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Hotfix version python in dockerfile #254

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Mar 20, 2024
Merged

Hotfix version python in dockerfile #254

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b9850fd
macapype_env 0.2 and 0.2-spm
davidmeunier79 Mar 20, 2024
1c9c26d
python and pip are already configured and shortcuted in macapype _env
davidmeunier79 Mar 20, 2024
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14 changes: 4 additions & 10 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
#
# Timestamp: 2020/12/02 18:33:44 UTC

FROM macatools/macapype_env:v0.1.2-spm
FROM macatools/macapype_env:v0.2-spm

USER root

Expand All @@ -18,17 +18,16 @@ ARG DEBIAN_FRONTEND="noninteractive"
MAINTAINER David Meunier "david.meunier@univ-amu.fr"
######################## Python packages

RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz

RUN apt-get install -y python3-pil python3-pil.imagetk


RUN python3 -m pip install -U pip
RUN python3 -m pip install -U pillow
RUN python -m pip install -U pillow
#RUN pip3 install pillow

#RUN apt-get install libx11-6 libxext6 libxt6 # matlab
RUN pip3 install xvfbwrapper \
RUN pip install xvfbwrapper \
psutil \
numpy \
scipy \
Expand Down Expand Up @@ -57,11 +56,6 @@ RUN pip3 install xvfbwrapper \

############################################# install macapype

RUN echo $(which python) && \
echo $(which python3) && \
ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip

RUN pip install --pre macapype && python -c "import macapype; print(macapype.__version__)"

################################################## Finishing
Expand Down
50 changes: 39 additions & 11 deletions Dockerfile_macapype_env
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Expand Up @@ -132,7 +132,6 @@ RUN apt-get install -y -q --no-install-recommends \
tcsh \
xfonts-base \
xvfb

RUN curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb
RUN dpkg -i /tmp/toinstall.deb
RUN rm /tmp/toinstall.deb
Expand Down Expand Up @@ -163,6 +162,45 @@ RUN echo "Downloading ANTs ..." \
&& curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
| tar -xz -C /opt/ants-2.3.1 --strip-components 1

######################## NiftiReg
RUN apt-get install --yes --no-install-recommends \
ca-certificates cmake gcc g++ git make \
&& git clone https://github.com/KCL-BMEIS/niftyreg.git /tmp/niftyreg-src \
&& mkdir /tmp/niftyreg-build \
&& cd /tmp/niftyreg-build \
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/niftyreg /tmp/niftyreg-src \
&& make \
&& make install
ENV PATH=/opt/niftyreg/bin:$PATH


####################### new: python 3.10

RUN wget https://www.python.org/ftp/python/3.10.8/Python-3.10.8.tgz
RUN tar xzf Python-3.10.8.tgz
#RUN cd Python-3.10.8
#RUN echo $(pwd)
RUN Python-3.10.8/configure --enable-optimizations
#RUN Python-3.10.8/make altinstall
RUN apt-get install zlib1g-dev
RUN make altinstall

RUN echo $(which python3.10)

RUN echo $(python3.10 -V )

RUN echo $(which pip3.10)
RUN echo $(pip3.10 -V )

RUN echo $(which python) && \
echo $(which python3.10) && \
ln -s /usr/local/bin/python3.10 /usr/bin/python && \
ln -s /usr/local/bin/pip3.10 /usr/bin/pip

RUN echo $(which python)
RUN echo $(which pip)


################################################## Install SPM12 as MCR
RUN apt-get -y install unzip xorg wget

Expand Down Expand Up @@ -193,16 +231,6 @@ RUN wget --no-check-certificate --progress=bar:force -P /opt https://www.fil.ion
&& chmod +x /opt/spm${SPM_VERSION}/spm${SPM_VERSION}
ENV SPM_DIR /opt/spm${SPM_VERSION}

######################## NiftiReg
RUN apt-get install --yes --no-install-recommends \
ca-certificates cmake gcc g++ git make \
&& git clone https://github.com/KCL-BMEIS/niftyreg.git /tmp/niftyreg-src \
&& mkdir /tmp/niftyreg-build \
&& cd /tmp/niftyreg-build \
&& cmake -DCMAKE_INSTALL_PREFIX=/opt/niftyreg /tmp/niftyreg-src \
&& make \
&& make install
ENV PATH=/opt/niftyreg/bin:$PATH

################################################## Finishing
RUN apt-get clean \
Expand Down
29 changes: 29 additions & 0 deletions Dockerfile_macapype_env_nomcr
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Expand Up @@ -173,6 +173,35 @@ RUN apt-get install --yes --no-install-recommends \
&& make install
ENV PATH=/opt/niftyreg/bin:$PATH


####################### new: python 3.10

RUN wget https://www.python.org/ftp/python/3.10.8/Python-3.10.8.tgz
RUN tar xzf Python-3.10.8.tgz
#RUN cd Python-3.10.8
#RUN echo $(pwd)
RUN Python-3.10.8/configure --enable-optimizations
#RUN Python-3.10.8/make altinstall
RUN apt-get install zlib1g-dev
RUN make altinstall

RUN echo $(which python3.10)

RUN echo $(python3.10 -V )

RUN echo $(which pip3.10)
RUN echo $(pip3.10 -V )

RUN echo $(which python) && \
echo $(which python3.10) && \
ln -s /usr/local/bin/python3.10 /usr/bin/python && \
ln -s /usr/local/bin/pip3.10 /usr/bin/pip

RUN echo $(which python)
RUN echo $(which pip)



################################################## Finishing
RUN apt-get clean \
&& rm -rf /var/lib/apt/lists/*
Expand Down
14 changes: 4 additions & 10 deletions Dockerfile_nomcr
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
#
# Timestamp: 2020/12/02 18:33:44 UTC

FROM macatools/macapype_env:v0.1.2
FROM macatools/macapype_env:v0.2

USER root

Expand All @@ -18,17 +18,16 @@ ARG DEBIAN_FRONTEND="noninteractive"
MAINTAINER David Meunier "david.meunier@univ-amu.fr"
######################## Python packages

RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz

RUN apt-get install -y python3-pil python3-pil.imagetk


RUN python3 -m pip install -U pip
RUN python3 -m pip install -U pillow
RUN python -m pip install -U pillow
#RUN pip3 install pillow

#RUN apt-get install libx11-6 libxext6 libxt6 # matlab
RUN pip3 install xvfbwrapper \
RUN pip install xvfbwrapper \
psutil \
numpy \
scipy \
Expand Down Expand Up @@ -57,11 +56,6 @@ RUN pip3 install xvfbwrapper \

############################################# install macapype

RUN echo $(which python) && \
echo $(which python3) && \
ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip

RUN pip install --pre macapype && python -c "import macapype; print(macapype.__version__)"

################################################## Finishing
Expand Down
15 changes: 4 additions & 11 deletions Dockerfile_testpypi
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Original file line number Diff line number Diff line change
Expand Up @@ -17,17 +17,16 @@ ARG DEBIAN_FRONTEND="noninteractive"
MAINTAINER David Meunier "david.meunier@univ-amu.fr"
######################## Python packages

RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz

RUN apt-get install -y python3-pil python3-pil.imagetk


RUN python3 -m pip install -U pip
RUN python3 -m pip install -U pillow
#RUN pip3 install pillow
RUN python -m pip install -U pillow
#RUN pip install pillow

#RUN apt-get install libx11-6 libxext6 libxt6 # matlab
RUN pip3 install xvfbwrapper \
RUN pip install xvfbwrapper \
psutil \
numpy \
scipy \
Expand Down Expand Up @@ -55,12 +54,6 @@ RUN pip3 install xvfbwrapper \
brain-slam

############################################# install macapype

RUN echo $(which python) && \
echo $(which python3) && \
ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip

RUN pip install --no-deps --index-url https://test.pypi.org/simple/ --pre macapype && python -c "import macapype; print(macapype.__version__)"

################################################## Finishing
Expand Down
15 changes: 4 additions & 11 deletions Dockerfile_testpypi_nomcr
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
#
# Timestamp: 2020/12/02 18:33:44 UTC

FROM macatools/macapype_env:v0.1.2
FROM macatools/macapype_env:v0.2

USER root

Expand All @@ -18,17 +18,15 @@ ARG DEBIAN_FRONTEND="noninteractive"
MAINTAINER David Meunier "david.meunier@univ-amu.fr"
######################## Python packages

RUN apt-get update && apt-get install -y git python3-pip libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz
RUN apt-get update && apt-get install -y git libpng-dev libfreetype6-dev libxft-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libxml2-dev libxslt1-dev wget graphviz

RUN apt-get install -y python3-pil python3-pil.imagetk


RUN python3 -m pip install -U pip
RUN python3 -m pip install -U pillow
RUN python -m pip install -U pillow
#RUN pip3 install pillow

#RUN apt-get install libx11-6 libxext6 libxt6 # matlab
RUN pip3 install xvfbwrapper \
RUN pip install xvfbwrapper \
psutil \
numpy \
scipy \
Expand Down Expand Up @@ -57,11 +55,6 @@ RUN pip3 install xvfbwrapper \

############################################# install macapype

RUN echo $(which python) && \
echo $(which python3) && \
ln -s /usr/bin/python3 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip

RUN pip install --no-deps --index-url https://test.pypi.org/simple/ --pre macapype && python -c "import macapype; print(macapype.__version__)"

################################################## Finishing
Expand Down
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