📚 tutorials: fix copy-paste run blockers

Address the copy-paste self-containment audit, a reader who pastes cells
into their own notebook hit avoidable failures.

- install notes: add matplotlib (the 7 plotting modules) and gsrd (all
  modules), plus a Graphviz `dot` note. These live in the build venv's
  extras, so CI was green while a documented `uv pip install` was not.
- module1: replace `!tree` (absent by default on macOS/minimal
  Linux/Windows) with a portable pure-Python directory listing.
- module5: guard the empty-DB case so it raises an actionable message
  ("run Module 2 first") instead of a cryptic `zip()` ValueError.
- module6b: un-hide the `pipeline_with_optional_fft` cell (was
  hide-input) so a copy-paste reader can see the code a later visible
  cell depends on.

Author: GeigerJ2

docs/source/tutorials/module1.md

@@ -38,10 +38,10 @@ After this module, you will be able to:
 This module needs AiiDA and `aiida-shell`:
 
 ```bash
-uv pip install aiida-core aiida-shell
+uv pip install aiida-core aiida-shell matplotlib git+https://github.com/aiidateam/gsrd
 ```
 
-It also uses the small `gsrd` simulator introduced in {ref}`Module 0 <tutorial:module0>`.
+It also uses the small `gsrd` simulator introduced in {ref}`Module 0 <tutorial:module0>`, and the Graphviz `dot` binary for the provenance-graph plots (`apt install graphviz`, `brew install graphviz`, or `conda install graphviz`).
 :::
 
 ## Setting up your AiiDA profile
@@ -322,8 +322,13 @@ AiiDA stores everything in its internal database and file repository (efficient
 ```
 
 ```{code-cell} ipython3
-# Show the directory tree of the dumped calculation data.
-!tree /tmp/aiida-tutorial/dump
+# Show the directory tree of the dumped data (pure Python, no `tree` binary needed).
+from pathlib import Path
+
+dump_dir = Path('/tmp/aiida-tutorial/dump')
+for path in sorted(dump_dir.rglob('*')):
+    indent = '    ' * (len(path.relative_to(dump_dir).parts) - 1)
+    print(f'{indent}{path.name}{"/" if path.is_dir() else ""}')
 ```
 
 All the relevant entities of the calculation are there: the input file, the simulation script, the submission script, captured stdout and stderr, and AiiDA metadata.

docs/source/tutorials/module2.md

@@ -49,7 +49,7 @@ After this module, you will be able to:
 Same requirements as {ref}`Module 1 <tutorial:module1>`:
 
 ```bash
-uv pip install aiida-core aiida-shell
+uv pip install aiida-core aiida-shell matplotlib git+https://github.com/aiidateam/gsrd
 ```
 :::
 

docs/source/tutorials/module3a.md

@@ -51,7 +51,7 @@ Running that workflow over *many* inputs, replacing the Python `for`-loop, is th
 This module uses `aiida-core`, `aiida-shell`, and `aiida-workgraph`. Install them with:
 
 ```bash
-uv pip install aiida-core aiida-shell aiida-workgraph
+uv pip install aiida-core aiida-shell aiida-workgraph matplotlib git+https://github.com/aiidateam/gsrd
 ```
 
 `aiida-workgraph` is currently a separate package; it is planned to become part of `aiida-core` with the v3.0 release.

docs/source/tutorials/module3b.md

@@ -41,7 +41,7 @@ After this module, you will be able to:
 This module uses AiiDA, `aiida-shell`, and `aiida-workgraph`:
 
 ```bash
-uv pip install aiida-core aiida-shell aiida-workgraph
+uv pip install aiida-core aiida-shell aiida-workgraph matplotlib git+https://github.com/aiidateam/gsrd
 ```
 :::
 

docs/source/tutorials/module4.md

@@ -49,7 +49,7 @@ After this module, you will be able to:
 This module uses AiiDA and `aiida-shell`, plus SSH access to a cluster:
 
 ```bash
-uv pip install aiida-core aiida-shell
+uv pip install aiida-core aiida-shell git+https://github.com/aiidateam/gsrd
 ```
 :::
 

docs/source/tutorials/module5.md

@@ -40,7 +40,7 @@ After this module, you will be able to:
 This module only needs AiiDA:
 
 ```bash
-uv pip install aiida-core
+uv pip install aiida-core aiida-shell matplotlib git+https://github.com/aiidateam/gsrd
 ```
 
 It reuses the sweep data created in {ref}`Module 2 <tutorial:module2>`.
@@ -350,6 +350,13 @@ qb = (
     )
 )
 rows = sorted(qb.all())
+if not rows:
+    msg = (
+        'No F-sweep data found in this profile. Module 5 queries the data that '
+        'Module 2 creates, run Module 2 first so this shared tutorial profile has '
+        'data to query.'
+    )
+    raise RuntimeError(msg)
 f_values, variances = zip(*rows)
 
 plot_transition_curve(list(f_values), list(variances))

docs/source/tutorials/module6a.md

@@ -37,7 +37,7 @@ Composing these into a workflow whose shape **emerges at runtime** (an `If` insi
 This module uses AiiDA, `aiida-shell`, and `aiida-workgraph`:
 
 ```bash
-uv pip install aiida-core aiida-shell aiida-workgraph
+uv pip install aiida-core aiida-shell aiida-workgraph matplotlib git+https://github.com/aiidateam/gsrd
 ```
 :::
 

docs/source/tutorials/module6b.md

@@ -35,7 +35,7 @@ After this module, you will be able to:
 This module uses AiiDA, `aiida-shell`, and `aiida-workgraph`:
 
 ```bash
-uv pip install aiida-core aiida-shell aiida-workgraph
+uv pip install aiida-core aiida-shell aiida-workgraph matplotlib git+https://github.com/aiidateam/gsrd
 ```
 :::
 
@@ -82,11 +82,9 @@ BASE_PARAMS = {
 F_VALUES = [0.038, 0.040, 0.042, 0.044, 0.046, 0.050, 0.055, 0.060]
 ```
 
-We also reuse `pipeline_with_optional_fft` from {ref}`Module 6a <tutorial:module6a>`, repeated here (folded) so this notebook runs standalone:
+We also reuse `pipeline_with_optional_fft` from {ref}`Module 6a <tutorial:module6a>`, repeated here so this notebook runs standalone:
 
 ```{code-cell} ipython3
-:tags: [hide-input]
-
 # The If-gated pipeline from Module 6a: run the pipeline, then run the FFT
 # only if the run's variance clears a threshold.
 @task.graph()

docs/source/tutorials/module7.md

@@ -40,7 +40,7 @@ This module is a survey, not a deep dive: each section is a concrete demo or ske
 This module touches AiiDA, `aiida-shell`, and `aiida-workgraph`:
 
 ```bash
-uv pip install aiida-core aiida-shell aiida-workgraph
+uv pip install aiida-core aiida-shell aiida-workgraph git+https://github.com/aiidateam/gsrd
 ```
 
 Install `aiida-core`, not `aiida` (the latter is an old meta-package).