diff --git a/docker/apmtools/Dockerfile b/docker/apmtools/Dockerfile
index 79ea0fc63c754422208ff54d6ffae110d0df77bd..04b4a7555998ef97970bf15da5c56a44d010d311 100644
--- a/docker/apmtools/Dockerfile
+++ b/docker/apmtools/Dockerfile
@@ -31,12 +31,12 @@ ENV PATH=/usr/local/miniconda3/bin:/home/atom_probe_tools/paraprobe-toolbox/code
RUN cd ~ \
&& apt update \
- && apt install -y curl=7.68.0-1ubuntu2.18 \
+ && apt install -y curl \
&& curl -sL https://deb.nodesource.com/setup_18.x -o nodesource_setup.sh \
&& chmod +x nodesource_setup.sh \
&& ./nodesource_setup.sh \
- && apt install -y nodejs=18.16.0-deb-1nodesource1 \
- && apt install -y m4=1.4.18-4 file=1:5.38-4 git=1:2.25.1-1ubuntu3.11 wget=1.20.3-1ubuntu2 libgl1-mesa-dev=21.2.6-0ubuntu0.1~20.04.2 libglu1-mesa-dev=9.0.1-1build1 build-essential=12.8ubuntu1.1 mpich=3.3.2-2build1 libgmp-dev=2:6.2.0+dfsg-4ubuntu0.1 libmpfr-dev=4.0.2-1 libssl-dev=1.1.1f-1ubuntu2.19 hwloc=2.1.0+dfsg-4 \
+ && apt install -y nodejs \
+ && apt install -y m4 file git wget libgl1-mesa-dev libglu1-mesa-dev build-essential mpich libgmp-dev libmpfr-dev libssl-dev hwloc \
&& wget https://repo.anaconda.com/miniconda/Miniconda3-py38_23.1.0-1-Linux-x86_64.sh \
&& mv Miniconda3-py38_23.1.0-1-Linux-x86_64.sh miniconda3-py38_23.1.0-1-Linux-x86_64.sh \
&& chmod +x miniconda3-py38_23.1.0-1-Linux-x86_64.sh \
diff --git a/docker/mpes/Dockerfile.jupyter b/docker/mpes/Dockerfile.jupyter
index b7eb10010117f56db228dc6d830a9e1e67174a9a..151e2661243cb199edf135f06996d795faa88f0e 100644
--- a/docker/mpes/Dockerfile.jupyter
+++ b/docker/mpes/Dockerfile.jupyter
@@ -11,5 +11,8 @@ RUN pip install -r requirements.jupyter.txt \
RUN rm requirements.jupyter.txt
USER root
-RUN apt-get install unzip
+RUN apt-get update --yes && \
+ apt-get install --yes --no-install-recommends \
+ unzip curl && \
+ apt-get clean && rm -rf /var/lib/apt/lists/*
USER $NB_UID
\ No newline at end of file
diff --git a/docker/mpes/generate_requirements.sh b/docker/mpes/generate_requirements.sh
index 4f66430f26ad41b7ebbfc4305a0cce3b551f45a7..8292decdf51f5d1d076313e4cb1a94c344578598 100755
--- a/docker/mpes/generate_requirements.sh
+++ b/docker/mpes/generate_requirements.sh
@@ -1,8 +1,8 @@
#!/bin/bash
docker run --rm --env HOME=/home/jovyan --mount type=bind,source="$(pwd)",target=/home/jovyan \
- --entrypoint bash jupyter/scipy-notebook:2023-04-10 -c \
+ --platform linux/amd64 --entrypoint bash jupyter/scipy-notebook:2023-04-10 -c \
"pip install pip-tools; pip-compile --resolver=backtracking --upgrade --output-file requirements.jupyter.txt requirements.jupyter.in"
docker run --rm --env HOME=/config --mount type=bind,source="$(pwd)",target=/config \
- --entrypoint bash gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop:v0.0.1 -c \
+ --platform linux/amd64 --entrypoint bash gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop:v0.0.1 -c \
"pip install pip-tools; pip-compile --output-file=requirements.webtop.txt --resolver=backtracking requirements.jupyter.txt requirements.webtop.in"
\ No newline at end of file
diff --git a/docker/mpes/requirements.jupyter.in b/docker/mpes/requirements.jupyter.in
index 2bad2e1f1ceac4a587786de4070d0302e947a646..cb9b252615d3645324acf336676f940e2066abe2 100644
--- a/docker/mpes/requirements.jupyter.in
+++ b/docker/mpes/requirements.jupyter.in
@@ -7,4 +7,5 @@ jupyterlab>=3.2.9
jupyterlab_h5web[full]>=6.0.0
punx>=0.2.5
mpes>=1.1.4
-silx>=1.1.2
\ No newline at end of file
+silx>=1.1.2
+numpy<1.24
\ No newline at end of file
diff --git a/docker/mpes/requirements.jupyter.txt b/docker/mpes/requirements.jupyter.txt
index 8e27f81182b3fdfb2401d805707bddc7c965152b..4bf3f89baf04ff79a60af98fe2f91f26b3ae3a73 100644
--- a/docker/mpes/requirements.jupyter.txt
+++ b/docker/mpes/requirements.jupyter.txt
@@ -2,11 +2,11 @@
# This file is autogenerated by pip-compile with Python 3.10
# by the following command:
#
-# pip-compile --output-file=requirements.jupyter.txt --resolver=backtracking requirements.jupyter.in
+# pip-compile --output-file=requirements.jupyter.txt requirements.jupyter.in
#
alabaster==0.7.13
# via sphinx
-anyio==3.6.2
+anyio==3.7.1
# via jupyter-server
argon2-cffi==21.3.0
# via
@@ -15,13 +15,17 @@ argon2-cffi==21.3.0
# notebook
argon2-cffi-bindings==21.2.0
# via argon2-cffi
-ase==3.19.0
+arrow==1.2.3
+ # via isoduration
+asciitree==0.3.3
+ # via zarr
+ase==3.22.1
# via
# ifes-apt-tc-data-modeling
# pynxtools
-asteval==0.9.29
+asteval==0.9.31
# via lmfit
-astropy==5.2.2
+astropy==5.3.1
# via
# mpes
# photutils
@@ -32,6 +36,7 @@ attrs==23.1.0
# via
# cattrs
# jsonschema
+ # referencing
# requests-cache
babel==2.12.1
# via
@@ -49,15 +54,15 @@ bokeh==2.4.3
# via
# dask
# mpes
-cattrs==22.2.0
+cattrs==23.1.2
# via requests-cache
-certifi==2023.5.7
+certifi==2023.7.22
# via requests
cffi==1.15.1
# via argon2-cffi-bindings
-charset-normalizer==3.1.0
+charset-normalizer==3.2.0
# via requests
-click==8.1.3
+click==8.1.6
# via
# dask
# distributed
@@ -70,17 +75,17 @@ comm==0.1.3
# via ipykernel
commonmark==0.9.1
# via recommonmark
-contourpy==1.0.7
+contourpy==1.1.0
# via matplotlib
-coverage==7.2.5
+coverage==7.2.7
# via mpes
cramjam==2.6.2
# via fastparquet
cycler==0.11.0
# via matplotlib
-cython==0.29.34
+cython==3.0.0
# via tables
-dask[array,complete,dataframe,diagnostics,distributed]==2023.4.1
+dask[array,complete,dataframe,diagnostics,distributed]==2023.7.1
# via
# distributed
# hyperspy
@@ -103,13 +108,13 @@ diffpy-structure==3.1.0
# diffsims
# kikuchipy
# orix
-diffsims==0.5.1
+diffsims==0.5.2
# via
# kikuchipy
# pyxem
-dill==0.3.6
+dill==0.3.7
# via hyperspy
-distributed==2023.4.1
+distributed==2023.7.1
# via dask
docutils==0.18.1
# via
@@ -117,26 +122,35 @@ docutils==0.18.1
# sphinx
# sphinx-rtd-theme
entrypoints==0.4
- # via ipyparallel
-exceptiongroup==1.1.1
- # via cattrs
+ # via
+ # ipyparallel
+ # jupyter-client
+ # numcodecs
+exceptiongroup==1.1.2
+ # via
+ # anyio
+ # cattrs
executing==1.2.0
# via stack-data
-fabio==2023.4.1
+fabio==2023.6.0
# via
# pyfai
# silx
fastdtw==0.3.4
# via mpes
-fastjsonschema==2.16.3
+fasteners==0.18
+ # via zarr
+fastjsonschema==2.18.0
# via nbformat
-fastparquet==2023.4.0
+fastparquet==2023.7.0
# via mpes
flatdict==4.0.1
# via pynxtools
-fonttools==4.39.3
+fonttools==4.41.1
# via matplotlib
-fsspec==2023.5.0
+fqdn==1.5.1
+ # via jsonschema
+fsspec==2023.6.0
# via
# dask
# fastparquet
@@ -147,7 +161,7 @@ future==0.18.3
# via uncertainties
gitdb==4.0.10
# via gitpython
-gitpython==3.1.31
+gitpython==3.1.32
# via pynxtools
h5glance==0.8.1
# via -r requirements.jupyter.in
@@ -155,7 +169,7 @@ h5grove==1.3.0
# via
# -r requirements.jupyter.in
# jupyterlab-h5web
-h5py==3.8.0
+h5py==3.9.0
# via
# h5glance
# h5grove
@@ -165,12 +179,13 @@ h5py==3.8.0
# jupyterlab-h5web
# kikuchipy
# mpes
+ # nionswift
# orix
# punx
# pyfai
# pynxtools
# silx
-hdf5plugin==4.1.1
+hdf5plugin==4.1.3
# via jupyterlab-h5web
htmlgen==2.0.0
# via h5glance
@@ -182,8 +197,9 @@ hyperspy==1.7.5
idna==3.4
# via
# anyio
+ # jsonschema
# requests
-ifes-apt-tc-data-modeling==0.0.8
+ifes-apt-tc-data-modeling==0.0.9
# via pynxtools
igor==0.3
# via mpes
@@ -192,14 +208,17 @@ imageio==2.27.0
# hyperspy
# kikuchipy
# mpes
+ # nionswift
+ # nionswift-io
+ # nionui
# scikit-image
imagesize==1.4.1
# via sphinx
-importlib-metadata==6.6.0
+importlib-metadata==6.8.0
# via
# dask
# hyperspy
-ipykernel==6.23.0
+ipykernel==6.25.0
# via
# ipyparallel
# ipywidgets
@@ -207,7 +226,7 @@ ipykernel==6.23.0
# notebook
ipyparallel==8.6.1
# via hyperspy
-ipython==8.13.2
+ipython==8.14.0
# via
# hyperspy
# ipykernel
@@ -223,6 +242,8 @@ ipywidgets==7.7.5
# via
# -r requirements.jupyter.in
# pyxem
+isoduration==20.11.0
+ # via jsonschema
jedi==0.18.2
# via ipython
jinja2==3.1.2
@@ -238,15 +259,20 @@ jinja2==3.1.2
# nbconvert
# notebook
# sphinx
-joblib==1.2.0
+joblib==1.3.1
# via scikit-learn
-json5==0.9.11
+json5==0.9.14
# via jupyterlab-server
-jsonschema==4.17.3
+jsonpointer==2.4
+ # via jsonschema
+jsonschema[format-nongpl]==4.18.4
# via
+ # jupyter-events
# jupyterlab-server
# nbformat
-jupyter-client==8.2.0
+jsonschema-specifications==2023.7.1
+ # via jsonschema
+jupyter-client==7.4.9
# via
# ipykernel
# ipyparallel
@@ -254,7 +280,7 @@ jupyter-client==8.2.0
# nbclassic
# nbclient
# notebook
-jupyter-core==5.3.0
+jupyter-core==5.3.1
# via
# ipykernel
# jupyter-client
@@ -265,40 +291,42 @@ jupyter-core==5.3.0
# nbconvert
# nbformat
# notebook
-jupyter-server==1.24.0
+jupyter-events==0.6.3
+ # via jupyter-server
+jupyter-server==2.7.0
# via
# jupyterlab
# jupyterlab-h5web
# jupyterlab-server
# nbclassic
# notebook-shim
+jupyter-server-terminals==0.4.4
+ # via jupyter-server
jupyterlab==3.5.3
# via
# -r requirements.jupyter.in
- # ifes-apt-tc-data-modeling
# pynxtools
-jupyterlab-h5web[full]==7.1.1
+jupyterlab-h5web[full]==10.0.0
# via
# -r requirements.jupyter.in
- # ifes-apt-tc-data-modeling
# pynxtools
jupyterlab-pygments==0.2.2
# via nbconvert
-jupyterlab-server==2.22.1
+jupyterlab-server==2.24.0
# via jupyterlab
jupyterlab-widgets==1.1.4
# via ipywidgets
-kikuchipy==0.8.4
+kikuchipy==0.8.7
# via pynxtools
kiwisolver==1.4.4
# via matplotlib
-lark==1.1.5
+lark==1.1.7
# via pynxtools
-lazy-loader==0.2
+lazy-loader==0.3
# via scikit-image
-llvmlite==0.40.0
+llvmlite==0.40.1
# via numba
-lmfit==1.2.1
+lmfit==1.2.2
# via
# mpes
# pyxem
@@ -306,17 +334,17 @@ locket==1.0.0
# via
# distributed
# partd
-lxml==4.9.2
+lxml==4.9.3
# via
# punx
# pyresttable
lz4==4.3.2
# via dask
-markupsafe==2.1.2
+markupsafe==2.1.3
# via
# jinja2
# nbconvert
-matplotlib==3.7.1
+matplotlib==3.7.2
# via
# ase
# diffsims
@@ -335,7 +363,7 @@ matplotlib-inline==0.1.6
# ipython
matplotlib-scalebar==0.8.1
# via orix
-mistune==2.0.5
+mistune==3.0.1
# via nbconvert
mpes==1.1.4
# via -r requirements.jupyter.in
@@ -345,7 +373,7 @@ msgpack==1.0.5
# via
# blosc2
# distributed
-natsort==8.3.1
+natsort==8.4.0
# via
# hyperspy
# mpes
@@ -353,14 +381,14 @@ nbclassic==1.0.0
# via
# jupyterlab
# notebook
-nbclient==0.7.4
+nbclient==0.8.0
# via nbconvert
-nbconvert==7.4.0
+nbconvert==7.7.3
# via
# jupyter-server
# nbclassic
# notebook
-nbformat==5.8.0
+nbformat==5.9.1
# via
# jupyter-server
# nbclassic
@@ -370,23 +398,40 @@ nbformat==5.8.0
nest-asyncio==1.5.6
# via
# ipykernel
+ # jupyter-client
# nbclassic
# notebook
networkx==3.1
# via
# radioactivedecay
# scikit-image
+niondata==0.15.5
+ # via
+ # nionswift
+ # nionswift-io
+nionswift==0.16.8
+ # via pynxtools
+nionswift-io==0.15.1
+ # via nionswift
+nionui==0.6.11
+ # via nionswift
+nionutils==0.4.7
+ # via
+ # niondata
+ # nionswift
+ # nionswift-io
+ # nionui
nodejs==0.1.1
# via -r requirements.jupyter.in
nose==1.3.7
# via mpes
-notebook==6.5.4
+notebook==6.5.5
# via
# jupyterlab
# widgetsnbextension
notebook-shim==0.2.3
# via nbclassic
-numba==0.57.0
+numba==0.57.1
# via
# diffsims
# hyperspy
@@ -395,13 +440,16 @@ numba==0.57.0
# orix
# pyxem
# sparse
+numcodecs==0.11.0
+ # via zarr
numexpr==2.8.4
# via
# hyperspy
# pyfai
# tables
-numpy==1.24.3
+numpy==1.23.5
# via
+ # -r requirements.jupyter.in
# ase
# astropy
# bokeh
@@ -421,7 +469,12 @@ numpy==1.24.3
# lmfit
# matplotlib
# mpes
+ # niondata
+ # nionswift
+ # nionswift-io
+ # nionui
# numba
+ # numcodecs
# numexpr
# numpy-quaternion
# opencv-python
@@ -446,9 +499,10 @@ numpy==1.24.3
# tables
# tifffile
# xarray
+ # zarr
numpy-quaternion==2022.4.3
# via orix
-opencv-python==4.7.0.72
+opencv-python==4.8.0.74
# via
# mpes
# symmetrize
@@ -459,8 +513,10 @@ orix==0.11.1
# diffsims
# kikuchipy
# pyxem
-orjson==3.8.12
+orjson==3.9.2
# via h5grove
+overrides==7.3.1
+ # via jupyter-server
packaging==23.1
# via
# astropy
@@ -480,7 +536,7 @@ packaging==23.1
# sphinx
# tables
# xarray
-pandas==2.0.1
+pandas==2.0.3
# via
# dask
# fastparquet
@@ -496,21 +552,22 @@ partd==1.4.0
# via dask
pexpect==4.8.0
# via ipython
-photutils==1.7.0
+photutils==1.8.0
# via
# mpes
# symmetrize
pickleshare==0.7.5
# via ipython
-pillow==9.5.0
+pillow==10.0.0
# via
# bokeh
# imageio
# matplotlib
+ # nionswift
# scikit-image
-pint==0.21
+pint==0.22
# via hyperspy
-platformdirs==3.5.0
+platformdirs==3.9.1
# via
# jupyter-core
# pooch
@@ -519,14 +576,14 @@ pooch==1.7.0
# via
# kikuchipy
# orix
-prettytable==3.7.0
+prettytable==3.8.0
# via hyperspy
-prometheus-client==0.16.0
+prometheus-client==0.17.1
# via
# jupyter-server
# nbclassic
# notebook
-prompt-toolkit==3.0.38
+prompt-toolkit==3.0.39
# via ipython
psutil==5.9.5
# via
@@ -545,7 +602,7 @@ pure-eval==0.2.2
# via stack-data
py-cpuinfo==9.0.0
# via tables
-pyarrow==12.0.0
+pyarrow==12.0.1
# via dask
pycifrw==4.4.5
# via diffpy-structure
@@ -553,46 +610,51 @@ pycparser==2.21
# via cffi
pyerfa==2.0.0.3
# via astropy
-pyfai==2023.3.0
+pyfai==2023.5.0
# via pyxem
pygments==2.15.1
# via
# ipython
# nbconvert
# sphinx
-pynxtools==0.0.2
+pynxtools==0.0.3
# via -r requirements.jupyter.in
pyparsing==3.0.9
# via matplotlib
pyresttable==2020.0.8
# via punx
-pyrsistent==0.19.3
- # via jsonschema
python-dateutil==2.8.2
# via
+ # arrow
# hyperspy
# ipyparallel
# jupyter-client
# matplotlib
# pandas
+python-json-logger==2.0.7
+ # via jupyter-events
pytz==2023.3
# via
+ # nionswift
# pandas
# pynxtools
+pytz-deprecation-shim==0.1.0.post0
+ # via tzlocal
pywavelets==1.4.1
# via scikit-image
-pyxem==0.15.0
+pyxem==0.15.1
# via pynxtools
-pyyaml==6.0
+pyyaml==6.0.1
# via
# astropy
# bokeh
# dask
# distributed
# hyperspy
+ # jupyter-events
# kikuchipy
# pynxtools
-pyzmq==25.0.2
+pyzmq==24.0.1
# via
# ipykernel
# ipyparallel
@@ -600,11 +662,15 @@ pyzmq==25.0.2
# jupyter-server
# nbclassic
# notebook
-radioactivedecay==0.4.17
+radioactivedecay==0.4.18
# via ifes-apt-tc-data-modeling
recommonmark==0.7.1
# via symmetrize
-requests==2.30.0
+referencing==0.30.0
+ # via
+ # jsonschema
+ # jsonschema-specifications
+requests==2.31.0
# via
# hyperspy
# jupyterlab-server
@@ -613,16 +679,28 @@ requests==2.30.0
# pynxtools
# requests-cache
# sphinx
-requests-cache==1.0.1
+requests-cache==1.1.0
# via pynxtools
-scikit-image==0.20.0
+rfc3339-validator==0.1.4
+ # via
+ # jsonschema
+ # jupyter-events
+rfc3986-validator==0.1.1
+ # via
+ # jsonschema
+ # jupyter-events
+rpds-py==0.9.2
+ # via
+ # jsonschema
+ # referencing
+scikit-image==0.21.0
# via
# hyperspy
# kikuchipy
# mpes
# pyxem
# symmetrize
-scikit-learn==1.2.2
+scikit-learn==1.3.0
# via
# kikuchipy
# pyxem
@@ -635,6 +713,8 @@ scipy==1.8.1
# kikuchipy
# lmfit
# mpes
+ # niondata
+ # nionswift
# orix
# pyfai
# pynxtools
@@ -660,6 +740,7 @@ six==1.16.0
# bleach
# diffpy-structure
# python-dateutil
+ # rfc3339-validator
# url-normalize
smmap==5.0.0
# via gitdb
@@ -680,7 +761,7 @@ sphinx==6.2.1
# sphinx-rtd-theme
# sphinxcontrib-jquery
# symmetrize
-sphinx-rtd-theme==1.2.0
+sphinx-rtd-theme==1.2.2
# via symmetrize
sphinxcontrib-applehelp==1.0.4
# via sphinx
@@ -700,24 +781,25 @@ stack-data==0.6.2
# via ipython
symmetrize==0.5.5
# via mpes
-sympy==1.11.1
+sympy==1.12
# via
# hyperspy
# radioactivedecay
tables==3.8.0
# via deepdish
-tblib==1.7.0
+tblib==2.0.0
# via distributed
terminado==0.17.1
# via
# jupyter-server
+ # jupyter-server-terminals
# nbclassic
# notebook
-threadpoolctl==3.1.0
+threadpoolctl==3.2.0
# via
# mpes
# scikit-learn
-tifffile==2023.4.12
+tifffile==2023.7.18
# via
# h5grove
# hyperspy
@@ -732,7 +814,7 @@ toolz==0.12.0
# distributed
# hyperspy
# partd
-tornado==6.3.1
+tornado==6.3.2
# via
# bokeh
# distributed
@@ -761,6 +843,7 @@ traitlets==5.9.0
# ipywidgets
# jupyter-client
# jupyter-core
+ # jupyter-events
# jupyter-server
# matplotlib-inline
# nbclassic
@@ -774,15 +857,26 @@ transforms3d==0.4.1
# via
# diffsims
# pyxem
-typing-extensions==4.5.0
- # via bokeh
+typing-extensions==4.7.1
+ # via
+ # bokeh
+ # cattrs
+ # pint
tzdata==2023.3
- # via pandas
+ # via
+ # pandas
+ # pytz-deprecation-shim
+tzlocal==4.3
+ # via
+ # nionswift
+ # pynxtools
uncertainties==3.1.7
# via lmfit
+uri-template==1.3.0
+ # via jsonschema
url-normalize==1.4.3
# via requests-cache
-urllib3==2.0.2
+urllib3==2.0.4
# via
# distributed
# requests
@@ -791,23 +885,27 @@ wcwidth==0.2.6
# via
# prettytable
# prompt-toolkit
+webcolors==1.13
+ # via jsonschema
webencodings==0.5.1
# via
# bleach
# tinycss2
-websocket-client==1.5.1
+websocket-client==1.6.1
# via jupyter-server
widgetsnbextension==3.6.4
# via ipywidgets
-xarray==2023.4.2
+xarray==2023.7.0
# via
# mpes
# pynxtools
+zarr==2.16.0
+ # via hyperspy
zict==3.0.0
# via distributed
zipfile37==0.1.3
# via pynxtools
-zipp==3.15.0
+zipp==3.16.2
# via importlib-metadata
# The following packages are considered to be unsafe in a requirements file: