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Merged
merged 3 commits into from
Apr 14, 2025
Merged

pyiron: set local folder as default project #67

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934a9b6
pyiron: set local folder as default project
jan-janssen Apr 14, 2025
62e41b4
Update pyiron_base.py
jan-janssen Apr 14, 2025
2aeee35
Update pyiron_base.py
jan-janssen Apr 14, 2025
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55 changes: 1 addition & 54 deletions aiida_nfdi.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -298,16 +298,6 @@
"source": "## Load Workflow with pyiron_base",
"metadata": {}
},
{
"id": "fdde6b82-b51d-434a-a9a8-5a8c31bbb429",
"cell_type": "code",
"source": "from pyiron_base import Project",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 20
},
{
"id": "be4d5d93-e9f6-4072-a6be-0ee5dc93590f",
"cell_type": "code",
Expand All @@ -318,34 +308,11 @@
"outputs": [],
"execution_count": 21
},
{
"id": "4db75587-5f4c-416d-a1f6-c949077fa2ca",
"cell_type": "code",
"source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
"metadata": {
"trusted": true
},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "0it [00:00, ?it/s]",
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "744782e84c574359874689c2242fb2d8"
}
},
"metadata": {}
}
],
"execution_count": 22
},
{
"id": "4452a648-d4c3-4f5f-8678-ffb54bef17dc",
"cell_type": "code",
"source": [
"delayed_object_lst = load_workflow_json(project=pr, file_name=workflow_json_filename)\n",
"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n",
"delayed_object_lst[-1].draw()"
],
"metadata": {
Expand Down Expand Up @@ -386,26 +353,6 @@
}
],
"execution_count": 24
},
{
"id": "b3bba27e-ece9-4c02-834c-53e69844b140",
"cell_type": "code",
"source": "pr.job_table()",
"metadata": {
"trusted": true
},
"outputs": [
{
"execution_count": 25,
"output_type": "execute_result",
"data": {
"text/plain": " id status chemicalformula \\\n0 1 finished None \n1 2 finished None \n2 3 finished None \n3 4 finished None \n4 5 finished None \n5 6 finished None \n\n job \\\n0 generate_mesh_0b48cf5155cd6802c17d20bb58104132 \n1 convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43 \n2 poisson_a0224b23ceb2119d105a5d98ef37f93e \n3 plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b \n4 substitute_macros_874fc185ecec04b4cb9537c58b7efb7b \n5 compile_paper_3cee534ffe692833d37faf1fd2170cb6 \n\n subjob projectpath \\\n0 /generate_mesh_0b48cf5155cd6802c17d20bb58104132 None \n1 /convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43 None \n2 /poisson_a0224b23ceb2119d105a5d98ef37f93e None \n3 /plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b None \n4 /substitute_macros_874fc185ecec04b4cb9537c58b7efb7b None \n5 /compile_paper_3cee534ffe692833d37faf1fd2170cb6 None \n\n project timestart timestop totalcputime \\\n0 /home/jovyan/test/ 2025-04-12 11:32:18.725836 None None \n1 /home/jovyan/test/ 2025-04-12 11:32:21.567671 None None \n2 /home/jovyan/test/ 2025-04-12 11:32:24.772144 None None \n3 /home/jovyan/test/ 2025-04-12 11:32:30.023925 None None \n4 /home/jovyan/test/ 2025-04-12 11:32:34.237777 None None \n5 /home/jovyan/test/ 2025-04-12 11:32:36.156992 None None \n\n computer \\\n0 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n1 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n2 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n3 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n4 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n5 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n\n hamilton hamversion parentid masterid \n0 PythonFunctionContainerJob 0.4 None None \n1 PythonFunctionContainerJob 0.4 None None \n2 PythonFunctionContainerJob 0.4 None None \n3 PythonFunctionContainerJob 0.4 None None \n4 PythonFunctionContainerJob 0.4 None None \n5 PythonFunctionContainerJob 0.4 None None ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>id</th>\n <th>status</th>\n <th>chemicalformula</th>\n <th>job</th>\n <th>subjob</th>\n <th>projectpath</th>\n <th>project</th>\n <th>timestart</th>\n <th>timestop</th>\n <th>totalcputime</th>\n <th>computer</th>\n <th>hamilton</th>\n <th>hamversion</th>\n <th>parentid</th>\n <th>masterid</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>1</td>\n <td>finished</td>\n <td>None</td>\n <td>generate_mesh_0b48cf5155cd6802c17d20bb58104132</td>\n <td>/generate_mesh_0b48cf5155cd6802c17d20bb58104132</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:18.725836</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>1</th>\n <td>2</td>\n <td>finished</td>\n <td>None</td>\n <td>convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43</td>\n <td>/convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:21.567671</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>2</th>\n <td>3</td>\n <td>finished</td>\n <td>None</td>\n <td>poisson_a0224b23ceb2119d105a5d98ef37f93e</td>\n <td>/poisson_a0224b23ceb2119d105a5d98ef37f93e</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:24.772144</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>3</th>\n <td>4</td>\n <td>finished</td>\n <td>None</td>\n <td>plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b</td>\n <td>/plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:30.023925</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>4</th>\n <td>5</td>\n <td>finished</td>\n <td>None</td>\n <td>substitute_macros_874fc185ecec04b4cb9537c58b7efb7b</td>\n <td>/substitute_macros_874fc185ecec04b4cb9537c58b7efb7b</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:34.237777</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>5</th>\n <td>6</td>\n <td>finished</td>\n <td>None</td>\n <td>compile_paper_3cee534ffe692833d37faf1fd2170cb6</td>\n <td>/compile_paper_3cee534ffe692833d37faf1fd2170cb6</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:32:36.156992</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
],
"execution_count": 25
}
]
}
34 changes: 3 additions & 31 deletions aiida_qe.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -348,15 +348,6 @@
"source": "## Load Workflow with pyiron_base",
"metadata": {}
},
{
"cell_type": "code",
"source": "from pyiron_base import Project",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 22
},
{
"cell_type": "code",
"source": "from python_workflow_definition.pyiron_base import load_workflow_json",
Expand All @@ -368,29 +359,10 @@
},
{
"cell_type": "code",
"source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
"metadata": {
"trusted": true
},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "0it [00:00, ?it/s]",
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "682a9c9d86fb4bc4823cd8112c5ffdf4"
}
},
"metadata": {}
}
"source": [
"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n",
"delayed_object_lst[-1].draw()"
],
"execution_count": 24
},
{
"cell_type": "code",
"source": "delayed_object_lst = load_workflow_json(project=pr, file_name=workflow_json_filename)\ndelayed_object_lst[-1].draw()",
"metadata": {
"trusted": true
},
Expand Down
33 changes: 1 addition & 32 deletions aiida_simple.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -175,15 +175,6 @@
"source": "## Load Workflow with pyiron_base",
"metadata": {}
},
{
"cell_type": "code",
"source": "from pyiron_base import Project",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 12
},
{
"cell_type": "code",
"source": "from python_workflow_definition.pyiron_base import load_workflow_json",
Expand All @@ -193,32 +184,10 @@
"outputs": [],
"execution_count": 13
},
{
"cell_type": "code",
"source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
"metadata": {
"trusted": true
},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "0it [00:00, ?it/s]",
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "1cebe3e991ff4d8aacbea78a858011fb"
}
},
"metadata": {}
}
],
"execution_count": 14
},
{
"cell_type": "code",
"source": [
"delayed_object_lst = load_workflow_json(project=pr, file_name=workflow_json_filename)\n",
"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n",
"delayed_object_lst[-1].draw()"
],
"metadata": {
Expand Down
55 changes: 1 addition & 54 deletions jobflow_nfdi.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -261,16 +261,6 @@
"source": "## Load Workflow with pyiron_base",
"metadata": {}
},
{
"id": "fdde6b82-b51d-434a-a9a8-5a8c31bbb429",
"cell_type": "code",
"source": "from pyiron_base import Project",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 18
},
{
"id": "be4d5d93-e9f6-4072-a6be-0ee5dc93590f",
"cell_type": "code",
Expand All @@ -281,34 +271,11 @@
"outputs": [],
"execution_count": 19
},
{
"id": "4db75587-5f4c-416d-a1f6-c949077fa2ca",
"cell_type": "code",
"source": "pr = Project(\"test\")\npr.remove_jobs(recursive=True, silently=True)",
"metadata": {
"trusted": true
},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "0it [00:00, ?it/s]",
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "9a6ea2489a6847ab8375930b499b9a7f"
}
},
"metadata": {}
}
],
"execution_count": 20
},
{
"id": "4452a648-d4c3-4f5f-8678-ffb54bef17dc",
"cell_type": "code",
"source": [
"delayed_object_lst = load_workflow_json(project=pr, file_name=workflow_json_filename)\n",
"delayed_object_lst = load_workflow_json(file_name=workflow_json_filename)\n",
"delayed_object_lst[-1].draw()"
],
"metadata": {
Expand Down Expand Up @@ -349,26 +316,6 @@
}
],
"execution_count": 22
},
{
"id": "b3bba27e-ece9-4c02-834c-53e69844b140",
"cell_type": "code",
"source": "pr.job_table()",
"metadata": {
"trusted": true
},
"outputs": [
{
"execution_count": 23,
"output_type": "execute_result",
"data": {
"text/plain": " id status chemicalformula \\\n0 1 finished None \n1 2 finished None \n2 3 finished None \n3 4 finished None \n4 5 finished None \n5 6 finished None \n\n job \\\n0 generate_mesh_0b48cf5155cd6802c17d20bb58104132 \n1 convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43 \n2 poisson_a0224b23ceb2119d105a5d98ef37f93e \n3 plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b \n4 substitute_macros_874fc185ecec04b4cb9537c58b7efb7b \n5 compile_paper_3cee534ffe692833d37faf1fd2170cb6 \n\n subjob projectpath \\\n0 /generate_mesh_0b48cf5155cd6802c17d20bb58104132 None \n1 /convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43 None \n2 /poisson_a0224b23ceb2119d105a5d98ef37f93e None \n3 /plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b None \n4 /substitute_macros_874fc185ecec04b4cb9537c58b7efb7b None \n5 /compile_paper_3cee534ffe692833d37faf1fd2170cb6 None \n\n project timestart timestop totalcputime \\\n0 /home/jovyan/test/ 2025-04-12 11:33:56.439299 None None \n1 /home/jovyan/test/ 2025-04-12 11:33:59.335257 None None \n2 /home/jovyan/test/ 2025-04-12 11:34:02.548200 None None \n3 /home/jovyan/test/ 2025-04-12 11:34:07.792544 None None \n4 /home/jovyan/test/ 2025-04-12 11:34:12.093499 None None \n5 /home/jovyan/test/ 2025-04-12 11:34:14.126943 None None \n\n computer \\\n0 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n1 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n2 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n3 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n4 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n5 pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1 \n\n hamilton hamversion parentid masterid \n0 PythonFunctionContainerJob 0.4 None None \n1 PythonFunctionContainerJob 0.4 None None \n2 PythonFunctionContainerJob 0.4 None None \n3 PythonFunctionContainerJob 0.4 None None \n4 PythonFunctionContainerJob 0.4 None None \n5 PythonFunctionContainerJob 0.4 None None ",
"text/html": "<div>\n<style scoped>\n .dataframe tbody tr th:only-of-type {\n vertical-align: middle;\n }\n\n .dataframe tbody tr th {\n vertical-align: top;\n }\n\n .dataframe thead th {\n text-align: right;\n }\n</style>\n<table border=\"1\" class=\"dataframe\">\n <thead>\n <tr style=\"text-align: right;\">\n <th></th>\n <th>id</th>\n <th>status</th>\n <th>chemicalformula</th>\n <th>job</th>\n <th>subjob</th>\n <th>projectpath</th>\n <th>project</th>\n <th>timestart</th>\n <th>timestop</th>\n <th>totalcputime</th>\n <th>computer</th>\n <th>hamilton</th>\n <th>hamversion</th>\n <th>parentid</th>\n <th>masterid</th>\n </tr>\n </thead>\n <tbody>\n <tr>\n <th>0</th>\n <td>1</td>\n <td>finished</td>\n <td>None</td>\n <td>generate_mesh_0b48cf5155cd6802c17d20bb58104132</td>\n <td>/generate_mesh_0b48cf5155cd6802c17d20bb58104132</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:33:56.439299</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>1</th>\n <td>2</td>\n <td>finished</td>\n <td>None</td>\n <td>convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43</td>\n <td>/convert_to_xdmf_29ad6ec6927268429dc9aef8166fde43</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:33:59.335257</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>2</th>\n <td>3</td>\n <td>finished</td>\n <td>None</td>\n <td>poisson_a0224b23ceb2119d105a5d98ef37f93e</td>\n <td>/poisson_a0224b23ceb2119d105a5d98ef37f93e</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:34:02.548200</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>3</th>\n <td>4</td>\n <td>finished</td>\n <td>None</td>\n <td>plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b</td>\n <td>/plot_over_line_82b37a42e0747f11d9a7f6318f63ac6b</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:34:07.792544</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>4</th>\n <td>5</td>\n <td>finished</td>\n <td>None</td>\n <td>substitute_macros_874fc185ecec04b4cb9537c58b7efb7b</td>\n <td>/substitute_macros_874fc185ecec04b4cb9537c58b7efb7b</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:34:12.093499</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n <tr>\n <th>5</th>\n <td>6</td>\n <td>finished</td>\n <td>None</td>\n <td>compile_paper_3cee534ffe692833d37faf1fd2170cb6</td>\n <td>/compile_paper_3cee534ffe692833d37faf1fd2170cb6</td>\n <td>None</td>\n <td>/home/jovyan/test/</td>\n <td>2025-04-12 11:34:14.126943</td>\n <td>None</td>\n <td>None</td>\n <td>pyiron@jupyter-pyiron-dev-pyth-flow-definition-a8grxfsa#1</td>\n <td>PythonFunctionContainerJob</td>\n <td>0.4</td>\n <td>None</td>\n <td>None</td>\n </tr>\n </tbody>\n</table>\n</div>"
},
"metadata": {}
}
],
"execution_count": 23
}
]
}
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