Atemerev/opts config (#115)

## Context
Options handling by `init.py`: `special` only supports positional
options. Attempting to specify a config file as a positional option led
to confusing error messages.

Now, using positional options in init.py lead to an error message
explaining that only keyword options are supported. --configFile can be
used anywhere on the command line after init.py, the rest of the options are passed
correctly to `neurodamus.commands`.

## Scope
Init.py is affected, no new dependencies added. Handling arguments is
extracted to a function for unit testing.

## Testing
tests/unit/test_init_py_config.py

## Review
* [X] PR description is complete
* [X] Coding style (imports, function length, New functions, classes or
files) are good
* [X] Unit/Scientific test added
* [N/A] Updated Readme, in-code, developer documentation

---------

Co-authored-by: Jorge Blanco Alonso <41900536+jorblancoa@users.noreply.github.com>

init.py

@@ -6,27 +6,18 @@
 """
 import sys
 from neurodamus import commands
+from neurodamus.utils.cli import extract_arguments
 from neuron import h
+import logging
 
 
 def main():
-    """Get the options for neurodamus and launch it.
-
-    We can't use positional arguments with special so we look for
-    --configFile=FILE, which defaults to simulation_config.json
-    """
-    first_argument_pos = 1
-    config_file = "simulation_config.json"
-
-    for i, arg in enumerate(sys.argv):
-        if arg.endswith("init.py"):
-            first_argument_pos = i + 1
-        elif arg.startswith("--configFile="):
-            config_file = arg.split('=')[1]
-            first_argument_pos = i + 1
-            break
-
-    args = [config_file] + sys.argv[first_argument_pos:]
+    args = []
+    try:
+        args = extract_arguments(sys.argv)
+    except ValueError as err:
+        logging.error(err)
+        return 1
 
     return commands.neurodamus(args)
 

neurodamus/utils/cli.py

@@ -0,0 +1,27 @@
+def extract_arguments(args):
+    """Get the options for neurodamus and launch it.
+
+    We can't use positional arguments with special so we look for
+    --configFile=FILE, which defaults to simulation_config.json
+    """
+    first_argument_pos = 1
+    init_py_reached = False
+    config_file = "simulation_config.json"
+    for i, arg in enumerate(args):
+        if not init_py_reached:
+            if arg.endswith("init.py"):
+                first_argument_pos = i + 1
+                init_py_reached = True
+            elif arg.startswith("--configFile="):
+                raise ValueError("Usage: ... init.py --configFile <config_file.json> ...")
+            continue
+
+        elif not arg.startswith("-"):
+            raise ValueError("Positional arguments are not supported by init.py. "
+                             f"Found positional argument: '{arg}'")
+        elif arg.startswith("--configFile="):
+            config_file = arg.split('=')[1]
+
+    result_args = ([config_file] +
+                   [x for x in args[first_argument_pos:] if not x.startswith("--configFile=")])
+    return result_args

tests/unit/conftest.py

@@ -1,6 +1,6 @@
 import pytest
 import sys
-import unittest
+import unittest.mock
 
 
 class MockParallelExec:

tests/unit/test_init_py_config.py

@@ -0,0 +1,51 @@
+import pytest
+
+from neurodamus.utils.cli import extract_arguments
+
+_default_config_file = 'simulation_config.json'
+
+
+def test_init_empty():
+    args = extract_arguments(['some/dir/init.py'])
+    assert len(args) == 1
+    assert args[0] == _default_config_file
+
+
+def test_init_non_positional():
+    with pytest.raises(ValueError):
+        extract_arguments(['init.py', 'simulation_config.json'])
+
+
+def test_init_config_only():
+    args = extract_arguments(['another/dir/init.py',
+                              '--configFile=conf/my_config.json'])
+    assert len(args) == 1
+    assert args[0] == 'conf/my_config.json'
+
+
+def test_init_pass_options():
+    args = extract_arguments(['another/dir/init.py', '--foo=bar',
+                              '--configFile=conf/my_config.json',
+                              '-v', '--baz=qux'])
+    assert len(args) == 4
+    assert args[0] == 'conf/my_config.json'
+    assert args[1] == '--foo=bar'
+    assert args[2] == '-v'
+    assert args[3] == '--baz=qux'
+
+
+def test_init_first_args():
+    args = extract_arguments(['dplace', 'special' 'another/dir/init.py', '--foo=bar',
+                              '--configFile=conf/my_config.json',
+                              '-v', '--baz=qux'])
+    assert len(args) == 4
+    assert args[0] == 'conf/my_config.json'
+    assert args[1] == '--foo=bar'
+    assert args[2] == '-v'
+    assert args[3] == '--baz=qux'
+
+
+def test_init_early_config_file():
+    with pytest.raises(ValueError):
+        extract_arguments(['dplace', 'special', '--configFile=my_config.json', '--some=pre',
+                              'etc', 'dir/init.py', '--foo=bar', '-v'])