Prep conduit manuscript

.editorconfig

@@ -9,13 +9,14 @@
  [*]
  end_of_line = lf
  insert_final_newline = true
+ max_line_length = 79
 
  # Matches multiple files with brace expansion notation
  # Set default charset and tab width
  [*.{js,py}]
  charset = utf-8
  indent_style = space
- indent_size = 2
+ indent_size = 4
 
  # cpp and hpp file indentation
  [*.{cpp,hpp}]

.github/workflows/CI.yml

@@ -45,34 +45,26 @@ jobs:
   binder:
     name: Notebooks
     runs-on: ubuntu-20.04
-    needs:
-      - docker-build
     container:
-      image: mmore500/conduit:GITHUB_ACTION_${{ github.run_number }}
+      image: mmore500/conduit:GITHUB_ACTION_706
       # github actions requires root to access mounted volumes
       options: --user root
     steps:
+      - uses: actions/checkout@v2
+        # with:
+        #   submodules: 'recursive'
       # Adapted from https://askubuntu.com/a/524368
-      - run: cd /opt/conduit/binder && ./execute_notebooks.sh
+      - run: ./binder/execute_notebooks.sh
+      # adapted from https://unix.stackexchange.com/a/545630
+      - run: find -type f -name "*.pdf" -exec bash -c 'gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dBATCH -dQUIET -sOutputFile="new.pdf" "{}"; rm "{}"; mv "new.pdf" "{}";' {} \;
+      - run: git config --global --add safe.directory "*"
       - run: git init
       - uses: fregante/setup-git-user@v1
       - run: git commit --allow-empty -m "Initial commit"
-      - run: cp -r /opt/conduit/ deploy/
       - uses: JamesIves/[email protected]
         with:
+          folder: .
           branch: binder # The branch the action should deploy to.
-          folder: deploy # The folder the action should deploy.
-      - run: mkdir -p deploy-artifacts/
-      - run: cp -r /opt/conduit/binder/. deploy-artifacts/binder/
-      # adapted from https://unix.stackexchange.com/a/107647
-      - run: find deploy-artifacts/binder/ -type f ! \( -name '*.csv' -o -name '*.png' -o -name '*.jpg' -o -name '*.pdf' -o -name '*.json' -o -name '*.meta' -o -name '*.txt' -o -name '*.out' -o -name '*.ipynb' \) -delete
-      # delete symlinks (Overleaf is not compatible with symlinks)
-      # adapted from https://superuser.com/a/586948
-      - run: find deploy-artifacts/binder -type l -delete
-      - uses: JamesIves/[email protected]
-        with:
-          branch: binder-artifacts # The branch the action should deploy to.
-          folder: deploy-artifacts # The folder the action should deploy.
 
   unit:
     name: Unit Tests

Dockerfile

@@ -1,5 +1,5 @@
 # Pull base image.
-FROM ubuntu:bionic-20180125@sha256:d6f6cc62b6bed64387d84ca227b76b9cc45049b0d0aefee0deec21ed19a300bf
+FROM ubuntu:focal-20231003@sha256:218bb51abbd1864df8be26166f847547b3851a89999ca7bfceb85ca9b5d2e95d
 
 COPY . /opt/conduit/
 
@@ -36,29 +36,27 @@ RUN \
     && \
   echo "buffed apt-get resiliency"
 
-RUN \
-  find /etc/apt -type f -name '*.list' -exec sed -i 's/\(^deb.*-backports.*\)/#\1/; s/\(^deb.*-updates.*\)/#\1/; s/\(^deb.*-proposed.*\)/#\1/; s/\(^deb.*-security.*\)/#\1/' {} + \
-    && \
-  rm -rf /var/lib/apt/lists/* \
-    && \
-  echo "removed -backports, -updates, -proposed, -security repositories"
-
 # adapted in part form https://www.cloudsavvyit.com/13461/how-to-run-puppeteer-and-headless-chrome-in-a-docker-container/
 RUN \
   apt-get update -qq \
     && \
-  apt-get install -y --allow-downgrades --no-install-recommends \
+  apt-get install -y aptitude git --allow-downgrades --no-install-recommends aptitude \
+    && \
+  aptitude install -y --without-recommends \
     build-essential \
     ca-certificates \
+    clang-7 \
     cmake \
     curl \
     doxygen \
     emacs \
     fonts-liberation \
     gconf-service \
     gdb \
+    ghostscript \
     gpg-agent \
     gzip \
+    g++-9 \
     hdf5-helpers \
     hdf5-tools \
     htop \
@@ -67,6 +65,7 @@ RUN \
     libatk1.0-0 \
     libc6 \
     libcairo2 \
+    libclang-7-dev \
     libcups2 \
     libcurl4 \
     libcurl4-openssl-dev \
@@ -80,28 +79,28 @@ RUN \
     libgtk-3-0 \
     libicu-dev \
     libjpeg-dev \
-    libhdf5-100 \
-    libhdf5-cpp-100 \
+    libhdf5-103 \
+    libhdf5-cpp-103 \
     libhdf5-dev \
     libhdf5-doc \
     libhdf5-mpi-dev \
-    libhdf5-mpich-100 \
+    libhdf5-mpich-103 \
     libhdf5-mpich-dev \
-    libhdf5-openmpi-100 \
+    libhdf5-openmpi-103 \
     libhdf5-openmpi-dev \
     libhdf5-serial-dev \
     libmpich-dev \
     libmpich12 \
     libnspr4 \
     libnss3 \
     libopenmpi-dev \
-    libopenmpi2 \
+    # libopenmpi2 \
     libpango-1.0-0 \
     libpangocairo-1.0-0 \
     libpng-dev \
     libpthread-stubs0-dev \
     libstdc++-7-dev \
-    libstdc++6=8-20180414-1ubuntu2 \
+    libstdc++6 \
     libx11-6 \
     libx11-xcb1 \
     libxcb1 \
@@ -115,6 +114,8 @@ RUN \
     libxrender1 \
     libxss1 \
     libxtst6 \
+    llvm-7 \
+    llvm-7-dev \
     locales \
     lsb-release \
     man \
@@ -128,90 +129,43 @@ RUN \
     openmpi-common \
     openmpi-doc \
     openssh-server \
-    python-dev \
-    python-h5py \
-    python-pip \
-    python-setuptools \
-    python-sphinx \
-    python-virtualenv \
-    python-wheel \
+    # python-dev \
+    # python-h5py \
+    # python-pip \
+    # python-setuptools \
+    # python-virtualenv \
+    # python-wheel \
     python3-dev \
     python3-h5py \
     python3-pip \
     python3-setuptools \
-    python3-sphinx \
     python3-virtualenv \
     python3-wheel \
     rename \
     rsync \
     slurm-client \
     software-properties-common \
+    sphinx-doc \
+    sphinx-common \
     tar \
     unzip \
     vim \
     wget \
     xdg-utils \
     && \
-  add-apt-repository ppa:git-core/ppa -y \
-    && \
-  apt-get update -qq \
-    && \
-  apt-get install -y --no-install-recommends git \
-    && \
   apt-get clean \
     && \
   rm -rf /var/lib/apt/lists/* \
     && \
   echo "installed fundamentals"
 
-# adapted in part from https://askubuntu.com/a/916451
-RUN \
-  apt-get update -qq \
-    && \
-  rm /etc/apt/apt.conf.d/docker-gzip-indexes \
-    && \
-  apt-get purge apt-show-versions \
-    && \
-  rm /var/lib/apt/lists/*lz4 \
-    && \
-  apt-get -o Acquire::GzipIndexes=false update \
-    && \
-  add-apt-repository -y ppa:ubuntu-toolchain-r/test \
-    && \
-  wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - \
-    && \
-  apt-add-repository "deb https://apt.llvm.org/xenial/ llvm-toolchain-xenial-7 main" \
-    && \
-  add-apt-repository -y ppa:ubuntu-toolchain-r/test \
-    && \
-  apt-get update -qq \
-    && \
-  apt-get clean \
-    && \
-  rm -rf /var/lib/apt/lists/* \
-    && \
-  echo "configured packaging system"
-
-RUN \
-  apt-get update -qq \
-    && \
-  apt-get install -qq \
-    libclang-7-dev=1:7.1.0~svn353565-1~exp1~20190408084827.60 \
-    llvm-7=1:7.1.0~svn353565-1~exp1~20190408084827.60 \
-    llvm-7-dev=1:7.1.0~svn353565-1~exp1~20190408084827.60 \
-    clang-7=1:7.1.0~svn353565-1~exp1~20190408084827.60 \
-    g++-9=9.4.0-1ubuntu1~18.04 \
-    && \
-  apt-get clean \
-    && \
-  rm -rf /var/lib/apt/lists/* \
-    && \
-  echo "installed llvm-7 dependencies"
-
 # magic from https://github.com/puppeteer/puppeteer/issues/3451#issuecomment-523961368
 RUN echo 'kernel.unprivileged_userns_clone=1' > /etc/sysctl.d/userns.conf
 
+# git confifg, see https://stackoverflow.com/a/76769867
 RUN \
+  git config --global url."https://".insteadOf git:// \
+    && \
   python3 -m pip install --timeout 60 --retries 100 --upgrade pip==21.3.1 \
     && \
   python3 -m pip install --timeout 60 --retries 100 --ignore-installed -r /opt/conduit/third-party/requirements.txt \
@@ -231,9 +185,11 @@ RUN \
     && \
   update-alternatives --install /usr/bin/llvm-cov llvm-cov /usr/bin/llvm-cov-7 90 \
     && \
-  npm install -g [email protected] \
+  npm install -g [email protected] [email protected] \
+    && \
+  npm cache clean --force \
     && \
-  n 12.18.2 \
+  PATH="$PATH" n 12.18.2 \
     && \
   export python="/usr/bin/python" \
     && \
@@ -291,6 +247,7 @@ RUN \
     && \
   echo "user added and granted permissions to /opt and /home/user"
 
+# git safe directory: https://stackoverflow.com/a/73100228/17332200
 RUN \
   mkdir /context/ \
     && \
@@ -300,6 +257,10 @@ RUN \
     && \
   chown user:user /__w/ \
     && \
+  git config --global --add safe.directory '*' \
+    && \
+  git config --global --add safe.directory /__w/conduit/conduit \
+    && \
   echo "/context/ /__w/ directories set up, user granted permissions"
 
 USER user

binder/clear_notebooks.sh

@@ -90,7 +90,7 @@ echo "-------------------------"
 shopt -s nullglob
 
 for script in "${script_dir}/"*/clear_notebooks.sh; do
-  "${script}"
+  "${script}" &
 done
 
 shopt -u nullglob