Added programmatic tests

src/pynxtools_apm/config/eln_cfg.py

@@ -48,7 +48,7 @@
     "map_to_str": [
         "alias",
         "description",
-        "method",
+        ("type", "method"),
         ("grain_diameter/@units", "grain_diameter/unit"),
         ("grain_diameter_error/@units", "grain_diameter/unit"),
         ("heat_treatment_temperature/@units", "heat_treatment_temperature/unit"),
@@ -77,7 +77,7 @@
         "alias",
         "preparation_date",
         "description",
-        "method",
+        ("type", "method"),
         ("initial_radius/@units", "initial_radius/unit"),
         ("shank_angle/@units", "shank_angle/unit"),
     ],

tests/run_tests.ipynb

@@ -0,0 +1,126 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fc9345cb-46bf-4df3-9dac-1bde062d9020",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "print(os.getcwd())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e69ad935-80fd-4e70-af69-ac98e0bf2e34",
+   "metadata": {},
+   "source": [
+    "## Define tests"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "48f6e922-52d3-412f-8345-0641d33e676e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tests = {\n",
+    "    # \"eln\": [(\"eln_data.yaml\", \"apm.oasis.specific.yaml\")],\n",
+    "    \"apt\": [\"Si.apt\"],\n",
+    "    \"csv\": [\"Annealed_CoCrNi_100.csv\"],\n",
+    "    \"env\": [\"ErMnO.env\"],\n",
+    "    \"epos\": [\"R45_04472-v03.epos\"],\n",
+    "    \"fig\": [\"Superalloy_MassSpec_ranged.fig.txt\"],\n",
+    "    \"imago\": [\"default.analysis\"],\n",
+    "    \"pos\": [\"ErMnO_pole.pos\"],\n",
+    "    # \"pyccapt\": [(\"1748_Al_range_.h5\", \"1748_Al.h5\")],\n",
+    "    \"rng\": [\"87D_1.rng\"],\n",
+    "    \"rrng\": [\"VAlN_film_plan-view_700C.rrng\"]\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6ae5057c-2101-4792-9804-3af046003db7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! mkdir -p log\n",
+    "! mkdir -p prod"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "36a351a5-940d-4891-bb7e-1f4ba4100f6d",
+   "metadata": {},
+   "source": [
+    "## Run tests"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "809a88fe-5e4f-4429-b668-8a7956210606",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for parser_type, list_of_tests in tests.items():\n",
+    "    for entry in list_of_tests:\n",
+    "        if isinstance(entry, str):  # no sidecar file          \n",
+    "            print(f\"Running test {parser_type}/{entry}\")\n",
+    "            curr_dir = f\"{os.getcwd()}/data/{parser_type}\"\n",
+    "            in_one = f\"{curr_dir}/{entry}\"\n",
+    "            out = f\"prod/data.{parser_type}.{entry}.nxs\"\n",
+    "            stdout = f\"log/stdout.{parser_type}.{entry}.txt\"\n",
+    "            stderr = f\"log/stderr.{parser_type}.{entry}.txt\"\n",
+    "            ! dataconverter $in_one --reader apm --nxdl NXapm --output $out 1>$stdout 2>$stderr            \n",
+    "            continue\n",
+    "        elif isinstance(entry, tuple):  # with sidecar file\n",
+    "            if len(entry) == 2 and all(isinstance(val, str) for val in entry):\n",
+    "                print(f\"Running test {parser_type}/{entry}\")\n",
+    "                curr_dir = f\"{os.getcwd()}/data/{parser_type}\"\n",
+    "                in_one = f\"{curr_dir}/{entry[0]}\"\n",
+    "                in_two = f\"{curr_dir}/{entry[1]}\"\n",
+    "                out = f\"prod/data.{parser_type}.{entry[0]}.nxs\"\n",
+    "                stdout = f\"log/stdout.{parser_type}.{entry[0]}.txt\"\n",
+    "                stderr = f\"log/stderr.{parser_type}.{entry[0]}.txt\"\n",
+    "                ! dataconverter $in_one $in_two --reader apm --nxdl NXapm --output $out 1>$stdout 2>$stderr\n",
+    "                continue\n",
+    "        print(f\"Skipping test {parser_type}/{entry}\")\n",
+    "print(\"Ran all tests\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "213077cb-6c43-42d0-8f0a-213c0f82696d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}