diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b0f7940..2d04211 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -323,7 +323,7 @@ jobs: - name: run-workflow shell: bash -l {0} run: | - conda install conda_subprocess=0.0.1 pyiron_base=0.7.11 + conda install conda_subprocess=0.0.1 pyiron_base=0.8.0 cd $GITHUB_WORKSPACE/exemplary_workflow/pyiron python workflow.py - name: upload-paper-artifact diff --git a/exemplary_workflow/pyiron/workflow.py b/exemplary_workflow/pyiron/workflow.py index 8a7f049..78ee019 100644 --- a/exemplary_workflow/pyiron/workflow.py +++ b/exemplary_workflow/pyiron/workflow.py @@ -38,14 +38,9 @@ # Processing ## poisson -def collect_output_poisson(working_directory): - with open(os.path.join(working_directory, "numdofs.txt"), "r") as f: - return {"numdofs": int(f.read())} - poisson = pr.wrap_executable( job_name="poisson", executable_str="python poisson.py --mesh square.xdmf --degree 2 --outputfile poisson.pvd --num-dofs numdofs.txt", - collect_output_funct=collect_output_poisson, conda_environment_path=pr.conda_environment.processing, input_file_lst=["../source/poisson.py", meshio.files.square_xdmf, meshio.files.square_h5], execute_job=True, @@ -65,7 +60,7 @@ def collect_output_poisson(working_directory): ## substitute macros macros = pr.wrap_executable( job_name="macros", - executable_str=f"python prepare_paper_macros.py --macro-template-file macros.tex.template --plot-data-path plotoverline.csv --domain-size {domain_size} --num-dofs {poisson.output['numdofs']} --output-macro-file macros.tex", + executable_str=f"python prepare_paper_macros.py --macro-template-file macros.tex.template --plot-data-path plotoverline.csv --domain-size {domain_size} --num-dofs {int(poisson.output['stdout'].split()[-1])} --output-macro-file macros.tex", conda_environment_path=pr.conda_environment.postprocessing, input_file_lst=["../source/macros.tex.template", "../source/prepare_paper_macros.py", pvbatch.files.plotoverline_csv], execute_job=True,