Drop support for old python, Fix style according to pylint update

.github/workflows/lint-pylint.yml

@@ -12,7 +12,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        # If new Python versions are added, update pylint accordingly
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -23,7 +24,11 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-          pip install pylint==2.17.3
+          pip install setuptools wheel
+          pip install pylint==3.3.0
       - name: Analysing the code with pylint
+        # Disable rule that limits to 5 the number of positional arguments
         run: |
-          pylint --rcfile=.pylintrc $(git ls-files '*.py')
+          pylint --rcfile=.pylintrc \
+            --disable=too-many-positional-arguments \
+            -- $(git ls-files '*.py')

SPRINTLOG.md

@@ -472,3 +472,4 @@ _Empty sprint_
 ## 2025-09-15 - 2025-09-26
 
 - Bump cryptography library from 42.0.4 to 44.0.1 to solve vulnerabities ([#845](https://github.com/ScilifelabDataCentre/dds_cli/pull/845))
+- Fix style according to guidelines and drop support for python 3.8 and 3.9 due to CVE, added new tests ([#843](https://github.com/ScilifelabDataCentre/dds_cli/pull/843))

WINDOWS.md

@@ -1,6 +1,6 @@
 # How to install the DDS CLI on Windows
 
-## 1. Download and install Python > 3.8
+## 1. Download and install Python > 3.10
 
 ### 1.1. Go to https://www.python.org/downloads/windows/
 
@@ -42,7 +42,7 @@
 
 ![Powershell 1](docs/_static/windows/powershell_top-1.png)
 
-> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.8 is shown or Python is not found, please consult the :ref:`Troubleshooting<troubleshooting>` section below.
+> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.10 is shown or Python is not found, please consult the :ref:`Troubleshooting<troubleshooting>` section below.
 
 ### 2.3. Python ships with a helper program called **pip** to install additional packages. In the next step, this software should be upgraded to its current version.
 

dds_cli/__main__.py

@@ -544,13 +544,14 @@ def configure():
             "Which method would you like to use?", choices=["Email", "Authenticator App", "Cancel"]
         ).ask()
 
+        auth_method: str | None = None  # type hint, initialized
         if auth_method_choice == "Cancel":
             LOG.info("Two-factor authentication method not configured.")
             sys.exit(0)
         elif auth_method_choice == "Authenticator App":
-            auth_method: str = "totp"
+            auth_method = "totp"
         elif auth_method_choice == "Email":
-            auth_method: str = "hotp"
+            auth_method = "hotp"
 
         with dds_cli.auth.Auth(authenticate=True, force_renew_token=False) as authenticator:
             authenticator.twofactor(auth_method=auth_method)
@@ -885,6 +886,8 @@ def activate_user(click_ctx, email):
     Super Admins: All users
     Unit Admins: Unit Admins / Personnel
     """
+    proceed_activation = False  # default assignment
+
     if click_ctx.get("NO_PROMPT", False):
         pass
     else:
@@ -925,6 +928,8 @@ def deactivate_user(click_ctx, email):
     Super Admins: All users
     Unit Admins: Unit Admins / Personnel
     """
+    proceed_deactivation = False  # default assignment
+
     if click_ctx.get("NO_PROMPT", False):
         pass
     else:

dds_cli/custom_decorators.py

@@ -154,6 +154,8 @@ def create_and_remove_task(self, *args, **kwargs):
             SpinnerColumn(spinner_name="dots12", style="white"),
             console=dds_cli.utils.stderr_console,
         ) as progress:
+
+            description: str | None = None  # type hint, initialized
             # Determine spinner text
             if func.__name__ == "remove_all":
                 description = f"Removing all files in project {self.project}"

dds_cli/file_compressor.py

@@ -104,8 +104,7 @@ def compress_file(
                     #     if not chunk:
                     #         break
                     #     yield
-                    for chunk in iter(lambda: compressor.read(chunk_size), b""):
-                        yield chunk
+                    yield from iter(lambda: compressor.read(chunk_size), b"")
         except Exception as err:  # pylint: disable=broad-exception-caught
             LOG.warning(str(err))
         else:

dds_cli/file_handler_local.py

@@ -92,8 +92,7 @@ def read_file(file, chunk_size: int = FileSegment.SEGMENT_SIZE_RAW):
 
         try:
             with file.open(mode="rb") as infile:
-                for chunk in iter(lambda: infile.read(chunk_size), b""):
-                    yield chunk
+                yield from iter(lambda: infile.read(chunk_size), b"")
         except OSError as err:
             LOG.warning(str(err))
 
@@ -278,11 +277,10 @@ def stream_from_file(self, file):
             # LOG.debug(
             #     "Test: %s",
             # )
-            for chunk in fc.Compressor.compress_file(file=file_info["path_raw"]):
-                # LOG.debug("Chunk type: %s", type(chunk))
-                # checksum.update(chunk)
-                # break
-                yield chunk
+            yield from fc.Compressor.compress_file(file=file_info["path_raw"])
+            # LOG.debug("Chunk type: %s", type(chunk))
+            # checksum.update(chunk)
+            # break
 
         # LOG.debug("Streaming file finished.")
         # Add checksum to file info

docs/installation.rst

@@ -29,7 +29,7 @@ As mentioned above, you can install ``dds-cli`` from PyPI or via an executable.
 Install from **PyPI**
 -----------------------
 
-1. To perform these steps you need to have Python version 3.8 or higher installed.
+1. To perform these steps you need to have Python version 3.10 or higher installed.
 
    * First check which Python version you have
 
@@ -39,7 +39,7 @@ Install from **PyPI**
 
       .. image:: ../img/python3-version.svg
 
-      If this does not return ``Python 3.8.x`` or higher, you will need to `install Python <https://www.python.org/downloads/>`_.
+      If this does not return ``Python 3.10.x`` or higher, you will need to `install Python <https://www.python.org/downloads/>`_.
 
    .. warning:: 
 

setup.py

@@ -24,11 +24,10 @@
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ],
     url="https://github.com/ScilifelabDataCentre/dds_cli",
     author="SciLifeLab Data Centre",

tests/test_commands.py

@@ -0,0 +1,184 @@
+"""Tests for CLI commands in dds_cli.__main__"""
+
+from click.testing import CliRunner
+from unittest.mock import MagicMock, patch
+import pytest
+
+
+import dds_cli.exceptions
+from dds_cli.__main__ import dds_main
+
+
+#### AUTH COMMANDS #####
+
+## TWOFACTOR subcommands ##
+
+
+# parametrized options to pass to the test
+@pytest.mark.parametrize(
+    "user_choice, expected_auth_method, expected_exit_code",
+    [
+        ("Email", "hotp", 0),
+        ("Authenticator App", "totp", 0),
+        ("Cancel", None, 0),  # Cancel exits with 0
+    ],
+)
+def test_auth_configure_ok(user_choice, expected_auth_method, expected_exit_code):
+    """Test of configure two factor method - ok"""
+
+    runner = CliRunner()
+    with patch("dds_cli.__main__.questionary.select") as mock_select, patch(
+        "dds_cli.auth.Auth"
+    ) as mock_auth:
+
+        # Mock the user selecting option
+        mock_select.return_value.ask.return_value = user_choice
+
+        # Mock the Auth context manager
+        mock_auth_instance = MagicMock()
+        mock_auth.return_value.__enter__.return_value = mock_auth_instance
+
+        result = runner.invoke(dds_main, ["auth", "twofactor", "configure"])
+
+        assert result.exit_code == expected_exit_code
+
+        if user_choice == "Cancel":
+            # No call to twofactor
+            mock_auth_instance.twofactor.assert_not_called()
+        else:
+            mock_auth_instance.twofactor.assert_called_once_with(auth_method=expected_auth_method)
+
+
+# parametrized options to pass to the test
+@pytest.mark.parametrize("user_choice", ["Email", "Authenticator App"])
+@pytest.mark.parametrize(
+    "exc_type", [dds_cli.exceptions.DDSCLIException, dds_cli.exceptions.ApiResponseError]
+)
+def test_auth_configure_exceptions(exc_type, user_choice):
+    """Test of configure two factor - fails with exceptions"""
+
+    runner = CliRunner()
+    with patch("dds_cli.__main__.questionary.select") as mock_select, patch(
+        "dds_cli.auth.Auth"
+    ) as mock_auth:
+
+        # Mock the user selecting option
+        mock_select.return_value.ask.return_value = user_choice
+
+        # Mock Auth context manager to raise exception
+        mock_auth_instance = MagicMock()
+        mock_auth.return_value.__enter__.return_value = mock_auth_instance
+        mock_auth_instance.twofactor.side_effect = exc_type("message")
+
+        result = runner.invoke(dds_main, ["auth", "twofactor", "configure"])
+
+        assert result.exit_code == 1
+
+
+#### USER COMMANDS #####
+
+## Activate and deativate users ##
+
+
+@pytest.mark.parametrize("confirm", [True, False])
+def test_user_activate_confirm_ok(confirm):
+    """Test user activation when confirmation is yes/no. - no errors"""
+
+    runner = CliRunner()
+    with patch(
+        "dds_cli.__main__.rich.prompt.Confirm.ask", return_value=confirm
+    ) as mock_confirm, patch("dds_cli.account_manager.AccountManager") as mock_manager:
+
+        mock_manager_instance = MagicMock()
+        mock_manager.return_value.__enter__.return_value = mock_manager_instance
+
+        result = runner.invoke(dds_main, ["user", "activate", "[email protected]"])
+
+        assert result.exit_code == 0
+        mock_confirm.assert_called_once()
+
+        if confirm:
+            mock_manager_instance.user_activation.assert_called_once_with(
+                email="[email protected]", action="reactivate"
+            )
+        else:
+            mock_manager_instance.user_activation.assert_not_called()
+
+
+@pytest.mark.parametrize("confirm", [True, False])
+def test_user_deactivate_confirm_ok(confirm):
+    """Test user de-activation when confirmation is yes/no. - no errors"""
+
+    runner = CliRunner()
+    with patch(
+        "dds_cli.__main__.rich.prompt.Confirm.ask", return_value=confirm
+    ) as mock_confirm, patch("dds_cli.account_manager.AccountManager") as mock_manager:
+
+        mock_manager_instance = MagicMock()
+        mock_manager.return_value.__enter__.return_value = mock_manager_instance
+
+        result = runner.invoke(dds_main, ["user", "deactivate", "[email protected]"])
+
+        assert result.exit_code == 0
+        mock_confirm.assert_called_once()
+
+        if confirm:
+            mock_manager_instance.user_activation.assert_called_once_with(
+                email="[email protected]", action="deactivate"
+            )
+        else:
+            mock_manager_instance.user_activation.assert_not_called()
+
+
+@pytest.mark.parametrize(
+    "exc_type",
+    [
+        dds_cli.exceptions.AuthenticationError,
+        dds_cli.exceptions.ApiResponseError,
+        dds_cli.exceptions.ApiRequestError,
+        dds_cli.exceptions.DDSCLIException,
+    ],
+)
+def test_user_activate_exceptions(exc_type):
+    """Test user activation when AccountManager raises errors."""
+
+    runner = CliRunner()
+    with patch("dds_cli.__main__.rich.prompt.Confirm.ask", return_value=True), patch(
+        "dds_cli.account_manager.AccountManager"
+    ) as mock_manager:
+
+        mock_manager_instance = MagicMock()
+        mock_manager_instance.user_activation.side_effect = exc_type("error")
+        mock_manager.return_value.__enter__.return_value = mock_manager_instance
+
+        result = runner.invoke(dds_main, ["user", "activate", "[email protected]"])
+
+        assert result.exit_code == 1
+        assert "error" in result.output
+
+
+@pytest.mark.parametrize(
+    "exc_type",
+    [
+        dds_cli.exceptions.AuthenticationError,
+        dds_cli.exceptions.ApiResponseError,
+        dds_cli.exceptions.ApiRequestError,
+        dds_cli.exceptions.DDSCLIException,
+    ],
+)
+def test_user_deactivate_exceptions(exc_type):
+    """Test user de-activation when AccountManager raises errors."""
+
+    runner = CliRunner()
+    with patch("dds_cli.__main__.rich.prompt.Confirm.ask", return_value=True), patch(
+        "dds_cli.account_manager.AccountManager"
+    ) as mock_manager:
+
+        mock_manager_instance = MagicMock()
+        mock_manager_instance.user_activation.side_effect = exc_type("error")
+        mock_manager.return_value.__enter__.return_value = mock_manager_instance
+
+        result = runner.invoke(dds_main, ["user", "deactivate", "[email protected]"])
+
+        assert result.exit_code == 1
+        assert "error" in result.output