Fix all typing issues

.pre-commit-config.yaml

@@ -17,6 +17,13 @@ repos:
       - id: black
         args: [--target-version=py39]
 
+  # Check python code static typing
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.931
+    hooks:
+      - id: mypy
+        additional_dependencies: ["pytest", "types-requests", "types-tabulate"]
+
   # Autoformat: YAML, JSON, Markdown, etc.
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v2.5.1

all-spark-notebook/test/test_spark_notebooks.py

@@ -3,7 +3,7 @@
 
 import logging
 
-import pytest
+import pytest  # type: ignore
 from pathlib import Path
 
 from conftest import TrackedContainer

base-notebook/jupyter_notebook_config.py

@@ -1,12 +1,12 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
-
+# mypy: ignore-errors
 from jupyter_core.paths import jupyter_data_dir
 import subprocess
 import os
-import errno
 import stat
 
+
 c = get_config()  # noqa: F821
 c.NotebookApp.ip = "0.0.0.0"
 c.NotebookApp.port = 8888
@@ -16,28 +16,21 @@ c.NotebookApp.open_browser = False
 c.FileContentsManager.delete_to_trash = False
 
 # Generate a self-signed certificate
+OPENSSL_CONFIG = """\
+[req]
+distinguished_name = req_distinguished_name
+[req_distinguished_name]
+"""
 if "GEN_CERT" in os.environ:
     dir_name = jupyter_data_dir()
     pem_file = os.path.join(dir_name, "notebook.pem")
-    try:
+    os.makedirs(dir_name, exist_ok=True)
-        os.makedirs(dir_name)
-    except OSError as exc:  # Python >2.5
-        if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
-            pass
-        else:
-            raise
 
     # Generate an openssl.cnf file to set the distinguished name
     cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
     if not os.path.isfile(cnf_file):
         with open(cnf_file, "w") as fh:
-            fh.write(
+            fh.write(OPENSSL_CONFIG)
-                """\
-[req]
-distinguished_name = req_distinguished_name
-[req_distinguished_name]
-"""
-            )
 
     # Generate a certificate if one doesn't exist on disk
     subprocess.check_call(

base-notebook/test/test_container_options.py

@@ -4,7 +4,7 @@ import pathlib
 import time
 import logging
 
-import pytest
+import pytest  # type: ignore
 import requests
 
 from conftest import TrackedContainer
@@ -303,6 +303,6 @@ def test_jupyter_env_vars_to_unset_as_root(
             "-c",
             "echo I like $FRUIT and ${SECRET_FRUIT:-stuff}, and love ${SECRET_ANIMAL:-to keep secrets}!",
         ],
-        **root_args,
+        **root_args,  # type: ignore
     )
     assert "I like bananas and stuff, and love to keep secrets!" in logs

base-notebook/test/test_package_managers.py

@@ -2,7 +2,7 @@
 # Distributed under the terms of the Modified BSD License.
 
 import logging
-import pytest
+import pytest  # type: ignore
 
 from conftest import TrackedContainer
 

base-notebook/test/test_python.py

@@ -2,7 +2,7 @@
 # Distributed under the terms of the Modified BSD License.
 import logging
 
-from packaging import version
+from packaging import version  # type: ignore
 
 from conftest import TrackedContainer
 

base-notebook/test/test_start_container.py

@@ -3,7 +3,7 @@
 
 import logging
 from typing import Optional
-import pytest
+import pytest  # type: ignore
 import requests
 import time
 

conftest.py

@@ -2,11 +2,11 @@
 # Distributed under the terms of the Modified BSD License.
 import os
 import logging
-import typing
+from typing import Any, Optional
 
 import docker
 from docker.models.containers import Container
-import pytest
+import pytest  # type: ignore
 import requests
 
 from requests.packages.urllib3.util.retry import Retry
@@ -35,7 +35,7 @@ def docker_client() -> docker.DockerClient:
 @pytest.fixture(scope="session")
 def image_name() -> str:
     """Image name to test"""
-    return os.getenv("TEST_IMAGE")
+    return os.environ["TEST_IMAGE"]
 
 
 class TrackedContainer:
@@ -56,14 +56,14 @@ class TrackedContainer:
         self,
         docker_client: docker.DockerClient,
         image_name: str,
-        **kwargs: typing.Any,
+        **kwargs: Any,
     ):
-        self.container = None
+        self.container: Optional[Container] = None
-        self.docker_client = docker_client
+        self.docker_client: docker.DockerClient = docker_client
-        self.image_name = image_name
+        self.image_name: str = image_name
-        self.kwargs = kwargs
+        self.kwargs: Any = kwargs
 
-    def run_detached(self, **kwargs: typing.Any) -> Container:
+    def run_detached(self, **kwargs: Any) -> Container:
         """Runs a docker container using the preconfigured image name
         and a mix of the preconfigured container options and those passed
         to this method.
@@ -94,11 +94,12 @@ class TrackedContainer:
         timeout: int,
         no_warnings: bool = True,
         no_errors: bool = True,
-        **kwargs: typing.Any,
+        **kwargs: Any,
     ) -> str:
         running_container = self.run_detached(**kwargs)
         rv = running_container.wait(timeout=timeout)
         logs = running_container.logs().decode("utf-8")
+        assert isinstance(logs, str)
         LOGGER.debug(logs)
         if no_warnings:
             assert not self.get_warnings(logs)
@@ -119,14 +120,14 @@ class TrackedContainer:
     def _lines_starting_with(logs: str, pattern: str) -> list[str]:
         return [line for line in logs.splitlines() if line.startswith(pattern)]
 
-    def remove(self):
+    def remove(self) -> None:
         """Kills and removes the tracked docker container."""
         if self.container:
             self.container.remove(force=True)
 
 
 @pytest.fixture(scope="function")
-def container(docker_client: docker.DockerClient, image_name: str):
+def container(docker_client: docker.DockerClient, image_name: str) -> Container:
     """Notebook container with initial configuration appropriate for testing
     (e.g., HTTP port exposed to the host for HTTP calls).
 

minimal-notebook/test/test_nbconvert.py

@@ -3,7 +3,7 @@
 
 import logging
 
-import pytest
+import pytest  # type: ignore
 from pathlib import Path
 
 from conftest import TrackedContainer

mypy.ini

@@ -0,0 +1,26 @@
+[mypy]
+python_version = 3.9
+follow_imports = normal
+strict = False
+no_incremental = True
+
+[mypy-docker.*]
+ignore_missing_imports = True
+
+[mypy-matplotlib.*]
+ignore_missing_imports = True
+
+[mypy-packaging.*]
+ignore_missing_imports = True
+
+[mypy-pandas.*]
+ignore_missing_imports = True
+
+[mypy-plumbum.*]
+ignore_missing_imports = True
+
+[mypy-pyspark.*]
+ignore_missing_imports = True
+
+[mypy-tensorflow.*]
+ignore_missing_imports = True

pyspark-notebook/ipython_kernel_config.py

@@ -10,4 +10,5 @@
 # Attempt to capture and forward low-level output, e.g. produced by Extension
 #  libraries.
 #  Default: True
+# type:ignore
 c.IPKernelApp.capture_fd_output = False  # noqa: F821

scipy-notebook/test/test_extensions.py

@@ -2,7 +2,7 @@
 # Distributed under the terms of the Modified BSD License.
 import logging
 
-import pytest
+import pytest  # type: ignore
 
 from conftest import TrackedContainer
 

scipy-notebook/test/test_matplotlib.py

@@ -3,7 +3,7 @@
 
 import logging
 
-import pytest
+import pytest  # type: ignore
 from pathlib import Path
 
 from conftest import TrackedContainer
@@ -29,7 +29,7 @@ THIS_DIR = Path(__file__).parent.resolve()
 )
 def test_matplotlib(
     container: TrackedContainer, test_file: str, expected_file: str, description: str
-):
+) -> None:
     """Various tests performed on matplotlib
 
     - Test that matplotlib is able to plot a graph and write it as an image

tagging/create_manifests.py

@@ -5,6 +5,7 @@ import argparse
 import datetime
 import logging
 import os
+from docker.models.containers import Container
 from .docker_runner import DockerRunner
 from .get_taggers_and_manifests import get_taggers_and_manifests
 from .git_helper import GitHelper
@@ -55,9 +56,9 @@ def create_manifest_file(
     owner: str,
     wiki_path: str,
     manifests: list[ManifestInterface],
-    container,
+    container: Container,
 ) -> None:
-    manifest_names = [manifest.__name__ for manifest in manifests]
+    manifest_names = [manifest.__class__.__name__ for manifest in manifests]
     LOGGER.info(f"Using manifests: {manifest_names}")
 
     commit_hash_tag = GitHelper.commit_hash_tag()

tagging/docker_runner.py

@@ -1,6 +1,7 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
 from typing import Optional
+from types import TracebackType
 import docker
 from docker.models.containers import Container
 import logging
@@ -13,7 +14,7 @@ class DockerRunner:
     def __init__(
         self,
         image_name: str,
-        docker_client=docker.from_env(),
+        docker_client: docker.DockerClient = docker.from_env(),
         command: str = "sleep infinity",
     ):
         self.container: Optional[Container] = None
@@ -31,7 +32,13 @@ class DockerRunner:
         LOGGER.info(f"Container {self.container.name} created")
         return self.container
 
-    def __exit__(self, exc_type, exc_value, traceback) -> None:
+    def __exit__(
+        self,
+        exc_type: Optional[type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[TracebackType],
+    ) -> None:
+        assert self.container is not None
         LOGGER.info(f"Removing container {self.container.name} ...")
         if self.container:
             self.container.remove(force=True)
@@ -44,6 +51,7 @@ class DockerRunner:
         LOGGER.info(f"Running cmd: '{cmd}' on container: {container}")
         out = container.exec_run(cmd)
         result = out.output.decode("utf-8").rstrip()
+        assert isinstance(result, str)
         if print_result:
             LOGGER.info(f"Command result: {result}")
         assert out.exit_code == 0, f"Command: {cmd} failed"

tagging/get_taggers_and_manifests.py

@@ -1,20 +1,22 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
+from typing import Optional
 from .images_hierarchy import ALL_IMAGES
 from .manifests import ManifestInterface
 from .taggers import TaggerInterface
 
 
 def get_taggers_and_manifests(
-    short_image_name: str,
+    short_image_name: Optional[str],
 ) -> tuple[list[TaggerInterface], list[ManifestInterface]]:
-    taggers: list[TaggerInterface] = []
+    if short_image_name is None:
-    manifests: list[ManifestInterface] = []
+        return [[], []]  # type: ignore
-    while short_image_name is not None:
-        image_description = ALL_IMAGES[short_image_name]
 
-        taggers = image_description.taggers + taggers
+    image_description = ALL_IMAGES[short_image_name]
-        manifests = image_description.manifests + manifests
+    parent_taggers, parent_manifests = get_taggers_and_manifests(
-
+        image_description.parent_image
-        short_image_name = image_description.parent_image
+    )
-    return taggers, manifests
+    return (
+        parent_taggers + image_description.taggers,
+        parent_manifests + image_description.manifests,
+    )

tagging/git_helper.py

@@ -7,7 +7,7 @@ from plumbum.cmd import git
 class GitHelper:
     @staticmethod
     def commit_hash() -> str:
-        return git["rev-parse", "HEAD"]().strip()
+        return git["rev-parse", "HEAD"]().strip()  # type: ignore
 
     @staticmethod
     def commit_hash_tag() -> str:
@@ -15,7 +15,7 @@ class GitHelper:
 
     @staticmethod
     def commit_message() -> str:
-        return git["log", -1, "--pretty=%B"]().strip()
+        return git["log", -1, "--pretty=%B"]().strip()  # type: ignore
 
 
 if __name__ == "__main__":

tagging/github_set_env.py

@@ -3,7 +3,7 @@
 import os
 
 
-def github_set_env(env_name, env_value):
+def github_set_env(env_name: str, env_value: str) -> None:
     if not os.environ.get("GITHUB_ACTIONS") or not os.environ.get("GITHUB_ENV"):
         return
 

tagging/images_hierarchy.py

@@ -39,39 +39,39 @@ ALL_IMAGES = {
     "base-notebook": ImageDescription(
         parent_image=None,
         taggers=[
-            SHATagger,
+            SHATagger(),
-            DateTagger,
+            DateTagger(),
-            UbuntuVersionTagger,
+            UbuntuVersionTagger(),
-            PythonVersionTagger,
+            PythonVersionTagger(),
-            JupyterNotebookVersionTagger,
+            JupyterNotebookVersionTagger(),
-            JupyterLabVersionTagger,
+            JupyterLabVersionTagger(),
-            JupyterHubVersionTagger,
+            JupyterHubVersionTagger(),
         ],
-        manifests=[CondaEnvironmentManifest, AptPackagesManifest],
+        manifests=[CondaEnvironmentManifest(), AptPackagesManifest()],
     ),
     "minimal-notebook": ImageDescription(parent_image="base-notebook"),
     "scipy-notebook": ImageDescription(parent_image="minimal-notebook"),
     "r-notebook": ImageDescription(
         parent_image="minimal-notebook",
-        taggers=[RVersionTagger],
+        taggers=[RVersionTagger()],
-        manifests=[RPackagesManifest],
+        manifests=[RPackagesManifest()],
     ),
     "tensorflow-notebook": ImageDescription(
-        parent_image="scipy-notebook", taggers=[TensorflowVersionTagger]
+        parent_image="scipy-notebook", taggers=[TensorflowVersionTagger()]
     ),
     "datascience-notebook": ImageDescription(
         parent_image="scipy-notebook",
-        taggers=[RVersionTagger, JuliaVersionTagger],
+        taggers=[RVersionTagger(), JuliaVersionTagger()],
-        manifests=[RPackagesManifest, JuliaPackagesManifest],
+        manifests=[RPackagesManifest(), JuliaPackagesManifest()],
     ),
     "pyspark-notebook": ImageDescription(
         parent_image="scipy-notebook",
-        taggers=[SparkVersionTagger, HadoopVersionTagger, JavaVersionTagger],
+        taggers=[SparkVersionTagger(), HadoopVersionTagger(), JavaVersionTagger()],
-        manifests=[SparkInfoManifest],
+        manifests=[SparkInfoManifest()],
     ),
     "all-spark-notebook": ImageDescription(
         parent_image="pyspark-notebook",
-        taggers=[RVersionTagger],
+        taggers=[RVersionTagger()],
-        manifests=[RPackagesManifest],
+        manifests=[RPackagesManifest()],
     ),
 }

tagging/manifests.py

@@ -1,11 +1,12 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
 from plumbum.cmd import docker
+from docker.models.containers import Container
 from .docker_runner import DockerRunner
 from .git_helper import GitHelper
 
 
-def quoted_output(container, cmd: str) -> str:
+def quoted_output(container: Container, cmd: str) -> str:
     return "\n".join(
         [
             "```",
@@ -50,13 +51,13 @@ class ManifestInterface:
     """Common interface for all manifests"""
 
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         raise NotImplementedError
 
 
 class CondaEnvironmentManifest(ManifestInterface):
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         return "\n".join(
             [
                 "## Python Packages",
@@ -72,7 +73,7 @@ class CondaEnvironmentManifest(ManifestInterface):
 
 class AptPackagesManifest(ManifestInterface):
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         return "\n".join(
             [
                 "## Apt Packages",
@@ -84,7 +85,7 @@ class AptPackagesManifest(ManifestInterface):
 
 class RPackagesManifest(ManifestInterface):
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         return "\n".join(
             [
                 "## R Packages",
@@ -101,7 +102,7 @@ class RPackagesManifest(ManifestInterface):
 
 class JuliaPackagesManifest(ManifestInterface):
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         return "\n".join(
             [
                 "## Julia Packages",
@@ -118,7 +119,7 @@ class JuliaPackagesManifest(ManifestInterface):
 
 class SparkInfoManifest(ManifestInterface):
     @staticmethod
-    def markdown_piece(container) -> str:
+    def markdown_piece(container: Container) -> str:
         return "\n".join(
             [
                 "## Apache Spark",

tagging/tag_image.py

@@ -28,11 +28,11 @@ def tag_image(short_image_name: str, owner: str) -> None:
     with DockerRunner(image) as container:
         tags = []
         for tagger in taggers:
-            tagger_name = tagger.__name__
+            tagger_name = tagger.__class__.__name__
             tag_value = tagger.tag_value(container)
             tags.append(tag_value)
             LOGGER.info(
-                f"Applying tag tagger_name: {tagger_name} tag_value: {tag_value}"
+                f"Applying tag, tagger_name: {tagger_name} tag_value: {tag_value}"
             )
             docker["tag", image, f"{owner}/{short_image_name}:{tag_value}"]()
 

tagging/taggers.py

@@ -1,15 +1,16 @@
 # Copyright (c) Jupyter Development Team.
 # Distributed under the terms of the Modified BSD License.
 from datetime import datetime
+from docker.models.containers import Container
 from .git_helper import GitHelper
 from .docker_runner import DockerRunner
 
 
-def _get_program_version(container, program: str) -> str:
+def _get_program_version(container: Container, program: str) -> str:
     return DockerRunner.run_simple_command(container, cmd=f"{program} --version")
 
 
-def _get_env_variable(container, variable: str) -> str:
+def _get_env_variable(container: Container, variable: str) -> str:
     env = DockerRunner.run_simple_command(
         container,
         cmd="env",
@@ -21,7 +22,7 @@ def _get_env_variable(container, variable: str) -> str:
     raise KeyError(variable)
 
 
-def _get_pip_package_version(container, package: str) -> str:
+def _get_pip_package_version(container: Container, package: str) -> str:
     VERSION_PREFIX = "Version: "
     package_info = DockerRunner.run_simple_command(
         container,
@@ -37,25 +38,25 @@ class TaggerInterface:
     """Common interface for all taggers"""
 
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         raise NotImplementedError
 
 
 class SHATagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return GitHelper.commit_hash_tag()
 
 
 class DateTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return datetime.utcnow().strftime("%Y-%m-%d")
 
 
 class UbuntuVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         os_release = DockerRunner.run_simple_command(
             container,
             "cat /etc/os-release",
@@ -63,63 +64,64 @@ class UbuntuVersionTagger(TaggerInterface):
         for line in os_release:
             if line.startswith("VERSION_ID"):
                 return "ubuntu-" + line.split("=")[1].strip('"')
+        raise RuntimeError(f"did not find ubuntu version in: {os_release}")
 
 
 class PythonVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "python-" + _get_program_version(container, "python").split()[1]
 
 
 class JupyterNotebookVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "notebook-" + _get_program_version(container, "jupyter-notebook")
 
 
 class JupyterLabVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "lab-" + _get_program_version(container, "jupyter-lab")
 
 
 class JupyterHubVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "hub-" + _get_program_version(container, "jupyterhub")
 
 
 class RVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "r-" + _get_program_version(container, "R").split()[2]
 
 
 class TensorflowVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "tensorflow-" + _get_pip_package_version(container, "tensorflow")
 
 
 class JuliaVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "julia-" + _get_program_version(container, "julia").split()[2]
 
 
 class SparkVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "spark-" + _get_env_variable(container, "APACHE_SPARK_VERSION")
 
 
 class HadoopVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "hadoop-" + _get_env_variable(container, "HADOOP_VERSION")
 
 
 class JavaVersionTagger(TaggerInterface):
     @staticmethod
-    def tag_value(container) -> str:
+    def tag_value(container: Container) -> str:
         return "java-" + _get_program_version(container, "java").split()[1]

test/package_helper.py

@@ -27,7 +27,8 @@ from collections import defaultdict
 from itertools import chain
 import logging
 import json
-from typing import Optional
+from typing import Any, Optional
+from docker.models.containers import Container
 
 from tabulate import tabulate
 
@@ -40,14 +41,16 @@ class CondaPackageHelper:
     """Conda package helper permitting to get information about packages"""
 
     def __init__(self, container: TrackedContainer):
-        self.running_container = CondaPackageHelper.start_container(container)
+        self.running_container: Container = CondaPackageHelper.start_container(
+            container
+        )
         self.requested: Optional[dict[str, set[str]]] = None
         self.installed: Optional[dict[str, set[str]]] = None
         self.available: Optional[dict[str, set[str]]] = None
         self.comparison: list[dict[str, str]] = []
 
     @staticmethod
-    def start_container(container: TrackedContainer):
+    def start_container(container: TrackedContainer) -> Container:
         """Start the TrackedContainer and return an instance of a running container"""
         LOGGER.info(f"Starting container {container.image_name} ...")
         return container.run_detached(
@@ -85,13 +88,13 @@ class CondaPackageHelper:
             )
         return self.requested
 
-    def _execute_command(self, command):
+    def _execute_command(self, command: list[str]) -> str:
         """Execute a command on a running container"""
         rc = self.running_container.exec_run(command)
-        return rc.output.decode("utf-8")
+        return rc.output.decode("utf-8")  # type: ignore
 
     @staticmethod
-    def _packages_from_json(env_export) -> dict[str, set[str]]:
+    def _packages_from_json(env_export: str) -> dict[str, set[str]]:
         """Extract packages and versions from the lines returned by the list of specifications"""
         # dependencies = filter(lambda x:  isinstance(x, str), json.loads(env_export).get("dependencies"))
         dependencies = json.loads(env_export).get("dependencies")
@@ -114,7 +117,7 @@ class CondaPackageHelper:
             packages_dict[package] = version
         return packages_dict
 
-    def available_packages(self):
+    def available_packages(self) -> dict[str, set[str]]:
         """Return the available packages"""
         if self.available is None:
             LOGGER.info("Grabing the list of available packages (can take a while) ...")
@@ -125,11 +128,13 @@ class CondaPackageHelper:
         return self.available
 
     @staticmethod
-    def _extract_available(lines):
+    def _extract_available(lines: str) -> dict[str, set[str]]:
         """Extract packages and versions from the lines returned by the list of packages"""
         ddict = defaultdict(set)
         for line in lines.splitlines()[2:]:
-            pkg, version = re.match(r"^(\S+)\s+(\S+)", line, re.MULTILINE).groups()
+            match = re.match(r"^(\S+)\s+(\S+)", line, re.MULTILINE)
+            assert match is not None
+            pkg, version = match.groups()
             ddict[pkg].add(version)
         return ddict
 
@@ -162,11 +167,11 @@ class CondaPackageHelper:
         return self.comparison
 
     @staticmethod
-    def semantic_cmp(version_string: str):
+    def semantic_cmp(version_string: str) -> Any:
         """Manage semantic versioning for comparison"""
 
-        def mysplit(string):
+        def mysplit(string: str) -> list[Any]:
-            def version_substrs(x):
+            def version_substrs(x: str) -> list[str]:
                 return re.findall(r"([A-z]+|\d+)", x)
 
             return list(chain(map(version_substrs, string.split("."))))
@@ -189,7 +194,9 @@ class CondaPackageHelper:
 
     def get_outdated_summary(self, requested_only: bool = True) -> str:
         """Return a summary of outdated packages"""
-        nb_packages = len(self.requested if requested_only else self.installed)
+        packages = self.requested if requested_only else self.installed
+        assert packages is not None
+        nb_packages = len(packages)
         nb_updatable = len(self.comparison)
         updatable_ratio = nb_updatable / nb_packages
         return f"{nb_updatable}/{nb_packages} ({updatable_ratio:.0%}) packages could be updated"

test/test_outdated.py

@@ -3,7 +3,7 @@
 
 import logging
 
-import pytest
+import pytest  # type: ignore
 from conftest import TrackedContainer
 
 from package_helper import CondaPackageHelper
@@ -12,7 +12,9 @@ LOGGER = logging.getLogger(__name__)
 
 
 @pytest.mark.info
-def test_outdated_packages(container: TrackedContainer, requested_only: bool = True):
+def test_outdated_packages(
+    container: TrackedContainer, requested_only: bool = True
+) -> None:
     """Getting the list of updatable packages"""
     LOGGER.info(f"Checking outdated packages in {container.image_name} ...")
     pkg_helper = CondaPackageHelper(container)

test/test_packages.py

@@ -37,8 +37,9 @@ Example:
 
 import logging
 
-import pytest
+import pytest  # type: ignore
 from conftest import TrackedContainer
+from typing import Callable, Iterable
 
 from package_helper import CondaPackageHelper
 
@@ -87,7 +88,7 @@ def packages(package_helper: CondaPackageHelper) -> dict[str, set[str]]:
     return package_helper.requested_packages()
 
 
-def package_map(package: str) -> str:
+def get_package_import_name(package: str) -> str:
     """Perform a mapping between the python package name and the name used for the import"""
     return PACKAGE_MAPPING.get(package, package)
 
@@ -113,7 +114,7 @@ def _check_import_package(
     """Generic function executing a command"""
     LOGGER.debug(f"Trying to import a package with [{command}] ...")
     rc = package_helper.running_container.exec_run(command)
-    return rc.exit_code
+    return rc.exit_code  # type: ignore
 
 
 def check_import_python_package(
@@ -130,10 +131,10 @@ def check_import_r_package(package_helper: CondaPackageHelper, package: str) ->
     )
 
 
-def _import_packages(
+def _check_import_packages(
     package_helper: CondaPackageHelper,
-    filtered_packages: dict[str, set[str]],
+    filtered_packages: Iterable[str],
-    check_function,
+    check_function: Callable[[CondaPackageHelper, str], int],
     max_failures: int,
 ) -> None:
     """Test if packages can be imported
@@ -157,33 +158,36 @@ def _import_packages(
 
 
 @pytest.fixture(scope="function")
-def r_packages(packages: dict[str, set[str]]):
+def r_packages(packages: dict[str, set[str]]) -> Iterable[str]:
     """Return an iterable of R packages"""
     # package[2:] is to remove the leading "r-" appended on R packages
     return map(
-        lambda package: package_map(package[2:]), filter(r_package_predicate, packages)
+        lambda package: get_package_import_name(package[2:]),
+        filter(r_package_predicate, packages),
     )
 
 
 def test_r_packages(
-    package_helper: CondaPackageHelper, r_packages, max_failures: int = 0
+    package_helper: CondaPackageHelper, r_packages: Iterable[str], max_failures: int = 0
-):
+) -> None:
     """Test the import of specified R packages"""
-    return _import_packages(
+    _check_import_packages(
         package_helper, r_packages, check_import_r_package, max_failures
     )
 
 
 @pytest.fixture(scope="function")
-def python_packages(packages: dict[str, set[str]]):
+def python_packages(packages: dict[str, set[str]]) -> Iterable[str]:
     """Return an iterable of Python packages"""
-    return map(package_map, filter(python_package_predicate, packages))
+    return map(get_package_import_name, filter(python_package_predicate, packages))
 
 
 def test_python_packages(
-    package_helper: CondaPackageHelper, python_packages, max_failures: int = 0
+    package_helper: CondaPackageHelper,
-):
+    python_packages: Iterable[str],
+    max_failures: int = 0,
+) -> None:
     """Test the import of specified python packages"""
-    return _import_packages(
+    _check_import_packages(
         package_helper, python_packages, check_import_python_package, max_failures
     )