From 3ab6a7b86d86636c080b62ec23d75786eb77a243 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 4 Nov 2023 22:29:57 -0500
Subject: [PATCH] Clean up lint and move tests out of source (#299)

---
 .github/workflows/main.yml                    |  18 +++++---
 .pre-commit-config.yaml                       |  15 ++++++
 docs/index.rst                                |   1 -
 docs/reference/nbclient.rst                   |   4 --
 docs/reference/nbclient.tests.rst             |  38 ----------------
 nbclient/cli.py                               |   2 +-
 nbclient/client.py                            |   4 +-
 pyproject.toml                                |  43 +++++++-----------
 {nbclient/tests => tests}/__init__.py         |   0
 {nbclient/tests => tests}/base.py             |   0
 {nbclient/tests => tests}/conftest.py         |   0
 .../tests => tests}/fake_kernelmanager.py     |   0
 .../tests => tests}/files/Autokill.ipynb      |   0
 .../files/Check History in Memory.ipynb       |   0
 .../tests => tests}/files/Clear Output.ipynb  |   0
 .../tests => tests}/files/Disable Stdin.ipynb |   0
 .../tests => tests}/files/Empty Cell.ipynb    |   0
 {nbclient/tests => tests}/files/Error.ipynb   |   0
 .../tests => tests}/files/Factorials.ipynb    |   0
 .../tests => tests}/files/HelloWorld.ipynb    |   0
 .../tests => tests}/files/Inline Image.ipynb  |   0
 .../tests => tests}/files/Interrupt.ipynb     |   0
 .../files/JupyterWidgets.ipynb                |   0
 .../tests => tests}/files/Other Comms.ipynb   |   0
 {nbclient/tests => tests}/files/Output.ipynb  |   0
 .../files/Parallel Execute A.ipynb            |   0
 .../files/Parallel Execute B.ipynb            |   0
 {nbclient/tests => tests}/files/SVG.ipynb     |   0
 .../Skip Exceptions with Cell Tags.ipynb      |   0
 .../files/Skip Exceptions.ipynb               |   0
 .../files/Skip Execution with Cell Tag.ipynb  |   0
 {nbclient/tests => tests}/files/Sleep1s.ipynb |   0
 {nbclient/tests => tests}/files/Unicode.ipynb |   0
 .../tests => tests}/files/UnicodePy3.ipynb    |   0
 {nbclient/tests => tests}/files/python.png    | Bin
 .../files/update-display-id.ipynb             |   0
 {nbclient/tests => tests}/test_client.py      |   3 ++
 {nbclient/tests => tests}/test_util.py        |   0
 38 files changed, 49 insertions(+), 79 deletions(-)
 delete mode 100644 docs/reference/nbclient.tests.rst
 rename {nbclient/tests => tests}/__init__.py (100%)
 rename {nbclient/tests => tests}/base.py (100%)
 rename {nbclient/tests => tests}/conftest.py (100%)
 rename {nbclient/tests => tests}/fake_kernelmanager.py (100%)
 rename {nbclient/tests => tests}/files/Autokill.ipynb (100%)
 rename {nbclient/tests => tests}/files/Check History in Memory.ipynb (100%)
 rename {nbclient/tests => tests}/files/Clear Output.ipynb (100%)
 rename {nbclient/tests => tests}/files/Disable Stdin.ipynb (100%)
 rename {nbclient/tests => tests}/files/Empty Cell.ipynb (100%)
 rename {nbclient/tests => tests}/files/Error.ipynb (100%)
 rename {nbclient/tests => tests}/files/Factorials.ipynb (100%)
 rename {nbclient/tests => tests}/files/HelloWorld.ipynb (100%)
 rename {nbclient/tests => tests}/files/Inline Image.ipynb (100%)
 rename {nbclient/tests => tests}/files/Interrupt.ipynb (100%)
 rename {nbclient/tests => tests}/files/JupyterWidgets.ipynb (100%)
 rename {nbclient/tests => tests}/files/Other Comms.ipynb (100%)
 rename {nbclient/tests => tests}/files/Output.ipynb (100%)
 rename {nbclient/tests => tests}/files/Parallel Execute A.ipynb (100%)
 rename {nbclient/tests => tests}/files/Parallel Execute B.ipynb (100%)
 rename {nbclient/tests => tests}/files/SVG.ipynb (100%)
 rename {nbclient/tests => tests}/files/Skip Exceptions with Cell Tags.ipynb (100%)
 rename {nbclient/tests => tests}/files/Skip Exceptions.ipynb (100%)
 rename {nbclient/tests => tests}/files/Skip Execution with Cell Tag.ipynb (100%)
 rename {nbclient/tests => tests}/files/Sleep1s.ipynb (100%)
 rename {nbclient/tests => tests}/files/Unicode.ipynb (100%)
 rename {nbclient/tests => tests}/files/UnicodePy3.ipynb (100%)
 rename {nbclient/tests => tests}/files/python.png (100%)
 rename {nbclient/tests => tests}/files/update-display-id.ipynb (100%)
 rename {nbclient/tests => tests}/test_client.py (99%)
 rename {nbclient/tests => tests}/test_util.py (100%)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bbec63ed..1663b379 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Run Linters
         run: |
           hatch run typing:test
-          hatch run lint:style
+          hatch run lint:build
           pipx run interrogate -v .
           pipx run doc8 --max-line-length=200
 
@@ -41,13 +41,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        exclude:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.11"]
+        include:
           - os: windows-latest
-            python-version: 3.8
-          - os: windows-latest
-            python-version: 3.9
+            python-version: "3.9"
+          - os: ubuntu-latest
+            python-version: "pypy-3.8"
+          - os: ubuntu-latest
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.10"
     steps:
       - name: Checkout
         uses: actions/checkout@v4
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 12f2648f..379f2cba 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -57,6 +57,21 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
 
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.6.1"
+    hooks:
+      - id: mypy
+        files: "^nbclient"
+        stages: [manual]
+        args: ["--install-types", "--non-interactive"]
+        additional_dependencies:
+          [
+            "traitlets>=5.13",
+            "jupyter_core>=5.3.2",
+            "jupyter_client",
+            "nbformat",
+          ]
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.1.3
     hooks:
diff --git a/docs/index.rst b/docs/index.rst
index e7992871..adab3887 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -64,7 +64,6 @@ this documentation section will help you.
    :caption: Table of Contents
 
    reference/index.rst
-   reference/nbclient.tests.rst
 
 Indices and tables
 ------------------
diff --git a/docs/reference/nbclient.rst b/docs/reference/nbclient.rst
index 636e7e60..e5744087 100644
--- a/docs/reference/nbclient.rst
+++ b/docs/reference/nbclient.rst
@@ -4,10 +4,6 @@ nbclient package
 Subpackages
 -----------
 
-.. toctree::
-
-   nbclient.tests
-
 Submodules
 ----------
 
diff --git a/docs/reference/nbclient.tests.rst b/docs/reference/nbclient.tests.rst
deleted file mode 100644
index 8ede97f1..00000000
--- a/docs/reference/nbclient.tests.rst
+++ /dev/null
@@ -1,38 +0,0 @@
-nbclient.tests package
-======================
-
-Submodules
-----------
-
-nbclient.tests.base module
---------------------------
-
-.. automodule:: nbclient.tests.base
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nbclient.tests.fake\_kernelmanager module
------------------------------------------
-
-.. automodule:: nbclient.tests.fake_kernelmanager
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-nbclient.tests.test\_client module
-----------------------------------
-
-.. automodule:: nbclient.tests.test_client
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: nbclient.tests
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/nbclient/cli.py b/nbclient/cli.py
index afe587fa..2151095f 100644
--- a/nbclient/cli.py
+++ b/nbclient/cli.py
@@ -47,7 +47,7 @@ class NbClientApp(JupyterApp):
     flags = nbclient_flags
 
     description = "An application used to execute notebook files (*.ipynb)"
-    notebooks = List([], help="Path of notebooks to convert").tag(config=True)
+    notebooks = List(Unicode(), help="Path of notebooks to convert").tag(config=True)
     timeout = Integer(
         None,
         allow_none=True,
diff --git a/nbclient/client.py b/nbclient/client.py
index 0b42dc2b..794f630c 100644
--- a/nbclient/client.py
+++ b/nbclient/client.py
@@ -494,9 +494,9 @@ def create_kernel_manager(self) -> KernelManager:
                 self.kernel_name = kn
 
         if not self.kernel_name:
-            self.km = self.kernel_manager_class(config=self.config)  # type:ignore[operator]
+            self.km = self.kernel_manager_class(config=self.config)
         else:
-            self.km = self.kernel_manager_class(kernel_name=self.kernel_name, config=self.config)  # type:ignore[operator]
+            self.km = self.kernel_manager_class(kernel_name=self.kernel_name, config=self.config)
         assert self.km is not None
         return self.km
 
diff --git a/pyproject.toml b/pyproject.toml
index 4e973f57..d53e5f38 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,6 +84,7 @@ path = "nbclient/_version.py"
 [tool.hatch.build.targets.sdist]
 include = [
     "/nbclient",
+    "/tests"
 ]
 
 [tool.hatch.envs.docs]
@@ -104,40 +105,27 @@ dependencies = ["coverage[toml]", "pytest-cov"]
 test = "python -m pytest -vv --cov nbclient --cov-branch --cov-report term-missing:skip-covered {args}"
 nowarn = "test -W default {args}"
 
-[tool.hatch.envs.typing]
-features = ["test"]
-dependencies = ["mypy~=1.6", "traitlets>=5.11.2", "jupyter_core>=5.3.2"]
-[tool.hatch.envs.typing.scripts]
-test = "mypy --install-types --non-interactive {args}"
-
 [tool.hatch.envs.lint]
-dependencies = [
-  "mdformat>0.7",
-  "mdformat-gfm>=0.3.5",
-  "ruff==0.1.3"
-]
 detached = true
+dependencies = ["pre-commit"]
 [tool.hatch.envs.lint.scripts]
-style = [
-  "ruff {args:.}",
-  "ruff format {args:.}",
-  "mdformat --check {args:docs *.md}"
-]
-fmt = [
-  "ruff --fix {args:.}",
-  "ruff format {args:.}",
-  "mdformat {args:docs *.md}"
-]
+build = "pre-commit run --all-files ruff"
+
+[tool.hatch.envs.typing]
+dependencies = [ "pre-commit"]
+detached = true
+[tool.hatch.envs.typing.scripts]
+test = "pre-commit run --all-files --hook-stage manual mypy"
 
 [tool.pytest.ini_options]
 minversion = "6.0"
 xfail_strict = true
 log_cli_level = "info"
 addopts = [
-  "-raXs", "--durations=10", "--color=yes", "--doctest-modules",
+  "-ra", "--durations=10", "--color=yes", "--doctest-modules",
    "--showlocals", "--strict-markers", "--strict-config"
 ]
-testpaths = ["nbclient/tests"]
+testpaths = ["tests"]
 filterwarnings= [
   # Fail on warnings
   "error",
@@ -146,7 +134,10 @@ filterwarnings= [
   "module:There is no current event loop:DeprecationWarning",
   "module:unclosed event loop:ResourceWarning",
   "module:Unclosed socket <zmq:ResourceWarning",
+  "module:zmq.eventloop.ioloop is deprecated:DeprecationWarning",
   "module:subprocess .* is still running:ResourceWarning",
+  "module:Unclosed context <zmq:ResourceWarning",
+  "module:datetime.datetime.utc:DeprecationWarning",
 ]
 asyncio_mode = "auto"
 
@@ -204,7 +195,7 @@ ignore = [
 
 [tool.ruff.lint.per-file-ignores]
 # S101 Use of `assert` detected
-"nbclient/tests/*" = ["S101"]
+"tests/*" = ["S101"]
 "nbclient/client.py" = ["S101"]
 
 [tool.interrogate]
@@ -215,7 +206,7 @@ ignore-property-decorators=true
 ignore-nested-functions=true
 ignore-nested-classes=true
 fail-under=100
-exclude = ["nbclient/tests", "docs"]
+exclude = ["tests", "docs"]
 
 [tool.repo-review]
-ignore = ["PY005", "PY007", "PP308", "GH102", "PC140"]
+ignore = ["PY005", "PY007", "GH102"]
diff --git a/nbclient/tests/__init__.py b/tests/__init__.py
similarity index 100%
rename from nbclient/tests/__init__.py
rename to tests/__init__.py
diff --git a/nbclient/tests/base.py b/tests/base.py
similarity index 100%
rename from nbclient/tests/base.py
rename to tests/base.py
diff --git a/nbclient/tests/conftest.py b/tests/conftest.py
similarity index 100%
rename from nbclient/tests/conftest.py
rename to tests/conftest.py
diff --git a/nbclient/tests/fake_kernelmanager.py b/tests/fake_kernelmanager.py
similarity index 100%
rename from nbclient/tests/fake_kernelmanager.py
rename to tests/fake_kernelmanager.py
diff --git a/nbclient/tests/files/Autokill.ipynb b/tests/files/Autokill.ipynb
similarity index 100%
rename from nbclient/tests/files/Autokill.ipynb
rename to tests/files/Autokill.ipynb
diff --git a/nbclient/tests/files/Check History in Memory.ipynb b/tests/files/Check History in Memory.ipynb
similarity index 100%
rename from nbclient/tests/files/Check History in Memory.ipynb
rename to tests/files/Check History in Memory.ipynb
diff --git a/nbclient/tests/files/Clear Output.ipynb b/tests/files/Clear Output.ipynb
similarity index 100%
rename from nbclient/tests/files/Clear Output.ipynb
rename to tests/files/Clear Output.ipynb
diff --git a/nbclient/tests/files/Disable Stdin.ipynb b/tests/files/Disable Stdin.ipynb
similarity index 100%
rename from nbclient/tests/files/Disable Stdin.ipynb
rename to tests/files/Disable Stdin.ipynb
diff --git a/nbclient/tests/files/Empty Cell.ipynb b/tests/files/Empty Cell.ipynb
similarity index 100%
rename from nbclient/tests/files/Empty Cell.ipynb
rename to tests/files/Empty Cell.ipynb
diff --git a/nbclient/tests/files/Error.ipynb b/tests/files/Error.ipynb
similarity index 100%
rename from nbclient/tests/files/Error.ipynb
rename to tests/files/Error.ipynb
diff --git a/nbclient/tests/files/Factorials.ipynb b/tests/files/Factorials.ipynb
similarity index 100%
rename from nbclient/tests/files/Factorials.ipynb
rename to tests/files/Factorials.ipynb
diff --git a/nbclient/tests/files/HelloWorld.ipynb b/tests/files/HelloWorld.ipynb
similarity index 100%
rename from nbclient/tests/files/HelloWorld.ipynb
rename to tests/files/HelloWorld.ipynb
diff --git a/nbclient/tests/files/Inline Image.ipynb b/tests/files/Inline Image.ipynb
similarity index 100%
rename from nbclient/tests/files/Inline Image.ipynb
rename to tests/files/Inline Image.ipynb
diff --git a/nbclient/tests/files/Interrupt.ipynb b/tests/files/Interrupt.ipynb
similarity index 100%
rename from nbclient/tests/files/Interrupt.ipynb
rename to tests/files/Interrupt.ipynb
diff --git a/nbclient/tests/files/JupyterWidgets.ipynb b/tests/files/JupyterWidgets.ipynb
similarity index 100%
rename from nbclient/tests/files/JupyterWidgets.ipynb
rename to tests/files/JupyterWidgets.ipynb
diff --git a/nbclient/tests/files/Other Comms.ipynb b/tests/files/Other Comms.ipynb
similarity index 100%
rename from nbclient/tests/files/Other Comms.ipynb
rename to tests/files/Other Comms.ipynb
diff --git a/nbclient/tests/files/Output.ipynb b/tests/files/Output.ipynb
similarity index 100%
rename from nbclient/tests/files/Output.ipynb
rename to tests/files/Output.ipynb
diff --git a/nbclient/tests/files/Parallel Execute A.ipynb b/tests/files/Parallel Execute A.ipynb
similarity index 100%
rename from nbclient/tests/files/Parallel Execute A.ipynb
rename to tests/files/Parallel Execute A.ipynb
diff --git a/nbclient/tests/files/Parallel Execute B.ipynb b/tests/files/Parallel Execute B.ipynb
similarity index 100%
rename from nbclient/tests/files/Parallel Execute B.ipynb
rename to tests/files/Parallel Execute B.ipynb
diff --git a/nbclient/tests/files/SVG.ipynb b/tests/files/SVG.ipynb
similarity index 100%
rename from nbclient/tests/files/SVG.ipynb
rename to tests/files/SVG.ipynb
diff --git a/nbclient/tests/files/Skip Exceptions with Cell Tags.ipynb b/tests/files/Skip Exceptions with Cell Tags.ipynb
similarity index 100%
rename from nbclient/tests/files/Skip Exceptions with Cell Tags.ipynb
rename to tests/files/Skip Exceptions with Cell Tags.ipynb
diff --git a/nbclient/tests/files/Skip Exceptions.ipynb b/tests/files/Skip Exceptions.ipynb
similarity index 100%
rename from nbclient/tests/files/Skip Exceptions.ipynb
rename to tests/files/Skip Exceptions.ipynb
diff --git a/nbclient/tests/files/Skip Execution with Cell Tag.ipynb b/tests/files/Skip Execution with Cell Tag.ipynb
similarity index 100%
rename from nbclient/tests/files/Skip Execution with Cell Tag.ipynb
rename to tests/files/Skip Execution with Cell Tag.ipynb
diff --git a/nbclient/tests/files/Sleep1s.ipynb b/tests/files/Sleep1s.ipynb
similarity index 100%
rename from nbclient/tests/files/Sleep1s.ipynb
rename to tests/files/Sleep1s.ipynb
diff --git a/nbclient/tests/files/Unicode.ipynb b/tests/files/Unicode.ipynb
similarity index 100%
rename from nbclient/tests/files/Unicode.ipynb
rename to tests/files/Unicode.ipynb
diff --git a/nbclient/tests/files/UnicodePy3.ipynb b/tests/files/UnicodePy3.ipynb
similarity index 100%
rename from nbclient/tests/files/UnicodePy3.ipynb
rename to tests/files/UnicodePy3.ipynb
diff --git a/nbclient/tests/files/python.png b/tests/files/python.png
similarity index 100%
rename from nbclient/tests/files/python.png
rename to tests/files/python.png
diff --git a/nbclient/tests/files/update-display-id.ipynb b/tests/files/update-display-id.ipynb
similarity index 100%
rename from nbclient/tests/files/update-display-id.ipynb
rename to tests/files/update-display-id.ipynb
diff --git a/nbclient/tests/test_client.py b/tests/test_client.py
similarity index 99%
rename from nbclient/tests/test_client.py
rename to tests/test_client.py
index 54197df7..bca96981 100644
--- a/nbclient/tests/test_client.py
+++ b/tests/test_client.py
@@ -352,6 +352,7 @@ def test_run_all_notebooks(input_name, opts):
     assert_notebooks_equal(input_nb, output_nb)
 
 
+@flaky
 def test_parallel_notebooks(capfd, tmpdir):
     """Two notebooks should be able to be run simultaneously without problems.
 
@@ -377,6 +378,7 @@ def test_parallel_notebooks(capfd, tmpdir):
     assert filter_messages_on_error_output(captured.err) == ""
 
 
+@flaky
 @pytest.mark.skipif(os.name == "nt", reason="warns about event loop on Windows")
 def test_many_parallel_notebooks(capfd):
     """Ensure that when many IPython kernels are run in parallel, nothing awful happens.
@@ -404,6 +406,7 @@ def test_many_parallel_notebooks(capfd):
     assert filter_messages_on_error_output(captured.err) == ""
 
 
+@flaky
 def test_async_parallel_notebooks(capfd, tmpdir):
     """Two notebooks should be able to be run simultaneously without problems.
 
diff --git a/nbclient/tests/test_util.py b/tests/test_util.py
similarity index 100%
rename from nbclient/tests/test_util.py
rename to tests/test_util.py