SOF-7756: runtime items

README.md

@@ -134,6 +134,36 @@ When developing in python the following should be taken into account:
     python -m unittest discover --verbose --catch --start-directory tests/py/esse/
     ```
 
+3. **Resolving Merge Conflicts in Auto-generated Python Models**: The Python model files in `src/py/mat3ra/esse/models/` are auto-generated from JSON schemas using `datamodel-codegen`. If merge conflicts occur in these files, they should be resolved by regenerating the models rather than manually editing them. To resolve conflicts:
+
+    ```bash
+    # Ensure you have the latest schemas built
+    npm run transpile-and-build-assets
+
+    # Regenerate Python models (requires datamodel-code-generator)
+    datamodel-codegen \
+        --input ./dist/js/schema/ \
+        --input-file-type jsonschema \
+        --output ./dist/py \
+        --output-model-type pydantic_v2.BaseModel \
+        --use-field-description \
+        --use-double-quotes \
+        --enable-version-header \
+        --use-title-as-name \
+        --class-name ESSE \
+        --disable-timestamp \
+        --use-default
+
+    # Sync regenerated files to src directory
+    rsync -av --delete dist/py/ src/py/mat3ra/esse/models/
+    ```
+
+    Alternatively, you can use the pre-commit hook which will regenerate models automatically when schema files change:
+
+    ```bash
+    pre-commit run generate-python-modules --all-files
+    ```
+
 ### 5.2. Development in Javascript/Typescript
 
 See [package.json](package.json) for the list of available npm commands. The JS modules are generated using the [build_schema.js](./build_schema.js) script. There is a setup for it to be run automatically when the package is installed (see "transpile" directive). To rebuild schemas manually, run:

dist/js/example/job.json

@@ -81,6 +81,7 @@
                     "shortName": "qe",
                     "summary": "Quantum Espresso",
                     "version": "5.1.1",
+                    "build": "GNU",
                     "hasAdvancedComputeOptions": true
                 },
                 "model": {
@@ -105,6 +106,7 @@
                             "shortName": "qe",
                             "summary": "Quantum Espresso",
                             "version": "5.1.1",
+                            "build": "GNU",
                             "hasAdvancedComputeOptions": true
                         },
                         "compute": null,
@@ -135,14 +137,32 @@
                                     "templateId": "dJ7HYz5pQ4AuN5qc9"
                                 }
                             ],
-                            "name": "pw_scf"
+                            "name": "pw_scf",
+                            "postProcessors": [],
+                            "preProcessors": [],
+                            "monitors": [],
+                            "results": []
                         },
                         "flowchartId": "execution",
                         "head": true,
                         "input": [
                             {
-                                "content": "K_POINTS automatic\n2 2 2 0 0 0",
-                                "name": "pw_scf.in"
+                                "template": {
+                                    "applicationName": "espresso",
+                                    "applicationVersions": [
+                                        "6.0"
+                                    ],
+                                    "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
+                                    "contextProviders": [
+                                        {
+                                            "name": "KGridManagerMixin"
+                                        }
+                                    ],
+                                    "executableName": "pw.x",
+                                    "name": "kpoints_grid"
+                                },
+                                "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+                                "isManuallyChanged": false
                             }
                         ],
                         "monitors": [
@@ -176,7 +196,11 @@
                 "_id": "LCthJ6E2QabYCZqf4",
                 "flowchartId": "05c362dc27ff1bb98d16fd60",
                 "type": "subworkflow",
-                "name": "subworkflow unit"
+                "name": "subworkflow unit",
+                "preProcessors": [],
+                "postProcessors": [],
+                "monitors": [],
+                "results": []
             }
         ]
     }

dist/js/example/software/application.json

@@ -3,5 +3,6 @@
     "shortName": "qe",
     "summary": "Quantum Espresso",
     "version": "5.1.1",
+    "build": "GNU",
     "hasAdvancedComputeOptions": true
 }

dist/js/example/software/flavor.json

@@ -5,5 +5,9 @@
             "templateId": "dJ7HYz5pQ4AuN5qc9"
         }
     ],
-    "name": "pw_scf"
+    "name": "pw_scf",
+    "postProcessors": [],
+    "preProcessors": [],
+    "monitors": [],
+    "results": []
 }

dist/js/example/software/template.json

@@ -4,7 +4,6 @@
         "6.0"
     ],
     "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
-    "rendered": "K_POINTS automatic\n10 10 10 0 0 0",
     "contextProviders": [
         {
             "name": "KGridManagerMixin"

dist/js/example/software_directory/modeling/espresso.json

@@ -2,5 +2,6 @@
     "name": "espresso",
     "shortName": "qe",
     "summary": "Quantum Espresso",
-    "version": "7.2"
+    "version": "7.2",
+    "build": "GNU"
 }

dist/js/example/software_directory/modeling/nwchem.json

@@ -1,6 +1,8 @@
 {
     "name": "NWChem",
     "summary": "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations",
+    "shortName": "nwchem",
     "version": "6.6",
-    "exec": "nwchem"
+    "exec": "nwchem",
+    "build": "GNU"
 }

dist/js/example/software_directory/modeling/unit/execution.json

@@ -3,28 +3,36 @@
         "name": "espresso",
         "shortName": "qe",
         "summary": "Quantum Espresso",
-        "version": "7.2"
+        "version": "7.2",
+        "build": "GNU"
     },
     "flowchartId": "modeling",
     "head": true,
     "input": [
         {
-            "applicationName": "espresso",
-            "applicationVersions": [
-                "6.0"
-            ],
-            "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
-            "rendered": "K_POINTS automatic\n10 10 10 0 0 0",
-            "contextProviders": [
-                {
-                    "name": "KGridManagerMixin"
-                }
-            ],
-            "executableName": "pw.x",
-            "name": "kpoints_grid"
+            "template": {
+                "applicationName": "espresso",
+                "applicationVersions": [
+                    "6.0"
+                ],
+                "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
+                "contextProviders": [
+                    {
+                        "name": "KGridManagerMixin"
+                    }
+                ],
+                "executableName": "pw.x",
+                "name": "kpoints_grid"
+            },
+            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+            "isManuallyChanged": false
         }
     ],
     "name": "modeling",
     "status": "idle",
-    "type": "execution"
+    "type": "execution",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

dist/js/example/software_directory/modeling/vasp.json

@@ -2,5 +2,6 @@
     "name": "vasp",
     "shortName": "vasp",
     "summary": "vienna ab-initio simulation package",
-    "version": "5.3.5"
+    "version": "5.3.5",
+    "build": "GNU"
 }

dist/js/example/software_directory/scripting/jupyter_lab.json

@@ -4,5 +4,6 @@
     "name": "jupyterLab",
     "shortName": "jl",
     "summary": "Jupyter Lab",
-    "version": "0.33.12"
+    "version": "0.33.12",
+    "build": "GNU"
 }

dist/js/example/software_directory/scripting/python.json

@@ -4,5 +4,6 @@
     "name": "python",
     "shortName": "py",
     "summary": "Python Script",
-    "version": "2.7.5"
+    "version": "2.7.5",
+    "build": "GNU"
 }

dist/js/example/software_directory/scripting/shell.json

@@ -4,5 +4,6 @@
     "name": "shell",
     "shortName": "sh",
     "summary": "Shell Script",
-    "version": "4.2.46"
+    "version": "4.2.46",
+    "build": "GNU"
 }

dist/js/example/software_directory/scripting/unit/execution.json

@@ -5,29 +5,37 @@
         "name": "python",
         "shortName": "py",
         "summary": "Python Script",
-        "version": "2.7.5"
+        "version": "2.7.5",
+        "build": "GNU"
     },
     "compute": null,
     "flowchartId": "scripting",
     "head": true,
     "input": [
         {
-            "applicationName": "espresso",
-            "applicationVersions": [
-                "6.0"
-            ],
-            "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
-            "rendered": "K_POINTS automatic\n10 10 10 0 0 0",
-            "contextProviders": [
-                {
-                    "name": "KGridManagerMixin"
-                }
-            ],
-            "executableName": "pw.x",
-            "name": "kpoints_grid"
+            "template": {
+                "applicationName": "espresso",
+                "applicationVersions": [
+                    "6.0"
+                ],
+                "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
+                "contextProviders": [
+                    {
+                        "name": "KGridManagerMixin"
+                    }
+                ],
+                "executableName": "pw.x",
+                "name": "kpoints_grid"
+            },
+            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+            "isManuallyChanged": false
         }
     ],
     "name": "scripting",
     "status": "idle",
-    "type": "execution"
+    "type": "execution",
+    "preProcessors": [],
+    "postProcessors": [],
+    "monitors": [],
+    "results": []
 }

dist/js/example/workflow/unit/runtime/runtime_items.json → dist/js/example/system/runtime_items.json

@@ -1,11 +1,11 @@
 {
+    "preProcessors": [],
+    "postProcessors": [],
     "monitors": [
         {
             "name": "standard_output"
         }
     ],
-    "postProcessors": [],
-    "preProcessors": [],
     "results": [
         {
             "name": "atomic_forces"

dist/js/example/workflow.json

@@ -28,6 +28,7 @@
                 "shortName": "qe",
                 "summary": "Quantum Espresso",
                 "version": "5.1.1",
+                "build": "GNU",
                 "hasAdvancedComputeOptions": true
             },
             "model": {
@@ -52,6 +53,7 @@
                         "shortName": "qe",
                         "summary": "Quantum Espresso",
                         "version": "5.1.1",
+                        "build": "GNU",
                         "hasAdvancedComputeOptions": true
                     },
                     "compute": null,
@@ -82,14 +84,32 @@
                                 "templateId": "dJ7HYz5pQ4AuN5qc9"
                             }
                         ],
-                        "name": "pw_scf"
+                        "name": "pw_scf",
+                        "postProcessors": [],
+                        "preProcessors": [],
+                        "monitors": [],
+                        "results": []
                     },
                     "flowchartId": "execution",
                     "head": true,
                     "input": [
                         {
-                            "content": "K_POINTS automatic\n2 2 2 0 0 0",
-                            "name": "pw_scf.in"
+                            "template": {
+                                "applicationName": "espresso",
+                                "applicationVersions": [
+                                    "6.0"
+                                ],
+                                "content": "K_POINTS automatic\n{{nkx}} {{nky}} {{nkz}} 0 0 0",
+                                "contextProviders": [
+                                    {
+                                        "name": "KGridManagerMixin"
+                                    }
+                                ],
+                                "executableName": "pw.x",
+                                "name": "kpoints_grid"
+                            },
+                            "rendered": "K_POINTS automatic\n2 2 2 0 0 0",
+                            "isManuallyChanged": false
                         }
                     ],
                     "monitors": [
@@ -123,7 +143,11 @@
             "_id": "LCthJ6E2QabYCZqf4",
             "flowchartId": "05c362dc27ff1bb98d16fd60",
             "type": "subworkflow",
-            "name": "subworkflow unit"
+            "name": "subworkflow unit",
+            "preProcessors": [],
+            "postProcessors": [],
+            "monitors": [],
+            "results": []
         }
     ]
 }