Deploying to gh-pages from @ 17f30ec 🚀

Author: jan-janssen

_sources/example_workflows/arithmetic/aiida.ipynb

@@ -63,7 +63,6 @@
    "source": [
     "get_prod_and_div_task = wg.add_task(\n",
     "    task(outputs=['prod', 'div'])(_get_prod_and_div),\n",
-    "    name=\"get_prod_and_div\",\n",
     "    x=orm.Float(1),\n",
     "    y=orm.Float(2),\n",
     ")"
@@ -79,7 +78,6 @@
    "source": [
     "get_sum_task = wg.add_task(\n",
     "    _get_sum,\n",
-    "    name=\"get_sum\",\n",
     "    x=get_prod_and_div_task.outputs.prod,\n",
     "    y=get_prod_and_div_task.outputs.div,\n",
     ")"
@@ -93,7 +91,6 @@
    "source": [
     "get_square_task = wg.add_task(\n",
     "    _get_square,\n",
-    "    name=\"get_square\",\n",
     "    x=get_sum_task.outputs.result,\n",
     ")"
    ]

_sources/example_workflows/nfdi/aiida.ipynb

@@ -98,7 +98,7 @@
   },
   {
    "cell_type": "code",
-   "source": "get_bulk_structure_task = wg.add_task(\n    get_bulk_structure,\n    name=\"get_bulk_structure\",\n    element=element,\n    a=a,\n    cubic=cubic,\n)",
+   "source": "get_bulk_structure_task = wg.add_task(\n    get_bulk_structure,\n    element=element,\n    a=a,\n    cubic=cubic,\n)",
    "metadata": {
     "trusted": true
    },
@@ -107,7 +107,7 @@
   },
   {
    "cell_type": "code",
-   "source": "relax_prepare_input_dict_task = wg.add_task(\n    get_dict,\n    name=\"relax_get_dict\",\n    structure=get_bulk_structure_task.outputs.result,\n    calculation=calc_type_relax,\n    kpts=kpts,\n    pseudopotentials=pseudopotentials,\n    smearing=smearing,\n)\n\nrelax_task = wg.add_task(\n    calculate_qe,\n    name=\"mini\",\n    input_dict=relax_prepare_input_dict_task.outputs.result,\n    working_directory=relax_workdir,\n)",
+   "source": "relax_prepare_input_dict_task = wg.add_task(\n    get_dict,\n    structure=get_bulk_structure_task.outputs.result,\n    calculation=calc_type_relax,\n    kpts=kpts,\n    pseudopotentials=pseudopotentials,\n    smearing=smearing,\n)\n\nrelax_task = wg.add_task(\n    calculate_qe,\n    input_dict=relax_prepare_input_dict_task.outputs.result,\n    working_directory=relax_workdir,\n)",
    "metadata": {
     "trusted": true
    },
@@ -116,7 +116,7 @@
   },
   {
    "cell_type": "code",
-   "source": "generate_structures_task = wg.add_task(\n    generate_structures,\n    name=\"generate_structures\",\n    structure=relax_task.outputs.structure,\n    strain_lst=strain_lst,\n)",
+   "source": "generate_structures_task = wg.add_task(\n    generate_structures,\n    structure=relax_task.outputs.structure,\n    strain_lst=strain_lst,\n)",
    "metadata": {
     "trusted": true
    },
@@ -125,7 +125,7 @@
   },
   {
    "cell_type": "code",
-   "source": "get_volumes_task = wg.add_task(get_list, name=\"get_volumes\")",
+   "source": "get_volumes_task = wg.add_task(get_list)",
    "metadata": {
     "trusted": true
    },
@@ -134,7 +134,7 @@
   },
   {
    "cell_type": "code",
-   "source": "get_energies_task = wg.add_task(get_list, name=\"get_energies\")",
+   "source": "get_energies_task = wg.add_task(get_list)",
    "metadata": {
     "trusted": true
    },
@@ -143,7 +143,7 @@
   },
   {
    "cell_type": "code",
-   "source": "strain_dir_tasks, scf_qe_tasks, scf_get_dict_tasks = [], [], []\n\nfor i, strain in enumerate(strain_lst):\n\n    structure_key = f\"s_{i}\"\n    strain_dir = orm.Str(f\"strain_{i}\")\n    generate_structures_task.add_output(\"workgraph.any\", structure_key)\n\n    scf_prepare_input_dict_task = wg.add_task(\n        get_dict,\n        name=f\"get_dict_{i}\",\n        structure=generate_structures_task.outputs[structure_key],\n        calculation=calc_type_scf,\n        kpts=kpts,\n        pseudopotentials=pseudopotentials,\n        smearing=smearing,\n    )\n\n    scf_qe_task = wg.add_task(\n        calculate_qe,\n        name=f\"qe_{i}\",\n        input_dict=scf_prepare_input_dict_task.outputs.result,\n        working_directory=strain_dir,\n    )\n\n    # collect energy and volume\n    get_energies_task.set({f\"{i}\": scf_qe_task.outputs.energy})\n    get_volumes_task.set({f\"{i}\": scf_qe_task.outputs.volume})",
+   "source": "strain_dir_tasks, scf_qe_tasks, scf_get_dict_tasks = [], [], []\n\nfor i, strain in enumerate(strain_lst):\n\n    structure_key = f\"s_{i}\"\n    strain_dir = orm.Str(f\"strain_{i}\")\n    generate_structures_task.add_output(\"workgraph.any\", structure_key)\n\n    scf_prepare_input_dict_task = wg.add_task(\n        get_dict,\n        structure=generate_structures_task.outputs[structure_key],\n        calculation=calc_type_scf,\n        kpts=kpts,\n        pseudopotentials=pseudopotentials,\n        smearing=smearing,\n    )\n\n    scf_qe_task = wg.add_task(\n        calculate_qe,\n        input_dict=scf_prepare_input_dict_task.outputs.result,\n        working_directory=strain_dir,\n    )\n\n    # collect energy and volume\n    get_energies_task.set({f\"{i}\": scf_qe_task.outputs.energy})\n    get_volumes_task.set({f\"{i}\": scf_qe_task.outputs.volume})",
    "metadata": {
     "trusted": true
    },
@@ -152,7 +152,7 @@
   },
   {
    "cell_type": "code",
-   "source": "plot_energy_volume_curve_task = wg.add_task(\n    plot_energy_volume_curve,\n    name=\"plot_energy_volume_curve\",\n    volume_lst=get_volumes_task.outputs.result,\n    energy_lst=get_energies_task.outputs.result,\n)",
+   "source": "plot_energy_volume_curve_task = wg.add_task(\n    plot_energy_volume_curve,\n    volume_lst=get_volumes_task.outputs.result,\n    energy_lst=get_energies_task.outputs.result,\n)",
    "metadata": {
     "trusted": true
    },

_sources/example_workflows/quantum_espresso/aiida.ipynb

@@ -426,7 +426,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_prod_and_div_task</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">task</span><span class="p">(</span><span class="n">outputs</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;prod&#39;</span><span class="p">,</span> <span class="s1">&#39;div&#39;</span><span class="p">])(</span><span class="n">_get_prod_and_div</span><span class="p">),</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;get_prod_and_div&quot;</span><span class="p">,</span>
     <span class="n">x</span><span class="o">=</span><span class="n">orm</span><span class="o">.</span><span class="n">Float</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span>
     <span class="n">y</span><span class="o">=</span><span class="n">orm</span><span class="o">.</span><span class="n">Float</span><span class="p">(</span><span class="mi">2</span><span class="p">),</span>
 <span class="p">)</span>
@@ -438,7 +437,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_sum_task</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">_get_sum</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;get_sum&quot;</span><span class="p">,</span>
     <span class="n">x</span><span class="o">=</span><span class="n">get_prod_and_div_task</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">prod</span><span class="p">,</span>
     <span class="n">y</span><span class="o">=</span><span class="n">get_prod_and_div_task</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">div</span><span class="p">,</span>
 <span class="p">)</span>
@@ -450,7 +448,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">get_square_task</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">_get_square</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;get_square&quot;</span><span class="p">,</span>
     <span class="n">x</span><span class="o">=</span><span class="n">get_sum_task</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">result</span><span class="p">,</span>
 <span class="p">)</span>
 </pre></div>

example_workflows/arithmetic/aiida.html

@@ -462,7 +462,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">gmsh_output_file</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">generate_mesh</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;generate_mesh&quot;</span><span class="p">,</span>
     <span class="n">domain_size</span><span class="o">=</span><span class="n">domain_size</span><span class="p">,</span>
     <span class="n">source_directory</span><span class="o">=</span><span class="n">source_directory</span><span class="p">,</span>
 <span class="p">)</span>
@@ -474,7 +473,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">meshio_output_dict</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">convert_to_xdmf</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;convert_to_xdmf&quot;</span><span class="p">,</span>
     <span class="n">gmsh_output_file</span><span class="o">=</span><span class="n">gmsh_output_file</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">result</span><span class="p">,</span>
 <span class="p">)</span>
 </pre></div>
@@ -485,7 +483,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">poisson_dict</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">poisson</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;poisson&quot;</span><span class="p">,</span>
     <span class="n">meshio_output_xdmf</span><span class="o">=</span><span class="n">meshio_output_dict</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">xdmf_file</span><span class="p">,</span> 
     <span class="n">meshio_output_h5</span><span class="o">=</span><span class="n">meshio_output_dict</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">h5_file</span><span class="p">,</span>
     <span class="n">source_directory</span><span class="o">=</span><span class="n">source_directory</span><span class="p">,</span>
@@ -498,7 +495,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">pvbatch_output_file</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">plot_over_line</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;plot_over_line&quot;</span><span class="p">,</span>
     <span class="n">poisson_output_pvd_file</span><span class="o">=</span><span class="n">poisson_dict</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">pvd_file</span><span class="p">,</span> 
     <span class="n">poisson_output_vtu_file</span><span class="o">=</span><span class="n">poisson_dict</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">vtu_file</span><span class="p">,</span>
     <span class="n">source_directory</span><span class="o">=</span><span class="n">source_directory</span><span class="p">,</span>
@@ -511,7 +507,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">macros_tex_file</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">substitute_macros</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;substitute_macros&quot;</span><span class="p">,</span>
     <span class="n">pvbatch_output_file</span><span class="o">=</span><span class="n">pvbatch_output_file</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> 
     <span class="n">ndofs</span><span class="o">=</span><span class="n">poisson_dict</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">numdofs</span><span class="p">,</span> 
     <span class="n">domain_size</span><span class="o">=</span><span class="n">domain_size</span><span class="p">,</span>
@@ -525,7 +520,6 @@ <h2>Define workflow with aiida<a class="headerlink" href="#define-workflow-with-
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">paper_output</span> <span class="o">=</span> <span class="n">wg</span><span class="o">.</span><span class="n">add_task</span><span class="p">(</span>
     <span class="n">compile_paper</span><span class="p">,</span>
-    <span class="n">name</span><span class="o">=</span><span class="s2">&quot;compile_paper&quot;</span><span class="p">,</span>
     <span class="n">macros_tex</span><span class="o">=</span><span class="n">macros_tex_file</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> 
     <span class="n">plot_file</span><span class="o">=</span><span class="n">pvbatch_output_file</span><span class="o">.</span><span class="n">outputs</span><span class="o">.</span><span class="n">result</span><span class="p">,</span>
     <span class="n">source_directory</span><span class="o">=</span><span class="n">source_directory</span><span class="p">,</span>