Tar home build

.dockerignore

@@ -0,0 +1,14 @@
+**/*.egg-info
+**/*.pyc
+**/*.tar.gz
+*.code-workspace
+**/.*.ipynb
+**/.ipynb*
+.venv/
+build/
+export/
+.do-not-setup-on-localhost
+
+# Sphinx documentation
+docs/html
+screenshots/

Dockerfile

@@ -1,48 +1,55 @@
 # syntax=docker/dockerfile:1
 FROM ghcr.io/astral-sh/uv:0.2.18 AS uv
-FROM ghcr.io/aiidalab/full-stack:2024.1019
-
-# Copy whole repo and pre-install the dependencies and app to the tmp folder.
-# In the before notebook scripts the app will be re-installed by moving it to the app folder.
-ENV PREINSTALL_APP_FOLDER=${CONDA_DIR}/aiidalab-qe
-COPY --chown=${NB_UID}:${NB_GID} . ${PREINSTALL_APP_FOLDER}
+FROM ghcr.io/aiidalab/full-stack:2024.1021
 
 USER ${NB_USER}
 
-# Using uv to speed up installation, per docs:
+ENV QE_VERSION="7.2"
+
+# 1. Install Quantum Espresso into a conda environment
+# (we do this here for better caching during Docker build)
+RUN mamba create -p /opt/conda/envs/quantum-espresso --yes \
+    qe=${QE_VERSION} && \
+    mkdir -p /home/${NB_USER}/.conda/envs && \
+    ln -s /opt/conda/envs/quantum-espresso /home/${NB_USER}/.conda/envs/quantum-espresso-${QE_VERSION} && \
+    mamba clean --all -f -y
+
+ENV QE_APP_FOLDER=${AIIDALAB_APPS}/quantum-espresso
+# 2. Copy files needed for installing stuff, the rest is copied at the end for better caching
+COPY --chown=${NB_UID}:${NB_GID} src/ ${QE_APP_FOLDER}/src
+COPY --chown=${NB_UID}:${NB_GID} setup.cfg pyproject.toml *yaml README.md ${QE_APP_FOLDER}
+
+WORKDIR "${QE_APP_FOLDER}"
+# 3.Install python dependencies
+# Use uv instead of pip to speed up installation, per docs:
 # https://github.com/astral-sh/uv/blob/main/docs/guides/docker.md#using-uv-temporarily
-# Use the same constraint file as PIP
+# Use the same constraint file as pip
 ENV UV_CONSTRAINT=${PIP_CONSTRAINT}
-RUN  --mount=from=uv,source=/uv,target=/bin/uv \
-     cd ${PREINSTALL_APP_FOLDER} && \
-     # Remove all untracked files and directories. For example the setup lock flag file.
-     git clean -fx && \
-     # It is important to install from `aiidalab install` to mimic the exact installation operation as
-     # from the app store.
-     # The command wil first install the dependencies from list by parsing setup config files,
-     # (for `aiidalab/aiidalab<23.03.2` the `setup.py` should be in the root folder of the app https://github.com/aiidalab/aiidalab/pull/382).
-     # and then the app and restart the daemon in the end.
-     # But since the aiida profile not yet exists, the daemon restart will fail but it is not a problem.
-     # Because we only need the dependencies to be installed.
-     # aiidalab install --yes --python ${CONDA_DIR}/bin/python  "quantum-espresso@file://${PREINSTALL_APP_FOLDER}" && \
-     # However, have to use `pip install` explicitly because `aiidalab install` call `pip install --user` which will install the app to `/home/${NB_USER}/.local`.
-     # It won't cause issue for docker but for k8s deployment the home folder is not bind mounted to the pod and the dependencies won't be found. (see issue in `jupyter/docker-stacks` https://github.com/jupyter/docker-stacks/issues/815)
-     uv pip install --system --no-cache . && \
-     fix-permissions "${CONDA_DIR}" && \
-     fix-permissions "/home/${NB_USER}"
+RUN --mount=from=uv,source=/uv,target=/bin/uv \
+    uv pip install --system --no-cache . && \
+    rm -rf build/ src/aiidalab_qe.egg-info/
+
+# 4. Prepare AiiDA profile and localhost computer
+# 5. Install the QE pseudopotentials and codes
+RUN bash /usr/local/bin/before-notebook.d/20_start-postgresql.sh && \
+    bash /usr/local/bin/before-notebook.d/40_prepare-aiida.sh && \
+    python -m aiidalab_qe install-qe && \
+    python -m aiidalab_qe install-pseudos && \
+    verdi daemon stop && \
+    mamba run -n aiida-core-services pg_ctl stop
 
-ENV QE_VERSION="7.2"
-RUN mamba create -p /opt/conda/envs/quantum-espresso --yes \
-        qe=${QE_VERSION} \
-     && mamba clean --all -f -y && \
-     fix-permissions "${CONDA_DIR}" && \
-     fix-permissions "/home/${NB_USER}"
 
-# Download the QE pseudopotentials to the folder for afterware installation.
-ENV PSEUDO_FOLDER=${CONDA_DIR}/pseudo
-RUN mkdir -p ${PSEUDO_FOLDER} && \
-    python -m aiidalab_qe download-pseudos --dest ${PSEUDO_FOLDER}
+# 6. Copy the whole repo
+COPY --chown=${NB_UID}:${NB_GID} . ${QE_APP_FOLDER}
+# Remove all untracked files and directories.
+RUN git clean -dffx || true
 
-COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
+USER root
+COPY ./before-notebook.d/* /usr/local/bin/before-notebook.d/
+RUN fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
 
 WORKDIR "/home/${NB_USER}"
+RUN tar -cf /opt/home.tar .
+
+USER ${NB_USER}

before-notebook.d/00_untar_home.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+#
+home="/home/${NB_USER}"
+
+if [[ ! -d ${home} ]]; then
+    echo "Directory $home does not exist!"
+    exit 1
+fi
+
+# Untar home archive file to restore home directory if it is empty
+if [[ $(ls -A ${home} | wc -l) = "0" ]];then
+  if [ -f /opt/home.tar.gz ]; then
+    echo "Extracting /opt/home.tar to /home/${NB_USER}"
+    tar -xf /opt/home.tar -C /home/${NB_USER}
+  fi
+fi