python312Packages.papermill: fix, cleanup (#400928)

pkgs/development/python-modules/bash-kernel/default.nix

@@ -1,14 +1,15 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
+  replaceVars,
+  bashInteractive,
   flit-core,
   filetype,
   ipykernel,
-  python,
   pexpect,
-  bashInteractive,
-  replaceVars,
+  writableTmpDirAsHomeHook,
+  python,
 }:
 
 buildPythonPackage rec {
@@ -16,10 +17,11 @@ buildPythonPackage rec {
   version = "0.10.0";
   pyproject = true;
 
-  src = fetchPypi {
-    pname = "bash_kernel";
-    inherit version;
-    hash = "sha256-LtWgpBbEGNHXUecVBb1siJ4SFXREtQxCh6aF2ndcKMo=";
+  src = fetchFromGitHub {
+    owner = "takluyver";
+    repo = "bash_kernel";
+    tag = version;
+    hash = "sha256-ugFMcQx1B1nKoO9rhb6PMllRcoZi0O4B9um8dOu5DU4=";
   };
 
   patches = [
@@ -36,9 +38,9 @@ buildPythonPackage rec {
     pexpect
   ];
 
-  preBuild = ''
-    export HOME=$TMPDIR
-  '';
+  nativeBuildInputs = [
+    writableTmpDirAsHomeHook
+  ];
 
   postInstall = ''
     ${python.pythonOnBuildForHost.interpreter} -m bash_kernel.install --prefix $out
@@ -59,6 +61,8 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
+  __darwinAllowLocalNetworking = true;
+
   meta = {
     description = "Bash Kernel for Jupyter";
     homepage = "https://github.com/takluyver/bash_kernel";

pkgs/development/python-modules/papermill/default.nix

@@ -1,32 +1,41 @@
 {
   lib,
   stdenv,
-  aiohttp,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   ansicolors,
+  click,
+  entrypoints,
+  nbclient,
+  nbformat,
+  pyyaml,
+  requests,
+  tenacity,
+  tqdm,
+  pythonAtLeast,
+  aiohttp,
+
+  # optional-dependencies
   azure-datalake-store,
   azure-identity,
   azure-storage-blob,
-  boto3,
-  buildPythonPackage,
-  click,
-  entrypoints,
-  fetchFromGitHub,
   gcsfs,
+  pygithub,
+  pyarrow,
+  boto3,
+
+  # tests
   ipykernel,
   moto,
-  nbclient,
-  nbformat,
-  pyarrow,
-  pygithub,
   pytest-mock,
   pytestCheckHook,
-  pythonAtLeast,
-  pythonOlder,
-  pyyaml,
-  requests,
-  setuptools,
-  tenacity,
-  tqdm,
+  versionCheckHook,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
@@ -34,8 +43,6 @@ buildPythonPackage rec {
   version = "2.6.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
   src = fetchFromGitHub {
     owner = "nteract";
     repo = "papermill";
@@ -46,15 +53,15 @@ buildPythonPackage rec {
   build-system = [ setuptools ];
 
   dependencies = [
-    click
-    pyyaml
-    nbformat
-    nbclient
-    tqdm
-    requests
-    entrypoints
-    tenacity
     ansicolors
+    click
+    entrypoints
+    nbclient
+    nbformat
+    pyyaml
+    requests
+    tenacity
+    tqdm
   ] ++ lib.optionals (pythonAtLeast "3.12") [ aiohttp ];
 
   optional-dependencies = {
@@ -75,17 +82,25 @@ buildPythonPackage rec {
       moto
       pytest-mock
       pytestCheckHook
+      versionCheckHook
+      writableTmpDirAsHomeHook
     ]
     ++ optional-dependencies.azure
     ++ optional-dependencies.s3
     ++ optional-dependencies.gcs;
-
-  preCheck = ''
-    export HOME=$(mktemp -d)
-  '';
+  versionCheckProgramArg = "--version";
 
   pythonImportsCheck = [ "papermill" ];
 
+  # Using pytestFlagsArray to prevent disabling false positives
+  pytestFlagsArray = [
+    # AssertionError: 'error' != 'display_data'
+    "--deselect=papermill/tests/test_execute.py::TestBrokenNotebook2::test"
+
+    # AssertionError: '\x1b[31mSystemExit\x1b[39m\x1b[31m:\x1b[39m 1\n' != '\x1b[0;31mSystemExit\x1b[0m\x1b[0;31m:\x1b[0m 1\n'
+    "--deselect=papermill/tests/test_execute.py::TestOutputFormatting::test_output_formatting"
+  ];
+
   disabledTests =
     [
       # pytest 8 compat
@@ -103,10 +118,11 @@ buildPythonPackage rec {
 
   __darwinAllowLocalNetworking = true;
 
-  meta = with lib; {
+  meta = {
     description = "Parametrize and run Jupyter and interact with notebooks";
     homepage = "https://github.com/nteract/papermill";
-    license = licenses.bsd3;
+    changelog = "https://papermill.readthedocs.io/en/latest/changelog.html";
+    license = lib.licenses.bsd3;
     maintainers = [ ];
     mainProgram = "papermill";
   };