Skip to content

Add support for Markdown in Sphinx-based documentation #16

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
samsrabin wants to merge 11 commits into
base: main
Choose a base branch
from
Draft

Add support for Markdown in Sphinx-based documentation #16

Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
aa78296
Use oraclelinux instead of centos.
samsrabin Oct 2, 2024
ca2f57c
Switch to oraclelinux 9.
samsrabin Oct 2, 2024
638e802
Explicitly request pip.
samsrabin Oct 2, 2024
ddfe1ce
Update repo for blas-devel and lapack-devel.
samsrabin Oct 2, 2024
08f226b
Resolve a gfortran error.
samsrabin Oct 2, 2024
ae71e60
Break up installation of HDF5, netCDF, and PnetCDF.
samsrabin Oct 2, 2024
a267984
Update netcdf package links.
samsrabin Oct 2, 2024
b455099
Failed attempt to resolve pnetcdf compiler error.
samsrabin Oct 2, 2024
c111b56
Update pnetcdf from 1.12.1 to 1.12.2.
samsrabin Oct 2, 2024
930606e
Replace CentOS references with OracleLinux.
samsrabin Oct 2, 2024
aa1c009
Add sphinx_mdinclude.
samsrabin Oct 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
42 changes: 23 additions & 19 deletions base/centos8/Dockerfile → base/oraclelinux9/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,10 @@
################################################################################################################
# escomp/base-centos8 Dockerfile #
# escomp/base-oraclelinux9e #
#--------------------------------------------------------------------------------------------------------------#
# A base CentOS8 install + MPI, HDF5, NetCDF and PNetCDF, as well as other core packages for escomp containers #
# A base OracleLinux9 install + MPI, HDF5, NetCDF and PNetCDF, plus other core packages for escomp containers #
################################################################################################################

# Use latest CentOS8:
FROM centos:8
FROM oraclelinux:9

# First, we upate the default packages and install some other necessary ones - while this may give
# some people updated versions of packages vs. others, these differences should not be numerically
Expand All @@ -14,15 +13,16 @@ FROM centos:8
RUN yum -y update && \
yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm && \
yum -y install vim emacs-nox git subversion which sudo csh make m4 cmake wget file byacc curl-devel zlib-devel && \
yum -y install perl-XML-LibXML gcc-gfortran gcc-c++ dnf-plugins-core python3 perl-core && \
yum -y install perl-XML-LibXML gcc-gfortran gcc-c++ dnf-plugins-core python3 pip perl-core && \
yum -y install ftp xmlstarlet diffutils && \
yum -y install git-lfs latexmk texlive-amscls texlive-anyfontsize texlive-cmap texlive-fancyhdr texlive-fncychap \
texlive-dvisvgm texlive-metafont texlive-ec texlive-titlesec texlive-babel-english texlive-tabulary \
texlive-framed texlive-wrapfig texlive-parskip texlive-upquote texlive-capt-of texlive-needspace \
texlive-times texlive-makeindex texlive-helvetic texlive-courier texlive-gsftopk texlive-dvips texlive-mfware texlive-dvisvgm && \
pip3 install rst2pdf sphinx sphinxcontrib-programoutput && \
pip3 install git+https://github.com/esmci/sphinx_rtd_theme.git@version-dropdown-with-fixes && \
dnf --enablerepo=powertools install -y blas-devel lapack-devel && \
pip3 install sphinx_mdinclude && \
dnf --enablerepo=ol9_codeready_builder install -y blas-devel lapack-devel && \
ln -s /usr/bin/python3 /usr/bin/python && \
echo '/usr/local/lib' > /etc/ld.so.conf.d/local.conf && \
ldconfig && \
Expand All @@ -38,6 +38,7 @@ RUN mkdir /tmp/sources && \
wget -q http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz && \
tar zxf mpich-3.3.2.tar.gz && \
cd mpich-3.3.2 && \
FFLAGS="-w -fallow-argument-mismatch -O2" \
./configure --prefix=/usr/local && \
make -j 2 install && \
rm -rf /tmp/sources
Expand All @@ -52,25 +53,28 @@ RUN mkdir /tmp/sources && \
tar zxf hdf5-1.12.0.tar.gz && \
cd hdf5-1.12.0 && \
./configure --prefix=/usr/local && \
make -j 2 install && \
cd /tmp/sources && \
wget -q ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.4.tar.gz && \
tar zxf netcdf-c-4.7.4.tar.gz && \
make -j 2 install

RUN cd /tmp/sources && \
wget -q https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz && \
tar zxf v4.7.4.tar.gz && \
cd netcdf-c-4.7.4 && \
./configure --prefix=/usr/local && \
make -j 2 install && \
ldconfig && \
cd /tmp/sources && \
wget -q ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.5.3.tar.gz && \
tar zxf netcdf-fortran-4.5.3.tar.gz && \
ldconfig

RUN cd /tmp/sources && \
wget -q https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.5.3.tar.gz && \
tar zxf v4.5.3.tar.gz && \
cd netcdf-fortran-4.5.3 && \
./configure --prefix=/usr/local && \
make -j 2 install && \
ldconfig && \
cd /tmp/sources && \
wget -q https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz && \
tar zxf pnetcdf-1.12.1.tar.gz && \
cd pnetcdf-1.12.1 && \
ldconfig

RUN cd /tmp/sources && \
wget -q https://parallel-netcdf.github.io/Release/pnetcdf-1.12.2.tar.gz && \
tar zxf pnetcdf-1.12.2.tar.gz && \
cd pnetcdf-1.12.2 && \
./configure --prefix=/usr/local && \
make -j 2 install && \
ldconfig && \
Expand Down