diff --git a/i14/templates/align-template.yaml b/i14/templates/align-template.yaml index bb0f233..81cf7d9 100644 --- a/i14/templates/align-template.yaml +++ b/i14/templates/align-template.yaml @@ -65,7 +65,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ inputs.parameters.inpath }}`}}" \ -p maskpath "{{`{{ inputs.parameters.maskpath }}`}}" \ -p complexpath "{{`{{ inputs.parameters.complexpath }}`}}" \ diff --git a/i14/templates/dpc-batch-template.yaml b/i14/templates/dpc-batch-template.yaml index f23c5e7..a2d7d61 100644 --- a/i14/templates/dpc-batch-template.yaml +++ b/i14/templates/dpc-batch-template.yaml @@ -72,7 +72,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ workflow.parameters.visitdir }}`}}/scan/i14-{{`{{ inputs.parameters.scanNumber }}`}}.nxs" \ -p process_configfile /tmp/config.yaml \ -p outpath "{{`{{ inputs.parameters.outputFolder }}`}}/i14-{{`{{ inputs.parameters.scanNumber }}`}}_dpc-phase.nxs" \ diff --git a/i14/templates/mask-template.yaml b/i14/templates/mask-template.yaml index 8a56429..e85d21b 100644 --- a/i14/templates/mask-template.yaml +++ b/i14/templates/mask-template.yaml @@ -73,7 +73,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ inputs.parameters.inpath }}`}}" \ -p outpath "{{`{{ inputs.parameters.outpath }}`}}" \ -p padding "{{`{{ inputs.parameters.padding }}`}}" \ diff --git a/i14/templates/phase-template.yaml b/i14/templates/phase-template.yaml index dcdca73..4e84fbb 100644 --- a/i14/templates/phase-template.yaml +++ b/i14/templates/phase-template.yaml @@ -65,7 +65,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ inputs.parameters.inpath }}`}}" \ -p maskpath "{{`{{ inputs.parameters.maskpath }}`}}" \ -p normalise "{{`{{ inputs.parameters.normalise }}`}}" \ diff --git a/i14/templates/xanes-auto-template.yaml b/i14/templates/xanes-auto-template.yaml index baa9eb2..35ade6e 100644 --- a/i14/templates/xanes-auto-template.yaml +++ b/i14/templates/xanes-auto-template.yaml @@ -128,7 +128,7 @@ spec: value: /opt/venv/lib64/python3.12/site-packages/hdf5plugin/plugins/ command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p first "{{`{{ inputs.parameters.first }}`}}" \ -p last "{{`{{ inputs.parameters.last }}`}}" \ -p exclude "{{`{{ inputs.parameters.exclude }}`}}" \ diff --git a/i14/templates/xanes-point-template.yaml b/i14/templates/xanes-point-template.yaml index 57dfd21..2466e7d 100644 --- a/i14/templates/xanes-point-template.yaml +++ b/i14/templates/xanes-point-template.yaml @@ -72,7 +72,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ workflow.parameters.visitdir }}`}}/scan/i14-{{`{{ inputs.parameters.scanNumber }}`}}.nxs" \ -p outpath "{{`{{ inputs.parameters.outputFolder }}`}}/i14-{{`{{ inputs.parameters.scanNumber }}`}}xanes_point.txt" \ -p edge_element "{{`{{ inputs.parameters.edgeElement }}`}}" \ diff --git a/i14/templates/xanes-sparse-template.yaml b/i14/templates/xanes-sparse-template.yaml index e6975d0..7c1b2ba 100644 --- a/i14/templates/xanes-sparse-template.yaml +++ b/i14/templates/xanes-sparse-template.yaml @@ -95,7 +95,7 @@ spec: value: /opt/venv/lib64/python3.12/site-packages/hdf5plugin/plugins/ command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p first "{{`{{ inputs.parameters.first }}`}}" \ -p last "{{`{{ inputs.parameters.last }}`}}" \ -p exclude "{{`{{ inputs.parameters.exclude }}`}}" \ diff --git a/i14/templates/xrd1d-batch-template.yaml b/i14/templates/xrd1d-batch-template.yaml index a83d2f1..dc866aa 100644 --- a/i14/templates/xrd1d-batch-template.yaml +++ b/i14/templates/xrd1d-batch-template.yaml @@ -100,7 +100,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ workflow.parameters.visitdir }}`}}/scan/i14-{{`{{ inputs.parameters.scanNumber }}`}}.nxs" \ -p process_configfile "{{`{{ inputs.parameters.xrdProcessConfigUpload }}`}}" \ -p outpath "{{`{{ inputs.parameters.outputFolder }}`}}/i14-{{`{{ inputs.parameters.scanNumber }}`}}-xrd1d.nxs" \ diff --git a/i14/templates/xrd2d-batch-template.yaml b/i14/templates/xrd2d-batch-template.yaml index 69e74cd..d48e040 100644 --- a/i14/templates/xrd2d-batch-template.yaml +++ b/i14/templates/xrd2d-batch-template.yaml @@ -89,7 +89,7 @@ spec: value: /tmp command: [bash] source: | - python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \ + python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb --prepare-only \ -p inpath "{{`{{ workflow.parameters.visitdir }}`}}/scan/i14-{{`{{ inputs.parameters.scanNumber }}`}}.nxs" \ -p process_configfile "{{`{{ inputs.parameters.xrdProcessConfigUpload }}`}}" \ -p outpath "{{`{{ inputs.parameters.outputFolder }}`}}/i14-{{`{{ inputs.parameters.scanNumber }}`}}-xrd2d.nxs" \