👌IMPROVE: data manage sections after Azure testing (#436)

docs/sections/managing_data/groups.md

@@ -104,10 +104,10 @@ $ verdi group relabel a_group my_group
 Success: Label changed to my_group
 ```
 
-Add one or more nodes to your new group using node PKs from the `tutorial_pbesol` group we inspected earlier:
+Add one or more nodes to your new group using node PKs from the `tutorial_pbesol` group we inspected earlier (the PK might be different for your database):
 
 ```{code-block} console
-$ verdi group add-nodes -G my_group 380 1273
+$ verdi group add-nodes -G my_group <PK> <PK>
 Do you really want to add 2 nodes to Group<my_group>? [y/N]: y
 ```
 
@@ -132,8 +132,8 @@ Group description  <no description>
 # Nodes:
 PK    Type         Created
 ----  -----------  -----------------
-74  CalcJobNode  2078D:17h:51m ago
-76  CalcJobNode  2078D:17h:57m ago
+ 380  CalcJobNode  2078D:17h:46m ago
+1273  CalcJobNode  2078D:18h:03m ago
 ...
 ```
 
@@ -157,6 +157,7 @@ Success: Group<my_group> deleted.
 Any deletion operation related to groups will not affect the nodes themselves.
 For example if you delete a group, the nodes that belonged to the group will remain in the database.
 The same happens if you remove nodes from the group -- they will remain in the database but won't belong to the group any more.
+You can delete all nodes in the group along with the group itself by adding option `--delete-nodes` to the `verdi group delete` command.
 
 :::
 

docs/sections/managing_data/querying.ipynb

@@ -177,8 +177,8 @@
     "    from aiida.orm import QueryBuilder\n",
     "    query = QueryBuilder()\n",
     "    query.append(StructureData, filters={'extras':{'!has_key':'formula'}})\n",
-    "    for structure, in query.iterall():\n",
-    "        structure.set_extra('formula', structure.get_formula(mode='count'))\n",
+    "    for structure, in query.all():\n",
+    "        structure.base.extras.set('formula', structure.get_formula(mode='count'))\n",
     "\n",
     "store_formula_in_extra()"
    ]
@@ -1774,8 +1774,8 @@
     "It will return a dictionary with all the attributes the node has.\n",
     "\n",
     "Note that a node also has a number of additional methods and attributes.\n",
-    "For instance, you can do `node.attributes_keys()` to get only the attribute keys or `node.get_attribute('wfc_cutoff')` to get the value of a single attribute (these two variants are more efficient if the node has a lot of attributes and you don't need all data).\n",
-    "Similarly, for `extras`, you have `node.extras`, `node.extras_keys()`, and `node.get_attribute('SOME_EXTRA_KEY')`."
+    "For instance, you can do `node.base.attributes.keys()` to get only the attribute keys or `node.base.attributes.get('wfc_cutoff')` to get the value of a single attribute (these two variants are more efficient if the node has a lot of attributes and you don't need all data).\n",
+    "Similarly, for `extras`, you have `node.base.extras.all`, `node.base.extras.keys()`, and `node.base.attributes.get('<SOME_EXTRA_KEY>')`."
    ]
   },
   {
@@ -1802,8 +1802,8 @@
     "query = QueryBuilder()\n",
     "query.append(PwCalculation)\n",
     "node, = query.first()\n",
-    "print('Attributes dictionary:', node.attributes, '\\n')\n",
-    "print('Extras dictionary:', node.extras)"
+    "print('Attributes dictionary:', node.base.attributes.all, '\\n')\n",
+    "print('Extras dictionary:', node.base.extras.all)"
    ]
   },
   {
@@ -1949,7 +1949,7 @@
     "\n",
     "Alternatively, the dataset is included in the virtual machine image of the AiiDA tutorial from [aiida-tutorials.readthedocs.io](https://aiida-tutorials.readthedocs.io) (choose the correct version of the tutorial, depending on which version of AiiDA you want to try).\n",
     "\n",
-    "If the data is not available yet, you can use the following command to import the required calculations:\n",
+    "If the data is not available yet, you can use the following command to import the required calculations (if you are in a notebook you can execute the command in a cell by adding an exclamation mark `!` in front)::\n",
     "\n",
     "```{code-block} console\n",
     "verdi archive import https://object.cscs.ch/v1/AUTH_b1d80408b3d340db9f03d373bbde5c1e/marvel-vms/tutorials/aiida_tutorial_2022_10_perovskites_main_0001.aiida\n",
@@ -1969,7 +1969,7 @@
     "These calculations are spin-polarized (without spin-orbit coupling), use a Gaussian smearing and perform a variable-cell relaxation of the full unit cell.\n",
     "The goal of this part of the tutorial is to have you utilize what you have learnt in the previous sections and “screen” for magnetic and metallic perovskites in a “high-throughput” way.\n",
     "As you learned previously in the tutorial, AiiDA allows to organize calculations into groups.\n",
-    "Once more check the list of groups in your database by typing:"
+    "Once more check the list of groups in your database by typing (From jupyter notebook or `IPython`):"
    ]
   },
   {
@@ -2282,14 +2282,6 @@
    "source": [
     "plot_results(results)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "461a8d21",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {