Merge pull request #373 from pyiron/main

Merge main

.github/workflows/push.yml

@@ -21,34 +21,41 @@ jobs:
       - name: Login to DockerHub Registry
         run: echo ${{ secrets.DOCKERHUB_PASSWORD }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
       - name: Build pyiron/base
+        timeout-minutes: 5
         run: |
           docker build -t pyiron/base:latest base/
           docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
       - name: Build pyiron/md
+        timeout-minutes: 5
         run: |
           tail --lines=+5 base/environment.yml >> md/environment.yml
           docker build -t pyiron/md:latest md/
           docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
       - name: Build pyiron/continuum
+        timeout-minutes: 5
         run: |
           docker build -t pyiron/continuum:latest continuum/
           docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
       - name: Build pyiron/pyiron
+        timeout-minutes: 5
         run: |
           tail --lines=+5 md/environment.yml >> pyiron/environment.yml
           docker build -t pyiron/pyiron:latest pyiron/
           docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
       - name: Build pyiron/potentialworkshop
+        timeout-minutes: 5
         run: | 
           tail --lines=+5 pyiron/environment.yml >> potentialworkshop/environment.yml
           docker build -t pyiron/potentialworkshop:latest potentialworkshop/
           docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
       - name: Build pyiron/experimental
+        timeout-minutes: 5
         run: |
           tail --lines=+5 base/environment.yml >> experimental/environment.yml
           docker build -t pyiron/experimental:latest experimental/
           docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
       - name: Build pyiron/mpie_cmti
+        timeout-minutes: 5
         run: |
           tail --lines=+5 pyiron/environment.yml >> mpie_cmti/environment.yml
           docker build -t pyiron/mpie_cmti:latest mpie_cmti/

.github/workflows/testing.yml

@@ -10,44 +10,59 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Build pyiron/base
+        timeout-minutes: 5
         run: |
           docker build -t pyiron/base:latest base/
           docker tag pyiron/base:latest pyiron/base:"$(date +%F)"
       - name: Build pyiron/md
+        timeout-minutes: 5
         run: |
           tail --lines=+5 base/environment.yml >> md/environment.yml
           docker build -t pyiron/md:latest md/
           docker tag pyiron/md:latest pyiron/md:"$(date +%F)"
       - name: Build pyiron/continuum
+        timeout-minutes: 5
         run: |
           docker build -t pyiron/continuum:latest continuum/
           docker tag pyiron/continuum:latest pyiron/continuum:"$(date +%F)"
       - name: Build pyiron/pyiron
+        timeout-minutes: 5
         run: |
           tail --lines=+5 md/environment.yml >> pyiron/environment.yml
           docker build -t pyiron/pyiron:latest pyiron/
           docker tag pyiron/pyiron:latest pyiron/pyiron:"$(date +%F)"
       - name: Build pyiron/potentialworkshop
+        timeout-minutes: 5
         run: | 
           tail --lines=+5 pyiron/environment.yml >> potentialworkshop/environment.yml
           docker build -t pyiron/potentialworkshop:latest potentialworkshop/
           docker tag pyiron/potentialworkshop:latest pyiron/potentialworkshop:"$(date +%F)"
       - name: Build pyiron/experimental
+        timeout-minutes: 5
         run: |
           tail --lines=+5 base/environment.yml >> experimental/environment.yml
           docker build -t pyiron/experimental:latest experimental/
           docker tag pyiron/experimental:latest pyiron/experimental:"$(date +%F)"
       - name: Build pyiron/mpie_cmti
+        timeout-minutes: 5
         run: |
           tail --lines=+5 pyiron/environment.yml >> mpie_cmti/environment.yml
           docker build -t pyiron/mpie_cmti:latest mpie_cmti/
           docker tag pyiron/mpie_cmti:latest pyiron/mpie_cmti:"$(date +%F)"
       # Testing
       - 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 --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;'
+      - name: Test pyiron/continuum
+        timeout-minutes: 5
+        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;'
+      - name: Test pyiron/base
+        timeout-minutes: 5
+        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;'  
+      - name: Test pyiron/pyiron
+        timeout-minutes: 20
+        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;'
+      - name: Test pyiron/experimental
+        timeout-minutes: 5
+        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;'
       # Export Environments
       - 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;' 

mpie_cmti/environment.yml

@@ -22,6 +22,6 @@ dependencies:
 - tensorflow =2.17.0
 - psycopg2 =2.9.9
 - numba =0.60.0
-- llama-index =0.11.2
-- jupyter-server-proxy =4.3.0
+- llama-index =0.11.3
+- jupyter-server-proxy =4.4.0
 - flux-core =0.64.0

requirements.txt

@@ -12,7 +12,7 @@ damask==3.0.0
 fenics==2019.1.0
 gpaw==24.6.0
 hyperspy==2.1.1
-jupyter-server-proxy==4.3.0
+jupyter-server-proxy==4.4.0
 nbgitpuller==1.2.1
 nglview==3.1.2
 pystem==0.0.26
@@ -27,4 +27,4 @@ temmeta==0.0.6
 vtk==9.2.6
 pytorch==2.1.2
 tensorflow==2.17.0
-llama-index==0.11.2
+llama-index==0.11.3