Docs: migrate tutorials using sphnix-gallery (#268)

To run calculation using QE, this PR
- Installs QE using conda
- Installs pseudo-potential using `aiida-pseudo`

Also, migrate one notebook in `howto` and `built-in task` sections.

.readthedocs.yaml

@@ -17,6 +17,9 @@ build:
       - verdi presto
       - verdi daemon start
       - verdi status
+      - aiida-pseudo install sssp -x PBEsol
+      - verdi group list
+      - cat /proc/cpuinfo | grep processor | wc -l
 
 conda:
   environment: docs/environment.yml

docs/environment.yml

@@ -5,3 +5,4 @@ channels:
 dependencies:
   - aiida-core
   - aiida-core.services
+  - qe

docs/gallery/autogen/quick_start.py

@@ -329,9 +329,7 @@ def multiply(x, y):
 
 
 try:
-    query_code = load_code(
-        "add@localhost"
-    )  # The computer label can also be omitted here
+    code = load_code("add@localhost")  # The computer label can also be omitted here
 except NotExistent:
     code = InstalledCode(
         computer=load_computer("localhost"),

docs/gallery/built-in/autogen/GALLERY_HEADER.rst

@@ -0,0 +1,3 @@
+==========
+HowTos
+==========

docs/gallery/built-in/autogen/shelljob.py

@@ -0,0 +1,141 @@
+"""
+=======================
+ShellJob
+=======================
+
+"""
+
+# %%
+# Introduction
+# ============
+# ``ShellJob`` is a built-in task, which uses the `aiida-shell <https://aiida-shell.readthedocs.io/en/latest/>`_ package to run shell commands easily. Run any shell executable without writing a dedicated plugin or parser.
+#
+# This tutorial is based on the `docs <https://aiida-shell.readthedocs.io/en/latest/howto.html#>`_ of the ``aiida-shell``.
+#
+# Load the AiiDA profile.
+
+from aiida import load_profile
+
+load_profile()
+
+# %%
+# Running a shell command
+# ========================
+# Run a shell command without any arguments. Here we run the `date` command to show the date.
+#
+
+
+from aiida_workgraph import WorkGraph
+
+wg = WorkGraph(name="test_shell_date")
+date_task = wg.add_task("ShellJob", command="date")
+wg.submit(wait=True)
+
+# Print out the result:
+print("\nResult: ", date_task.outputs["stdout"].value.get_content())
+
+# %%
+# Running a shell command with arguments
+# =======================================
+# To pass arguments to the shell command, pass them as a list of strings to the arguments keyword:
+#
+
+
+wg = WorkGraph(name="test_shell_date_with_arguments")
+date_task = wg.add_task("ShellJob", command="date", arguments=["--iso-8601"])
+wg.submit(wait=True)
+
+# Print out the result:
+print("\nResult: ", date_task.outputs["stdout"].value.get_content())
+
+# %%
+# Running a shell command with files as arguments
+# ===============================================
+# For commands that take arguments that refer to files, pass those files using the nodes keyword. The keyword takes a dictionary of SinglefileData nodes. To specify where on the command line the files should be passed, use placeholder strings in the arguments keyword.
+#
+
+
+from aiida.orm import SinglefileData
+
+wg = WorkGraph(name="test_shell_cat_with_file_arguments")
+cat_task = wg.add_task(
+    "ShellJob",
+    command="cat",
+    arguments=["{file_a}", "{file_b}"],
+    nodes={
+        "file_a": SinglefileData.from_string("string a"),
+        "file_b": SinglefileData.from_string("string b"),
+    },
+)
+wg.submit(wait=True)
+
+# Print out the result:
+print("\nResult: ", cat_task.outputs["stdout"].value.get_content())
+
+# %%
+# Create a workflow
+# =================
+# We want to calculate `(x+y)*z` in two steps using the `expr` command. Each step will invole one `ShellJob`.
+#
+# If one wanted to run this workflow in AiiDA using CalcJob and WorkChain, one would have to write plugins for `expr` command, and a WorkChain to handle the workflow. With aiida-workgraph, this can be run with the following workgraph:
+#
+
+from aiida_workgraph import WorkGraph
+from aiida.orm import Int
+from aiida_shell.data import PickledData
+from aiida import load_profile
+
+load_profile()
+
+
+def parser(self, dirpath):
+    from aiida.orm import Int
+
+    return {"result": Int((dirpath / "stdout").read_text().strip())}
+
+
+# Create a workgraph
+wg = WorkGraph(name="shell_add_mutiply_workflow")
+expr_1 = wg.add_task(
+    "ShellJob",
+    name="expr_1",
+    command="expr",
+    arguments=["{x}", "+", "{y}"],
+    nodes={"x": Int(2), "y": Int(3)},
+    parser=PickledData(parser),
+    parser_outputs=[{"name": "result"}],
+)
+expr_2 = wg.add_task(
+    "ShellJob",
+    name="expr_2",
+    command="expr",
+    arguments=["{result}", "*", "{z}"],
+    nodes={"z": Int(4), "result": expr_1.outputs["result"]},
+    parser=PickledData(parser),
+    parser_outputs=[{"name": "result"}],
+)
+wg.to_html()
+
+
+# %%
+# Submit the workgraph
+#
+
+wg.submit(wait=True, timeout=100)
+print("State of WorkGraph    : {}".format(wg.state))
+print("Result               : {}".format(expr_2.node.outputs.result.value))
+
+
+# %%
+# Generate node graph from the AiiDA process
+#
+
+from aiida_workgraph.utils import generate_node_graph
+
+generate_node_graph(wg.pk)
+
+# %%
+# What's Next
+# ===========
+# For more examples of ``aiida-shell``, please refer to its `docs <https://aiida-shell.readthedocs.io/en/latest/howto.html#>`_.
+#

docs/gallery/concept/autogen/workgraph.py

@@ -0,0 +1,76 @@
+"""
+WorkGraph
+=================
+
+This :class:`~aiida_workgraph.workgraph.WorkGraph` object is a collection of tasks and links.
+
+Create and launch workgraph
+----------------------------
+"""
+
+# %%
+# First, create an empty workgraph:
+#
+
+from aiida_workgraph import WorkGraph, task
+
+wg = WorkGraph(name="my_first_workgraph")
+
+# %%
+# Define and use tasks
+#
+
+# Define a task using a `calcfunction`:
+@task.calcfunction()
+def add(x, y):
+    return x + y
+
+
+# Add tasks to the workgraph
+add1 = wg.add_task(add, name="add1")
+add2 = wg.add_task(add, name="add2")
+
+# %%
+# Add a link between tasks:
+
+wg.add_link(add1.outputs["result"], add2.inputs["x"])
+wg.to_html()
+
+# %%
+# Submit the workgraph:
+
+wg.submit(inputs={"add1": {"x": 1, "y": 2}, "add2": {"y": 3}}, wait=True)
+
+# %%
+# Load workgraph from the AiiDA process
+# -------------------------------------
+#
+# WorkGraph saves its data as an extra attribute in its process, allowing reconstruction of the WorkGraph from the process.
+
+from aiida_workgraph import WorkGraph
+
+wg_loaded = WorkGraph.load(wg.pk)
+
+# %%
+# Execute order
+# -------------
+# The tasks will be executed under the following conditions:
+#
+# - No input task
+# - All input tasks are finished.
+# Group outputs
+# -------------
+# You can output the results of the tasks as the output of the WorkGraph.
+
+wg = WorkGraph("test_workgraph_group_outputs")
+wg.add_task(add, "add1", x=2, y=3)
+wg.group_outputs = [{"name": "sum", "from": "add1.result"}]
+wg.submit(wait=True)
+assert wg.process.outputs.sum.value == 5
+
+# %%
+# List of all Methods
+# ----------------------------
+#
+# .. autoclass:: aiida_workgraph.workgraph.WorkGraph
+#    :members:

docs/gallery/howto/autogen/GALLERY_HEADER.rst

@@ -0,0 +1,3 @@
+===============
+Built-in tasks
+===============