RUN apt-get -q install -y libvips libvips-dev
 
 ### Install BioFormats wrapper
 
@@ -70,6 +16,7 @@ RUN python3 compile_bfbridge.py
 
 WORKDIR /root/src/
 
+RUN pip install pyvips --break-system-packages
 RUN pip install flask --break-system-packages
 RUN pip install gunicorn --break-system-packages
 RUN pip install greenlet --break-system-packages

From daaf690172516327c56ae2462e75e1f00fed394d Mon Sep 17 00:00:00 2001
From: CGDogan <126820728+CGDogan@users.noreply.github.com>
Date: Tue, 5 Sep 2023 17:31:45 +0100
Subject: [PATCH 2/2] fix build

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index 4dbfb67..550ce32 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,6 +10,7 @@ RUN apt-get -q install -y libvips libvips-dev
 ### Install BioFormats wrapper
 
 WORKDIR /root/src/BFBridge/python
+RUN pip install -r requirements.txt --break-system-packages
 RUN python3 compile_bfbridge.py
 
 ### Set up the server