Issue 219: add debian 13 tests and documentation (#220)

* add debian13 tests and documentation

* remove python2 tests

* update debian packages

* update debian packages

Author: jkotan

.ci/debian13_py3/Dockerfile

@@ -0,0 +1,46 @@
+FROM debian:trixie
+
+MAINTAINER DESY, Jan Kotanski <jankotan@gmail.com>
+
+
+RUN apt-get update
+RUN apt-get install -y base-passwd apt-utils dialog -y
+RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
+RUN apt-get -qq update && apt-get -qq install -y libterm-readline-gnu-perl coreutils gnupg2 procps curl apt-transport-https gnupg2 ca-certificates wget
+RUN curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
+RUN chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
+# RUN add-apt-repository "deb http://repos.pni-hdri.de/apt/debian trixie main" -y
+RUN cd /etc/apt/sources.list.d && wget http://repos.pni-hdri.de/trixie-pni-hdri.list
+RUN apt-get -qq update && apt-get -qq -y dist-upgrade
+RUN apt-get -qq update && apt-get -qq install -y python3-sphinx  apt-utils net-tools
+RUN apt-get install -y libpninexus3.3.0-dev libpninexus3.3.0 libh5cpp0.7.1-dev libh5cpp0.7.1 python3-numpy libhdf5-dev libboost-regex-dev libboost-program-options-dev libboost-system-dev libboost-date-time-dev libboost-filesystem-dev libblas-dev  cython3 python3-setuptools libboost-python-dev python3-numpy-dev g++ python3-h5py  git python3-pytest cmake doxygen python3-sphinx libboost-all-dev hdf5-filter-plugin bitshuffle
+# hdf5-plugin-bz2 hdf5-plugin-lz4
+
+RUN useradd -ms /bin/bash tango
+RUN apt-get -qq install -y adduser
+RUN  /bin/bash -c 'sleep 10'
+
+# # install latest h5cpp
+# RUN mkdir -p /opt/h5cpp
+# RUN mkdir -p /h5cpp-src
+# RUN cd /h5cpp-src && git clone https://github.com/ess-dmsc/h5cpp && mkdir build
+# RUN cd /h5cpp-src/build && cmake -DCMAKE_INSTALL_PREFIX=/opt/h5cpp -DCMAKE_BUILD_TYPE=Release -DH5CPP_CONAN=DISABLE -DH5CPP_DISABLE_TESTS=True  ../h5cpp && make install -j4
+# ENV CPLUS_INCLUDE_PATH=/opt/h5cpp/include
+# ENV LD_LIBRARY_PATH=/opt/h5cpp/lib
+# ENV H5CPP=/opt/h5cpp/lib/cmake/h5cpp-0.5
+# ENV H5CPP_LOCAL_PATH=/opt/h5cpp
+# ENV HDF5_HL_LOCAL_PATH=/usr/lib/x86_64-linux-gnu/hdf5/serial/
+
+# # install latest linpninexus
+# RUN mkdir -p /opt/libpninexus
+# RUN mkdir -p /libpninexus-src
+# RUN cd /libpninexus-src && git clone https://github.com/pni-libraries/libpninexus && mkdir build
+# RUN cd /libpninexus-src/build && cmake -DCMAKE_BUILD_TYPE=Release  -DPNINEXUS_CONAN=DISABLE -DCMAKE_INSTALL_PREFIX=/opt/libpninexus/ ../libpninexus  && make -j4 && make install -j4
+# # RUN cd /libpninexus-src/build && cmake -Dh5cpp_DIR=$H5CPP  -DCMAKE_BUILD_TYPE=Release  -DPNINEXUS_CONAN=DISABLE -DCMAKE_INSTALL_PREFIX=/opt/h5cpp/ ../libpninexus  && make -j4 && make install -j4
+# ENV CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:/opt/libpninexus/include
+# ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/libpninexus/lib
+# ENV PNINEXUS_LOCAL_PATH=/opt/libpninexus
+
+ENV PKG_CONFIG_PATH=/home/tango/lib/pkgconfig
+USER tango
+WORKDIR /home/tango

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [debian12, debian11, debian10, ubuntu25.04, ubuntu24.04, ubuntu22.04]
+        os: [debian13, debian12, debian11, ubuntu25.04, ubuntu24.04, ubuntu22.04]
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
@@ -44,7 +44,7 @@ jobs:
         run: .ci/run.sh 3
 
       - name: Append documentation for the latest release version
-        if: github.ref == 'refs/heads/develop' &&  matrix.os == 'debian12'
+        if: github.ref == 'refs/heads/develop' &&  matrix.os == 'debian13'
         run: |
              docker  exec ndts /bin/bash -c "cp doc/index.html doc/_config.yml build"
              docker  exec ndts /bin/bash -c "git config remote.origin.fetch '+refs/heads/*:refs/remotes/origin/*'"
@@ -57,13 +57,13 @@ jobs:
              docker  exec --user root ndts /bin/bash -c "rm -rf build build_tools *.h5 src test"
 
       - name: Extract the code version from the branch name
-        if: startsWith(github.ref, 'refs/heads/docs_') && matrix.os == 'debian12'
+        if: startsWith(github.ref, 'refs/heads/docs_') && matrix.os == 'debian13'
         shell: bash
         run: echo "##[set-output name=docver;]$(echo ${GITHUB_REF#refs/heads/docs_})"
         id: extract_docver
 
       - name: Append documentation for the extracted release version
-        if: startsWith(github.ref, 'refs/heads/docs_') &&  matrix.os == 'debian12'
+        if: startsWith(github.ref, 'refs/heads/docs_') &&  matrix.os == 'debian13'
         run: |
              echo Version: ${{ steps.extract_docver.outputs.docver }}
              docker  exec ndts /bin/bash -c "git config remote.origin.fetch '+refs/heads/*:refs/remotes/origin/*'"
@@ -76,7 +76,7 @@ jobs:
              docker  exec  --user root  ndts /bin/bash -c "rm -rf build build_tools *.h5 src test"
 
       - name: Deploy documentation
-        if: (github.ref == 'refs/heads/develop' || startsWith(github.ref, 'refs/heads/docs_'))  &&  matrix.os == 'debian12'
+        if: (github.ref == 'refs/heads/develop' || startsWith(github.ref, 'refs/heads/docs_'))  &&  matrix.os == 'debian13'
         uses: s0/git-publish-subdir-action@develop
         env:
           REPO: self
@@ -88,28 +88,3 @@ jobs:
       - name: Stop the docker
         run: docker container stop ndts
 
-  python2_tests:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        os: [debian10]
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-
-      - name: Build the docker
-        env:
-          OS: ${{ matrix.os }}
-        run: docker build -t ndts .ci/${OS}_py2
-
-      - name: Run the docker
-        run: docker run --name  ndts -d -it -v `pwd`:/home/tango  ndts
-
-      - name: install python-pninexus
-        run: .ci/install.sh 2
-
-      - name: run tests
-        run: .ci/run.sh 2
-
-      - name: Stop the docker
-        run: docker container stop ndts

README.rst

@@ -78,7 +78,7 @@ For Python3 just replace python with python3 in the above instructions.
 Debian and Ubuntu packages
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Debian ``bookworm``, ``bullseye``, ``buster`` or Ubuntu ``oracular``,
+Debian ``trixie``, ``bookworm``, ``bullseye`` or Ubuntu ``plucky``,
 ``noble``, ``jammy`` packages can be found in the HDRI repository.
 
 To install the debian packages, add the PGP repository key
@@ -89,12 +89,12 @@ To install the debian packages, add the PGP repository key
        $ curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
        $ chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
 
-and then download the corresponding source list, e.g. for ``bookworm``
+and then download the corresponding source list, e.g. for ``trixie``
 
 ::
 
        $ cd /etc/apt/sources.list.d
-       $ wget http://repos.pni-hdri.de/bookworm-pni-hdri.list
+       $ wget http://repos.pni-hdri.de/trixie-pni-hdri.list
 
 or ``noble``
 

doc/sphinx/installation.rst

@@ -66,19 +66,19 @@ keyring
 The return value of this command line should be `OK`.
 In a next step you have to add new package sources to your system. For this
 purpose go to :file:`/etc/apt/sources.list.d` and download the sources file.
-For Debian (Bookworm) use
+For Debian (Trixie) use
 
 .. code-block:: bash
 
-   $ wget http://repos.pni-hdri.de/bookworm-hdri.list
+   $ wget http://repos.pni-hdri.de/trixie-hdri.list
 
-and for Ubuntu (Jammy)
+and for Ubuntu (Noble)
 
 .. code-block:: bash
 
-   $ wget http://repos.pni-hdri.de/jammy-pni-hdri.list
+   $ wget http://repos.pni-hdri.de/noble-pni-hdri.list
 
-Similarly, proceed for Bookworm, Bullseye, Buster, Lunar, Jammy, Focal.
+Similarly, proceed for Trixie, Bookworm, Bullseye, Plucky, Jammy.
 Once you have downloaded the file use
 
 .. code-block:: bash