Testing dockerfile for baselibs

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,10 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci.yml

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+name: CI Regression
+
+on: [push, pull_request]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        # 3.6 will reach EoL in December 2021
+        # https://devguide.python.org/#status-of-python-branches
+        python-version: [ "3.8", "3.9" ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install test dependencies
+        run: |
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install -y gdal-bin libgdal-dev build-essential
+          python -m pip install --upgrade pip
+          pip install https://github.com/rasterio/rasterio/archive/master.zip
+          pip install .[test]
+          pip install coveralls
+      - name: Run tests
+        run: coverage run -m pytest -v
+      - name: Submit coveralls
+        if: github.event_name != 'pull_request'
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '29 15 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+        
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/dockerhub.yml

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+name: CI to Docker Hub Baselibs
+
+on:
+  push:
+  schedule:
+    - cron: '30 5 * * 1,3'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - 
+        name: Lower github-runner storage
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+      -
+        name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ./requirements/Dockerfile.baselibs
+          push: true
+          tags: nasanccs/wrf-baselibs:latest

.github/workflows/lint.yml

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+name: Code style - PEP8
+
+on: [push, pull_request]
+
+jobs:
+
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Set up Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+      - name: flake8 Lint
+        uses: py-actions/flake8@v2

.github/workflows/pypi-publish.yml

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+name: Publish package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install build package
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build --user
+    - name: Build distribution
+      run: |
+        python -m build --sdist --wheel --outdir dist/ .
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

requirements/Dockerfile.baselibs

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+FROM rockylinux:8
+MAINTAINER Jordan A Caraballo-Vega <[email protected]>
+
+ENV NML_VERSION 4.4
+ENV MPI_SHORT_VERSION 4.0
+ENV MPI_VERSION 4.0.0
+ENV J 4
+
+# Set up base OS environment
+RUN dnf -y update \
+    && dnf install -y --setopt=tsflags=nodocs --enablerepo=powertools,epel \
+        gcc gcc-gfortran gcc-c++ \
+        glibc.i686 libgcc.i686 libpng-devel jasper jasper-devel hostname \
+        m4 make perl tar bash tcsh time wget which zlib zlib-devel \
+        openssh-clients openssh-server net-tools fontconfig libgfortran \
+        libXext libXrender ImageMagick ImageMagick-devel epel-release git flex \
+        flex-devel byacc bzip2-devel gzip-devel \
+        php-devel php-pear \
+    && dnf -y clean all --enablerepo='*' \
+    && rm -rf /var/cache/dnf
+
+# Setting system
+RUN groupadd wrf -g 9999
+RUN useradd -u 9999 -g wrf -G wheel -M -d /wrf wrfuser
+RUN mkdir /wrf \
+ &&  chown -R wrfuser:wrf /wrf \
+ &&  chmod 6755 /wrf
+
+# Build OpenMPI
+RUN mkdir -p /wrf/libs/openmpi/BUILD_DIR
+RUN cd /wrf/libs/openmpi/BUILD_DIR \
+ && curl -L -O https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.0.tar.gz \
+ && tar -xf openmpi-4.0.0.tar.gz \
+ && cd openmpi-4.0.0 \
+ && ./configure --prefix=/usr/local &> /wrf/libs/build_log_openmpi_config \
+ && echo dummy printout to keep travis happy openmpi config \
+ && make all install \
+ && echo "make all install | awk 'NR % 1000 == 0'" \
+ && echo "make all install &> /wrf/libs/build_log_openmpi_make" \
+ && echo dummy printout to keep travis happy openmpi make \
+ && cd / \
+ && rm -rf /wrf/libs/openmpi/BUILD_DIR
+
+# Set up base OS environment
+
+#RUN yum -y update
+# Install SCL release package and python SCL
+#RUN yum -y install centos-release-scl \
+# && yum -y install --setopt=tsflags=nodocs rh-python38
+# Enable rh-python scl binary
+#COPY entrypoint.sh /usr/bin/entrypoint.sh
+#RUN chmod +x /usr/bin/entrypoint.sh
+#ENTRYPOINT [ "/usr/bin/entrypoint.sh" ]
+
+
+
+# Install version 10 of GNU compiler
+
+#RUN yum -y install centos-release-scl \
+# && yum -y install devtoolset-10 \
+# && yum -y install devtoolset-10-gcc devtoolset-10-gcc-gfortran devtoolset-10-gcc-c++ \
+# && scl enable devtoolset-10 bash \
+# && scl enable devtoolset-10 tcsh 
+
+
+# Build HDF5 libraries
+#RUN mkdir -p /wrf/libs/hdf5/BUILD_DIR
+#RUN source /opt/rh/devtoolset-10/enable \
+# && cd /wrf/libs/hdf5/BUILD_DIR \
+# && wget https://www2.mmm.ucar.edu/people/duda/files/mpas/sources/hdf5-1.10.5.tar.bz2 \
+# && tar -xf hdf5-1.10.5.tar.bz2 \
+# && cd hdf5-1.10.5 \
+# && ./configure --enable-fortran --enable-cxx --enable-shared --prefix=/usr/local/ &> /wrf/libs/build_log_hdf5_config \
+# && echo dummy printout to keep travis happy hdf5 config \
+# && make install &> /wrf/libs/build_log_hdf5_make \
+# && echo dummy printout to keep travis happy hdf5 make \
+# && cd / \
+# && rm -rf /wrf/libs/hdf5/BUILD_DIR
+#ENV LD_LIBRARY_PATH /usr/local/lib
+
+# Build netCDF C libraries
+#RUN yum -y install libcurl-devel zlib-devel
+#ENV NETCDF /wrf/libs/netcdf
+#RUN mkdir -p ${NETCDF}/BUILD_DIR
+#RUN source /opt/rh/devtoolset-10/enable \
+# && cd ${NETCDF}/BUILD_DIR \
+# && curl -L -O https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz \
+# && curl -L -O https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.6.0.tar.gz \
+# && curl -L -O https://github.com/Unidata/netcdf4-python/archive/v1.5.3rel.tar.gz \
+# && tar -xf v4.7.4.tar.gz \
+# && cd netcdf-c-4.7.4 \
+# && ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncc_config \
+# && echo dummy printout to keep travis happy ncc config \
+# && make install &> /wrf/libs/build_log_ncc_make \
+# && echo dummy printout to keep travis happy ncc make \
+# && cd /
+
+# Build netCDF Fortran libraries
+#RUN source /opt/rh/devtoolset-10/enable \
+# && env \
+# && cd ${NETCDF}/BUILD_DIR \
+# && tar -xf v4.6.0.tar.gz \
+# && cd netcdf-fortran-4.6.0/ \
+# && export LD_LIBRARY_PATH=${NETCDF}/lib:/usr/local/lib:${LD_LIBRARY_PATH} \
+# && CPPFLAGS=-I${NETCDF}/include LDFLAGS=-L${NETCDF}/lib ./configure --enable-shared --prefix=${NETCDF} &> /wrf/libs/build_log_ncf_config \
+# && echo dummy printout to keep travis happy ncf config \
+# && make install &> /wrf/libs/build_log_ncf_make \
+# && echo dummy printout to keep travis happy ncf make \
+# && cd /
+
+# Install and setup Python3.8
+#RUN yum -y groupinstall "Development Tools"
+#RUN yum -y install openssl-devel bzip2-devel libffi-devel xz-devel
+#RUN mkdir -p /wrf/libs/python/BUILD_DIR \
+#  && cd /wrf/libs/python/BUILD_DIR \
+#  && wget https://www.python.org/ftp/python/3.8.12/Python-3.8.12.tgz \
+#  && tar -xf Python-3.8.12.tgz \
+#  && cd Python-3.8.12 \
+#  && ./configure --enable-optimizations --prefix=/usr/local  \
+#  && make altinstall \
+#  && cd / \
+#  && rm -rf /wrf/libs/python/BUILD_DIR
+#RUN python3.8 -m pip install numpy \
+# && python3.8 -m pip install --upgrade pip \
+# && python3.8 -m pip install --upgrade setuptools
+#RUN ldconfig -v
+
+# Build netCDF4-python libraries
+#RUN source /opt/rh/devtoolset-10/enable \
+# && cd ${NETCDF}/BUILD_DIR \
+# && tar -xf v1.5.3rel.tar.gz \
+# && cd netcdf4-python-1.5.3rel/ \
+# && export LD_LIBRARY_PATH=${NETCDF}/lib:${LD_LIBRARY_PATH} \
+# && export NETCDF4_DIR=${NETCDF} \
+# && export HDF5_DIR=/usr/local \
+# && python3.8 -m pip install wheel \
+# && python3.8 setup.py build \
+# && CPPFLAGS="-I${NETCDF}/include -I/usr/local/include" LDFLAGS="-L${NETCDF}/lib -L/usr/local/lib" python3.8 setup.py install \
+# && echo dummy printout to keep travis happy ncf4-python install \
+# && cd / \
+# && rm -rf ${NETCDF}/BUILD_DIR
+
+#RUN mkdir -p /var/run/sshd \
+#    && ssh-keygen -A \
+#    && sed -i 's/#PermitRootLogin yes/PermitRootLogin yes/g' /etc/ssh/sshd_config \
+#    && sed -i 's/#RSAAuthentication yes/RSAAuthentication yes/g' /etc/ssh/sshd_config \
+#    && sed -i 's/#PubkeyAuthentication yes/PubkeyAuthentication yes/g' /etc/ssh/sshd_config
+
+#RUN mkdir -p  /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput \
+# &&  chown -R wrfuser:wrf /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local \
+# &&  chmod 6755 /wrf /wrf/WPS_GEOG /wrf/wrfinput /wrf/wrfoutput /usr/local
+
+# Download NCL
+#RUN curl -SL https://www.earthsystemgrid.org/api/v1/dataset/ncl.662.dap/file/ncl_ncarg-6.6.2-CentOS7.6_64bit_gnu485.tar.gz | tar zxC /usr/local 
+#ENV NCARG_ROOT /usr/local
+
+# Set environment for interactive container shells
+#RUN echo export LDFLAGS="-lm" >> /etc/bashrc \
+# && echo export NETCDF=${NETCDF} >> /etc/bashrc \
+# && echo export JASPERINC=/usr/include/jasper/ >> /etc/bashrc \
+# && echo export JASPERLIB=/usr/lib64/ >> /etc/bashrc \
+# && echo export LD_LIBRARY_PATH="/opt/rh/devtoolset-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/bashrc  \
+# && echo export PATH=".:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/bashrc \
+# && echo export NCARG_ROOT=/usr/local >> /etc/bashrc
+
+#RUN echo setenv LDFLAGS "-lm" >> /etc/csh.cshrc \
+# && echo setenv NETCDF "${NETCDF}" >> /etc/csh.cshrc \
+# && echo setenv JASPERINC "/usr/include/jasper/" >> /etc/csh.cshrc \
+# && echo setenv JASPERLIB "/usr/lib64/" >> /etc/csh.cshrc \
+# && echo setenv LD_LIBRARY_PATH "/opt/rh/devtoolset-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}" >> /etc/csh.cshrc \
+# && echo setenv PATH ".:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH" >> /etc/csh.cshrc \
+# && echo setenv NCARG_ROOT /usr/local >> /etc/csh.cshrc
+
+#RUN mkdir /wrf/.ssh ; echo "StrictHostKeyChecking no" > /wrf/.ssh/config
+#COPY default-mca-params.conf /wrf/.openmpi/mca-params.conf
+#RUN mkdir -p /wrf/.openmpi
+#RUN chown -R wrfuser:wrf /wrf/
+
+# all root steps completed above, now below as regular userID wrfuser
+#USER wrfuser
+#WORKDIR /wrf
+
+# Download data
+#ARG argname=tutorial
+#RUN echo DAVE $argname
+#RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/src/wps_files/geog_low_res_mandatory.tar.gz | tar -xzC /wrf/WPS_GEOG ; fi
+#RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/colorado_march16.new.tar.gz | tar -xzC /wrf/wrfinput ; fi
+#RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/src/namelists_v$NML_VERSION.tar.gz  | tar -xzC /wrf/wrfinput ; fi
+#RUN if [ "$argname" = "tutorial" ] ; then curl -SL https://www2.mmm.ucar.edu/wrf/TUTORIAL_DATA/WRF_NCL_scripts.tar.gz | tar -xzC /wrf ; fi
+#RUN if [ "$argname" = "regtest" ]  ; then curl -SL https://www2.mmm.ucar.edu/wrf/dave/data_smaller.tar.gz | tar -xzC /wrf ; fi
+
+#ENV JASPERINC /usr/include/jasper
+#ENV JASPERLIB /usr/lib64
+#ENV NETCDF_classic 1
+#ENV LD_LIBRARY_PATH /opt/rh/devtoolset-10/root/usr/lib/gcc/aarch64-redhat-linux/10:/usr/lib64/openmpi/lib:${NETCDF}/lib:${LD_LIBRARY_PATH}
+#ENV PATH  .:/opt/rh/devtoolset-10/root/usr/bin:/usr/lib64/openmpi/bin:${NETCDF}/bin:$PATH
+
+#RUN ssh-keygen -f /wrf/.ssh/id_rsa -t rsa -N '' \
+#    && chmod 600 /wrf/.ssh/config \
+#    && chmod 700 /wrf/.ssh \
+#    && cp /wrf/.ssh/id_rsa.pub /wrf/.ssh/authorized_keys
+#