rename all

Author: pdiercks

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: run-simple-use-case
+name: run-exemplary-workflow
 
 on:
   push:
@@ -23,21 +23,21 @@ jobs:
       - name: setup-conda-environment
         uses: conda-incubator/setup-miniconda@v2
         with:
-          environment-file: simple_use_case/source/envs/default_env.yaml
+          environment-file: exemplary_workflow/source/envs/default_env.yaml
           miniforge-version: latest
-          activate-environment: simple_use_case
+          activate-environment: exemplary_workflow
 
       - name: run-workflow
         shell: bash -l {0}
         run: |
           conda install --channel conda-forge doit=0.33.1
-          cd $GITHUB_WORKSPACE/simple_use_case/pydoit
+          cd $GITHUB_WORKSPACE/exemplary_workflow/pydoit
           doit
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/pydoit/paper.pdf
+          path: ./exemplary_workflow/pydoit/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -54,21 +54,21 @@ jobs:
       - name: setup-conda-environment
         uses: conda-incubator/setup-miniconda@v2
         with:
-          environment-file: simple_use_case/source/envs/default_env.yaml
+          environment-file: exemplary_workflow/source/envs/default_env.yaml
           miniforge-version: latest
-          activate-environment: simple_use_case
+          activate-environment: exemplary_workflow
 
       - name: run-workflow
         shell: bash -l {0}
         run: |
           conda install --channel conda-forge cwltool
-          cd $GITHUB_WORKSPACE/simple_use_case/cwl
-          cwltool wf_run_use_case.cwl
+          cd $GITHUB_WORKSPACE/exemplary_workflow/cwl
+          cwltool wf_run_exemplary_wf.cwl
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/cwl/paper.pdf
+          path: ./exemplary_workflow/cwl/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -90,14 +90,14 @@ jobs:
         run: |
           sudo apt-get update && sudo apt-get install --no-install-recommends --yes python3-pip
           python3 -m pip install cwltool[deps]
-          cd $GITHUB_WORKSPACE/simple_use_case/cwl
-          python3 -m cwltool --debug --beta-conda-dependencies wf_run_use_case.cwl
+          cd $GITHUB_WORKSPACE/exemplary_workflow/cwl
+          python3 -m cwltool --debug --beta-conda-dependencies wf_run_exemplary_wf.cwl
 
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/cwl/paper.pdf
+          path: ./exemplary_workflow/cwl/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -115,19 +115,19 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniforge-version: latest
-          activate-environment: simple_use_case
+          activate-environment: exemplary_workflow
 
       - name: run-workflow
         shell: bash -l {0}
         run: |
           conda install --channel bioconda nextflow=21.04.0
-          cd $GITHUB_WORKSPACE/simple_use_case/nextflow
-          nextflow run simplecase.nf
+          cd $GITHUB_WORKSPACE/exemplary_workflow/nextflow
+          nextflow run exemplarywf.nf
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/nextflow/paper.pdf
+          path: ./exemplary_workflow/nextflow/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -146,21 +146,21 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniforge-version: latest
-          activate-environment: simple_use_case
+          activate-environment: exemplary_workflow
           channels: conda-forge,bioconda
           channel-priority: strict
 
       - name: run-workflow
         shell: bash -l {0}
         run: |
           conda install snakemake
-          cd $GITHUB_WORKSPACE/simple_use_case/snakemake
+          cd $GITHUB_WORKSPACE/exemplary_workflow/snakemake
           snakemake --cores 1 --use-conda --conda-frontend conda ./paper.pdf
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/snakemake/paper.pdf
+          path: ./exemplary_workflow/snakemake/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -177,22 +177,22 @@ jobs:
       - name: setup-conda-environment
         uses: conda-incubator/setup-miniconda@v2
         with:
-          environment-file: simple_use_case/source/envs/default_env.yaml
+          environment-file: exemplary_workflow/source/envs/default_env.yaml
           miniforge-version: latest
-          activate-environment: simple_use_case
+          activate-environment: exemplary_workflow
 
       - name: run-workflow
         shell: bash -l -i {0}
         run: |
-          bash $GITHUB_WORKSPACE/simple_use_case/kadistudio/install_components.sh
+          bash $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/install_components.sh
           mkdir $GITHUB_WORKSPACE/run
-          process_engine run $GITHUB_WORKSPACE/simple_use_case/kadistudio/simple_use_case.flow -p $GITHUB_WORKSPACE/run
+          process_engine run $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/exemplary_workflow.flow -p $GITHUB_WORKSPACE/run
 
       - name: upload-paper-artifact
         uses: actions/upload-artifact@v2
         with:
           name: paper
-          path: ./simple_use_case/kadistudio/paper.pdf
+          path: ./exemplary_workflow/kadistudio/paper.pdf
           retention-days: 1
           if-no-files-found: error
 
@@ -237,9 +237,9 @@ jobs:
     - name: setup-conda-environment
       uses: conda-incubator/setup-miniconda@v2
       with:
-        environment-file: simple_use_case/source/envs/default_env.yaml
+        environment-file: exemplary_workflow/source/envs/default_env.yaml
         miniforge-version: latest
-        activate-environment: simple_use_case
+        activate-environment: exemplary_workflow
 
     - name: install-aiida-shell
       # the shell directive is necessary to properly activate the shell
@@ -254,16 +254,16 @@ jobs:
         verdi quicksetup --non-interactive --profile default --email aiida@localhost --first-name Giuseppe --last-name Verdi --institution Khedivial --db-backend psql_dos
 
     - name: run-workflow
-      working-directory: simple_use_case/aiida
+      working-directory: exemplary_workflow/aiida
       shell: bash -l {0}
       run:
-        ./simple_use_case.py
+        ./exemplary_workflow.py
 
     - name: upload-paper-artifact
       uses: actions/upload-artifact@v2
       with:
         name: paper
-        path: ./simple_use_case/aiida/paper.pdf
+        path: ./exemplary_workflow/aiida/paper.pdf
         retention-days: 1
         if-no-files-found: error
 
@@ -293,11 +293,11 @@ jobs:
 
     - name: run-workflow
       run: |
-        cd simple_use_case/gwl
+        cd exemplary_workflow/gwl
         guix workflow run workflow.w
 
     - name: upload-paper-artifact
       uses: actions/upload-artifact@v2
       with:
         name: paper
-        path: simple_use_case/gwl/paper.pdf
+        path: exemplary_workflow/gwl/paper.pdf

README.md

@@ -48,7 +48,7 @@ reproducible research workflows, by anyone, anywhere and anytime.
 We greatly appreciate and encourage contributions by any users or developers of 
 workflow tools. 
 A list of preselected tools can be found in the [documentation](https://nfdi4ingscientificworkflowrequirements.readthedocs.io/en/latest/).
-If you would like to add an implementation of the [simple use case](https://nfdi4ingscientificworkflowrequirements.readthedocs.io/en/latest/docs/simpleusecase.html) for a tool
+If you would like to add an implementation of the [exemplary workflow](https://nfdi4ingscientificworkflowrequirements.readthedocs.io/en/latest/docs/exemplarywf.html) for a tool
 (not limited to the given list), or if you suggest changes to one of the
 existing implementations, please raise an issue and/or submit a pull request.
 We also encourage to start a new [discussion](https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/discussions)

conf.py

@@ -47,7 +47,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['conda-env','conda-env', '_build', 'Thumbs.db', '.DS_Store', 'simple_use_case']
+exclude_patterns = ['conda-env','conda-env', '_build', 'Thumbs.db', '.DS_Store', 'exemplary_workflow']
 
 
 # The master toctree document.

docs/simpleusecase.rst docs/exemplarywf.rstdocs/simpleusecase.rst renamed to docs/exemplarywf.rst

@@ -1,8 +1,8 @@
 
-.. _simpleusecase:
+.. _exemplarywf:
 
-Simple use case
-===============
+Exemplary workflow
+==================
 As a minimal working example representative of workflows in computational science, the 
 poisson equation is solved using the finite element method for a set of predefined boundary conditions :math:`u_{\mathrm{D}}`
 on a square domain :math:`\varOmega={(0, s)}^2, s\in\mathbb{R}^+`.
@@ -17,10 +17,10 @@ The final output of the workflow is a PDF document showing the solution :math:`u
 line :math:`L=\{(x, y)\in\varOmega\,\vert\,x=y\}` and the number of degrees of freedom used in the finite element model.
 The (directed acyclic graph of the) workflow is shown below and consists of the following processes:
 
-.. |DAG| image:: ./../img/simple_use_case_dag.png
+.. |DAG| image:: ./../img/exemplary_wf_dag.png
     :class: align-right
     :width: 95%
-    :alt: simple_use_case_dag
+    :alt: exemplary_wf_dag
 
 1. Partition of the computational domain using `Gmsh <http://gmsh.info/>`_, |DAG|
 
@@ -66,13 +66,13 @@ The (directed acyclic graph of the) workflow is shown below and consists of the
     cp source/paper.tex ./paper.tex
     tectonic ./paper.tex 
 
-It is important to note that the `source files <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/simple_use_case/source>`_ are
+It is important to note that the `source files <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/exemplary_workflow/source>`_ are
 regarded as static inputs, i.e. changing them may break the workflow and thus
 only the variable domain size should be exposed as an actual input parameter.
 The number of degrees of freedom is written to stdout
 by the FEniCS script `source/poisson.py`
 and used here to showcase how one might deal with output of integer type (i.e. non-file output).
 If the tool does not support this the number of degrees of freedom is written to a file.
 
-Details on the specific versions used for each software package can be found in the `conda environment specification file <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/simple_use_case/source/envs/default_env.yaml>`_.
-Exemplary implementations with various tools can be found `here <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/tree/main/simple_use_case>`_.
+Details on the specific versions used for each software package can be found in the `conda environment specification file <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/exemplary_workflow/source/envs/default_env.yaml>`_.
+Exemplary implementations with various tools can be found `here <https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/tree/main/exemplary_workflow>`_.

simple_use_case/README.md exemplary_workflow/README.mdsimple_use_case/README.md renamed to exemplary_workflow/README.md

@@ -1,4 +1,4 @@
-# Simple use case
+# Exemplary workflow
 As a minimal working example representative of workflows in computational science,
 the poisson equation is solved using the finite element method.
 The workflow consists of the following processes:
@@ -10,14 +10,14 @@ The workflow consists of the following processes:
 5. Preparation of macro definitions,
 6. Generation of a PDF using [LaTeX](https://www.latex-project.org/), [Tectonic](https://tectonic-typesetting.github.io/en-US/) respectively.
 
-A more extensive description can be found in the [documentation](https://nfdi4ingscientificworkflowrequirements.readthedocs.io/en/latest/docs/simpleusecase.html).
+A more extensive description can be found in the [documentation](https://nfdi4ingscientificworkflowrequirements.readthedocs.io/en/latest/docs/exemplarywf.html).
 
 ## Compute environment
 Details about how the compute environment is built (using [conda](https://docs.conda.io/en/latest/)) can be found in the respective sub-directory for each tool.
 
 ## Headless operation
-The ParaView version used in the examples (see the [conda environment specification file](https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/simple_use_case/source/envs/default_env.yaml)) is linked against EGL to also support offscreen rendering.
+The ParaView version used in the examples (see the [conda environment specification file](https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/exemplary_workflow/source/envs/default_env.yaml)) is linked against EGL to also support offscreen rendering.
 Usually, these libraries exist in case of a desktop pc where an actual screen or monitor is available.
-However, for headless operation, i.e. when executing the simple use case in a container, it is necessary to install aforementioned libraries since these are not installed automatically as a dependency by conda.
+However, for headless operation, i.e. when executing the exemplary workflow in a container, it is necessary to install aforementioned libraries since these are not installed automatically as a dependency by conda.
 We refer to the installation of the basic dependencies in our [github action](https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/.github/actions/install-basic-deps/action.yml) to give an example.
 For more information about offscreen rendering with ParaView go to the [ParaView documentation](https://kitware.github.io/paraview-docs/latest/cxx/Offscreen.html).

simple_use_case/aiida/.gitignore exemplary_workflow/aiida/.gitignoresimple_use_case/aiida/.gitignore renamed to exemplary_workflow/aiida/.gitignore

@@ -1,5 +1,5 @@
 # AiiDA
-This directory contains an implementation of the simple use case with [AiiDA](https://www.aiida.net/).
+This directory contains an implementation of the exemplary workflow with [AiiDA](https://www.aiida.net/).
 
 ## Implementation
 Since the implementation of workflows in AiiDA is quite different from the other file
@@ -11,7 +11,7 @@ According to the [documentation](https://aiida.readthedocs.io/projects/aiida-cor
 > The calcfunction in AiiDA is a function decorator that transforms a regular python function in a calculation process, which automatically stores the provenance of its output in the provenance graph when executed.
 
 Typically `calcfunction`s are used for short running processes to be run on the local machine, like preprocessing and postprocessing steps.
-One could think of a workaround, using `os.subprocess` inside a `calcfunction` to run the processes of the simple use case.
+One could think of a workaround, using `os.subprocess` inside a `calcfunction` to run the processes of the exemplary workflow.
 However, `calcfunction`s are not intended to be used to run external codes and the use of `os.subprocess` is discouraged since in this case the provenance cannot be properly captured by AiiDA.    
 
 ### Calculation jobs
@@ -38,10 +38,10 @@ sudo apt install \
     git python3-dev python3-pip \
     postgresql postgresql-server-dev-all postgresql-client rabbitmq-server
 ```
-Next, we prepare a conda environment with all the software required to run the simple use case.
+Next, we prepare a conda environment with all the software required to run the exemplary workflow.
 ```sh
-conda env create --name aiida_simplecase --file ../source/envs/default_env.yaml
-conda activate aiida_simplecase
+conda env create --name aiida_env --file ../source/envs/default_env.yaml
+conda activate aiida_env
 ```
 Make sure that the python version is greater than 3.8, since this is required by the `aiida-shell` plugin.
 Next we install the `aiida-shell` plugin, which will automatically install AiiDA as a dependency.
@@ -58,14 +58,14 @@ to setup a profile and see if everything was installed correctly by running
 verdi status
 ```
 
-## Running the simple use case
+## Running the exemplary workflow
 If you are using `conda`, activate your environment.
 ```
-conda activate aiida_simplecase
+conda activate aiida_env
 ```
-Make the workflow script executable (`chmod +x ./simple_use_case.py`) and run it with
+Make the workflow script executable (`chmod +x ./exemplary_workflow.py`) and run it with
 ```
-./simple_use_case.py
+./exemplary_workflow.py
 ```
 By default all `ShellJob`s are run on the `localhost`.
 Some useful commands to inspect the status of the processes run and their results stored in the database are listed below.

simple_use_case/aiida/README.md exemplary_workflow/aiida/README.mdsimple_use_case/aiida/README.md renamed to exemplary_workflow/aiida/README.md

@@ -6,16 +6,16 @@ If you have [`miniconda`](https://docs.conda.io/projects/conda/en/latest/user-gu
 installed, you can simply create a respective environment by typing
 
 ```sh
-conda env create --file default_env.yml --prefix ./simpleusecase
-conda activate ./simpleusecase
+conda env create --file default_env.yml --prefix ./exemplarywf
+conda activate ./exemplarywf
 ```
 
 Note that by specifying the `--prefix` option you can simply remove all downloaded packages afterwards
 by removing the folder given to `prefix`. To execute the workflow after activating the environment,
 simply type
 
 ```sh
-cwltool wf_run_use_case.cwl
+cwltool wf_run_exemplary_wf.cwl
 ```
 
 into your terminal.
@@ -24,7 +24,7 @@ Or you can use the conda dependency feature of the CWL reference runner to obtai
 the dependencies dynamically:
 
 ```sh
-cwltool --beta-conda-dependencies wf_run_use_case.cwl
+cwltool --beta-conda-dependencies wf_run_exemplary_wf.cwl
 ```
 
 Note that there exist tools to visualize, edit or create cwl workflows. For instance, you can
@@ -33,4 +33,4 @@ or you can use the [Rabix Composer](https://github.com/rabix/composer) to compos
 on your machine.
 
 Example: ![Workflow Diagram](workflow.svg)
-[source](https://view.commonwl.org/workflows/github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/simple_use_case/cwl/wf_run_use_case.cwl)
+[source](https://view.commonwl.org/workflows/github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements/blob/main/exemplary_workflow/cwl/wf_run_exemplary_wf.cwl)