From 868c302898a94c1697c1998a7faaa09802552ae5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Sep 2024 04:40:13 +0000 Subject: [PATCH 1/6] Bump jupyter-server-proxy from 4.3.0 to 4.4.0 Bumps [jupyter-server-proxy](https://github.com/jupyterhub/jupyter-server-proxy) from 4.3.0 to 4.4.0. - [Release notes](https://github.com/jupyterhub/jupyter-server-proxy/releases) - [Changelog](https://github.com/jupyterhub/jupyter-server-proxy/blob/main/RELEASE.md) - [Commits](https://github.com/jupyterhub/jupyter-server-proxy/compare/v4.3.0...v4.4.0) --- updated-dependencies: - dependency-name: jupyter-server-proxy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3e662952..099b235b 100644 --- a/requirements.txt +++ b/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 From bcfc39bf07499f254c02dc1be406044a2c0ced00 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Sep 2024 04:40:23 +0000 Subject: [PATCH 2/6] Bump llama-index from 0.11.2 to 0.11.3 Bumps [llama-index](https://github.com/run-llama/llama_index) from 0.11.2 to 0.11.3. - [Release notes](https://github.com/run-llama/llama_index/releases) - [Changelog](https://github.com/run-llama/llama_index/blob/main/CHANGELOG.md) - [Commits](https://github.com/run-llama/llama_index/compare/v0.11.2...v0.11.3) --- updated-dependencies: - dependency-name: llama-index dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 3e662952..2262d868 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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 From d9584c5744ad8482da50d92df11498365d4b8205 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Mon, 2 Sep 2024 04:40:27 +0000 Subject: [PATCH 3/6] [dependabot skip] Update environment --- mpie_cmti/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml index b6cd2683..fb4aa28e 100644 --- a/mpie_cmti/environment.yml +++ b/mpie_cmti/environment.yml @@ -23,5 +23,5 @@ dependencies: - psycopg2 =2.9.9 - numba =0.60.0 - llama-index =0.11.2 -- jupyter-server-proxy =4.3.0 +- jupyter-server-proxy =4.4.0 - flux-core =0.64.0 From 329db6a5e1e47062e1ebf63a5265e509956a5304 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Mon, 2 Sep 2024 04:40:36 +0000 Subject: [PATCH 4/6] [dependabot skip] Update environment --- mpie_cmti/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml index b6cd2683..2f78d137 100644 --- a/mpie_cmti/environment.yml +++ b/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 +- llama-index =0.11.3 - jupyter-server-proxy =4.3.0 - flux-core =0.64.0 From d5f86033fec640ba21ed193d496df08ab197f571 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 2 Sep 2024 08:38:03 +0200 Subject: [PATCH 5/6] Add timeout in testing.yml --- .github/workflows/testing.yml | 23 +++++++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index d1bb8b3d..cb5b0611 100644 --- a/.github/workflows/testing.yml +++ b/.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;' From 73da45781ed3f8e30cafe9aaa664a2116679c12d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 2 Sep 2024 08:38:56 +0200 Subject: [PATCH 6/6] Add timeout in push.yml --- .github/workflows/push.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index 304edd65..02469872 100644 --- a/.github/workflows/push.yml +++ b/.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/