updated sage build

.gitea/workflows/build-jupyter-sage.yaml

@@ -9,14 +9,6 @@ jobs:
   "Build Jupyter Sage docker images":
     runs-on: woryzen
     steps:
-      -
-        name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      -
-        name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-        with:
-          driver: docker-container
       -
         name: Login to Gitea container registry
         uses: docker/login-action@v3
@@ -28,10 +20,12 @@ jobs:
         name: Build and push jupyter-sage image
         uses: docker/build-push-action@v5.3.0
         with:
+          builder: multiplatform-builder
           context: "{{defaultContext}}:jupyter-sage"
-          platforms: linux/amd64,linux/arm64
+          platforms: linux/amd64
           push: true
-          pull: true
-          tags: gitea.woggioni.net/woggioni/jupyter-sage:latest
-          cache-from: type=registry,ref=gitea.woggioni.net/woggioni/jupyter-sage:buildx
-          cache-to: type=registry,mode=max,compression=zstd,image-manifest=true,oci-mediatypes=true,ref=gitea.woggioni.net/woggioni/jupyter-sage:buildx          
+          build-args: "VERSION=10.8"
+          ssh: default=/home/luser/.ssh/id_ed25519
+          tags: |
+            gitea.woggioni.net/woggioni/jupyter-sage:latest
+            gitea.woggioni.net/woggioni/jupyter-sage:10.8

jupyter-sage/Dockerfile

@@ -1,36 +1,44 @@
-FROM debian:latest
-RUN apt-get update && apt-get upgrade
-RUN apt-get install -y bc binutils bzip2 ca-certificates cliquer cmake curl \
-        ecl eclib-tools fflas-ffpack g++ gap gcc gengetopt gfan gfortran \
-        glpk-utils gmp-ecm lcalc libatomic-ops-dev libboost-dev \
-        libbraiding-dev libbrial-dev libbrial-groebner-dev libbz2-dev \
-        libcdd-dev libcdd-tools libcliquer-dev libcurl4-openssl-dev libec-dev \
-        libecm-dev libffi-dev libflint-dev libfplll-dev libfreetype-dev \
-        libgap-dev libgc-dev libgd-dev libgf2x-dev libgiac-dev libgivaro-dev \
-        libglpk-dev libgmp-dev libgsl-dev libhomfly-dev libiml-dev \
-        liblfunction-dev liblinbox-dev liblrcalc-dev liblzma-dev libm4ri-dev \
-        libm4rie-dev libmpc-dev libmpfi-dev libmpfr-dev libncurses5-dev \
-        libntl-dev libopenblas-dev libpari-dev libplanarity-dev libppl-dev \
-        libprimesieve-dev libpython3-dev libqhull-dev libreadline-dev \
-        librw-dev libsingular4-dev libsqlite3-dev libssl-dev \
-        libsuitesparse-dev libsymmetrica2-dev libz-dev libzmq3-dev m4 make \
-        maxima maxima-sage meson nauty ninja-build openssl palp pari-doc \
-        pari-elldata pari-galdata pari-galpol pari-gp2c pari-seadata patch \
-        patchelf perl pkg-config planarity ppl-dev python3 python3-setuptools \
-        python3-venv singular singular-doc sqlite3 sympow tachyon tar texinfo \
-        tox xcas xz-utils git
-RUN apt-get install -y default-jdk dvipng ffmpeg fonts-freefont-otf \
-        imagemagick latexmk libavdevice-dev libjpeg-dev pandoc tex-gyre \
-        texlive-fonts-recommended texlive-lang-cyrillic texlive-lang-english \
-        texlive-lang-european texlive-lang-french texlive-lang-german \
-        texlive-lang-italian texlive-lang-japanese texlive-lang-polish \
-        texlive-lang-portuguese texlive-lang-spanish texlive-latex-extra \
-        texlive-luatex texlive-xetex xindy
-RUN useradd jovyan -u 1000 -s /bin/bash -m -h /home/jovyan
+FROM debian:stable AS build
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked \
+    apt update &&\
+    apt install -y python3 python3-dev pipx gcc g++ libffi-dev cargo cmake autoconf swig ninja-build patchelf meson python3-faiss adduser
+RUN adduser -u 1000 --system --shell /bin/sh --home /home/jovyan jovyan
 USER jovyan
 WORKDIR /home/jovyan
-COPY build.sh build.sh
-RUN git clone -c core.symlinks=true --filter blob:none  \
-    --origin upstream --branch master --tags \
-    https://github.com/sagemath/sage.git
-RUN export srcdir=/home/jovyan/sage source build.sh && prepare && build
+RUN python3 -m venv venv
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install sagemath
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install jupyter-core
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install jupyterhub
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install jupyterlab
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install notebook
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install ipywidgets
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install jupyterlab-lsp
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install python-lsp-server[yapf,rope,pyflakes] 
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install jupyter-ai
+RUN --mount=type=cache,target=/home/jovyan/.cache/pip,uid=1000,gid=1000 venv/bin/pip install langchain-openai langchain_ollama
+
+ENV PATH="/home/jovyan/venv/bin/:$PATH"
+
+FROM debian:stable
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    --mount=type=cache,target=/var/lib/apt,sharing=locked \
+    apt update &&\
+    apt install -y python3 adduser
+RUN adduser -u 1000 --system --shell /bin/sh --home /home/jovyan jovyan
+USER jovyan
+COPY --from=build /home/jovyan /home/jovyan
+COPY jupyter_server_config.py docker_healthcheck.py /etc/jupyter/
+COPY start-notebook.py start-singleuser.py /usr/local/bin/
+RUN mkdir /home/jovyan/work
+WORKDIR /home/jovyan/work
+ENV JUPYTER_PORT=8888
+EXPOSE $JUPYTER_PORT
+ENV PATH="/home/jovyan/venv/bin/:$PATH"
+CMD ["start-notebook.py"]
+
+# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
+# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server`, and `retro` jupyter commands
+# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
+HEALTHCHECK --interval=3s --timeout=1s --start-period=3s --retries=3 \
+    CMD /etc/jupyter/docker_healthcheck.py || exit 1

jupyter-sage/build.sh

@@ -1,15 +1,18 @@
 #!/usr/bin/env sh
+set -e
 
-pkgs=(standard
-       bliss
-       coxeter3
-       mcqd
-       meataxe
-       sirocco
-       tdlib)
+# pkgs=(
+#   standard
+#   bliss
+#   coxeter3
+#   mcqd
+#   meataxe
+#   sirocco
+#   tdlib
+# )
 
-prepare(){
-  cd sage
+prepare() {
+  cd "${srcdir}"
 # use correct latte-count binary name
 #  patch -p1 -i ../latte-count.patch
 # update to tdlib 0.9 (Fedora)
@@ -23,29 +26,17 @@ prepare(){
 }
 
 build() {
-  export SAGE_NUM_THREADS=$(($(nproc)/2))
-  export PYTHONPATH="$PWD"/sage/pkgs/sage-setup
-
-  for _pkg in ${_pkgs[@]}; do
-    cd "$srcdir"/sage/pkgs/sagemath-$_pkg
-    python setup.py build
-  done
+  #export SAGE_NUM_THREADS=$(($(nproc)/2))
+  #export PYTHONPATH="$PWD"/sage/pkgs/sage-setup
+  python3 -m build --wheel --no-isolation -C setup-args=-Dbuild-docs=false
 }
 
 package() {
-  for _pkg in ${_pkgs[@]}; do
-    cd "$srcdir"/sage/pkgs/sagemath-$_pkg
-    python setup.py install --root="$pkgdir" --optimize=1
-  done
-
-# fix symlinks to assets
-#  _pythonpath=`python -c "from sysconfig import get_path; print(get_path('platlib'))"`
-#  for _i in $(ls "$srcdir"/sage/src/sage/ext_data/notebook-ipython); do
-#    rm "$pkgdir"/usr/share/jupyter/kernels/sagemath/$_i
-#    ln -s $_pythonpath/sage/ext_data/notebook-ipython/$_i "$pkgdir"/usr/share/jupyter/kernels/sagemath/
-#  done
-
-# adjust threejs version
-#  rm "$pkgdir"$_pythonpath/sage/ext_data/threejs/threejs-version.txt
-#  ln -s /usr/share/threejs-sage/version "$pkgdir"$_pythonpath/sage/ext_data/threejs/threejs-version.txt
+    python -m installer dist/*.whl
 }
+
+# prepare
+
+build
+
+package

jupyter-sage/start-notebook.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+import os
+import shlex
+import sys
+
+# If we are in a JupyterHub, we pass on to `start-singleuser.py` instead so it does the right thing
+if "JUPYTERHUB_API_TOKEN" in os.environ:
+    print(
+        "WARNING: using start-singleuser.py instead of start-notebook.py to start a server associated with JupyterHub."
+    )
+    command = ["/usr/local/bin/start-singleuser.py"] + sys.argv[1:]
+    os.execvp(command[0], command)
+
+
+# Entrypoint is start.sh
+command = []
+
+# If we want to survive restarts, launch the command using `run-one-constantly`
+if os.environ.get("RESTARTABLE") == "yes":
+    command.append("run-one-constantly")
+
+# We always launch a jupyter subcommand from this script
+command.append("jupyter")
+
+# Launch the configured subcommand.
+# Note that this should be a single string, so we don't split it.
+# We default to `lab`.
+jupyter_command = os.environ.get("DOCKER_STACKS_JUPYTER_CMD", "lab")
+command.append(jupyter_command)
+
+# Append any optional NOTEBOOK_ARGS we were passed in.
+# This is supposed to be multiple args passed on to the notebook command,
+# so we split it correctly with shlex
+if "NOTEBOOK_ARGS" in os.environ:
+    command += shlex.split(os.environ["NOTEBOOK_ARGS"])
+
+# Pass through any other args we were passed on the command line
+command += sys.argv[1:]
+
+# Execute the command!
+print("Executing: " + " ".join(command))
+os.execvp(command[0], command)