Dev (#45)

* Add tdqm python package * Add mysql python package * Add lftp ubuntu package * Fix vcpkg install * Add quarto vs-code extension * Add sstudentt python package * Add numba python package * Bump ubuntu from `6d7b5d3` to `a6d2b38` Bumps ubuntu from `6d7b5d3` to `a6d2b38`. --- updated-dependencies: - dependency-name: ubuntu dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump R to 4.4.0 * Add scoringrules python package * Add python packages for building packages * Add python3-venv to the list of dependencies * Add ruff and black python packages * Bump docker/build-push-action from 5 to 6 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@v5...v6) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> * Bump ubuntu from `a6d2b38` to `19478ce` Bumps ubuntu from `a6d2b38` to `19478ce`. --- updated-dependencies: - dependency-name: ubuntu dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump RSPM snapshot and R to 4.4.1 * Add more recent pandoc version * Add latex packages for rjtools template * Add h5py python package * Bump pandoc version * Bump ubuntu from `19478ce` to `340d9b0` Bumps ubuntu from `19478ce` to `340d9b0`. --- updated-dependencies: - dependency-name: ubuntu dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Downgrade pandoc * Add covr R package and dependencies --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BerriJ · Aug 14, 2024 · 3d16d2f · 3d16d2f
1 parent 963280f
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -51,7 +51,9 @@
                 // Live Share
                 "ms-vsliveshare.vsliveshare",
                 // Copilot
-                "GitHub.copilot"
+                "GitHub.copilot",
+                // Quarto
+                "quarto.quarto"
             ],
             // Set *default* container specific settings
             // Important for radian and latex

diff --git a/.github/workflows/build_deploy_dev.yml b/.github/workflows/build_deploy_dev.yml
@@ -36,7 +36,7 @@ jobs:
           echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV
       -
         name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

diff --git a/.github/workflows/build_deploy_master.yml b/.github/workflows/build_deploy_master.yml
@@ -36,7 +36,7 @@ jobs:
           echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV
       -
         name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

diff --git a/.github/workflows/build_deploy_size.yml b/.github/workflows/build_deploy_size.yml
@@ -35,7 +35,7 @@ jobs:
           echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV
       -
         name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

diff --git a/.github/workflows/build_on_pr.yml b/.github/workflows/build_on_pr.yml
@@ -34,7 +34,7 @@ jobs:
           echo "IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')" >> $GITHUB_ENV
       -
         name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,9 @@
-FROM ubuntu:jammy@sha256:6d7b5d3317a71adb5e175640150e44b8b9a9401a7dd394f44840626aff9fa94d
+FROM ubuntu:jammy@sha256:340d9b015b194dc6e2a13938944e0d016e57b9679963fdeb9ce021daac430221
 
 SHELL ["/bin/bash", "-c"]
 
 ENV DISPLAY=:0 \
-    TZ=Europe/Berlin
+  TZ=Europe/Berlin
 
 ARG USERNAME=vscode
 ARG USER_UID=1000
@@ -12,53 +12,54 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 # Add non root user
 RUN groupadd --gid $USER_GID $USERNAME \
-    && useradd -rm -d /home/$USERNAME -s /bin/bash -g root --uid $USER_UID --gid $USER_GID $USERNAME \
-    && addgroup $USERNAME staff
+  && useradd -rm -d /home/$USERNAME -s /bin/bash -g root --uid $USER_UID --gid $USER_GID $USERNAME \
+  && addgroup $USERNAME staff
 
 # Create folders to mount extensions
 RUN mkdir -p /home/$USERNAME/.vscode-server/extensions \
-    /home/$USERNAME/.vscode-server-insiders/extensions \
-    workspaces \
-    && chown -R $USERNAME \
-    /home/$USERNAME/.vscode-server \
-    /home/$USERNAME/.vscode-server-insiders \
-    workspaces
+  /home/$USERNAME/.vscode-server-insiders/extensions \
+  workspaces \
+  && chown -R $USERNAME \
+  /home/$USERNAME/.vscode-server \
+  /home/$USERNAME/.vscode-server-insiders \
+  workspaces
 
 # Ubuntu Setup
 RUN echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections &&\
-    apt-get update &&\
-    apt-get -y --no-install-recommends install \
-    ca-certificates \
-    git \
-    build-essential \
-    cmake \
-    ninja-build \
-    ccache \
-    gfortran \
-    netbase \
-    zip \
-    unzip \
-    xclip \
-    zsh \
-    gnupg2 \
-    nano \
-    gdb \
-    ssh-client \
-    fontconfig \
-    pkg-config \
-    default-libmysqlclient-dev \
-    ttf-mscorefonts-installer \
-    locales &&\
-    locale-gen en_US.UTF-8 &&\
-    locale-gen de_DE.UTF-8 &&\
-    update-locale LANG=en_US.UTF-8 &&\
-    git clone --depth=1 https://github.com/sindresorhus/pure.git /home/$USERNAME/.zsh/pure \
-    && rm -rf /home/$USERNAME/.zsh/pure/.git \
-    && apt-get autoclean -y \
-    && rm -rf /var/lib/apt/lists/*
+  apt-get update &&\
+  apt-get -y --no-install-recommends install \
+  ca-certificates \
+  git \
+  build-essential \
+  cmake \
+  ninja-build \
+  ccache \
+  gfortran \
+  netbase \
+  zip \
+  unzip \
+  xclip \
+  zsh \
+  lftp \
+  gnupg2 \
+  nano \
+  gdb \
+  ssh-client \
+  fontconfig \
+  pkg-config \
+  default-libmysqlclient-dev \
+  ttf-mscorefonts-installer \
+  locales &&\
+  locale-gen en_US.UTF-8 &&\
+  locale-gen de_DE.UTF-8 &&\
+  update-locale LANG=en_US.UTF-8 &&\
+  git clone --depth=1 https://github.com/sindresorhus/pure.git /home/$USERNAME/.zsh/pure \
+  && rm -rf /home/$USERNAME/.zsh/pure/.git \
+  && apt-get autoclean -y \
+  && rm -rf /var/lib/apt/lists/*
 
 ENV LC_ALL=en_US.UTF-8 \
-    LANG=en_US.UTF-8
+  LANG=en_US.UTF-8
 
 # Font config
 # "LM Roman 10", "Times New Roman" ... use `showtext` package in R
@@ -71,53 +72,54 @@ RUN fc-cache -f -v
 
 # Install quarto
 ENV QUARTO_VERSION="1.4.551"
-
 COPY install_scripts/install_quarto.sh /install_scripts/install_quarto.sh
-
 RUN chmod +x install_scripts/install_quarto.sh &&\
-    install_scripts/install_quarto.sh
+  install_scripts/install_quarto.sh
 
+RUN wget https://github.com/jgm/pandoc/releases/download/3.1.6.2/pandoc-3.1.6.2-1-amd64.deb &&\
+  dpkg -i pandoc-3.1.6.2-1-amd64.deb
 
 # Install phantomjs
 COPY install_scripts/install_phantomjs.sh /install_scripts/install_phantomjs.sh
 
 RUN chmod +x install_scripts/install_phantomjs.sh &&\
-    install_scripts/install_phantomjs.sh
+  install_scripts/install_phantomjs.sh
 
 # Install vcpkg C++ dependency manager
-RUN git clone --depth=1 https://github.com/Microsoft/vcpkg /usr/local/vcpkg \
-    && rm -rf /usr/local/vcpkg/.git \
-    && cd /usr/local/vcpkg \
-    && ./bootstrap-vcpkg.sh \
-    && ./vcpkg integrate install \
-    && /usr/local/vcpkg/vcpkg install armadillo \
-    && /usr/local/vcpkg/vcpkg install pybind11 \
-    && chown --recursive $USERNAME:$USERNAME /usr/local/vcpkg
+RUN git clone --depth=1 https://github.com/Microsoft/vcpkg --branch 2024.04.26 /usr/local/vcpkg \
+  && rm -rf /usr/local/vcpkg/.git \
+  && cd /usr/local/vcpkg \
+  && ./bootstrap-vcpkg.sh \
+  && ./vcpkg integrate install \
+  && /usr/local/vcpkg/vcpkg install armadillo \
+  && /usr/local/vcpkg/vcpkg install pybind11 \
+  && chown --recursive $USERNAME:$USERNAME /usr/local/vcpkg
 
 ENV PATH="/usr/local/vcpkg:${PATH}"
 
 # Install Python CARMA
 RUN git clone --depth=1 https://github.com/RUrlus/carma.git /usr/local/carma \
-    && rm -rf /usr/local/carma/.git \
-    && cd /usr/local/carma \
-    && mkdir build \
-    && cd build \
-    && cmake -DCARMA_INSTALL_LIB=ON .. \
-    && cmake --build . --config Release --target install \
-    && rm -rf /usr/local/carma
+  && rm -rf /usr/local/carma/.git \
+  && cd /usr/local/carma \
+  && mkdir build \
+  && cd build \
+  && cmake -DCARMA_INSTALL_LIB=ON .. \
+  && cmake --build . --config Release --target install \
+  && rm -rf /usr/local/carma
 
 # Install Python
 COPY package_lists/python_packages.txt /package_lists/python_packages.txt
 
 RUN apt-get update &&\
-    apt-get -y --no-install-recommends install \
-    python3-pip  \
-    python3-dev && \
-    # Python packages
-    pip3 install -U --no-cache-dir \
-    $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')  \
-    && apt-get autoclean -y \
-    && rm -rf /var/lib/apt/lists/*
+  apt-get -y --no-install-recommends install \
+  python3-pip  \
+  python3-dev \
+  python3-venv && \
+  # Python packages
+  pip3 install -U --no-cache-dir \
+  $(grep -o '^[^#]*' package_lists/python_packages.txt | tr '\n' ' ')  \
+  && apt-get autoclean -y \
+  && rm -rf /var/lib/apt/lists/*
 
 # Set PATH for user installed python packages
 ENV PATH="/home/vscode/.local/bin:${PATH}"
@@ -127,31 +129,31 @@ COPY install_scripts/install_latex.sh /install_scripts/install_latex.sh
 COPY package_lists/latex_packages.txt /package_lists/latex_packages.txt
 
 RUN chmod +x install_scripts/install_latex.sh &&\
-    install_scripts/install_latex.sh \
-    && export PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}" \
-    && tlmgr option -- autobackup 0 \
-    && tlmgr option -- docfiles 0 \
-    && tlmgr option -- srcfiles 0 \
-    && tlmgr install \
-    $(grep -o '^[^#]*' package_lists/latex_packages.txt | tr '\n' ' ') \
-    && chown --recursive $USERNAME:$USERNAME /usr/local/texlive
+  install_scripts/install_latex.sh \
+  && export PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}" \
+  && tlmgr option -- autobackup 0 \
+  && tlmgr option -- docfiles 0 \
+  && tlmgr option -- srcfiles 0 \
+  && tlmgr install \
+  $(grep -o '^[^#]*' package_lists/latex_packages.txt | tr '\n' ' ') \
+  && chown --recursive $USERNAME:$USERNAME /usr/local/texlive
 
 # Set Latex Path
 ENV PATH="/usr/local/texlive/bin/x86_64-linux:${PATH}"
 
 # Install R
-ENV R_VERSION=4.3.3
+ENV R_VERSION=4.4.1
 
 # Set RSPM snapshot see:
 # https://packagemanager.posit.co/client/#/repos/cran/setup?r_environment=other&snapshot=2023-10-04&distribution=ubuntu-22.04
-ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2024-03-21
+ENV R_REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/2024-07-14
 
 COPY install_scripts/install_r.sh /install_scripts/install_r.sh
 COPY package_lists/r_packages.txt /package_lists/r_packages.txt
 COPY package_lists/r_packages_github.txt /package_lists/r_packages_github.txt
 
 RUN chmod +x install_scripts/install_r.sh &&\
-    install_scripts/install_r.sh
+  install_scripts/install_r.sh
 
 COPY --chown=$USERNAME .misc/.zshrc /home/$USERNAME/.
 

diff --git a/install_scripts/install_latex.sh b/install_scripts/install_latex.sh
@@ -3,8 +3,7 @@
 # Install build dependencies
 apt-get update
 apt-get install -y --no-install-recommends \
-wget \
-pandoc
+wget 
 
 # Install Latex
 wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz

diff --git a/install_scripts/install_r.sh b/install_scripts/install_r.sh
@@ -17,7 +17,6 @@ RUNDEPS="ca-certificates \
       vim-tiny \
       wget \
       dirmngr \
-      pandoc \
       libmagick++-dev \
       libpoppler-cpp-dev \
       libudunits2-dev \

diff --git a/package_lists/latex_packages.txt b/package_lists/latex_packages.txt
@@ -57,6 +57,8 @@ ieeetran
 ifoddpage
 inconsolata
 koma-script
+l3backend
+l3backend-dev
 latexindent # Indentation
 latexmk
 latex-tools-dev
@@ -99,9 +101,11 @@ textpos
 threeparttable
 threeparttablex
 thumbpdf
+titlesec
 #! To find packages: tlmgr search --global --file "authblk.sty"
 tracklang
 ulem
+upquote
 varwidth
 was
 wrapfig

diff --git a/package_lists/python_packages.txt b/package_lists/python_packages.txt
@@ -1,22 +1,27 @@
 aiofiles
 autopep8
+black
 bspline
+build
 celery
 fastapi
 flower
 google-api-python-client 
 google-auth-httplib2 
 google-auth-oauthlib
+h5py
 investiny
 investpy
 ipykernel
 Jinja2
 kaleido
 matplotlib
 meteostat
+mysql
 mysqlclient
 nbclient
 nbformat
+numba
 numdifftools
 numpy
 pandas
@@ -28,9 +33,14 @@ pyparsing==2.4.7
 pytest
 redis
 requests
+ruff
 scikit-learn
 scipy
+scoringrules
+setuptools
 sqlalchemy
+sstudentt
 statsmodels
 tdqm
+tqdm
 uvicorn
diff --git a/package_lists/r_packages.txt b/package_lists/r_packages.txt
@@ -7,6 +7,7 @@ cli
 conflicted
 copula
 corrplot
+covr
 cowplot
 crayon
 crosstalk
@@ -17,6 +18,7 @@ devtools
 DiceKriging
 doParallel
 doSNOW
+DT
 energy
 eurostat
 evir
@@ -47,6 +49,7 @@ gridSVG
 grImport2
 gt
 Hmisc
+htmltools
 htmlwidgets
 igraph
 inline