Merge main

.github/workflows/testing.yml

@@ -24,10 +24,10 @@ jobs:
       - run: docker build -t pyiron/mpie_cmti:latest mpie_cmti/
       - run: docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
       - run: docker images
-      - run: docker run --rm pyiron/continuum /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
-      - run: docker run --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'  
-      - run: docker run --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
-      - run: docker run --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
+      - run: docker run --rm pyiron/continuum /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
+      - run: docker run --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'  
+      - run: docker run --rm pyiron/pyiron /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
+      - run: docker run --rm pyiron/experimental /bin/bash -c 'source /opt/conda/bin/activate; i=0; for f in $(ls "${HOME}"/notebooks_*/*.ipynb); do jupyter nbconvert --ExecutePreprocessor.timeout=9999999 --ExecutePreprocessor.kernel_name=python3 --to notebook --execute $f || i=$((i+1)); done; if [ $i -gt 0 ]; then exit 1; fi;'
       - run: mkdir -p environment; chmod 777 environment
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/base /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_base_$(date +%F).yml;' 
       - run: docker run -v $(pwd)/environment:/home/jovyan/ --rm pyiron/md /bin/bash -c 'source /opt/conda/bin/activate; conda env export > /home/jovyan/pyiron_md_$(date +%F).yml;' 

base/environment.yml

@@ -1,4 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- pyiron_base =0.8.4
+- pyiron_base =0.9.10
+- git =2.42.0
+- openmpi =4.1.6
+- hdf5 =1.14.3=mpi_openmpi_*

continuum/Dockerfile

@@ -25,7 +25,8 @@ RUN mamba env update -n base -f ${HOME}/environment.yml && \
 
 USER root
 ENV NOTEBOOK_DIR=${HOME}/notebooks_continuum
-RUN chmod +x ${HOME}/include_notebooks.sh && \
+RUN rm -rf ${HOME}/notebooks_atomistics && \
+    chmod +x ${HOME}/include_notebooks.sh && \
     /bin/bash ${HOME}/include_notebooks.sh && \
     fix-permissions ${HOME} && \
     fix-permissions $CONDA_DIR

continuum/environment.yml

@@ -4,8 +4,11 @@ dependencies:
 - damask =3.0.0a8
 - fenics =2019.1.0=*_42
 - mshr =2019.1.0=*_9
+- pyiron_base =0.8.2
+- pyiron_atomistics =0.5.3
 - pyiron_continuum =0.0.8
 - pyiron_gpl =0.0.5
 - pyvista =0.43.6
 - sqsgenerator =0.3
 - vtk =9.2.6
+- seaborn =0.13.2

experimental/Dockerfile

@@ -15,7 +15,8 @@ RUN mamba env update -n base -f ${HOME}/environment.yml && \
 
 USER root
 ENV NOTEBOOK_DIR=${HOME}/notebooks_experimental
-RUN chmod +x ${HOME}/include_notebooks.sh && \
+RUN rm -rf ${HOME}/notebooks_base && \
+    chmod +x ${HOME}/include_notebooks.sh && \
     /bin/bash ${HOME}/include_notebooks.sh && \
     fix-permissions $CONDA_DIR && \
     fix-permissions ${HOME}

md/Dockerfile

@@ -19,7 +19,8 @@ RUN mamba env update -n base -f ${HOME}/environment.yml && \
 
 USER root
 ENV NOTEBOOK_DIR=${HOME}/notebooks_atomistics
-RUN chmod +x ${HOME}/include_notebooks.sh && \
+RUN rm -rf ${HOME}/notebooks_base && \
+    chmod +x ${HOME}/include_notebooks.sh && \
     /bin/bash include_notebooks.sh &&\
     fix-permissions ${HOME} && \
     fix-permissions $CONDA_DIR

md/environment.yml

@@ -2,8 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - pyiron =0.5.2
-- pyiron_atomistics =0.5.4
-- pyscal =2.10.18
+- pyiron_atomistics =0.6.9
 - pyiron-data =0.0.29
 - nglview =3.1.2
 - lammps =2023.11.21=*openmpi*

mpie_cmti/environment.yml

@@ -5,12 +5,12 @@ dependencies:
 - calphy =1.3.8
 - fitsnap3 =3.1.0.1
 - nbgitpuller =1.2.1
-- pyiron_base =0.9.1
-- pyiron_atomistics =0.6.1
-- pyiron_snippets =0.1.1
+- pyiron_base =0.9.10
+- pyiron_atomistics =0.6.9
+- pyiron_snippets =0.1.3
 - pyiron_contrib =0.1.16
 - pyiron_potentialfit =0.3.2
-- pyiron_workflow =0.9.1
+- pyiron_workflow =0.9.4
 - pyiron_gui =0.0.12
 - matgl =0.9.2
 - mlip =2.0

potentialworkshop/Dockerfile

@@ -15,7 +15,8 @@ RUN mamba env update -n base -f ${HOME}/environment.yml && \
 
 USER root
 ENV NOTEBOOK_DIR=${HOME}/notebooks_potentialworkshop
-RUN chmod +x ${HOME}/include_notebooks.sh && \
+RUN rm -rf ${HOME}/notebooks_pyiron && \
+    chmod +x ${HOME}/include_notebooks.sh && \
     /bin/bash include_notebooks.sh &&\
     fix-permissions $CONDA_DIR && \
     fix-permissions ${HOME}

potentialworkshop/environment.yml

@@ -7,7 +7,6 @@ dependencies:
 - pyiron_contrib =0.1.16
 - pyiron_gpl =0.0.5
 - nbgitpuller =1.2.1
-- python-ace =0.2.8
-- tensorpotential =0.2.0
+- python-ace =0.3.0
 - calphy =1.3.7
 - pyxtal =0.6.7

pyiron/Dockerfile

@@ -16,7 +16,8 @@ RUN mamba install -n base -c defaults mkl=2023.2.0 && \
 
 USER root
 ENV NOTEBOOK_DIR=${HOME}/notebooks_pyiron
-RUN chmod +x ${HOME}/include_notebooks.sh && \
+RUN rm -rf ${HOME}/notebooks_atomistics && \
+    chmod +x ${HOME}/include_notebooks.sh && \
     /bin/bash include_notebooks.sh &&\
     fix-permissions $CONDA_DIR && \
     fix-permissions ${HOME}

pyiron/environment.yml

@@ -1,5 +1,5 @@
 channels:
 - conda-forge
 dependencies:
-- sphinxdft =3.0.7
-- gpaw =24.1.0=*openmpi*
+- sphinxdft =3.1
+- gpaw =24.6.0=*openmpi*

requirements.txt

@@ -1,23 +1,23 @@
 pyiron==0.5.2
-pyiron_base==0.9.1
-pyiron-atomistics==0.6.1
+pyiron_base==0.9.10
+pyiron-atomistics==0.6.9
 pyiron-continuum==0.0.8
 pyiron-contrib==0.1.16
 pyiron_experimental==0.0.3
-pyiron_workflow==0.9.1
+pyiron_workflow==0.9.4
 pyiron-gpl==0.0.5
 pyiron_snippets==0.1.1
 pyiron_potentialfit==0.3.2
 calphy==1.3.8
 damask==3.0.0a8
 fenics==2019.1.0
-gpaw==24.1.0
+gpaw==24.6.0
 hyperspy==2.1.1
 jupyter-server-proxy==4.1.2
 nbgitpuller==1.2.1
 nglview==3.1.2
 pystem==0.0.26
-python-ace==0.2.8
+python-ace==0.3.0
 pyvista==0.43.6
 pyxem==0.19.1
 pyxtal==0.6.7