- Requirements now in a file rather than inline

  (matches the way sygnature requirements are added)

Author: Alan Christie

Dockerfile-obabel

@@ -9,9 +9,15 @@ USER root
 
 # Copy the obabel pipeline implementation into the image
 COPY src/python /opt/python-obabel
-RUN apt-get update && apt-get install -y --no-install-recommends python-setuptools gzip python-pip && pip install -e /opt/python-obabel
-# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
-RUN pip install im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        python-setuptools \
+        gzip \
+        python-pip && \
+    pip install -e /opt/python-obabel
+# And the project pip requirements
+COPY requirements-obabel.txt /root/
+RUN pip install -r /root/requirements-obabel.txt
 
 # The CMD is simply to run 'execute' in the WORKDIR.
 # The user would normally mount a volume with their own execute

Dockerfile-rdkit

@@ -8,10 +8,11 @@ RUN apt-get -y update && apt-get -y install zip unzip procps
 
 # Copy the pipeline implementation into the image
 COPY src/python /opt/python
+COPY requirements-rdkit.txt /root/
 RUN pip install -e /opt/python
-# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
-RUN pip install molvs standardiser matplotlib \
-        im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7
+# And the pip packages from the project requirements
+# NOTE: matplotlib is missing
+RUN pip install -r /root/requirements-rdkit.txt
 
 # The CMD is simply to run 'execute' in the WORKDIR.
 # The user would normally mount a volume with their own execute

Dockerfile-rdkit-centos

@@ -8,10 +8,11 @@ RUN yum -y update && yum -y install zip unzip python-devel python2-pip python-se
 
 # Copy the pipeline implementation into the image
 COPY src/python /opt/python
+COPY requirements-rdkit.txt /root/
 RUN pip install -e /opt/python
-# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
+# And the pip packages from the project requirements
 # NOTE: matplotlib is missing
-RUN pip install molvs standardiser im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7
+RUN pip install -r /root/requirements-rdkit.txt
 
 # The CMD is simply to run 'execute' in the WORKDIR.
 # The user would normally mount a volume with their own execute

requirements-obabel.txt

@@ -0,0 +1,2 @@
+im-pipelines-utils==2.4.*
+im-pipelines-utils-rdkit==1.5.*

requirements.txt renamed to requirements-rdkit.txt

@@ -1,7 +1,5 @@
 im-pipelines-utils==2.4.*
 im-pipelines-utils-rdkit==1.5.*
 matplotlib==2.2.*
-scipy==1.1.*
-numpy==1.14.*
-scikit-learn==0.19.*
-pandas==0.23.*
+molvs==0.1.1
+standardiser==0.1.9