Don't install pypi packages to ~/.local

Dockerfile

@@ -17,13 +17,10 @@ ARG UV_CACHE_DIR=/tmp/uv_cache
 ARG QE_APP_SRC=/tmp/quantum-espresso
 ARG COMPUTER_LABEL="localhost"
 
-#
-# We'll define the possible HQ download URLs (for x86_64 and ARM64).
-#
 ARG HQ_URL_AMD64="https://github.com/It4innovations/hyperqueue/releases/download/v${HQ_VER}/hq-v${HQ_VER}-linux-x64.tar.gz"
 ARG HQ_URL_ARM64="https://github.com/It4innovations/hyperqueue/releases/download/v${HQ_VER}/hq-v${HQ_VER}-linux-arm64-linux.tar.gz"
-ARG VIBROSCOPY_PKG="aiidalab-qe-vibroscopy@git+https://github.com/mikibonacci/aiidalab-qe-vibroscopy@v1.2.0"
-ARG MUON_PKG="aiidalab-qe-muon@git+https://github.com/mikibonacci/aiidalab-qe-muon@v1.0.0"
+ARG VIBROSCOPY_PKG="aiidalab-qe-vibroscopy@git+https://github.com/aiidalab/aiidalab-qe-vibroscopy@v1.2.1"
+ARG MUON_PKG="aiidalab-qe-muon@git+https://github.com/aiidalab/aiidalab-qe-muon@v1.0.1"
 ARG AIIDA_HQ_PKG="aiida-hyperqueue~=0.3.0"
 
 ###############################################################################
@@ -112,7 +109,8 @@ ENV UV_CONSTRAINT=${PIP_CONSTRAINT}
 # Install the aiida-hyperqueue
 RUN --mount=from=uv,source=/uv,target=/bin/uv \
     --mount=from=build_deps,source=${UV_CACHE_DIR},target=${UV_CACHE_DIR},rw \
-    uv pip install --system --strict --cache-dir=${UV_CACHE_DIR} ${AIIDA_HQ_PKG}
+    uv pip install --system --strict --cache-dir=${UV_CACHE_DIR} \
+      ${AIIDA_HQ_PKG} ${MUON_PKG} aiida-bader
 
 COPY ./before-notebook.d/* /usr/local/bin/before-notebook.d/
 
@@ -127,18 +125,16 @@ RUN --mount=from=qe_conda_env,source=${QE_DIR},target=${QE_DIR} \
     verdi code create core.code.installed --label python --computer=localhost --default-calc-job-plugin pythonjob.pythonjob --filepath-executable=/opt/conda/bin/python -n && \
     verdi code create core.code.installed --label bader --computer=localhost --default-calc-job-plugin bader.bader --filepath-executable=${QE_DIR}/bin/bader -n && \
     verdi code create core.code.installed --label wannier90 --computer=localhost --default-calc-job-plugin wannier90.wannier90 --filepath-executable=/opt/conda/bin/wannier90.x -n && \
-    # Additional plugins
-    pip uninstall -y phonopy && \
-    pip install aiida-bader ${VIBROSCOPY_PKG} ${MUON_PKG} && \
+    pip install --no-user ${VIBROSCOPY_PKG} && \
     # run post_install for plugin
     python -m aiida_bader post-install && \
     python -m aiidalab_qe_vibroscopy setup-phonopy && \
     python -m aiidalab_qe_muon setup-python3 && \
     # wannier90 plugin need SSSP 1.1
+    # Install this earlier as part of the pseudo installation
     aiida-pseudo install sssp -v 1.1 -x PBE && \
     aiida-pseudo install sssp -v 1.1 -x PBEsol && \
     verdi daemon stop && \
-    pip install spglib==2.5.0 && \
     mamba run -n aiida-core-services pg_ctl stop && \
     touch /home/${NB_USER}/.FLAG_HOME_INITIALIZED && \
     # NOTE: The work folder is empty but if included clashes with the work folder in a Renku
@@ -147,7 +143,7 @@ RUN --mount=from=qe_conda_env,source=${QE_DIR},target=${QE_DIR} \
     # It is usually safe (and preferable) to let .conda be recreated on the fly each time,
     # because .conda typically just holds local environment information, caches, or references
     # to available environments.
-    cd /home/${NB_USER} && tar -cf /opt/conda/home.tar --exclude work --exclude .conda .
+    cd /home/${NB_USER} && tar -cf /opt/conda/home.tar --exclude .cache --exclude work --exclude .conda .
 
 ###############################################################################
 # 6) Final stage
@@ -166,19 +162,27 @@ ARG MUON_PKG
 
 USER ${NB_USER}
 WORKDIR /tmp
-# Install python dependencies
+
+# Install common dependencies such as pymatgen and pandas via conda,
+# to avoid building them when installing via pip
+# TODO: Remove this once it is part of the full-stack image.
+RUN mamba install aiida-core.atomic_tools --y && \
+    mamba clean --all -f -y
+
+# Install dependencies in the final image.
+# It is important that these are installed in /opt/conda, not ~/.local
 # Use uv cache from the previous build step
-# # Install the aiida-hyperqueue
+# NOTE: uv refuses the install aiidalab-qe-vibroscopy due to invalid RECORD file,
+# pyproject.toml is likely invalid as it contains direct git dependency.
 ENV UV_CONSTRAINT=${PIP_CONSTRAINT}
 RUN --mount=from=uv,source=/uv,target=/bin/uv \
     --mount=from=build_deps,source=${UV_CACHE_DIR},target=${UV_CACHE_DIR},rw \
     --mount=from=build_deps,source=${QE_APP_SRC},target=${QE_APP_SRC},rw \
     uv pip install --strict --system --compile-bytecode --cache-dir=${UV_CACHE_DIR} \
-      ${QE_APP_SRC} ${AIIDA_HQ_PKG}
-# Install plugins in the final image
-RUN pip install aiida-bader ${VIBROSCOPY_PKG} ${MUON_PKG} && \
-    mamba install scipy==1.13.1 --y && \
-    mamba clean --all -f -y
+      ${QE_APP_SRC} aiida-bader ${AIIDA_HQ_PKG} ${MUON_PKG}
+
+# This fails on arm with `uv pip` so is installed separately
+RUN pip install --no-user ${VIBROSCOPY_PKG}
 
 # copy hq binary
 COPY --from=home_build /opt/conda/hq /usr/local/bin/