libAtoms · bernstei · Dec 12, 2022 · Dec 13, 2022 · Jan 31, 2023 · Jan 31, 2023
diff --git a/docs/source/examples.cli.ipynb b/docs/source/examples.cli.ipynb
@@ -0,0 +1,123 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "72125898",
+   "metadata": {},
+   "source": [
+    "# command line examples"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ad34d6f2",
+   "metadata": {},
+   "source": [
+    "## evaluating configurations"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "699abc83",
+   "metadata": {},
+   "source": [
+    "A very simple example of evaluating energies/forces of a configuration with a machine learning potential.\n",
+    "\n",
+    "Potential and input files are stored in `docs/example_files/cli`, and example is written assuming that jupyter server has the current working directory set to the directory containing this example notebook."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "54564961",
+   "metadata": {},
+   "source": [
+    "### clean up files from previous runs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fa31f4c8",
+   "metadata": {},
+   "source": [
+    "Make sure that old output files are not there, otherwise autoparallelization of workflow will skip the evaluation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "197b7226",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "Path(\"GAP_evaluated_wfl_eval_configs.xyz\").unlink(missing_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "39ed76f2",
+   "metadata": {},
+   "source": [
+    "### evaluate using the command line"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b7147883",
+   "metadata": {},
+   "source": [
+    "Run a `wfl` command line one liner with standardized arguments for input and output files (all commands), and potential filename (standardized for all machine learning potentials subcommands: `ace`, `gap`, and `mace`)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "6dec15c0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!wfl eval gap -pf ../example_files/cli/GAP.xml \\\n",
+    "              -i ../example_files/cli/wfl_eval_configs.xyz \\\n",
+    "              -o GAP_evaluated_wfl_eval_configs.xyz"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f91acc7b",
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
+   "outputs": [],
+   "source": [
+    "# test that output is correct (hidden from nbsphinx autogenerated documentation)\n",
+    "import numpy as np\n",
+    "import ase.io\n",
+    "\n",
+    "for atoms in ase.io.read(\"GAP_evaluated_wfl_eval_configs.xyz\", \":\"):\n",
+    "    assert np.allclose(atoms.arrays[\"ref_error_calc_forces\"], atoms.arrays[\"gap_forces\"], atol=1.0e-6)"
+   ]
+  }
+ ],
+ "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": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/tests/test_doc_examples.py b/tests/test_doc_examples.py
@@ -1,5 +1,7 @@
 import os
 import shutil
+import re
+from pathlib import Path
 import json
 import pytest
 
@@ -10,21 +12,52 @@ def _get_coding_blocks(nb_file):
         nb = json.load(fo)
     return [''.join(cell['source']) for cell in nb['cells'] if cell['cell_type'] == 'code']
 
+def _fix_wfl(code_block):
+    if re.match(r"!\s*wfl\s+", code_block):
+        # join lines
+        code_block = re.sub(r"\\\n", " ", code_block)
+        # find args for cli runner
+        args_str = re.sub(r"^!\s*wfl\s+", "", code_block)
+        # run cli comand
+        code_block = ("from click.testing import CliRunner\n" +
+                      "from wfl.cli.cli import cli\n" +
+                      "import shlex\n" +
+                      "runner = CliRunner()\n" +
+                      f"runner.invoke(cli, shlex.split(\"\"\"{args_str}\"\"\"))")
+
+    return code_block
+
 @pytest.mark.parametrize(
-    ('nb_file', 'idx_execute'),
+    ('nb_file', 'idx_execute', 'wfl_cli'),
     (
-        pytest.param('examples.buildcell.ipynb', 'all', id='buildcell',
+        pytest.param('examples.buildcell.ipynb', 'all', False, id='buildcell',
             marks=pytest.mark.skipif(not shutil.which("buildcell"), reason="buildcell not in PATH")),
-        pytest.param('examples.dimers.ipynb', 'all', id='dimer structures'),
-        pytest.param('examples.select_fps.ipynb', 'all', id='select fps')
+        pytest.param('examples.dimers.ipynb', 'all', False, id='dimer structures'),
+        pytest.param('examples.cli.ipynb', 'all', True, id='command line interface')
     )
 )
-def test_example(tmp_path, nb_file, idx_execute):
+
+def test_example(tmp_path, monkeypatch, nb_file, idx_execute, wfl_cli):
     basepath = os.path.join(f'{os.path.dirname(__file__)}/../docs/source')
     coding_blocks = _get_coding_blocks(f'{basepath}/{nb_file}')
-    code = '\n'.join([cb_i for idx_i, cb_i in enumerate(coding_blocks) if idx_execute == 'all' or idx_i in idx_execute])
+    if wfl_cli:
+        coding_blocks_exec = [_fix_wfl(cb_i) for idx_i, cb_i in enumerate(coding_blocks) if idx_execute == 'all' or idx_i in idx_execute]
+
+        example_name = nb_file.replace("examples.", "").replace(".ipynb", "")
+
+        source_example_files_dir = (Path(__file__).parent.parent / "docs" / "example_files" / example_name)
+        if source_example_files_dir.is_dir():
+            pytest_example_files_dir = tmp_path / "example_files" / example_name
+            shutil.copytree(source_example_files_dir, pytest_example_files_dir)
+
+            # examples look for their files under "../example_files/<example_name>/", so move
+            # down one to allow the ".." to work
+            (tmp_path / "run").mkdir()
+            monkeypatch.chdir(tmp_path / "run")
+    else:
+        coding_blocks_exec = [cb_i for idx_i, cb_i in enumerate(coding_blocks) if idx_execute == 'all' or idx_i in idx_execute]
+
+    code = '\n'.join(coding_blocks_exec)
     assert code is not ''
 
-    os.chdir(tmp_path)
     exec(code)
-    os.chdir('..')