Merge pull request #343 from pyiron/debug_tests

Debug docker stack - try to fix notebook execution

Author: niklassiemer

.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