DevOps: Fix tutorial scripts and CI/CD

Make the exercise/solution conversion script reversible. Remove empty tutorial code cells.
espressomd · Oct 4, 2024 · 5fb1106 · 5fb1106
1 parent 03033c4
commit 5fb1106
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Showing 4 changed files with 33 additions and 73 deletions.
diff --git a/doc/tutorials/Readme.md b/doc/tutorials/Readme.md
@@ -70,7 +70,7 @@ physical systems.
   Measuring the excess chemical potential of a salt solution using the Widom particle insertion method.  
   [Guide](widom_insertion/widom_insertion.ipynb)
 * **Grand-Canonical Monte Carlo**
-  Simulating a polyelectrolyte solution coupled to a reservoir of salt.
+  Simulating a polyelectrolyte solution coupled to a reservoir of salt.  
   [Guide](grand_canonical_monte_carlo/grand_canonical_monte_carlo.ipynb)
 
 [comment]: # (End of tutorials landing page)

diff --git a/doc/tutorials/convert.py b/doc/tutorials/convert.py
@@ -75,7 +75,7 @@ def add_cell_from_script(nb, filepath):
 
 
 def remove_empty_cells(nb):
-    for i in range(len(nb['cells']) - 1, 0, -1):
+    for i in range(len(nb["cells"]))[::-1]:
         cell = nb['cells'][i]
         if cell['source'].strip() == '':
             nb['cells'].pop(i)
@@ -90,11 +90,19 @@ def parse_solution_cell(cell):
 
 
 def convert_exercise2_to_code(nb):
-    for i in range(len(nb["cells"]) - 1, 0, -1):
+    for i in range(len(nb["cells"]))[::-1]:
         cell = nb["cells"][i]
-        solution = parse_solution_cell(cell)
-        if solution is not None:
-            cell["source"] = solution
+        if cell["cell_type"] != "markdown":
+            continue
+        source = cell["source"]
+        if source.startswith("<details") and source.endswith("</details>"):
+            m = re.search("```python\n(.+)\n```", source, flags=re.DOTALL)
+            solution = "# SOLUTION CELL\n" + m.group(1)
+            nb["cells"][i] = nbformat.v4.new_code_cell(source=solution)
+            if (i + 1) != len(nb["cells"]) and \
+                    nb["cells"][i + 1]["cell_type"] == "code" and \
+                    not nb["cells"][i + 1]["source"]:
+                del nb["cells"][i + 1]
 
 
 def disable_plot_interactivity(nb):

diff --git a/doc/tutorials/lennard_jones/lennard_jones.ipynb b/doc/tutorials/lennard_jones/lennard_jones.ipynb
@@ -273,14 +273,6 @@
     "system = espressomd.System(box_l=BOX_L)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "13275327",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -356,14 +348,6 @@
     "particles = system.part.add(type=[0] * N_PART, pos=np.random.random((N_PART, 3)) * system.box_l)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "655d49e6",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -498,14 +482,6 @@
     "    epsilon=LJ_EPS, sigma=LJ_SIG, cutoff=LJ_CUT, shift=0)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "91ac5e57",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "id": "5e6332fb",
@@ -717,14 +693,6 @@
     "T_inst = 2. / 3. * e_kin / N_PART"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c53290b6",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -843,14 +811,6 @@
     "steps_per_subsample = int(np.ceil(3 * corr_time / system.time_step))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "94fc76b6",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -923,14 +883,6 @@
     "SEM_pot_energy = np.std(pot_energies) / np.sqrt(len(pot_energies))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3e4a203c",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1034,14 +986,6 @@
     "system.auto_update_accumulators.add(rdf_acc)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "8de0795a",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "id": "51edfcf1",
@@ -1082,14 +1026,6 @@
     "rs = rdf_obs.bin_centers()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "18a10a12",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/testsuite/scripts/tutorials/test_convert.py b/testsuite/scripts/tutorials/test_convert.py
@@ -188,7 +188,7 @@ def test_cells_prepare_for_html(self):
         self.assertEqual(cell['source'], 'Question 1')
         cell = next(cells)
         self.assertEqual(cell['cell_type'], 'code')
-        self.assertEqual(cell['source'], '1')
+        self.assertEqual(cell['source'], '# SOLUTION CELL\n1')
         cell = next(cells)
         self.assertEqual(cell['cell_type'], 'markdown')
         self.assertEqual(cell['source'], '1b')
@@ -199,7 +199,7 @@ def test_cells_prepare_for_html(self):
         self.assertEqual(cell['cell_type'], 'code')
         self.assertEqual(
             cell['source'],
-            '2\nimport matplotlib.pyplot\nglobal_var = 20')
+            '# SOLUTION CELL\n2\nimport matplotlib.pyplot\nglobal_var = 20')
         cell = next(cells)
         self.assertEqual(cell['cell_type'], 'code')
         self.assertEqual(cell['source'], '3')
@@ -231,7 +231,7 @@ def test_cells_conversion(self):
         self.assertEqual(cell['source'], 'Question 1')
         cell = next(cells)
         self.assertEqual(cell['cell_type'], 'code')
-        self.assertEqual(cell['source'], '1')
+        self.assertEqual(cell['source'], '# SOLUTION CELL\n1')
         self.assertEqual(next(cells, 'EOF'), 'EOF')
 
         with open(f_input, 'w', encoding='utf-8') as f:
@@ -255,6 +255,22 @@ def test_cells_conversion(self):
         self.assertEqual(cell['source'], '')
         self.assertEqual(next(cells, 'EOF'), 'EOF')
 
+        # check operation is reversible
+        cmd = ['cells', '--to-py', str(f_input)]
+        self.run_command(cmd, f_input)
+        # read processed notebook
+        with open(f_input, encoding='utf-8') as f:
+            nb_output = nbformat.read(f, as_version=4)
+        # check cells
+        cells = iter(nb_output['cells'])
+        cell = next(cells)
+        self.assertEqual(cell['cell_type'], 'markdown')
+        self.assertEqual(cell['source'], 'Question 1')
+        cell = next(cells)
+        self.assertEqual(cell['cell_type'], 'code')
+        self.assertEqual(cell['source'], '# SOLUTION CELL\n1')
+        self.assertEqual(next(cells, 'EOF'), 'EOF')
+
     @skipIfMissingModules
     def test_cells_autopep8(self):
         root = pathlib.Path("@CMAKE_CURRENT_BINARY_DIR@")