From 22c4c714ed823e6ed8c81c6e08ab6802c0dd790c Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 6 Dec 2022 21:42:27 +0000
Subject: [PATCH 01/38] First draft with test outline

---
 skops/io/_cli.py               | 76 ++++++++++++++++++++++++++++++++++
 skops/io/tests/test_cli.py     | 40 ++++++++++++++++++
 skops/io/tests/test_persist.py |  7 +++-
 3 files changed, 122 insertions(+), 1 deletion(-)
 create mode 100644 skops/io/_cli.py
 create mode 100644 skops/io/tests/test_cli.py

diff --git a/skops/io/_cli.py b/skops/io/_cli.py
new file mode 100644
index 00000000..75d99d27
--- /dev/null
+++ b/skops/io/_cli.py
@@ -0,0 +1,76 @@
+from __future__ import annotations
+
+import argparse
+import logging
+import os
+import pathlib
+import pickle as pkl
+from typing import Optional
+
+from skops.io import dumps, get_untrusted_types
+
+
+def _convert(
+    input_file: os.PathLike, output_dir: pathlib.Path, is_trusted: bool = False
+):
+    model_name = pathlib.Path(input_file).stem
+
+    logging.info(f"Converting {model_name}")
+
+    with open(input_file, "rb") as f:
+        obj = pkl.load(f)
+    skops_dump = dumps(obj)
+
+    if not is_trusted:
+        untrusted_types = get_untrusted_types(data=skops_dump)
+        if len(untrusted_types) > 0:
+            # Print out untrusted types to command line
+            untrusted_str = "\n".join(untrusted_types)
+            print(untrusted_str)
+            logging.warning(
+                "Unsafe Types Detected!\n"
+                f"While converting {model_name}, "
+                "the following unsafe types were found: \n"
+                f"{untrusted_str}\n"
+                "To convert this anyway, add `-t` to this command."
+            )
+            return
+
+        logging.debug(f"No unsafe types found in {model_name}.")
+
+    with open(output_dir / f"{model_name}.skops", "wb") as out_file:
+        print(f"Writing to {output_dir/model_name}.skops")
+        out_file.write(skops_dump)
+
+
+def main_convert(command_line_args: Optional[list[str]] = None):
+    parser = argparse.ArgumentParser(
+        description="Convert input Pickle files to .skops files"
+    )
+    parser.add_argument("input-files", type=argparse.FileType("r"), nargs="+")
+    parser.add_argument("-t", "--trusted", action="store_true", default=False)
+    parser.add_argument(
+        "-d",
+        "--debug",
+        help="Enable debug logging",
+        action="store_const",
+        dest="loglevel",
+        const=logging.DEBUG,
+        default=logging.WARNING,
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        help="Enable verbose logging",
+        action="store_const",
+        dest="loglevel",
+        const=logging.INFO,
+    )
+    args = parser.parse_args()
+
+    for input_file in args.input_files:
+        _convert(
+            input_file=input_file,
+            output_dir=pathlib.Path.cwd(),
+            is_trusted=args.trusted,
+        )
diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
new file mode 100644
index 00000000..eee3ca2b
--- /dev/null
+++ b/skops/io/tests/test_cli.py
@@ -0,0 +1,40 @@
+import pickle as pkl
+
+import numpy as np
+import pytest
+
+from skops.io._cli import _convert
+
+
+class MockUnsafeType:
+    def __init__(self):
+        pass
+
+
+class TestConvert:
+    model_name = "a_model"
+
+    @pytest.fixture
+    def pkl_path(self, tmp_path):
+        return tmp_path / f"{self.model_name}.pkl"
+
+    @pytest.fixture
+    def skops_path(self, tmp_path):
+        return tmp_path / f"{self.model_name}.skops"
+
+    @pytest.fixture
+    def write_safe_file(self, pkl_path):
+        obj = np.ndarray([1, 2, 3, 4])
+        with open(pkl_path, "wb") as f:
+            pkl.dump(obj, f)
+
+    @pytest.fixture
+    def write_unsafe_file(self, pkl_path):
+        obj = MockUnsafeType()
+        with open(pkl_path, "wb") as f:
+            pkl.dump(obj, f)
+
+    def test_base_case_works_as_expected(
+        self, write_safe_file, pkl_path, skops_path, tmp_path
+    ):
+        _convert(pkl_path, tmp_path)
diff --git a/skops/io/tests/test_persist.py b/skops/io/tests/test_persist.py
index c38871c6..2160e259 100644
--- a/skops/io/tests/test_persist.py
+++ b/skops/io/tests/test_persist.py
@@ -419,7 +419,12 @@ def get_input(estimator):
         )
     else:
         X, y = make_classification(
-            n_samples=N_SAMPLES, n_features=N_FEATURES, random_state=0
+            n_samples=N_SAMPLES,
+            n_features=N_FEATURES,
+            random_state=0,
+            n_classes=3,
+            n_redundant=1,
+            n_informative=N_FEATURES - 1,
         )
     y = _enforce_estimator_tags_y(estimator, y)
     tags = _safe_tags(estimator)

From eacedf8b67fff6192d3b54b7a08e89730cc1a5f8 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Fri, 9 Dec 2022 21:53:23 +0000
Subject: [PATCH 02/38] Add in tests for both main and method

---
 skops/io/_cli.py           | 38 ++++++++++--------
 skops/io/tests/test_cli.py | 79 ++++++++++++++++++++++++++++++++++----
 2 files changed, 92 insertions(+), 25 deletions(-)

diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index 75d99d27..65a2dee1 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -21,25 +21,29 @@ def _convert(
         obj = pkl.load(f)
     skops_dump = dumps(obj)
 
-    if not is_trusted:
-        untrusted_types = get_untrusted_types(data=skops_dump)
-        if len(untrusted_types) > 0:
-            # Print out untrusted types to command line
-            untrusted_str = "\n".join(untrusted_types)
-            print(untrusted_str)
+    untrusted_types = get_untrusted_types(data=skops_dump)
+
+    if not untrusted_types:
+        logging.debug(f"No unsafe types found in {model_name}.")
+    else:
+        untrusted_str = "\n".join(untrusted_types)
+
+        logging.warning(
+            "Unsafe Types Detected!\n"
+            f"While converting {model_name}, "
+            "the following unsafe types were found: \n"
+            f"{untrusted_str}\n"
+        )
+
+        if not is_trusted:
             logging.warning(
-                "Unsafe Types Detected!\n"
-                f"While converting {model_name}, "
-                "the following unsafe types were found: \n"
-                f"{untrusted_str}\n"
+                f"Model {model_name} will not be converted due to unsafe types.\n"
                 "To convert this anyway, add `-t` to this command."
             )
             return
 
-        logging.debug(f"No unsafe types found in {model_name}.")
-
     with open(output_dir / f"{model_name}.skops", "wb") as out_file:
-        print(f"Writing to {output_dir/model_name}.skops")
+        logging.info(f"Writing to {output_dir/model_name}.skops")
         out_file.write(skops_dump)
 
 
@@ -47,7 +51,7 @@ def main_convert(command_line_args: Optional[list[str]] = None):
     parser = argparse.ArgumentParser(
         description="Convert input Pickle files to .skops files"
     )
-    parser.add_argument("input-files", type=argparse.FileType("r"), nargs="+")
+    parser.add_argument("inputs", nargs="+")
     parser.add_argument("-t", "--trusted", action="store_true", default=False)
     parser.add_argument(
         "-d",
@@ -66,9 +70,9 @@ def main_convert(command_line_args: Optional[list[str]] = None):
         dest="loglevel",
         const=logging.INFO,
     )
-    args = parser.parse_args()
-
-    for input_file in args.input_files:
+    args = parser.parse_args(command_line_args)
+    print(args.inputs)
+    for input_file in args.inputs:
         _convert(
             input_file=input_file,
             output_dir=pathlib.Path.cwd(),
diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
index eee3ca2b..171696e6 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/io/tests/test_cli.py
@@ -1,8 +1,15 @@
+import logging
+import os.path
+import pathlib
 import pickle as pkl
+from typing import Optional
+from unittest import mock
+from unittest.mock import call, patch
 
 import numpy as np
 import pytest
 
+import skops
 from skops.io._cli import _convert
 
 
@@ -12,7 +19,15 @@ def __init__(self):
 
 
 class TestConvert:
-    model_name = "a_model"
+    model_name = "some_model_name"
+
+    @pytest.fixture
+    def safe_obj(self):
+        return np.ndarray([1, 2, 3, 4])
+
+    @pytest.fixture
+    def unsafe_obj(self):
+        return MockUnsafeType()
 
     @pytest.fixture
     def pkl_path(self, tmp_path):
@@ -23,18 +38,66 @@ def skops_path(self, tmp_path):
         return tmp_path / f"{self.model_name}.skops"
 
     @pytest.fixture
-    def write_safe_file(self, pkl_path):
-        obj = np.ndarray([1, 2, 3, 4])
+    def write_safe_file(self, pkl_path, safe_obj):
         with open(pkl_path, "wb") as f:
-            pkl.dump(obj, f)
+            pkl.dump(safe_obj, f)
 
     @pytest.fixture
-    def write_unsafe_file(self, pkl_path):
-        obj = MockUnsafeType()
+    def write_unsafe_file(self, pkl_path, unsafe_obj):
         with open(pkl_path, "wb") as f:
-            pkl.dump(obj, f)
+            pkl.dump(unsafe_obj, f)
 
     def test_base_case_works_as_expected(
-        self, write_safe_file, pkl_path, skops_path, tmp_path
+        self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj
     ):
         _convert(pkl_path, tmp_path)
+        persisted_obj = skops.io.load(skops_path)
+        assert np.array_equal(persisted_obj, safe_obj)
+
+    def test_unsafe_case_works_as_expected(
+        self, pkl_path, tmp_path, skops_path, write_unsafe_file, caplog
+    ):
+        caplog.set_level(logging.WARNING)
+        _convert(pkl_path, tmp_path)
+        assert not os.path.isfile(skops_path)
+
+        # check logging has warned that an unsafe type was found
+        assert MockUnsafeType.__name__ in caplog.text
+
+
+class TestMainConvert:
+    @staticmethod
+    def assert_called_correctly(
+        mock_convert: mock.MagicMock,
+        paths: list,
+        output_dir: Optional[pathlib.Path] = pathlib.Path.cwd(),
+        trusted: Optional[bool] = False,
+    ):
+        assert mock_convert.call_count == len(paths)
+
+        mock_convert.assert_has_calls(
+            [
+                call(input_file=p, output_dir=output_dir, is_trusted=trusted)
+                for p in paths
+            ]
+        )
+
+    @patch("skops.io._cli._convert")
+    def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
+        args = [
+            "123.pkl",
+            "abc.pkl",
+        ]
+
+        skops.io._cli.main_convert(command_line_args=args)
+        self.assert_called_correctly(mock_convert, args)
+
+    @patch("skops.io._cli._convert")
+    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted"])
+    def test_with_trusted_works_as_expected(
+        self, mock_convert: mock.MagicMock, trusted_flag
+    ):
+        paths = ["abc.123", "234.567", "d/object_1.pkl"]
+        args = paths + [trusted_flag]
+        skops.io._cli.main_convert(command_line_args=args)
+        self.assert_called_correctly(mock_convert, paths=paths, trusted=True)

From 453728d3b6aaec553123bee13e131d40e9e74a1c Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Fri, 9 Dec 2022 22:07:15 +0000
Subject: [PATCH 03/38] Add entrypoint to setup.py

---
 setup.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index df25333b..17a13116 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 # This is a bit (!) hackish: we are setting a global variable so that the
 # main modelcard __init__ can detect if it is being loaded by the setup
 # routine, to avoid attempting to load components.
-builtins.__SKOPS_SETUP__ = True
+builtins.__SKOPS_SETUP__ = True  # type: ignore
 
 
 import skops  # noqa
@@ -34,6 +34,14 @@
 
 
 def setup_package():
+    package_data = dict(
+        entry_points={
+            "console_scripts": [
+                "convert = skops.io._cli._convert:main_convert",
+            ],
+        }
+    )
+
     metadata = dict(
         name=DISTNAME,
         maintainer=MAINTAINER,
@@ -73,7 +81,7 @@ def setup_package():
         include_package_data=True,
     )
 
-    setup(**metadata)
+    setup(**package_data, **metadata)
 
 
 if __name__ == "__main__":

From da6da30b0bfdefea97f1f89e9f705042d6bede57 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Fri, 9 Dec 2022 22:22:53 +0000
Subject: [PATCH 04/38] Get entrypoint working

---
 setup.py         | 2 +-
 skops/io/_cli.py | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 17a13116..9e94c001 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ def setup_package():
     package_data = dict(
         entry_points={
             "console_scripts": [
-                "convert = skops.io._cli._convert:main_convert",
+                "skops-convert = skops.io._cli:main_convert",
             ],
         }
     )
diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index 65a2dee1..d66b777c 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -71,7 +71,6 @@ def main_convert(command_line_args: Optional[list[str]] = None):
         const=logging.INFO,
     )
     args = parser.parse_args(command_line_args)
-    print(args.inputs)
     for input_file in args.inputs:
         _convert(
             input_file=input_file,

From 5a9c0fc3db94b5f7628fc5632acce497a73eb857 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Fri, 9 Dec 2022 22:46:41 +0000
Subject: [PATCH 05/38] Undo change in _persist

---
 skops/io/tests/test_persist.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/skops/io/tests/test_persist.py b/skops/io/tests/test_persist.py
index 2160e259..c38871c6 100644
--- a/skops/io/tests/test_persist.py
+++ b/skops/io/tests/test_persist.py
@@ -419,12 +419,7 @@ def get_input(estimator):
         )
     else:
         X, y = make_classification(
-            n_samples=N_SAMPLES,
-            n_features=N_FEATURES,
-            random_state=0,
-            n_classes=3,
-            n_redundant=1,
-            n_informative=N_FEATURES - 1,
+            n_samples=N_SAMPLES, n_features=N_FEATURES, random_state=0
         )
     y = _enforce_estimator_tags_y(estimator, y)
     tags = _safe_tags(estimator)

From b3a561eea8d668b4ee6f19bc335ef08dadd18383 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sun, 11 Dec 2022 13:24:57 +0000
Subject: [PATCH 06/38] Add output dir argument

---
 skops/io/_cli.py           | 32 +++++++++++++++++++++++++++++---
 skops/io/tests/test_cli.py | 21 ++++++++++++++++++++-
 2 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index d66b777c..e2a0673e 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -51,8 +51,18 @@ def main_convert(command_line_args: Optional[list[str]] = None):
     parser = argparse.ArgumentParser(
         description="Convert input Pickle files to .skops files"
     )
-    parser.add_argument("inputs", nargs="+")
-    parser.add_argument("-t", "--trusted", action="store_true", default=False)
+    parser.add_argument("inputs", nargs="+", help="Input files to convert.")
+    parser.add_argument(
+        "-t",
+        "--trusted",
+        help=(
+            "Automatically trust all files, "
+            "and convert all inputs, even if an "
+            "untrusted type is detected."
+        ),
+        action="store_true",
+        default=False,
+    )
     parser.add_argument(
         "-d",
         "--debug",
@@ -70,10 +80,26 @@ def main_convert(command_line_args: Optional[list[str]] = None):
         dest="loglevel",
         const=logging.INFO,
     )
+    parser.add_argument(
+        "--output-dir",
+        help=(
+            "Specify a directory to save converted files to. "
+            "Default will save files to the current working directory."
+        ),
+        type=str,
+        default=None,
+    )
     args = parser.parse_args(command_line_args)
+
+    output_dir = args.output_dir
+    if not output_dir:
+        output_dir = pathlib.Path.cwd()
+    else:
+        output_dir = pathlib.Path(output_dir)
+
     for input_file in args.inputs:
         _convert(
             input_file=input_file,
-            output_dir=pathlib.Path.cwd(),
+            output_dir=output_dir,
             is_trusted=args.trusted,
         )
diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
index 171696e6..1fa565d9 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/io/tests/test_cli.py
@@ -73,6 +73,7 @@ def assert_called_correctly(
         output_dir: Optional[pathlib.Path] = pathlib.Path.cwd(),
         trusted: Optional[bool] = False,
     ):
+        breakpoint()
         assert mock_convert.call_count == len(paths)
 
         mock_convert.assert_has_calls(
@@ -93,7 +94,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         self.assert_called_correctly(mock_convert, args)
 
     @patch("skops.io._cli._convert")
-    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted"])
+    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted", None])
     def test_with_trusted_works_as_expected(
         self, mock_convert: mock.MagicMock, trusted_flag
     ):
@@ -101,3 +102,21 @@ def test_with_trusted_works_as_expected(
         args = paths + [trusted_flag]
         skops.io._cli.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, paths=paths, trusted=True)
+
+    @patch("skops.io._cli._convert")
+    @pytest.mark.parametrize(
+        "output_dir, expected_dir",
+        [("a/b/c", pathlib.Path("a/b/c")), (None, pathlib.Path.cwd())],
+    )
+    def test_with_output_dir_works_as_expected(
+        self, mock_convert: mock.MagicMock, output_dir, expected_dir
+    ):
+        paths = ["abc.123", "234.567", "d/object_1.pkl"]
+
+        if output_dir is not None:
+            args = paths + ["--output-dir", output_dir]
+        else:
+            args = paths
+
+        skops.io._cli.main_convert(command_line_args=args)
+        self.assert_called_correctly(mock_convert, paths=paths, output_dir=expected_dir)

From 1d01ff5bae5c07d7294c808386ab6bba9a3a87c5 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sun, 11 Dec 2022 13:29:26 +0000
Subject: [PATCH 07/38] fix tests

---
 skops/io/tests/test_cli.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
index 1fa565d9..56a31305 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/io/tests/test_cli.py
@@ -73,7 +73,6 @@ def assert_called_correctly(
         output_dir: Optional[pathlib.Path] = pathlib.Path.cwd(),
         trusted: Optional[bool] = False,
     ):
-        breakpoint()
         assert mock_convert.call_count == len(paths)
 
         mock_convert.assert_has_calls(
@@ -94,7 +93,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         self.assert_called_correctly(mock_convert, args)
 
     @patch("skops.io._cli._convert")
-    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted", None])
+    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted"])
     def test_with_trusted_works_as_expected(
         self, mock_convert: mock.MagicMock, trusted_flag
     ):

From 91d1b0f9c57dfc8796de679e4264dd8a920dab26 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sun, 11 Dec 2022 13:41:42 +0000
Subject: [PATCH 08/38] adjust format of log message

---
 skops/io/_cli.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index e2a0673e..225a1186 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -57,8 +57,8 @@ def main_convert(command_line_args: Optional[list[str]] = None):
         "--trusted",
         help=(
             "Automatically trust all files, "
-            "and convert all inputs, even if an "
-            "untrusted type is detected."
+            "and convert all inputs, "
+            "even if an untrusted type is detected."
         ),
         action="store_true",
         default=False,
@@ -66,7 +66,7 @@ def main_convert(command_line_args: Optional[list[str]] = None):
     parser.add_argument(
         "-d",
         "--debug",
-        help="Enable debug logging",
+        help="Enable debug logging.",
         action="store_const",
         dest="loglevel",
         const=logging.DEBUG,
@@ -75,7 +75,7 @@ def main_convert(command_line_args: Optional[list[str]] = None):
     parser.add_argument(
         "-v",
         "--verbose",
-        help="Enable verbose logging",
+        help="Enable verbose logging.",
         action="store_const",
         dest="loglevel",
         const=logging.INFO,
@@ -97,6 +97,8 @@ def main_convert(command_line_args: Optional[list[str]] = None):
     else:
         output_dir = pathlib.Path(output_dir)
 
+    logging.basicConfig(format="%(message)s", level=args.loglevel)
+
     for input_file in args.inputs:
         _convert(
             input_file=input_file,

From 7af9c268113740ac1b74006614ae35157082f52e Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sun, 11 Dec 2022 15:09:51 +0000
Subject: [PATCH 09/38] Update main entrypoint and parent structure

---
 setup.py            |  2 +-
 skops/entrypoint.py | 21 +++++++++++++++++++++
 skops/io/_cli.py    | 12 +++++++++---
 3 files changed, 31 insertions(+), 4 deletions(-)
 create mode 100644 skops/entrypoint.py

diff --git a/setup.py b/setup.py
index 9e94c001..32f9db1c 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ def setup_package():
     package_data = dict(
         entry_points={
             "console_scripts": [
-                "skops-convert = skops.io._cli:main_convert",
+                "skops = skops.entrypoint:main_entrypoint",
             ],
         }
     )
diff --git a/skops/entrypoint.py b/skops/entrypoint.py
new file mode 100644
index 00000000..5e751bbb
--- /dev/null
+++ b/skops/entrypoint.py
@@ -0,0 +1,21 @@
+import argparse
+
+import skops.io._cli
+
+
+def main_entrypoint(command_line_args=None):
+    """Main entrypoint for all command line Skops methods."""
+    parser = argparse.ArgumentParser(
+        prog="Skops",
+        description="Main entrypoint for all command line Skops methods.",
+        add_help=False,
+    )
+
+    function_map = {"convert": skops.io._cli.main_convert}
+
+    parser.add_argument(
+        "function", help="Function to call.", choices=function_map.keys()
+    )
+
+    arg, _ = parser.parse_known_args()
+    function_map.get(arg.function)(parent=parser)
diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index 225a1186..45040262 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -43,14 +43,20 @@ def _convert(
             return
 
     with open(output_dir / f"{model_name}.skops", "wb") as out_file:
-        logging.info(f"Writing to {output_dir/model_name}.skops")
+        logging.info(f"Writing to {output_dir / model_name}.skops")
         out_file.write(skops_dump)
 
 
-def main_convert(command_line_args: Optional[list[str]] = None):
+def main_convert(
+    command_line_args: Optional[list[str]] = None,
+    parent: Optional[argparse.ArgumentParser] = None,
+):
+    parents = [parent] if parent else []
+
     parser = argparse.ArgumentParser(
-        description="Convert input Pickle files to .skops files"
+        description="Convert input Pickle files to .skops files", parents=parents
     )
+
     parser.add_argument("inputs", nargs="+", help="Input files to convert.")
     parser.add_argument(
         "-t",

From 8ad10cdfcc1c4f2e33da18889572e5cebbfc11fa Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Mon, 12 Dec 2022 21:06:29 +0000
Subject: [PATCH 10/38] Add test that covers main entrypoint

---
 setup.py                             |  2 +-
 skops/io/tests/test_cli.py           |  9 ++++----
 skops/utils/__init__.py              |  0
 skops/{ => utils}/entrypoint.py      |  6 ++----
 skops/utils/tests/test_entrypoint.py | 32 ++++++++++++++++++++++++++++
 5 files changed, 39 insertions(+), 10 deletions(-)
 create mode 100644 skops/utils/__init__.py
 rename skops/{ => utils}/entrypoint.py (76%)
 create mode 100644 skops/utils/tests/test_entrypoint.py

diff --git a/setup.py b/setup.py
index 32f9db1c..efde11e1 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ def setup_package():
     package_data = dict(
         entry_points={
             "console_scripts": [
-                "skops = skops.entrypoint:main_entrypoint",
+                "skops = skops.utils.entrypoint:main_entrypoint",
             ],
         }
     )
diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
index 56a31305..7b186b6d 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/io/tests/test_cli.py
@@ -4,7 +4,6 @@
 import pickle as pkl
 from typing import Optional
 from unittest import mock
-from unittest.mock import call, patch
 
 import numpy as np
 import pytest
@@ -77,12 +76,12 @@ def assert_called_correctly(
 
         mock_convert.assert_has_calls(
             [
-                call(input_file=p, output_dir=output_dir, is_trusted=trusted)
+                mock.call(input_file=p, output_dir=output_dir, is_trusted=trusted)
                 for p in paths
             ]
         )
 
-    @patch("skops.io._cli._convert")
+    @mock.patch("skops.io._cli._convert")
     def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         args = [
             "123.pkl",
@@ -92,7 +91,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         skops.io._cli.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, args)
 
-    @patch("skops.io._cli._convert")
+    @mock.patch("skops.io._cli._convert")
     @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted"])
     def test_with_trusted_works_as_expected(
         self, mock_convert: mock.MagicMock, trusted_flag
@@ -102,7 +101,7 @@ def test_with_trusted_works_as_expected(
         skops.io._cli.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, paths=paths, trusted=True)
 
-    @patch("skops.io._cli._convert")
+    @mock.patch("skops.io._cli._convert")
     @pytest.mark.parametrize(
         "output_dir, expected_dir",
         [("a/b/c", pathlib.Path("a/b/c")), (None, pathlib.Path.cwd())],
diff --git a/skops/utils/__init__.py b/skops/utils/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/skops/entrypoint.py b/skops/utils/entrypoint.py
similarity index 76%
rename from skops/entrypoint.py
rename to skops/utils/entrypoint.py
index 5e751bbb..0933a804 100644
--- a/skops/entrypoint.py
+++ b/skops/utils/entrypoint.py
@@ -12,10 +12,8 @@ def main_entrypoint(command_line_args=None):
     )
 
     function_map = {"convert": skops.io._cli.main_convert}
-
     parser.add_argument(
         "function", help="Function to call.", choices=function_map.keys()
     )
-
-    arg, _ = parser.parse_known_args()
-    function_map.get(arg.function)(parent=parser)
+    args, _ = parser.parse_known_args(command_line_args)
+    function_map.get(args.function)(parent=parser, command_line_args=command_line_args)
diff --git a/skops/utils/tests/test_entrypoint.py b/skops/utils/tests/test_entrypoint.py
new file mode 100644
index 00000000..396636e9
--- /dev/null
+++ b/skops/utils/tests/test_entrypoint.py
@@ -0,0 +1,32 @@
+import pathlib
+import sys
+from unittest import mock
+
+import pytest
+
+from skops.utils.entrypoint import main_entrypoint
+
+
+class TestEntrypoint:
+    """Integration tests that check that entrypoint calls pass through correctly.
+
+    Full coverage of individual entrypoint calls should be done in their own classes.
+    """
+
+    @pytest.fixture(autouse=True)
+    def clear_argv(self):
+        # Required to clear argv in case Pytest is called on this specific function.
+        # Otherwise, clogs parser.parse_known_args() in argparse
+        sys.argv = [""]
+
+    @mock.patch("skops.io._cli._convert")
+    def test_convert_works_as_expected(self, mocked_convert: mock.MagicMock):
+        args = ["convert", "abc.def", "-t"]
+
+        main_entrypoint(args)
+
+        mocked_convert.assert_called_once_with(
+            input_file="abc.def",
+            output_dir=pathlib.Path.cwd(),
+            is_trusted=True,
+        )

From 864d8ca6b570d21507d379893b473a8ca282121e Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Thu, 15 Dec 2022 09:51:52 +0000
Subject: [PATCH 11/38] Update skops/io/_cli.py

Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>
---
 skops/io/_cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skops/io/_cli.py b/skops/io/_cli.py
index 45040262..673a1580 100644
--- a/skops/io/_cli.py
+++ b/skops/io/_cli.py
@@ -29,7 +29,7 @@ def _convert(
         untrusted_str = "\n".join(untrusted_types)
 
         logging.warning(
-            "Unsafe Types Detected!\n"
+            "Unknown Types Detected!\n"
             f"While converting {model_name}, "
             "the following unsafe types were found: \n"
             f"{untrusted_str}\n"

From b39ec14fafcc4c4a53c5e7184f0da5754651675c Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sat, 17 Dec 2022 18:30:19 +0000
Subject: [PATCH 12/38] WIP for merging from main

---
 skops/cli/__init__.py                         |  0
 skops/{io/_cli.py => cli/_convert.py}         |  1 +
 skops/{utils => cli}/entrypoint.py            |  4 ++--
 skops/cli/tests/__init__.py                   |  0
 skops/{utils => cli}/tests/test_entrypoint.py |  2 +-
 skops/io/tests/test_cli.py                    | 10 +++++-----
 6 files changed, 9 insertions(+), 8 deletions(-)
 create mode 100644 skops/cli/__init__.py
 rename skops/{io/_cli.py => cli/_convert.py} (97%)
 rename skops/{utils => cli}/entrypoint.py (86%)
 create mode 100644 skops/cli/tests/__init__.py
 rename skops/{utils => cli}/tests/test_entrypoint.py (94%)

diff --git a/skops/cli/__init__.py b/skops/cli/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/skops/io/_cli.py b/skops/cli/_convert.py
similarity index 97%
rename from skops/io/_cli.py
rename to skops/cli/_convert.py
index 45040262..80a6129c 100644
--- a/skops/io/_cli.py
+++ b/skops/cli/_convert.py
@@ -13,6 +13,7 @@
 def _convert(
     input_file: os.PathLike, output_dir: pathlib.Path, is_trusted: bool = False
 ):
+    """Function that is called by the ``skops convert`` entrypoint"""
     model_name = pathlib.Path(input_file).stem
 
     logging.info(f"Converting {model_name}")
diff --git a/skops/utils/entrypoint.py b/skops/cli/entrypoint.py
similarity index 86%
rename from skops/utils/entrypoint.py
rename to skops/cli/entrypoint.py
index 0933a804..5e5c8335 100644
--- a/skops/utils/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -1,6 +1,6 @@
 import argparse
 
-import skops.io._cli
+import skops.cli._convert
 
 
 def main_entrypoint(command_line_args=None):
@@ -11,7 +11,7 @@ def main_entrypoint(command_line_args=None):
         add_help=False,
     )
 
-    function_map = {"convert": skops.io._cli.main_convert}
+    function_map = {"convert": skops.cli._cli.main_convert}
     parser.add_argument(
         "function", help="Function to call.", choices=function_map.keys()
     )
diff --git a/skops/cli/tests/__init__.py b/skops/cli/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/skops/utils/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
similarity index 94%
rename from skops/utils/tests/test_entrypoint.py
rename to skops/cli/tests/test_entrypoint.py
index 396636e9..febf9164 100644
--- a/skops/utils/tests/test_entrypoint.py
+++ b/skops/cli/tests/test_entrypoint.py
@@ -4,7 +4,7 @@
 
 import pytest
 
-from skops.utils.entrypoint import main_entrypoint
+from skops.cli.entrypoint import main_entrypoint
 
 
 class TestEntrypoint:
diff --git a/skops/io/tests/test_cli.py b/skops/io/tests/test_cli.py
index 7b186b6d..1a8ffaf2 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/io/tests/test_cli.py
@@ -9,7 +9,7 @@
 import pytest
 
 import skops
-from skops.io._cli import _convert
+from skops.cli._convert import _convert
 
 
 class MockUnsafeType:
@@ -81,14 +81,14 @@ def assert_called_correctly(
             ]
         )
 
-    @mock.patch("skops.io._cli._convert")
+    @mock.patch("skops.cli._convert._convert")
     def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         args = [
             "123.pkl",
             "abc.pkl",
         ]
 
-        skops.io._cli.main_convert(command_line_args=args)
+        skops.cli._convert.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, args)
 
     @mock.patch("skops.io._cli._convert")
@@ -98,7 +98,7 @@ def test_with_trusted_works_as_expected(
     ):
         paths = ["abc.123", "234.567", "d/object_1.pkl"]
         args = paths + [trusted_flag]
-        skops.io._cli.main_convert(command_line_args=args)
+        skops.cli._convert.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, paths=paths, trusted=True)
 
     @mock.patch("skops.io._cli._convert")
@@ -116,5 +116,5 @@ def test_with_output_dir_works_as_expected(
         else:
             args = paths
 
-        skops.io._cli.main_convert(command_line_args=args)
+        skops.cli._convert.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, paths=paths, output_dir=expected_dir)

From aa240502bce76b76bf136a0f07bc2dc5dc3da791 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sat, 17 Dec 2022 20:07:43 +0000
Subject: [PATCH 13/38] Address PR comments 1

---
 skops/cli/__init__.py               |  4 ++
 skops/cli/_convert.py               | 82 ++++++++++++++---------------
 skops/cli/entrypoint.py             |  2 +-
 skops/{io => cli}/tests/test_cli.py | 66 +++++++++++------------
 skops/cli/tests/test_entrypoint.py  |  7 ++-
 5 files changed, 80 insertions(+), 81 deletions(-)
 rename skops/{io => cli}/tests/test_cli.py (55%)

diff --git a/skops/cli/__init__.py b/skops/cli/__init__.py
index e69de29b..93938a52 100644
--- a/skops/cli/__init__.py
+++ b/skops/cli/__init__.py
@@ -0,0 +1,4 @@
+from ._convert import _convert_file, main_convert
+from .entrypoint import main_entrypoint
+
+__all__ = ["_convert_file", "main_convert", "main_entrypoint"]
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 58565e2d..7890b98e 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -10,10 +10,22 @@
 from skops.io import dumps, get_untrusted_types
 
 
-def _convert(
-    input_file: os.PathLike, output_dir: pathlib.Path, is_trusted: bool = False
-):
-    """Function that is called by the ``skops convert`` entrypoint"""
+def _convert_file(input_file: os.PathLike, output_file: pathlib.Path):
+    """
+    Function that is called by ``skops convert`` entrypoint.
+
+    Loads a pickle model from the input path, converts to skops format, and saves to
+    output file.
+
+    Parameters
+    ----------
+    input_file : os.PathLike
+        Path of input .pkl model to load.
+
+    output_file : os.PathLike
+        Path to save .skops model to.
+
+    """
     model_name = pathlib.Path(input_file).stem
 
     logging.info(f"Converting {model_name}")
@@ -33,18 +45,12 @@ def _convert(
             "Unknown Types Detected!\n"
             f"While converting {model_name}, "
             "the following unsafe types were found: \n"
-            f"{untrusted_str}\n"
+            f"{untrusted_str}\n\n"
+            f"When loading{output_file}, add ``--trusted`` to the skops.load call."
         )
 
-        if not is_trusted:
-            logging.warning(
-                f"Model {model_name} will not be converted due to unsafe types.\n"
-                "To convert this anyway, add `-t` to this command."
-            )
-            return
-
-    with open(output_dir / f"{model_name}.skops", "wb") as out_file:
-        logging.info(f"Writing to {output_dir / model_name}.skops")
+    with open(output_file, "wb") as out_file:
+        logging.info(f"Writing to {output_file}")
         out_file.write(skops_dump)
 
 
@@ -60,15 +66,15 @@ def main_convert(
 
     parser.add_argument("inputs", nargs="+", help="Input files to convert.")
     parser.add_argument(
-        "-t",
-        "--trusted",
+        "-o",
+        "--output-files",
+        nargs="+",
         help=(
-            "Automatically trust all files, "
-            "and convert all inputs, "
-            "even if an untrusted type is detected."
+            "Specify output file names for the converted skops files."
+            "If not provided, will default to using the same name as the input file, "
+            "and saving to the current working directory."
         ),
-        action="store_true",
-        default=False,
+        default=None,
     )
     parser.add_argument(
         "-d",
@@ -87,28 +93,22 @@ def main_convert(
         dest="loglevel",
         const=logging.INFO,
     )
-    parser.add_argument(
-        "--output-dir",
-        help=(
-            "Specify a directory to save converted files to. "
-            "Default will save files to the current working directory."
-        ),
-        type=str,
-        default=None,
-    )
-    args = parser.parse_args(command_line_args)
-
-    output_dir = args.output_dir
-    if not output_dir:
-        output_dir = pathlib.Path.cwd()
-    else:
-        output_dir = pathlib.Path(output_dir)
 
+    args = parser.parse_args(command_line_args)
+    output_files = args.output_files
+    input_files = args.inputs
     logging.basicConfig(format="%(message)s", level=args.loglevel)
 
-    for input_file in args.inputs:
-        _convert(
+    for input_file_index in range(len(args.inputs)):
+        input_file = input_files[input_file_index]
+        if output_files and len(output_files) >= input_file_index:
+            output_file = output_files[input_file_index]
+        else:
+            # No filename provided, defaulting to base file path
+            file_name = pathlib.Path(input_file).stem
+            output_file = pathlib.Path.cwd() / f"{file_name}.skops"
+
+        _convert_file(
             input_file=input_file,
-            output_dir=output_dir,
-            is_trusted=args.trusted,
+            output_file=output_file,
         )
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index 5e5c8335..9ef95c5c 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -11,7 +11,7 @@ def main_entrypoint(command_line_args=None):
         add_help=False,
     )
 
-    function_map = {"convert": skops.cli._cli.main_convert}
+    function_map = {"convert": skops.cli._convert.main_convert}
     parser.add_argument(
         "function", help="Function to call.", choices=function_map.keys()
     )
diff --git a/skops/io/tests/test_cli.py b/skops/cli/tests/test_cli.py
similarity index 55%
rename from skops/io/tests/test_cli.py
rename to skops/cli/tests/test_cli.py
index 1a8ffaf2..ff2a31e7 100644
--- a/skops/io/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -1,5 +1,4 @@
 import logging
-import os.path
 import pathlib
 import pickle as pkl
 from typing import Optional
@@ -8,8 +7,8 @@
 import numpy as np
 import pytest
 
-import skops
-from skops.cli._convert import _convert
+from skops import cli
+from skops.io import load
 
 
 class MockUnsafeType:
@@ -49,16 +48,18 @@ def write_unsafe_file(self, pkl_path, unsafe_obj):
     def test_base_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj
     ):
-        _convert(pkl_path, tmp_path)
-        persisted_obj = skops.io.load(skops_path)
+        cli._convert_file(pkl_path, skops_path)
+        persisted_obj = load(skops_path)
         assert np.array_equal(persisted_obj, safe_obj)
 
     def test_unsafe_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_unsafe_file, caplog
     ):
         caplog.set_level(logging.WARNING)
-        _convert(pkl_path, tmp_path)
-        assert not os.path.isfile(skops_path)
+        cli._convert_file(pkl_path, skops_path)
+        persisted_obj = load(skops_path, trusted=True)
+
+        assert isinstance(persisted_obj, MockUnsafeType)
 
         # check logging has warned that an unsafe type was found
         assert MockUnsafeType.__name__ in caplog.text
@@ -69,52 +70,47 @@ class TestMainConvert:
     def assert_called_correctly(
         mock_convert: mock.MagicMock,
         paths: list,
-        output_dir: Optional[pathlib.Path] = pathlib.Path.cwd(),
-        trusted: Optional[bool] = False,
+        output_files: Optional[list] = None,
     ):
+        if not output_files:
+            output_files = [
+                pathlib.Path.cwd() / f"{pathlib.Path(p).stem}.skops" for p in paths
+            ]
         assert mock_convert.call_count == len(paths)
-
         mock_convert.assert_has_calls(
             [
-                mock.call(input_file=p, output_dir=output_dir, is_trusted=trusted)
-                for p in paths
+                mock.call(input_file=paths[i], output_file=output_files[i])
+                for i in range(len(paths))
             ]
         )
 
-    @mock.patch("skops.cli._convert._convert")
+    @mock.patch("skops.cli._convert._convert_file")
     def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         args = [
             "123.pkl",
             "abc.pkl",
         ]
 
-        skops.cli._convert.main_convert(command_line_args=args)
+        cli.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, args)
 
-    @mock.patch("skops.io._cli._convert")
-    @pytest.mark.parametrize("trusted_flag", ["-t", "--trusted"])
-    def test_with_trusted_works_as_expected(
-        self, mock_convert: mock.MagicMock, trusted_flag
-    ):
-        paths = ["abc.123", "234.567", "d/object_1.pkl"]
-        args = paths + [trusted_flag]
-        skops.cli._convert.main_convert(command_line_args=args)
-        self.assert_called_correctly(mock_convert, paths=paths, trusted=True)
-
-    @mock.patch("skops.io._cli._convert")
+    @mock.patch("skops.cli._convert._convert_file")
     @pytest.mark.parametrize(
-        "output_dir, expected_dir",
-        [("a/b/c", pathlib.Path("a/b/c")), (None, pathlib.Path.cwd())],
+        "input_paths, output_files, expected_paths",
+        [
+            (["abc.123"], ["a/b/c"], ["a/b/c"]),
+            (["abc.123"], None, [pathlib.Path.cwd() / "abc.skops"]),
+        ],
     )
     def test_with_output_dir_works_as_expected(
-        self, mock_convert: mock.MagicMock, output_dir, expected_dir
+        self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
     ):
-        paths = ["abc.123", "234.567", "d/object_1.pkl"]
-
-        if output_dir is not None:
-            args = paths + ["--output-dir", output_dir]
+        if output_files is not None:
+            args = input_paths + ["--output-files"] + output_files
         else:
-            args = paths
+            args = input_paths
 
-        skops.cli._convert.main_convert(command_line_args=args)
-        self.assert_called_correctly(mock_convert, paths=paths, output_dir=expected_dir)
+        cli.main_convert(command_line_args=args)
+        self.assert_called_correctly(
+            mock_convert, paths=input_paths, output_files=expected_paths
+        )
diff --git a/skops/cli/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
index febf9164..51d065c7 100644
--- a/skops/cli/tests/test_entrypoint.py
+++ b/skops/cli/tests/test_entrypoint.py
@@ -19,14 +19,13 @@ def clear_argv(self):
         # Otherwise, clogs parser.parse_known_args() in argparse
         sys.argv = [""]
 
-    @mock.patch("skops.io._cli._convert")
+    @mock.patch("skops.cli._convert._convert_file")
     def test_convert_works_as_expected(self, mocked_convert: mock.MagicMock):
-        args = ["convert", "abc.def", "-t"]
+        args = ["convert", "abc.def"]
 
         main_entrypoint(args)
 
         mocked_convert.assert_called_once_with(
             input_file="abc.def",
-            output_dir=pathlib.Path.cwd(),
-            is_trusted=True,
+            output_file=pathlib.Path.cwd() / "abc.skops",
         )

From 02b3cf8d5f095a85f25b64867e67bd9a99dc7dee Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sat, 17 Dec 2022 20:38:12 +0000
Subject: [PATCH 14/38] Add test to check for multiple output file types

---
 skops/cli/_convert.py       |  2 +-
 skops/cli/tests/test_cli.py | 26 ++++++++++++++++++++++++++
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 7890b98e..72590408 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -101,7 +101,7 @@ def main_convert(
 
     for input_file_index in range(len(args.inputs)):
         input_file = input_files[input_file_index]
-        if output_files and len(output_files) >= input_file_index:
+        if output_files and len(output_files) > input_file_index:
             output_file = output_files[input_file_index]
         else:
             # No filename provided, defaulting to base file path
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_cli.py
index ff2a31e7..6893b1bc 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -101,6 +101,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
             (["abc.123"], ["a/b/c"], ["a/b/c"]),
             (["abc.123"], None, [pathlib.Path.cwd() / "abc.skops"]),
         ],
+        ids=["Given an output path", "No output path"],
     )
     def test_with_output_dir_works_as_expected(
         self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
@@ -114,3 +115,28 @@ def test_with_output_dir_works_as_expected(
         self.assert_called_correctly(
             mock_convert, paths=input_paths, output_files=expected_paths
         )
+
+    @mock.patch("skops.cli._convert._convert_file")
+    @pytest.mark.parametrize(
+        "input_paths, output_files, expected_paths",
+        [
+            (
+                ["model_a.pkl", "model_b.pkl"],
+                ["a.skops", "b.skops"],
+                ["a.skops", "b.skops"],
+            ),
+            (
+                ["model_a.pkl", "model_b.pkl", "model_c.pkl"],
+                ["a.skops", "b.skops"],
+                ["a.skops", "b.skops", pathlib.Path.cwd() / "model_c.skops"],
+            ),
+        ],
+        ids=["With enough output paths", "With only some output paths"],
+    )
+    def test_for_multiple_inputs_and_outputs_works_as_expected(
+        self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
+    ):
+        args = input_paths + ["--output-files"] + output_files
+        cli.main_convert(args)
+
+        self.assert_called_correctly(mock_convert, input_paths, expected_paths)

From 245197f019d9d5cf2cc69e7f2d6127b3a3eae2d3 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Sat, 17 Dec 2022 20:49:30 +0000
Subject: [PATCH 15/38] Update entrypoint name in setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 535162fe..7df920c6 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ def setup_package():
     package_data = dict(
         entry_points={
             "console_scripts": [
-                "skops = skops.utils.entrypoint:main_entrypoint",
+                "skops = skops.cli.entrypoint:main_entrypoint",
             ],
         }
     )

From 2b681ced8fe7ca7de8d194057a4ee4fd05a0ab2f Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 3 Jan 2023 21:23:58 +0000
Subject: [PATCH 16/38] PR comments before reworking to support only single
 files

---
 skops/cli/__init__.py       |  4 ----
 skops/cli/_convert.py       | 12 ++++++------
 skops/cli/tests/test_cli.py | 12 ++++++------
 3 files changed, 12 insertions(+), 16 deletions(-)
 delete mode 100644 skops/cli/__init__.py

diff --git a/skops/cli/__init__.py b/skops/cli/__init__.py
deleted file mode 100644
index 93938a52..00000000
--- a/skops/cli/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from ._convert import _convert_file, main_convert
-from .entrypoint import main_entrypoint
-
-__all__ = ["_convert_file", "main_convert", "main_entrypoint"]
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 72590408..c54afd4c 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -4,13 +4,13 @@
 import logging
 import os
 import pathlib
-import pickle as pkl
+import pickle
 from typing import Optional
 
 from skops.io import dumps, get_untrusted_types
 
 
-def _convert_file(input_file: os.PathLike, output_file: pathlib.Path):
+def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
     """
     Function that is called by ``skops convert`` entrypoint.
 
@@ -31,22 +31,22 @@ def _convert_file(input_file: os.PathLike, output_file: pathlib.Path):
     logging.info(f"Converting {model_name}")
 
     with open(input_file, "rb") as f:
-        obj = pkl.load(f)
+        obj = pickle.load(f)
     skops_dump = dumps(obj)
 
     untrusted_types = get_untrusted_types(data=skops_dump)
 
     if not untrusted_types:
-        logging.debug(f"No unsafe types found in {model_name}.")
+        logging.debug(f"No unknown types found in {model_name}.")
     else:
         untrusted_str = "\n".join(untrusted_types)
 
         logging.warning(
             "Unknown Types Detected!\n"
             f"While converting {model_name}, "
-            "the following unsafe types were found: \n"
+            "the following unknown types were found: \n"
             f"{untrusted_str}\n\n"
-            f"When loading{output_file}, add ``--trusted`` to the skops.load call."
+            f"When loading {output_file}, add ``trusted=True`` to the skops.load call."
         )
 
     with open(output_file, "wb") as out_file:
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_cli.py
index 6893b1bc..80234fb2 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -7,7 +7,7 @@
 import numpy as np
 import pytest
 
-from skops import cli
+from skops.cli import _convert
 from skops.io import load
 
 
@@ -48,7 +48,7 @@ def write_unsafe_file(self, pkl_path, unsafe_obj):
     def test_base_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj
     ):
-        cli._convert_file(pkl_path, skops_path)
+        _convert._convert_file(pkl_path, skops_path)
         persisted_obj = load(skops_path)
         assert np.array_equal(persisted_obj, safe_obj)
 
@@ -56,7 +56,7 @@ def test_unsafe_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_unsafe_file, caplog
     ):
         caplog.set_level(logging.WARNING)
-        cli._convert_file(pkl_path, skops_path)
+        _convert._convert_file(pkl_path, skops_path)
         persisted_obj = load(skops_path, trusted=True)
 
         assert isinstance(persisted_obj, MockUnsafeType)
@@ -91,7 +91,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
             "abc.pkl",
         ]
 
-        cli.main_convert(command_line_args=args)
+        _convert.main_convert(command_line_args=args)
         self.assert_called_correctly(mock_convert, args)
 
     @mock.patch("skops.cli._convert._convert_file")
@@ -111,7 +111,7 @@ def test_with_output_dir_works_as_expected(
         else:
             args = input_paths
 
-        cli.main_convert(command_line_args=args)
+        _convert.main_convert(command_line_args=args)
         self.assert_called_correctly(
             mock_convert, paths=input_paths, output_files=expected_paths
         )
@@ -137,6 +137,6 @@ def test_for_multiple_inputs_and_outputs_works_as_expected(
         self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
     ):
         args = input_paths + ["--output-files"] + output_files
-        cli.main_convert(args)
+        _convert.main_convert(args)
 
         self.assert_called_correctly(mock_convert, input_paths, expected_paths)

From 25b539c4ec66175bb6ed2c838c0dbaa9019c79ef Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Wed, 4 Jan 2023 20:25:00 +0000
Subject: [PATCH 17/38] Pre-parser rework]

---
 setup.py                           |  2 +-
 skops/cli/_convert.py              | 22 ++++++++++++---------
 skops/cli/entrypoint.py            | 18 ++++++++++++-----
 skops/cli/tests/__init__.py        |  0
 skops/cli/tests/test_cli.py        |  9 +++++----
 skops/cli/tests/test_entrypoint.py | 31 ------------------------------
 6 files changed, 32 insertions(+), 50 deletions(-)
 delete mode 100644 skops/cli/tests/__init__.py

diff --git a/setup.py b/setup.py
index 7df920c6..ce368f12 100644
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@ def setup_package():
     package_data = dict(
         entry_points={
             "console_scripts": [
-                "skops = skops.cli.entrypoint:main_entrypoint",
+                "skops = skops.cli.entrypoint:main_cli",
             ],
         }
     )
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index c54afd4c..aa434c3c 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -54,17 +54,12 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
         out_file.write(skops_dump)
 
 
-def main_convert(
-    command_line_args: Optional[list[str]] = None,
-    parent: Optional[argparse.ArgumentParser] = None,
-):
-    parents = [parent] if parent else []
-
+def get_parser() -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(
-        description="Convert input Pickle files to .skops files", parents=parents
+        description="Convert input Pickle files to .skops files"
     )
 
-    parser.add_argument("inputs", nargs="+", help="Input files to convert.")
+    parser.add_argument("inputs", nargs="+", help="Input files to convert. ")
     parser.add_argument(
         "-o",
         "--output-files",
@@ -72,7 +67,7 @@ def main_convert(
         help=(
             "Specify output file names for the converted skops files."
             "If not provided, will default to using the same name as the input file, "
-            "and saving to the current working directory."
+            "and saving to the current working directory with the suffix ``.skops``. "
         ),
         default=None,
     )
@@ -93,6 +88,15 @@ def main_convert(
         dest="loglevel",
         const=logging.INFO,
     )
+    return parser
+
+
+def main(
+    command_line_args: Optional[list[str]] = None,
+    parser: Optional[argparse.ArgumentParser] = None,
+):
+    if not parser:
+        parser = get_parser()
 
     args = parser.parse_args(command_line_args)
     output_files = args.output_files
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index 9ef95c5c..032610c8 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -3,17 +3,25 @@
 import skops.cli._convert
 
 
-def main_entrypoint(command_line_args=None):
-    """Main entrypoint for all command line Skops methods."""
+def main_cli(command_line_args=None):
+    """Main command line interface entrypoint for all command line Skops methods."""
     parser = argparse.ArgumentParser(
         prog="Skops",
         description="Main entrypoint for all command line Skops methods.",
-        add_help=False,
+        add_help=True,
     )
 
-    function_map = {"convert": skops.cli._convert.main_convert}
+    # NB: methods should be functions, parsers should be objects
+    function_map = {
+        "convert": {
+            "method": skops.cli._convert.main,
+            "parser": skops.cli._convert.get_parser,
+        },
+    }
+
     parser.add_argument(
         "function", help="Function to call.", choices=function_map.keys()
     )
+    # subparsers = parser.add_subparsers(help="sub-command help")
+
     args, _ = parser.parse_known_args(command_line_args)
-    function_map.get(args.function)(parent=parser, command_line_args=command_line_args)
diff --git a/skops/cli/tests/__init__.py b/skops/cli/tests/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_cli.py
index 80234fb2..f15d94bd 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -46,11 +46,12 @@ def write_unsafe_file(self, pkl_path, unsafe_obj):
             pkl.dump(unsafe_obj, f)
 
     def test_base_case_works_as_expected(
-        self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj
+        self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj, caplog
     ):
         _convert._convert_file(pkl_path, skops_path)
         persisted_obj = load(skops_path)
         assert np.array_equal(persisted_obj, safe_obj)
+        assert MockUnsafeType.__name__ not in caplog.text
 
     def test_unsafe_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_unsafe_file, caplog
@@ -91,7 +92,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
             "abc.pkl",
         ]
 
-        _convert.main_convert(command_line_args=args)
+        _convert.main(command_line_args=args)
         self.assert_called_correctly(mock_convert, args)
 
     @mock.patch("skops.cli._convert._convert_file")
@@ -111,7 +112,7 @@ def test_with_output_dir_works_as_expected(
         else:
             args = input_paths
 
-        _convert.main_convert(command_line_args=args)
+        _convert.main(command_line_args=args)
         self.assert_called_correctly(
             mock_convert, paths=input_paths, output_files=expected_paths
         )
@@ -137,6 +138,6 @@ def test_for_multiple_inputs_and_outputs_works_as_expected(
         self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
     ):
         args = input_paths + ["--output-files"] + output_files
-        _convert.main_convert(args)
+        _convert.main(args)
 
         self.assert_called_correctly(mock_convert, input_paths, expected_paths)
diff --git a/skops/cli/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
index 51d065c7..e69de29b 100644
--- a/skops/cli/tests/test_entrypoint.py
+++ b/skops/cli/tests/test_entrypoint.py
@@ -1,31 +0,0 @@
-import pathlib
-import sys
-from unittest import mock
-
-import pytest
-
-from skops.cli.entrypoint import main_entrypoint
-
-
-class TestEntrypoint:
-    """Integration tests that check that entrypoint calls pass through correctly.
-
-    Full coverage of individual entrypoint calls should be done in their own classes.
-    """
-
-    @pytest.fixture(autouse=True)
-    def clear_argv(self):
-        # Required to clear argv in case Pytest is called on this specific function.
-        # Otherwise, clogs parser.parse_known_args() in argparse
-        sys.argv = [""]
-
-    @mock.patch("skops.cli._convert._convert_file")
-    def test_convert_works_as_expected(self, mocked_convert: mock.MagicMock):
-        args = ["convert", "abc.def"]
-
-        main_entrypoint(args)
-
-        mocked_convert.assert_called_once_with(
-            input_file="abc.def",
-            output_file=pathlib.Path.cwd() / "abc.skops",
-        )

From 50bf18916548b89e0f316c5d90d1f87e0778a3af Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Wed, 4 Jan 2023 20:25:34 +0000
Subject: [PATCH 18/38] Remove empty test file

---
 skops/cli/tests/test_entrypoint.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 skops/cli/tests/test_entrypoint.py

diff --git a/skops/cli/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
deleted file mode 100644
index e69de29b..00000000

From 227f23cbe18cc9dc576ed56f6cbb08f78aae17d9 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Mon, 9 Jan 2023 20:51:20 +0000
Subject: [PATCH 19/38] Pre-test reintroduction

---
 skops/cli/_convert.py       | 88 ++++++++++++++++++-------------------
 skops/cli/entrypoint.py     | 29 ++++++++----
 skops/cli/tests/test_cli.py | 69 +++++++----------------------
 3 files changed, 80 insertions(+), 106 deletions(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index aa434c3c..a4875bc9 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -28,7 +28,7 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
     """
     model_name = pathlib.Path(input_file).stem
 
-    logging.info(f"Converting {model_name}")
+    logging.debug(f"Converting {model_name}")
 
     with open(input_file, "rb") as f:
         obj = pickle.load(f)
@@ -37,41 +37,53 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
     untrusted_types = get_untrusted_types(data=skops_dump)
 
     if not untrusted_types:
-        logging.debug(f"No unknown types found in {model_name}.")
+        logging.info(f"No unknown types found in {model_name}.")
     else:
-        untrusted_str = "\n".join(untrusted_types)
+        untrusted_str = ", ".join(untrusted_types)
 
         logging.warning(
-            "Unknown Types Detected!\n"
+            "Unknown Types Detected! "
             f"While converting {model_name}, "
-            "the following unknown types were found: \n"
-            f"{untrusted_str}\n\n"
-            f"When loading {output_file}, add ``trusted=True`` to the skops.load call."
+            "the following unknown types were found: "
+            f"{untrusted_str}. "
+            f"When loading {output_file}, add 'trusted=True' to the skops.load call. "
         )
 
     with open(output_file, "wb") as out_file:
-        logging.info(f"Writing to {output_file}")
+        logging.debug(f"Writing to {output_file}")
         out_file.write(skops_dump)
 
 
-def get_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(
-        description="Convert input Pickle files to .skops files"
-    )
+def format_parser(
+    parser: Optional[argparse.ArgumentParser] = None,
+) -> argparse.ArgumentParser:
+    """Adds arguments and help to parent CLI parser for the convert method."""
+
+    if not parser:  # used in tests
+        parser = argparse.ArgumentParser()
 
-    parser.add_argument("inputs", nargs="+", help="Input files to convert. ")
-    parser.add_argument(
+    parser_subgroup = parser.add_argument_group("convert")
+    parser_subgroup.add_argument("input", help="Input file to convert. ")
+
+    parser_subgroup.add_argument(
         "-o",
-        "--output-files",
-        nargs="+",
+        "--output-file",
         help=(
-            "Specify output file names for the converted skops files."
+            "Specify the output file name for the converted skops file. "
             "If not provided, will default to using the same name as the input file, "
-            "and saving to the current working directory with the suffix ``.skops``. "
+            "and saving to the current working directory with the suffix '.skops'."
         ),
         default=None,
     )
-    parser.add_argument(
+    parser_subgroup.add_argument(
+        "-v",
+        "--verbose",
+        help="Enable verbose logging.",
+        action="store_const",
+        dest="loglevel",
+        const=logging.INFO,
+    )
+    parser_subgroup.add_argument(
         "-d",
         "--debug",
         help="Enable debug logging.",
@@ -80,14 +92,6 @@ def get_parser() -> argparse.ArgumentParser:
         const=logging.DEBUG,
         default=logging.WARNING,
     )
-    parser.add_argument(
-        "-v",
-        "--verbose",
-        help="Enable verbose logging.",
-        action="store_const",
-        dest="loglevel",
-        const=logging.INFO,
-    )
     return parser
 
 
@@ -96,23 +100,19 @@ def main(
     parser: Optional[argparse.ArgumentParser] = None,
 ):
     if not parser:
-        parser = get_parser()
+        parser = format_parser(argparse.ArgumentParser())
 
-    args = parser.parse_args(command_line_args)
-    output_files = args.output_files
-    input_files = args.inputs
+    args, _ = parser.parse_known_args(command_line_args)
+    output_file = args.output_file
+    input_file = args.input
     logging.basicConfig(format="%(message)s", level=args.loglevel)
 
-    for input_file_index in range(len(args.inputs)):
-        input_file = input_files[input_file_index]
-        if output_files and len(output_files) > input_file_index:
-            output_file = output_files[input_file_index]
-        else:
-            # No filename provided, defaulting to base file path
-            file_name = pathlib.Path(input_file).stem
-            output_file = pathlib.Path.cwd() / f"{file_name}.skops"
-
-        _convert_file(
-            input_file=input_file,
-            output_file=output_file,
-        )
+    if not output_file:
+        # No filename provided, defaulting to base file path
+        file_name = pathlib.Path(input_file).stem
+        output_file = pathlib.Path.cwd() / f"{file_name}.skops"
+
+    _convert_file(
+        input_file=input_file,
+        output_file=output_file,
+    )
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index 032610c8..cdcb5608 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -4,24 +4,35 @@
 
 
 def main_cli(command_line_args=None):
-    """Main command line interface entrypoint for all command line Skops methods."""
-    parser = argparse.ArgumentParser(
+    """
+    Main command line interface entrypoint for all command line Skops methods.
+
+    To add a new entrypoint:
+        1. Create a new main
+    """
+    entry_parser = argparse.ArgumentParser(
         prog="Skops",
         description="Main entrypoint for all command line Skops methods.",
         add_help=True,
     )
 
-    # NB: methods should be functions, parsers should be objects
+    subparsers = entry_parser.add_subparsers(
+        title="Command",
+        description="Skops command to call",
+        dest="cmd",
+        help="Sub-commands help",
+    )
+
     function_map = {
         "convert": {
             "method": skops.cli._convert.main,
-            "parser": skops.cli._convert.get_parser,
+            "format_parser": skops.cli._convert.format_parser,
         },
     }
 
-    parser.add_argument(
-        "function", help="Function to call.", choices=function_map.keys()
-    )
-    # subparsers = parser.add_subparsers(help="sub-command help")
+    for func_name, values in function_map.items():
+        subparser = subparsers.add_parser(func_name)
+        subparser.set_defaults(func=values["method"])
+        values["format_parser"](subparser)
 
-    args, _ = parser.parse_known_args(command_line_args)
+    args, _ = entry_parser.parse_known_args(command_line_args)
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_cli.py
index f15d94bd..b4838665 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -1,7 +1,6 @@
 import logging
 import pathlib
 import pickle as pkl
-from typing import Optional
 from unittest import mock
 
 import numpy as np
@@ -70,74 +69,38 @@ class TestMainConvert:
     @staticmethod
     def assert_called_correctly(
         mock_convert: mock.MagicMock,
-        paths: list,
-        output_files: Optional[list] = None,
+        path,
+        output_file=None,
     ):
-        if not output_files:
-            output_files = [
-                pathlib.Path.cwd() / f"{pathlib.Path(p).stem}.skops" for p in paths
-            ]
-        assert mock_convert.call_count == len(paths)
-        mock_convert.assert_has_calls(
-            [
-                mock.call(input_file=paths[i], output_file=output_files[i])
-                for i in range(len(paths))
-            ]
-        )
+        if not output_file:
+            output_file = pathlib.Path.cwd() / f"{pathlib.Path(path).stem}.skops"
+        mock_convert.assert_called_once_with(input_file=path, output_file=output_file)
 
     @mock.patch("skops.cli._convert._convert_file")
     def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
-        args = [
-            "123.pkl",
-            "abc.pkl",
-        ]
+        path = "123.pkl"
 
-        _convert.main(command_line_args=args)
-        self.assert_called_correctly(mock_convert, args)
+        _convert.main(command_line_args=[path])
+        self.assert_called_correctly(mock_convert, path)
 
     @mock.patch("skops.cli._convert._convert_file")
     @pytest.mark.parametrize(
-        "input_paths, output_files, expected_paths",
+        "input_path, output_file, expected_path",
         [
-            (["abc.123"], ["a/b/c"], ["a/b/c"]),
-            (["abc.123"], None, [pathlib.Path.cwd() / "abc.skops"]),
+            ("abc.123", "a/b/c", "a/b/c"),
+            ("abc.123", None, pathlib.Path.cwd() / "abc.skops"),
         ],
         ids=["Given an output path", "No output path"],
     )
     def test_with_output_dir_works_as_expected(
-        self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
+        self, mock_convert: mock.MagicMock, input_path, output_file, expected_path
     ):
-        if output_files is not None:
-            args = input_paths + ["--output-files"] + output_files
+        if output_file is not None:
+            args = [input_path, "--output", output_file]
         else:
-            args = input_paths
+            args = [input_path]
 
         _convert.main(command_line_args=args)
         self.assert_called_correctly(
-            mock_convert, paths=input_paths, output_files=expected_paths
+            mock_convert, path=input_path, output_file=expected_path
         )
-
-    @mock.patch("skops.cli._convert._convert_file")
-    @pytest.mark.parametrize(
-        "input_paths, output_files, expected_paths",
-        [
-            (
-                ["model_a.pkl", "model_b.pkl"],
-                ["a.skops", "b.skops"],
-                ["a.skops", "b.skops"],
-            ),
-            (
-                ["model_a.pkl", "model_b.pkl", "model_c.pkl"],
-                ["a.skops", "b.skops"],
-                ["a.skops", "b.skops", pathlib.Path.cwd() / "model_c.skops"],
-            ),
-        ],
-        ids=["With enough output paths", "With only some output paths"],
-    )
-    def test_for_multiple_inputs_and_outputs_works_as_expected(
-        self, mock_convert: mock.MagicMock, input_paths, output_files, expected_paths
-    ):
-        args = input_paths + ["--output-files"] + output_files
-        _convert.main(args)
-
-        self.assert_called_correctly(mock_convert, input_paths, expected_paths)

From 426d663ca5e387230a129faecf6866c29207b3ff Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Mon, 9 Jan 2023 22:06:06 +0000
Subject: [PATCH 20/38] Pre-test reintroduction

---
 skops/cli/_convert.py              | 13 ++++-------
 skops/cli/entrypoint.py            |  5 ++--
 skops/cli/tests/test_cli.py        |  7 ++++--
 skops/cli/tests/test_entrypoint.py | 37 ++++++++++++++++++++++++++++++
 4 files changed, 49 insertions(+), 13 deletions(-)
 create mode 100644 skops/cli/tests/test_entrypoint.py

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index a4875bc9..6852d81b 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -96,16 +96,11 @@ def format_parser(
 
 
 def main(
-    command_line_args: Optional[list[str]] = None,
-    parser: Optional[argparse.ArgumentParser] = None,
+    parsed_args: argparse.Namespace,
 ):
-    if not parser:
-        parser = format_parser(argparse.ArgumentParser())
-
-    args, _ = parser.parse_known_args(command_line_args)
-    output_file = args.output_file
-    input_file = args.input
-    logging.basicConfig(format="%(message)s", level=args.loglevel)
+    output_file = parsed_args.output_file
+    input_file = parsed_args.input
+    logging.basicConfig(format="%(message)s", level=parsed_args.loglevel)
 
     if not output_file:
         # No filename provided, defaulting to base file path
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index cdcb5608..ed50c445 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -17,7 +17,7 @@ def main_cli(command_line_args=None):
     )
 
     subparsers = entry_parser.add_subparsers(
-        title="Command",
+        title="Commands",
         description="Skops command to call",
         dest="cmd",
         help="Sub-commands help",
@@ -35,4 +35,5 @@ def main_cli(command_line_args=None):
         subparser.set_defaults(func=values["method"])
         values["format_parser"](subparser)
 
-    args, _ = entry_parser.parse_known_args(command_line_args)
+    args = entry_parser.parse_args(command_line_args)
+    args.func(args)
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_cli.py
index b4838665..fe76953e 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_cli.py
@@ -79,8 +79,9 @@ def assert_called_correctly(
     @mock.patch("skops.cli._convert._convert_file")
     def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
         path = "123.pkl"
+        namespace, _ = _convert.format_parser().parse_known_args([path])
 
-        _convert.main(command_line_args=[path])
+        _convert.main(namespace)
         self.assert_called_correctly(mock_convert, path)
 
     @mock.patch("skops.cli._convert._convert_file")
@@ -100,7 +101,9 @@ def test_with_output_dir_works_as_expected(
         else:
             args = [input_path]
 
-        _convert.main(command_line_args=args)
+        namespace, _ = _convert.format_parser().parse_known_args(args)
+
+        _convert.main(namespace)
         self.assert_called_correctly(
             mock_convert, path=input_path, output_file=expected_path
         )
diff --git a/skops/cli/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
new file mode 100644
index 00000000..0947307a
--- /dev/null
+++ b/skops/cli/tests/test_entrypoint.py
@@ -0,0 +1,37 @@
+import pathlib
+import sys
+from unittest import mock
+
+import pytest
+
+from skops.cli.entrypoint import main_cli
+
+
+class TestEntrypoint:
+    """Integration tests that check that entrypoint calls pass through correctly.
+    Full coverage of individual entrypoint calls should be done in their own classes.
+    """
+
+    @pytest.fixture(autouse=True)
+    def clear_argv(self):
+        # Required to clear argv in case Pytest is called on this specific function.
+        # Otherwise, clogs parser.parse_known_args() in argparse
+        sys.argv = [""]
+
+    @mock.patch("skops.cli._convert._convert_file")
+    def test_convert_works_as_expected(
+        self,
+        convert_file_mock: mock.MagicMock,
+    ):
+        """
+        Intended as a unit test to make sure,
+        given 'convert' as the first argument,
+        the parser is configured correctly
+        """
+
+        args = ["convert", "abc.def"]
+
+        main_cli(args)
+        convert_file_mock.assert_called_once_with(
+            input_file="abc.def", output_file=pathlib.Path.cwd() / "abc.skops"
+        )

From 37d3a871ac8f5459c887e0320c17baf55b1651f5 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 09:01:32 +0000
Subject: [PATCH 21/38] Change verbosity to work as discussed in PR

---
 skops/cli/_convert.py                         | 17 +++-------
 skops/cli/_utils.py                           | 15 +++++++++
 .../tests/{test_cli.py => test_convert.py}    | 31 ++++++++++++++++++-
 skops/cli/tests/test_entrypoint.py            |  4 +++
 4 files changed, 54 insertions(+), 13 deletions(-)
 create mode 100644 skops/cli/_utils.py
 rename skops/cli/tests/{test_cli.py => test_convert.py} (76%)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 6852d81b..9000f57b 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -7,6 +7,7 @@
 import pickle
 from typing import Optional
 
+from skops.cli._utils import get_log_level
 from skops.io import dumps, get_untrusted_types
 
 
@@ -79,18 +80,9 @@ def format_parser(
         "-v",
         "--verbose",
         help="Enable verbose logging.",
-        action="store_const",
+        action="count",
         dest="loglevel",
-        const=logging.INFO,
-    )
-    parser_subgroup.add_argument(
-        "-d",
-        "--debug",
-        help="Enable debug logging.",
-        action="store_const",
-        dest="loglevel",
-        const=logging.DEBUG,
-        default=logging.WARNING,
+        default=0,
     )
     return parser
 
@@ -100,7 +92,8 @@ def main(
 ):
     output_file = parsed_args.output_file
     input_file = parsed_args.input
-    logging.basicConfig(format="%(message)s", level=parsed_args.loglevel)
+
+    logging.basicConfig(format="%(message)s", level=get_log_level(parsed_args.loglevel))
 
     if not output_file:
         # No filename provided, defaulting to base file path
diff --git a/skops/cli/_utils.py b/skops/cli/_utils.py
new file mode 100644
index 00000000..82a371ab
--- /dev/null
+++ b/skops/cli/_utils.py
@@ -0,0 +1,15 @@
+import logging
+
+
+def get_log_level(level: int = 0):
+    """Takes in verbosity from a CLI entrypoint (number of times -v specified),
+    and sets the logger to the required log level"""
+
+    all_levels = [logging.WARNING, logging.INFO, logging.DEBUG]
+
+    if level > len(all_levels):
+        level = len(all_levels)
+    elif level < 0:
+        level = 0
+
+    return all_levels[level]
diff --git a/skops/cli/tests/test_cli.py b/skops/cli/tests/test_convert.py
similarity index 76%
rename from skops/cli/tests/test_cli.py
rename to skops/cli/tests/test_convert.py
index fe76953e..049d44b8 100644
--- a/skops/cli/tests/test_cli.py
+++ b/skops/cli/tests/test_convert.py
@@ -65,7 +65,7 @@ def test_unsafe_case_works_as_expected(
         assert MockUnsafeType.__name__ in caplog.text
 
 
-class TestMainConvert:
+class TestMain:
     @staticmethod
     def assert_called_correctly(
         mock_convert: mock.MagicMock,
@@ -107,3 +107,32 @@ def test_with_output_dir_works_as_expected(
         self.assert_called_correctly(
             mock_convert, path=input_path, output_file=expected_path
         )
+
+    @mock.patch("skops.cli._convert._convert_file")
+    @pytest.mark.parametrize(
+        "verbosity, expected_level",
+        [
+            ("", logging.WARNING),
+            ("-v", logging.INFO),
+            ("--verbose", logging.INFO),
+            ("-vv", logging.DEBUG),
+            ("-v -v", logging.DEBUG),
+            ("-vvv", logging.DEBUG),
+            ("--verbose --verbose", logging.DEBUG),
+        ],
+    )
+    def test_given_log_levels_works_as_expected(
+        self, mock_convert: mock.MagicMock, verbosity, expected_level, caplog
+    ):
+        input_path = "abc.def"
+        output_path = "bde.skops"
+        args = [input_path, "--output", output_path, verbosity.split()]
+
+        namespace, _ = _convert.format_parser().parse_known_args(args)
+
+        _convert.main(namespace)
+        self.assert_called_correctly(
+            mock_convert, path=input_path, output_file=output_path
+        )
+
+        assert caplog.at_level(expected_level)
diff --git a/skops/cli/tests/test_entrypoint.py b/skops/cli/tests/test_entrypoint.py
index 0947307a..2fd3cb60 100644
--- a/skops/cli/tests/test_entrypoint.py
+++ b/skops/cli/tests/test_entrypoint.py
@@ -1,3 +1,4 @@
+import logging
 import pathlib
 import sys
 from unittest import mock
@@ -22,6 +23,7 @@ def clear_argv(self):
     def test_convert_works_as_expected(
         self,
         convert_file_mock: mock.MagicMock,
+        caplog,
     ):
         """
         Intended as a unit test to make sure,
@@ -35,3 +37,5 @@ def test_convert_works_as_expected(
         convert_file_mock.assert_called_once_with(
             input_file="abc.def", output_file=pathlib.Path.cwd() / "abc.skops"
         )
+
+        assert caplog.at_level(logging.WARNING)

From 9b9f342bc775fdc3ed2cfbf4ffd6bfc23deccea0 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 09:37:30 +0000
Subject: [PATCH 22/38] Add needed __init__ file

---
 skops/cli/__init__.py | 0
 skops/cli/_convert.py | 5 ++++-
 2 files changed, 4 insertions(+), 1 deletion(-)
 create mode 100644 skops/cli/__init__.py

diff --git a/skops/cli/__init__.py b/skops/cli/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 9000f57b..ca2f0548 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -79,7 +79,10 @@ def format_parser(
     parser_subgroup.add_argument(
         "-v",
         "--verbose",
-        help="Enable verbose logging.",
+        help=(
+            "Increases verbosity of logging. Can be used multiple times to increase "
+            "further."
+        ),
         action="count",
         dest="loglevel",
         default=0,

From 6f5b71e377a81e9b7237006d18b241a76afe2509 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 09:40:41 +0000
Subject: [PATCH 23/38] Update docstrings

---
 skops/cli/entrypoint.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index ed50c445..ec7c0305 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -8,7 +8,9 @@ def main_cli(command_line_args=None):
     Main command line interface entrypoint for all command line Skops methods.
 
     To add a new entrypoint:
-        1. Create a new main
+        1. Create a new method to call that accepts a namespace
+        2. Create a new subparser formatter to define the expected CL arguments
+        3. Add those to the function map.
     """
     entry_parser = argparse.ArgumentParser(
         prog="Skops",
@@ -23,6 +25,9 @@ def main_cli(command_line_args=None):
         help="Sub-commands help",
     )
 
+    # function_map should map the expected CL command to
+    #   method: the command to call
+    #   format_parser: the function used to create a subparser for that command
     function_map = {
         "convert": {
             "method": skops.cli._convert.main,

From aa7c3ba5205a88fce78b3c5036c19a214d898971 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 09:44:53 +0000
Subject: [PATCH 24/38] Make names of files uniform

---
 skops/cli/_convert.py   | 4 ++--
 skops/cli/entrypoint.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index ca2f0548..594edaf9 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -64,7 +64,7 @@ def format_parser(
         parser = argparse.ArgumentParser()
 
     parser_subgroup = parser.add_argument_group("convert")
-    parser_subgroup.add_argument("input", help="Input file to convert. ")
+    parser_subgroup.add_argument("input-file", help="Input file to convert. ")
 
     parser_subgroup.add_argument(
         "-o",
@@ -94,7 +94,7 @@ def main(
     parsed_args: argparse.Namespace,
 ):
     output_file = parsed_args.output_file
-    input_file = parsed_args.input
+    input_file = parsed_args.input_file
 
     logging.basicConfig(format="%(message)s", level=get_log_level(parsed_args.loglevel))
 
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index ec7c0305..f2a7ac17 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -25,7 +25,7 @@ def main_cli(command_line_args=None):
         help="Sub-commands help",
     )
 
-    # function_map should map the expected CL command to
+    # function_map should map a command to
     #   method: the command to call
     #   format_parser: the function used to create a subparser for that command
     function_map = {

From 1c0352d359723b56ca6228d120ffa55ecd9f7356 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 18:55:01 +0000
Subject: [PATCH 25/38] Update help docstrings

---
 docs/changes.rst      | 9 ++++++++-
 skops/cli/_convert.py | 6 +++---
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/docs/changes.rst b/docs/changes.rst
index f1aa7739..86f78ded 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -9,6 +9,12 @@ skops Changelog
     :depth: 1
     :local:
 
+v0.5
+----
+- Added CLI entrypoint support (:func:`.cli.entrypoint.main_cli`)
+  and a command line function to convert Pickle files
+  to Skops files (:func:`.cli._convert.main`). :pr:`249` by `Erin Aho`_
+
 v0.4
 ----
 - :func:`.io.dump` and :func:`.io.load` now work with file like objects,
@@ -83,4 +89,5 @@ Contributors
 
 :user:`Adrin Jalali <adrinjalali>`, :user:`Merve Noyan <merveenoyan>`,
 :user:`Benjamin Bossan <BenjaminBossan>`, :user:`Ayyuce Demirbas
-<ayyucedemirbas>`, :user:`Prajjwal Mishra <p-mishra1>`
+<ayyucedemirbas>`, :user:`Prajjwal Mishra <p-mishra1>`,
+:user:`Erin Aho <E-Aho>`,
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 594edaf9..e68d2760 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -64,7 +64,7 @@ def format_parser(
         parser = argparse.ArgumentParser()
 
     parser_subgroup = parser.add_argument_group("convert")
-    parser_subgroup.add_argument("input-file", help="Input file to convert. ")
+    parser_subgroup.add_argument("input", help="Path to an input file to convert. ")
 
     parser_subgroup.add_argument(
         "-o",
@@ -81,7 +81,7 @@ def format_parser(
         "--verbose",
         help=(
             "Increases verbosity of logging. Can be used multiple times to increase "
-            "further."
+            "verbosity further."
         ),
         action="count",
         dest="loglevel",
@@ -94,7 +94,7 @@ def main(
     parsed_args: argparse.Namespace,
 ):
     output_file = parsed_args.output_file
-    input_file = parsed_args.input_file
+    input_file = parsed_args.input
 
     logging.basicConfig(format="%(message)s", level=get_log_level(parsed_args.loglevel))
 

From 8d9b3c52de0a3d5069dc7b94e31e36cd9dc0f717 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 10 Jan 2023 19:07:30 +0000
Subject: [PATCH 26/38] Add documentation for CLI

---
 docs/persistence.rst | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 07aa3e2c..0c2871ad 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -110,6 +110,22 @@ you have custom functions (say, a custom function to be used with
 most ``numpy`` and ``scipy`` functions should work. Therefore, you can save
 objects having references to functions such as ``numpy.sqrt``.
 
+Command Line Interface
+########
+Skops has a command line interface to convert SciKit-Learn models persisted with
+``Pickle`` to ``Skops`` files.
+
+To convert a file from the command line, use the ``skops convert`` entrypoint.
+
+Below is an example call to convert a file ``my_model.pkl`` to ``new_model.skops``:
+
+.. code:: console
+    skops convert my_model.pkl
+
+Further help for the different supported options can be found by calling
+``skops convert --help`` in a terminal.
+
+
 Supported libraries
 -------------------
 

From 8150f9a429941a5dae084c1f77ae092435639e59 Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 11:17:22 +0000
Subject: [PATCH 27/38] Update docs/persistence.rst

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>
---
 docs/persistence.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 0c2871ad..86fed026 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -111,7 +111,8 @@ most ``numpy`` and ``scipy`` functions should work. Therefore, you can save
 objects having references to functions such as ``numpy.sqrt``.
 
 Command Line Interface
-########
+######################
+
 Skops has a command line interface to convert SciKit-Learn models persisted with
 ``Pickle`` to ``Skops`` files.
 

From 88e7be05e0eaa5e73ab9bc490d592c9d4217cd4b Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 11:17:35 +0000
Subject: [PATCH 28/38] Update docs/persistence.rst

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>
---
 docs/persistence.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 86fed026..8332a6a4 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -113,7 +113,7 @@ objects having references to functions such as ``numpy.sqrt``.
 Command Line Interface
 ######################
 
-Skops has a command line interface to convert SciKit-Learn models persisted with
+Skops has a command line interface to convert scikit-learn models persisted with
 ``Pickle`` to ``Skops`` files.
 
 To convert a file from the command line, use the ``skops convert`` entrypoint.

From c38cb735133f7739e038da88e0e0f524bc898036 Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 11:18:56 +0000
Subject: [PATCH 29/38] Update docs/persistence.rst

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>
---
 docs/persistence.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 8332a6a4..04f1234e 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -118,7 +118,7 @@ Skops has a command line interface to convert scikit-learn models persisted with
 
 To convert a file from the command line, use the ``skops convert`` entrypoint.
 
-Below is an example call to convert a file ``my_model.pkl`` to ``new_model.skops``:
+Below is an example call to convert a file ``my_model.pkl`` to ``my_model.skops``:
 
 .. code:: console
     skops convert my_model.pkl

From 5233230806f4181633cea1a9264d7e43369d7833 Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 11:32:32 +0000
Subject: [PATCH 30/38] Apply suggestions from code review

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>
---
 docs/persistence.rst    | 1 +
 skops/cli/_convert.py   | 7 +++----
 skops/cli/_utils.py     | 2 +-
 skops/cli/entrypoint.py | 3 +--
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 04f1234e..943a2196 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -121,6 +121,7 @@ To convert a file from the command line, use the ``skops convert`` entrypoint.
 Below is an example call to convert a file ``my_model.pkl`` to ``my_model.skops``:
 
 .. code:: console
+
     skops convert my_model.pkl
 
 Further help for the different supported options can be found by calling
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index e68d2760..1e2095ee 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -11,9 +11,8 @@
 from skops.io import dumps, get_untrusted_types
 
 
-def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
-    """
-    Function that is called by ``skops convert`` entrypoint.
+def _convert_file(input_file: os.PathLike, output_file: os.PathLike) -> None:
+    """Function that is called by ``skops convert`` entrypoint.
 
     Loads a pickle model from the input path, converts to skops format, and saves to
     output file.
@@ -92,7 +91,7 @@ def format_parser(
 
 def main(
     parsed_args: argparse.Namespace,
-):
+) -> None:
     output_file = parsed_args.output_file
     input_file = parsed_args.input
 
diff --git a/skops/cli/_utils.py b/skops/cli/_utils.py
index 82a371ab..205b836a 100644
--- a/skops/cli/_utils.py
+++ b/skops/cli/_utils.py
@@ -1,7 +1,7 @@
 import logging
 
 
-def get_log_level(level: int = 0):
+def get_log_level(level: int = 0) -> int:
     """Takes in verbosity from a CLI entrypoint (number of times -v specified),
     and sets the logger to the required log level"""
 
diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index f2a7ac17..3e9acaf8 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -4,8 +4,7 @@
 
 
 def main_cli(command_line_args=None):
-    """
-    Main command line interface entrypoint for all command line Skops methods.
+    """Main command line interface entrypoint for all command line Skops methods.
 
     To add a new entrypoint:
         1. Create a new method to call that accepts a namespace

From 95a5ff3815e3e1d6b048f827cd9b7ed763524e3a Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 11:41:40 +0000
Subject: [PATCH 31/38] Local changes

---
 skops/cli/_convert.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index e68d2760..0c27eb59 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -43,7 +43,6 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike):
         untrusted_str = ", ".join(untrusted_types)
 
         logging.warning(
-            "Unknown Types Detected! "
             f"While converting {model_name}, "
             "the following unknown types were found: "
             f"{untrusted_str}. "

From 7e631783a2f2bf58cb39045ba674512f7073ac06 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 12:02:16 +0000
Subject: [PATCH 32/38] Add test coverage for very verbose logging

---
 skops/cli/_utils.py             | 2 +-
 skops/cli/tests/test_convert.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/skops/cli/_utils.py b/skops/cli/_utils.py
index 205b836a..55173532 100644
--- a/skops/cli/_utils.py
+++ b/skops/cli/_utils.py
@@ -8,7 +8,7 @@ def get_log_level(level: int = 0) -> int:
     all_levels = [logging.WARNING, logging.INFO, logging.DEBUG]
 
     if level > len(all_levels):
-        level = len(all_levels)
+        level = len(all_levels) - 1
     elif level < 0:
         level = 0
 
diff --git a/skops/cli/tests/test_convert.py b/skops/cli/tests/test_convert.py
index 049d44b8..d7a3a69e 100644
--- a/skops/cli/tests/test_convert.py
+++ b/skops/cli/tests/test_convert.py
@@ -117,7 +117,7 @@ def test_with_output_dir_works_as_expected(
             ("--verbose", logging.INFO),
             ("-vv", logging.DEBUG),
             ("-v -v", logging.DEBUG),
-            ("-vvv", logging.DEBUG),
+            ("-vvvvv", logging.DEBUG),
             ("--verbose --verbose", logging.DEBUG),
         ],
     )

From 6e357705feb0d75cbb8c12000371427886d0a597 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 12:10:25 +0000
Subject: [PATCH 33/38] Add comments to make entrypoint more clear

---
 skops/cli/entrypoint.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/skops/cli/entrypoint.py b/skops/cli/entrypoint.py
index 3e9acaf8..c98ef8d3 100644
--- a/skops/cli/entrypoint.py
+++ b/skops/cli/entrypoint.py
@@ -25,7 +25,7 @@ def main_cli(command_line_args=None):
     )
 
     # function_map should map a command to
-    #   method: the command to call
+    #   method: the command to call (gets set to default 'func')
     #   format_parser: the function used to create a subparser for that command
     function_map = {
         "convert": {
@@ -35,9 +35,13 @@ def main_cli(command_line_args=None):
     }
 
     for func_name, values in function_map.items():
+        # Add subparser for each function in func map,
+        # and assigns default func to be "method" from function_map
         subparser = subparsers.add_parser(func_name)
         subparser.set_defaults(func=values["method"])
         values["format_parser"](subparser)
 
+    # Parse arguments with arg parser for given function in function map,
+    # Then call the matching method in the function_map with the argument namespace
     args = entry_parser.parse_args(command_line_args)
     args.func(args)

From 02c95ad014e5d6d0c84f2925a6a0aabc5295f8df Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 12:14:20 +0000
Subject: [PATCH 34/38] Adjust test to be more clear

---
 skops/cli/tests/test_convert.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/skops/cli/tests/test_convert.py b/skops/cli/tests/test_convert.py
index d7a3a69e..f7ee3a46 100644
--- a/skops/cli/tests/test_convert.py
+++ b/skops/cli/tests/test_convert.py
@@ -1,6 +1,6 @@
 import logging
 import pathlib
-import pickle as pkl
+import pickle
 from unittest import mock
 
 import numpy as np
@@ -37,12 +37,12 @@ def skops_path(self, tmp_path):
     @pytest.fixture
     def write_safe_file(self, pkl_path, safe_obj):
         with open(pkl_path, "wb") as f:
-            pkl.dump(safe_obj, f)
+            pickle.dump(safe_obj, f)
 
     @pytest.fixture
     def write_unsafe_file(self, pkl_path, unsafe_obj):
         with open(pkl_path, "wb") as f:
-            pkl.dump(unsafe_obj, f)
+            pickle.dump(unsafe_obj, f)
 
     def test_base_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj, caplog
@@ -88,7 +88,7 @@ def test_base_works_as_expected(self, mock_convert: mock.MagicMock):
     @pytest.mark.parametrize(
         "input_path, output_file, expected_path",
         [
-            ("abc.123", "a/b/c", "a/b/c"),
+            ("abc.123", "some/file/path.out", "some/file/path.out"),
             ("abc.123", None, pathlib.Path.cwd() / "abc.skops"),
         ],
         ids=["Given an output path", "No output path"],

From c3491efe4005fed8f515538f435ddab1042067a5 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Tue, 17 Jan 2023 12:42:17 +0000
Subject: [PATCH 35/38] Add example script to convert all pkl files in working
 dir

---
 docs/persistence.rst            |  7 +++++++
 skops/cli/_convert.py           | 14 +++++++++-----
 skops/cli/tests/test_convert.py |  8 ++++++--
 3 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/docs/persistence.rst b/docs/persistence.rst
index 943a2196..473b9b6f 100644
--- a/docs/persistence.rst
+++ b/docs/persistence.rst
@@ -124,6 +124,13 @@ Below is an example call to convert a file ``my_model.pkl`` to ``my_model.skops`
 
     skops convert my_model.pkl
 
+To convert multiple files, you can use bash commands to iterate the above call.
+For example, to convert all ``.pkl`` flies in the current directory:
+
+.. code:: console
+
+    for FILE in *.pkl; do skops convert FILE; done
+
 Further help for the different supported options can be found by calling
 ``skops convert --help`` in a terminal.
 
diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 7f6708ad..946c8948 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -11,7 +11,11 @@
 from skops.io import dumps, get_untrusted_types
 
 
-def _convert_file(input_file: os.PathLike, output_file: os.PathLike) -> None:
+def _convert_file(
+    input_file: os.PathLike,
+    output_file: os.PathLike,
+    logger: logging.Logger = logging.getLogger(),
+) -> None:
     """Function that is called by ``skops convert`` entrypoint.
 
     Loads a pickle model from the input path, converts to skops format, and saves to
@@ -28,7 +32,7 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike) -> None:
     """
     model_name = pathlib.Path(input_file).stem
 
-    logging.debug(f"Converting {model_name}")
+    logger.debug(f"Converting {model_name}")
 
     with open(input_file, "rb") as f:
         obj = pickle.load(f)
@@ -37,11 +41,11 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike) -> None:
     untrusted_types = get_untrusted_types(data=skops_dump)
 
     if not untrusted_types:
-        logging.info(f"No unknown types found in {model_name}.")
+        logger.info(f"No unknown types found in {model_name}.")
     else:
         untrusted_str = ", ".join(untrusted_types)
 
-        logging.warning(
+        logger.warning(
             f"While converting {model_name}, "
             "the following unknown types were found: "
             f"{untrusted_str}. "
@@ -49,7 +53,7 @@ def _convert_file(input_file: os.PathLike, output_file: os.PathLike) -> None:
         )
 
     with open(output_file, "wb") as out_file:
-        logging.debug(f"Writing to {output_file}")
+        logger.debug(f"Writing to {output_file}")
         out_file.write(skops_dump)
 
 
diff --git a/skops/cli/tests/test_convert.py b/skops/cli/tests/test_convert.py
index f7ee3a46..6395dd3d 100644
--- a/skops/cli/tests/test_convert.py
+++ b/skops/cli/tests/test_convert.py
@@ -47,10 +47,14 @@ def write_unsafe_file(self, pkl_path, unsafe_obj):
     def test_base_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_safe_file, safe_obj, caplog
     ):
-        _convert._convert_file(pkl_path, skops_path)
+        mock_logger = mock.MagicMock()
+        _convert._convert_file(pkl_path, skops_path, logger=mock_logger)
         persisted_obj = load(skops_path)
         assert np.array_equal(persisted_obj, safe_obj)
-        assert MockUnsafeType.__name__ not in caplog.text
+
+        # Check no warnings or errors raised
+        mock_logger.warning.assert_not_called()
+        mock_logger.error.assert_not_called()
 
     def test_unsafe_case_works_as_expected(
         self, pkl_path, tmp_path, skops_path, write_unsafe_file, caplog

From 7e072da43e96c432b2bec46443086ecd46d27677 Mon Sep 17 00:00:00 2001
From: Erin Aho <erinaho@outlook.com>
Date: Wed, 18 Jan 2023 12:50:14 +0000
Subject: [PATCH 36/38] Update skops/cli/_convert.py to be more clear in
 warning message

Co-authored-by: Benjamin Bossan <BenjaminBossan@users.noreply.github.com>
---
 skops/cli/_convert.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 946c8948..d1f7a4e7 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -46,7 +46,7 @@ def _convert_file(
         untrusted_str = ", ".join(untrusted_types)
 
         logger.warning(
-            f"While converting {model_name}, "
+            f"While converting {input_file}, "
             "the following unknown types were found: "
             f"{untrusted_str}. "
             f"When loading {output_file}, add 'trusted=True' to the skops.load call. "

From 799f91bcaf8f71befc17b022e510357d559f1792 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Wed, 18 Jan 2023 17:06:24 +0000
Subject: [PATCH 37/38] Update log message

---
 skops/cli/_convert.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 946c8948..d8388d2d 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -98,7 +98,9 @@ def main(
     output_file = parsed_args.output_file
     input_file = parsed_args.input
 
-    logging.basicConfig(format="%(message)s", level=get_log_level(parsed_args.loglevel))
+    logging.basicConfig(
+        format="%(levelname)-8s: %(message)s", level=get_log_level(parsed_args.loglevel)
+    )
 
     if not output_file:
         # No filename provided, defaulting to base file path

From 8ddc6b9cfb9115f7fbb4be06f8403a1beab55312 Mon Sep 17 00:00:00 2001
From: = <erinaho@outlook.com>
Date: Wed, 18 Jan 2023 17:10:18 +0000
Subject: [PATCH 38/38] Adjust warning message to not use Trusted=True

---
 skops/cli/_convert.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/skops/cli/_convert.py b/skops/cli/_convert.py
index 4e8f0855..7d630c15 100644
--- a/skops/cli/_convert.py
+++ b/skops/cli/_convert.py
@@ -49,7 +49,8 @@ def _convert_file(
             f"While converting {input_file}, "
             "the following unknown types were found: "
             f"{untrusted_str}. "
-            f"When loading {output_file}, add 'trusted=True' to the skops.load call. "
+            f"When loading {output_file} with skops.load, these types must be "
+            "specified as 'trusted'"
         )
 
     with open(output_file, "wb") as out_file: