From c53917ca054a33f7e59d2836d434bf543dc315af Mon Sep 17 00:00:00 2001
From: Kohulan <kohulan.rajan@uni-jena.de>
Date: Mon, 13 Mar 2023 20:24:02 +0100
Subject: [PATCH] fix: Docker dependencies

---
 Dockerfile       | 29 ++++++++++-------------------
 requirements.txt | 17 +++++++++--------
 2 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 6fd80d9..d632073 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,21 +1,10 @@
-FROM debian:buster-slim AS nmrxiv-python-ms
+FROM debian:buster-20230227-slim AS cheminf-python-ms
 
 # Install runtime dependencies
 RUN apt-get update \
- && apt-get install -yq --no-install-recommends \
-    libboost-atomic1.67.0 \
-    libboost-chrono1.67.0 \
-    libboost-date-time1.67.0 \
-    libboost-iostreams1.67.0 \
-    libboost-python1.67.0 \
-    libboost-regex1.67.0 \
-    libboost-serialization1.67.0 \
-    libboost-system1.67.0 \
-    libboost-thread1.67.0 \
-    libcairo2-dev \
-    python3-dev \
-    python3-numpy \
-    python3-cairo \
+ && apt-get upgrade -y \
+ && apt-get install -y --no-install-recommends \
+    python3 \
     python3-pip \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
@@ -24,17 +13,19 @@ RUN apt-get update && \
     apt-get install -y software-properties-common && \
     apt-get update -y && \
     apt-get install -y openjdk-11-jre
-    
+
+RUN python3 -m pip install -U pip
+
 ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
 RUN export JAVA_HOME
 
 WORKDIR /code
 
-RUN python3 -m pip install -U pip 
-
 COPY ./requirements.txt /code/requirements.txt
 RUN pip3 install --upgrade setuptools pip
-RUN pip3 install --no-cache-dir --upgrade -r /code/requirements.txt
+RUN pip3 install --no-cache-dir -r /code/requirements.txt
+RUN python3 -m pip uninstall -y imantics
+RUN pip3 install imantics==0.1.12
 RUN pip3 install --no-deps decimer-segmentation
 RUN pip3 install --no-deps decimer>=2.2.0
 RUN pip3 install --no-deps STOUT-pypi>=2.0.5
diff --git a/requirements.txt b/requirements.txt
index df11670..b81c436 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,14 +5,15 @@ psycopg2>=2.7,<2.8
 fastapi-pagination==0.10.0
 rdkit-pypi>=2022.09.4
 websockets==10.4
-pillow
-opencv-python
-matplotlib
+pillow==9.4.0
+opencv-python==4.7.0.68
+jpype1==1.4.1
+matplotlib==3.4.3
 scikit-image
-imantics
-pdf2image
+pdf2image==1.16.2
 IPython
-pystow
-unicodedata2
+pystow>=0.4.9
+unicodedata2==15.0.0
 efficientnet
-tensorflow==2.10.0
\ No newline at end of file
+tensorflow==2.10.0
+pyheif==0.7.1
\ No newline at end of file