Combine csv example into main examples notebook (#4022)

* Combine csv example into examples.ipynb and update test accordingly

* fix

Author: clmould

examples/csv_output.ipynb

@@ -120,22 +120,12 @@
     ")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Delete temp dir\n",
-    "temp_dir.cleanup()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## View key output variables\n",
-    "Run the large tokamak scenario using `SingleRun` to set some values on the `CostModel` instance and then print them."
+    "Using the `MFILE` we generated by running the large tokamak scenario above, we have set some values on the `CostModel` instance and can print them."
    ]
   },
   {
@@ -144,14 +134,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Define input file name relative to project dir\n",
-    "input_rel = script_dir / \"data/large_tokamak_IN.DAT\"\n",
-    "print(input_rel)\n",
-    "temp_dir, temp_input_path, _ = copy_to_temp_dir(input_rel)\n",
+    "import process.data_structure\n",
     "\n",
-    "# Run process on an input file\n",
-    "single_run = SingleRun(temp_input_path.as_posix())\n",
-    "single_run.run()"
+    "# Print some values on the CostModel instance\n",
+    "print(f\"Heat transport system: {process.data_structure.cost_variables.c226:.3e} M$\")\n",
+    "print(f\"Electrical plant equipment: {process.data_structure.cost_variables.c24:.3e} M$\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Convert to CSV format\n",
+    "This demonstrates how you would read from a PROCESS MFILE and write specified values into a csv using the `mfile_to_csv` function"
    ]
   },
   {
@@ -160,11 +155,28 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import process.data_structure\n",
-    "\n",
-    "# Print some values on the CostModel instance\n",
-    "print(f\"Heat transport system: {process.data_structure.cost_variables.c226:.3e} M$\")\n",
-    "print(f\"Electrical plant equipment: {process.data_structure.cost_variables.c24:.3e} M$\")"
+    "from process.io import mfile_to_csv\n",
+    "\n",
+    "data_dir = Path(\"data\")\n",
+    "\n",
+    "# mfile_to_csv requires two inputs:\n",
+    "# - path to the MFILE\n",
+    "# - .json containing the variable names to include in the csv file\n",
+    "\n",
+    "# This routine attempts to find every variable listed in the json file\n",
+    "# in the MFILE and writes the variable name, description and value\n",
+    "# to the output csv.\n",
+    "# Any listed variable that isn't in that MFILE will be skipped.\n",
+    "# The .csv file is saved to the directory of the input file\n",
+    "\n",
+    "mfile_to_csv.main(\n",
+    "    args=[\n",
+    "        \"-f\",\n",
+    "        (data_dir / \"large_tokamak_1_MFILE.DAT\").as_posix(),\n",
+    "        \"-v\",\n",
+    "        (data_dir / \"mfile_to_csv_vars.json\").as_posix(),\n",
+    "    ]\n",
+    ")"
    ]
   },
   {

examples/examples.ipynb

@@ -44,40 +44,12 @@ def test_examples(examples_temp_data):
     """
     example_notebook_location = examples_temp_data / "examples.ipynb"
     with testbook(example_notebook_location, execute=True, timeout=600):
-        pass
-
-
-def test_scan(examples_temp_data):
-    """Run scan.ipynb notebook check no exceptions are raised and that an MFILE is created.
-
-    scan.ipynb intentionally produces files when running the notebook, but remove
-    them when testing.
-    :param examples_temp_data: temporary dir containing examples files
-    :type examples_temp_data: Path
-    """
-    scan_notebook_location = examples_temp_data / "scan.ipynb"
-    with testbook(scan_notebook_location, execute=True, timeout=1200):
-        # Run entire scan.ipynb notebook and assert an MFILE is created
-        assert os.path.exists(examples_temp_data / "data/scan_example_file_MFILE.DAT")
-
-
-def test_csv(examples_temp_data):
-    """Run csv_output.ipynb, check no exceptions are raised, check a csv file exists and check the csv file contains data.
-
-    csv_output.ipynb intentionally produces files when running the notebook, but remove
-    them when testing.
-    :param examples_temp_data: temporary dir containing examples files
-    :type examples_temp_data: Path
-    """
-    csv_notebook_location = examples_temp_data / "csv_output.ipynb"
-    with testbook(csv_notebook_location, execute=True, timeout=600):
         # Check csv file is created
         assert os.path.exists(examples_temp_data / "data/large_tokamak_1_MFILE.csv")
 
         # Read in the csv file created by test and check it contains positive floats
         readcsv = pd.read_csv(examples_temp_data / "data/large_tokamak_1_MFILE.csv")
-        values = readcsv["Value"]
-        value_array = np.array(values)
+        value_array = np.array(readcsv["Value"])
         check_float = False
         check_positive = False
         value_array_type = value_array.dtype
@@ -91,6 +63,20 @@ def test_csv(examples_temp_data):
         assert check_positive
 
 
+def test_scan(examples_temp_data):
+    """Run scan.ipynb notebook check no exceptions are raised and that an MFILE is created.
+
+    scan.ipynb intentionally produces files when running the notebook, but remove
+    them when testing.
+    :param examples_temp_data: temporary dir containing examples files
+    :type examples_temp_data: Path
+    """
+    scan_notebook_location = examples_temp_data / "scan.ipynb"
+    with testbook(scan_notebook_location, execute=True, timeout=1200):
+        # Run entire scan.ipynb notebook and assert an MFILE is created
+        assert os.path.exists(examples_temp_data / "data/scan_example_file_MFILE.DAT")
+
+
 def test_plot_solutions(examples_temp_data):
     """Run plot_solutions.ipynb and check no exceptions are raised.