Merge pull request #244209 from dotlambda/jupyterlab-4.0.3

python310Packages.jupyterlab: 3.6.3 -> 4.0.3

pkgs/development/python-modules/experiment-utilities/default.nix

@@ -5,6 +5,7 @@
 , fasteners
 , fetchFromGitLab
 , qgrid
+, ipynbname
 , ipywidgets
 , odfpy
 , scipy
@@ -28,6 +29,10 @@ buildPythonPackage rec {
     hash = "sha256-zjmmLUpGjUhpw2+stLJE6cImesnBSvrcid5bHMftX/Q=";
   };
 
+  patches = [
+    ./unvendor-ipynbname.patch
+  ];
+
   # This dependency constraint (<=7.6.5) was due to a bug in qgrid that has been patched in its
   # owned derivation
   postPatch = ''
@@ -39,6 +44,7 @@ buildPythonPackage rec {
     cloudpickle
     dill
     fasteners
+    ipynbname
     ipywidgets
     odfpy
     plotly

pkgs/development/python-modules/experiment-utilities/unvendor-ipynbname.patch

@@ -0,0 +1,117 @@
+diff --git a/exputils/gui/jupyter/__init__.py b/exputils/gui/jupyter/__init__.py
+index 6e9aefb..fdfdd28 100644
+--- a/exputils/gui/jupyter/__init__.py
++++ b/exputils/gui/jupyter/__init__.py
+@@ -30,8 +30,8 @@ from exputils.gui.jupyter.misc import remove_children_from_widget
+ from exputils.gui.jupyter.misc import set_children_of_widget
+ from exputils.gui.jupyter.misc import generate_random_state_backup_name
+ 
+-from exputils.gui.jupyter.ipynbname import get_notebook_name
+-from exputils.gui.jupyter.ipynbname import get_notebook_path
++from ipynbname import name as get_notebook_name
++from ipynbname import path as get_notebook_path
+ 
+ DEFAULT_CONFIG_DIRECTORY = '.ipython_config'
+ 
+diff --git a/exputils/gui/jupyter/ipynbname.py b/exputils/gui/jupyter/ipynbname.py
+deleted file mode 100644
+index 51e21b7..0000000
+--- a/exputils/gui/jupyter/ipynbname.py
++++ /dev/null
+@@ -1,86 +0,0 @@
+-##
+-## This file is part of the exputils package.
+-##
+-## Copyright: INRIA
+-## Year: 2022, 2023
+-## Contact: chris.reinke@inria.fr
+-##
+-## exputils is provided under GPL-3.0-or-later
+-##
+-# Taken from https://pypi.org/project/ipynbname/
+-# TODO: add them to licence
+-
+-from notebook import notebookapp
+-import urllib, json, os, ipykernel, ntpath
+-
+-FILE_ERROR = "Can't identify the notebook {}."
+-CONN_ERROR = "Unable to access server;\n \
+-            + ipynbname requires either no security or token based security."
+-
+-def _get_kernel_id():
+-    """ Returns the kernel ID of the ipykernel.
+-    """
+-    connection_file = os.path.basename(ipykernel.get_connection_file())
+-    kernel_id = connection_file.split('-', 1)[1].split('.')[0]
+-    return kernel_id
+-
+-
+-def _get_sessions(srv):
+-    """ Given a server, returns sessions, or HTTPError if access is denied.
+-        NOTE: Works only when either there is no security or there is token
+-        based security. An HTTPError is raised if unable to connect to a
+-        server.
+-    """
+-    try:
+-        qry_str = ""
+-        token = srv['token']
+-        if token:
+-            qry_str = f"?token={token}"
+-        url = f"{srv['url']}api/sessions{qry_str}"
+-        req = urllib.request.urlopen(url)
+-        return json.load(req)
+-    except:
+-        raise urllib.error.HTTPError(CONN_ERROR)
+-
+-
+-def _get_nb_path(sess, kernel_id):
+-    """ Given a session and kernel ID, returns the notebook path for the
+-        session, or None if there is no notebook for the session.
+-    """
+-    if sess['kernel']['id'] == kernel_id:
+-        return sess['notebook']['path']
+-    return None
+-
+-
+-def get_notebook_name():
+-    """ Returns the short name of the notebook w/o the .ipynb extension,
+-        or raises a FileNotFoundError exception if it cannot be determined.
+-    """
+-    kernel_id = _get_kernel_id()
+-    for srv in notebookapp.list_running_servers():
+-        try:
+-            sessions = _get_sessions(srv)
+-            for sess in sessions:
+-                nb_path = _get_nb_path(sess, kernel_id)
+-                if nb_path:
+-                    return ntpath.basename(nb_path).replace('.ipynb', '')
+-        except:
+-            pass  # There may be stale entries in the runtime directory
+-    raise FileNotFoundError(FILE_ERROR.format('name'))
+-
+-
+-def get_notebook_path():
+-    """ Returns the absolute path of the notebook,
+-        or raises a FileNotFoundError exception if it cannot be determined.
+-    """
+-    kernel_id = _get_kernel_id()
+-    for srv in notebookapp.list_running_servers():
+-        try:
+-            sessions = _get_sessions(srv)
+-            for sess in sessions:
+-                nb_path = _get_nb_path(sess, kernel_id)
+-                if nb_path:
+-                    return os.path.join(srv['notebook_dir'], nb_path)
+-        except:
+-            pass  # There may be stale entries in the runtime directory
+-    raise FileNotFoundError(FILE_ERROR.format('path'))
+\ No newline at end of file
+diff --git a/setup.cfg b/setup.cfg
+index 9d9cbb0..6080ed6 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -25,3 +25,4 @@ install_requires =
+   tensorboard >= 1.15.0
+   fasteners >= 0.18
+   pyyaml >= 6.0
++  ipynbname

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

@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, ipykernel
+}:
+
+buildPythonPackage rec {
+  pname = "ipynbname";
+  version = "2023.2.0.0";
+  format = "setuptools";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-Riu915VmJIdtxOqB+nkoRas4cOREyh9res2uo32Mnr8=";
+  };
+
+  propagatedBuildInputs = [
+    ipykernel
+  ];
+
+  pythonImportsCheck = [ "ipynbname" ];
+
+  # upstream has no tests
+  doCheck = false;
+
+  meta = {
+    description = "Simply returns either notebook filename or the full path to the notebook";
+    homepage = "https://github.com/msm1089/ipynbname";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ dotlambda ];
+  };
+}

pkgs/development/python-modules/jupyter-collaboration/default.nix

@@ -1,29 +1,33 @@
 { lib
 , buildPythonPackage
 , pythonOlder
-, fetchFromGitHub
+, fetchPypi
+, hatch-jupyter-builder
+, hatch-nodejs-version
 , hatchling
 , pythonRelaxDepsHook
+, jupyter-events
+, jupyter-server
 , jupyter-server-fileid
 , jupyter-ydoc
 , ypy-websocket
+, pytest-asyncio
 , pytest-jupyter
 , pytestCheckHook
 }:
 
 buildPythonPackage rec {
-  pname = "jupyter-server-ydoc";
-  version = "0.8.0";
+  pname = "jupyter-collaboration";
+  version = "1.0.1";
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   format = "pyproject";
 
-  src = fetchFromGitHub {
-    owner = "jupyterlab";
-    repo = "jupyter_collaboration";
-    rev = "refs/tags/v${version}";
-    hash = "sha256-KLb7kU5jsj6ihGO6HU3Y7uF+0PcwKoQlqQAhtO0oaJw=";
+  src = fetchPypi {
+    pname = "jupyter_collaboration";
+    inherit version;
+    hash = "sha256-cf7BpF6WSoHQJQW0IXdpCAGTdkX9RNWZ4JovTHvcPho=";
   };
 
   postPatch = ''
@@ -31,6 +35,8 @@ buildPythonPackage rec {
   '';
 
   nativeBuildInputs = [
+    hatch-jupyter-builder
+    hatch-nodejs-version
     hatchling
     pythonRelaxDepsHook
   ];
@@ -40,14 +46,17 @@ buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = [
+    jupyter-events
+    jupyter-server
     jupyter-server-fileid
     jupyter-ydoc
     ypy-websocket
   ];
 
-  pythonImportsCheck = [ "jupyter_server_ydoc" ];
+  pythonImportsCheck = [ "jupyter_collaboration" ];
 
   nativeCheckInputs = [
+    pytest-asyncio
     pytest-jupyter
     pytestCheckHook
   ];
@@ -57,10 +66,10 @@ buildPythonPackage rec {
   '';
 
   meta = {
-    changelog = "https://github.com/jupyterlab/jupyter_collaboration/blob/${src.rev}/CHANGELOG.md";
-    description = "A Jupyter Server Extension Providing Y Documents";
+    changelog = "https://github.com/jupyterlab/jupyter_collaboration/blob/v${version}/CHANGELOG.md";
+    description = "JupyterLab Extension enabling Real-Time Collaboration";
     homepage = "https://github.com/jupyterlab/jupyter_collaboration";
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ dotlambda ];
+    maintainers = lib.teams.jupyter.members;
   };
 }

pkgs/development/python-modules/jupyter-nbextensions-configurator/default.nix

@@ -1,7 +1,13 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, fetchpatch
 , jupyter-contrib-core
+, jupyter-core
+, jupyter-server
+, notebook
+, pyyaml
+, tornado
 }:
 
 buildPythonPackage rec {
@@ -15,7 +21,23 @@ buildPythonPackage rec {
     hash = "sha256-ovKYHATRAC5a5qTMv32ohU2gJd15/fRKXa5HI0zGp/0=";
   };
 
-  propagatedBuildInputs = [ jupyter-contrib-core ];
+  patches = [
+    # https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator/pull/166
+    (fetchpatch {
+      name = "notebook-v7-compat.patch";
+      url = "https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator/commit/a600cef9222ca0c61a6912eb29d8fa0323409705.patch";
+      hash = "sha256-Rt9r5ZOgnhBcs18+ET5+k0/t980I2DiVN8oHkGLp0iw=";
+    })
+  ];
+
+  propagatedBuildInputs = [
+    jupyter-contrib-core
+    jupyter-core
+    jupyter-server
+    notebook
+    pyyaml
+    tornado
+  ];
 
   pythonImportsCheck = [ "jupyter_nbextensions_configurator" ];
 

pkgs/development/python-modules/jupyter-server/default.nix

@@ -23,24 +23,27 @@
 , jupyter-server-terminals
 , nbformat
 , nbconvert
+, packaging
 , send2trash
 , terminado
 , prometheus-client
 , anyio
 , websocket-client
+, overrides
 , requests
+, flaky
 }:
 
 buildPythonPackage rec {
   pname = "jupyter-server";
-  version = "2.0.6";
+  version = "2.7.0";
   format = "pyproject";
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     pname = "jupyter_server";
     inherit version;
-    hash= "sha256-jddZkukLfKVWeUoe1cylEmPGl6vG0N9WGvV0qhwKAz8=";
+    hash = "sha256-NtoKJm0xpBrDNaNmyIkzwX36W7gXpI9cAsFtMDvJR38=";
   };
 
   nativeBuildInputs = [
@@ -60,22 +63,23 @@ buildPythonPackage rec {
     jupyter-server-terminals
     nbformat
     nbconvert
+    packaging
     send2trash
     terminado
     prometheus-client
     anyio
     websocket-client
+    overrides
   ];
 
   nativeCheckInputs = [
     ipykernel
-    pandoc
     pytestCheckHook
     pytest-console-scripts
     pytest-jupyter
     pytest-timeout
-    pytest-tornasync
     requests
+    flaky
   ];
 
   preCheck = ''
@@ -85,11 +89,16 @@ buildPythonPackage rec {
 
   disabledTests = [
     "test_cull_idle"
+    "test_server_extension_list"
   ] ++ lib.optionals stdenv.isDarwin [
     # attempts to use trashcan, build env doesn't allow this
     "test_delete"
     # test is presumable broken in sandbox
     "test_authorized_requests"
+    # Insufficient access privileges for operation
+    "test_regression_is_hidden"
+  ] ++ lib.optionals (stdenv.isLinux && stdenv.isAarch64) [
+    "test_copy_big_dir"
   ];
 
   disabledTestPaths = [
@@ -103,9 +112,10 @@ buildPythonPackage rec {
   __darwinAllowLocalNetworking = true;
 
   meta = with lib; {
+    changelog = "https://github.com/jupyter-server/jupyter_server/blob/v${version}/CHANGELOG.md";
     description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications";
     homepage = "https://github.com/jupyter-server/jupyter_server";
     license = licenses.bsdOriginal;
-    maintainers = [ maintainers.elohmeier ];
+    maintainers = lib.teams.jupyter.members;
   };
 }

pkgs/development/python-modules/jupyter-ydoc/default.nix

@@ -11,14 +11,14 @@
 
 buildPythonPackage rec {
   pname = "jupyter-ydoc";
-  version = "0.3.4";
+  version = "1.0.2";
 
   format = "pyproject";
 
   src = fetchPypi {
     pname = "jupyter_ydoc";
     inherit version;
-    hash = "sha256-WiJi5wvwBLgsxs5xZ16TMKoFj+MNsuh82BJa1N0a5OE=";
+    hash = "sha256-D5W+3j8eCB4H1cV8A8ZY46Ukfg7xiIkHT776IN0+ylM=";
   };
 
   nativeBuildInputs = [
@@ -46,6 +46,6 @@ buildPythonPackage rec {
     description = "Document structures for collaborative editing using Ypy";
     homepage = "https://github.com/jupyter-server/jupyter_ydoc";
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ dotlambda ];
+    maintainers = lib.teams.jupyter.members;
   };
 }

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

@@ -1,54 +1,50 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, ipython
+, hatch-jupyter-builder
+, hatchling
+, async-lru
 , packaging
 , tornado
+, ipykernel
 , jupyter-core
+, jupyter-lsp
 , jupyterlab_server
 , jupyter-server
-, jupyter-server-ydoc
-, notebook
+, notebook-shim
 , jinja2
 , tomli
 , pythonOlder
 , jupyter-packaging
-, pythonRelaxDepsHook
-, nbclassic
 }:
 
 buildPythonPackage rec {
   pname = "jupyterlab";
-  version = "3.6.3";
-  format = "setuptools";
+  version = "4.0.3";
+  format = "pyproject";
 
-  disabled = pythonOlder "3.7";
+  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-Nz6c+4py7dKUvhTxZmJWOiIM7PD7Jt56qxr5optom4I=";
+    hash = "sha256-4U0c5GphMCgRHQ1Hah19awlAA7dGK6xmn1tHgxeryzk=";
   };
 
   nativeBuildInputs = [
-    jupyter-packaging
-    pythonRelaxDepsHook
-  ];
-
-  pythonRelaxDeps = [
-    "jupyter-ydoc"
-    "jupyter-server-ydoc"
+    hatch-jupyter-builder
+    hatchling
   ];
 
   propagatedBuildInputs = [
-    ipython
+    async-lru
     packaging
     tornado
+    ipykernel
     jupyter-core
+    jupyter-lsp
     jupyterlab_server
     jupyter-server
-    jupyter-server-ydoc
-    nbclassic
-    notebook
+    notebook-shim
     jinja2
   ] ++ lib.optionals (pythonOlder "3.11") [
     tomli
@@ -68,10 +64,10 @@ buildPythonPackage rec {
   ];
 
   meta = with lib; {
-    changelog = "https://github.com/jupyterlab/jupyterlab/releases/tag/v${version}";
+    changelog = "https://github.com/jupyterlab/jupyterlab/blob/v${version}/CHANGELOG.md";
     description = "Jupyter lab environment notebook server extension";
-    license = with licenses; [ bsd3 ];
+    license = licenses.bsd3;
     homepage = "https://jupyter.org/";
-    maintainers = with maintainers; [ zimbatm ];
+    maintainers = lib.teams.jupyter.members;
   };
 }

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

@@ -19,14 +19,14 @@
 
 buildPythonPackage rec {
   pname = "jupyterlab_server";
-  version = "2.19.0";
+  version = "2.24.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-muwhohg7vt2fkahmKDVUSVdfGGLYiyitX5BQGdMebCE=";
+    hash = "sha256-Tm+Z4KVXm7vDLkScTbsDlWHU8aeCfVczJz7VZzjyHwc=";
   };
 
   nativeBuildInputs = [
@@ -77,6 +77,6 @@ buildPythonPackage rec {
     homepage = "https://jupyterlab-server.readthedocs.io/";
     changelog = "https://github.com/jupyterlab/jupyterlab_server/blob/v${version}/CHANGELOG.md";
     license = licenses.bsdOriginal;
-    maintainers = with maintainers; [ ];
+    maintainers = lib.teams.jupyter.members;
   };
 }

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

@@ -3,97 +3,66 @@
 , buildPythonPackage
 , pythonOlder
 , fetchPypi
-, argon2-cffi
-, glibcLocales
-, mock
-, jinja2
+, hatch-jupyter-builder
+, hatchling
+, jupyter-server
+, jupyterlab
+, jupyterlab_server
+, notebook-shim
 , tornado
-, ipython_genutils
-, traitlets
-, jupyter-core
-, jupyter-client
-, nbformat
-, nbclassic
-, nbconvert
-, ipykernel
-, terminado
-, requests
-, send2trash
-, pexpect
-, prometheus-client
+, pytest-jupyter
 , pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "notebook";
-  version = "6.5.2";
-  disabled = pythonOlder "3.7";
+  version = "7.0.1";
+  disabled = pythonOlder "3.8";
+
+  format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-wYl+UxfiJfx4tFVJpqtLZo5MmW/QOgTpOP5eevK//9A=";
+    hash = "sha256-LhatTmPqiffvviEu58FpP8+lq1X/73UEdTD3SvS9kmw=";
   };
 
-  LC_ALL = "en_US.utf8";
-
-  nativeCheckInputs = [ pytestCheckHook glibcLocales ];
-
-  propagatedBuildInputs = [
-    jinja2
-    tornado
-    ipython_genutils
-    traitlets
-    jupyter-core
-    send2trash
-    jupyter-client
-    nbformat
-    nbclassic
-    nbconvert
-    ipykernel
-    terminado
-    requests
-    pexpect
-    prometheus-client
-    argon2-cffi
-  ];
-
   postPatch = ''
-    # Remove selenium tests
-    rm -rf notebook/tests/selenium
-    export HOME=$TMPDIR
+    substituteInPlace pyproject.toml \
+      --replace "timeout = 300" ""
   '';
 
-  disabledTests = [
-    # a "system_config" is generated, and fails many tests
-    "config"
-    "load_ordered"
-    # requires jupyter, but will cause circular imports
-    "test_run"
-    "TestInstallServerExtension"
-    "launch_socket"
-    "sock_server"
-    "test_list_formats" # tries to find python MIME type
-    "KernelCullingTest" # has a race condition failing on slower hardware
-    "test_connections" # tornado.simple_httpclient.HTTPTimeoutError: Timeout during request"
-  ] ++ lib.optionals stdenv.isDarwin [
-    "test_delete"
-    "test_checkpoints_follow_file"
+  nativeBuildInputs = [
+    hatch-jupyter-builder
+    hatchling
+    jupyterlab
   ];
 
-  disabledTestPaths = lib.optionals stdenv.isDarwin [
-    # requires local networking
-    "notebook/auth/tests/test_login.py"
-    "notebook/bundler/tests/test_bundler_api.py"
+  propagatedBuildInputs = [
+    jupyter-server
+    jupyterlab
+    jupyterlab_server
+    notebook-shim
+    tornado
   ];
 
+  nativeCheckInputs = [
+    pytest-jupyter
+    pytestCheckHook
+  ];
+
+  env = {
+    JUPYTER_PLATFORM_DIRS = 1;
+  };
+
   # Some of the tests use localhost networking.
   __darwinAllowLocalNetworking = true;
 
   meta = {
-    description = "The Jupyter HTML notebook is a web-based notebook environment for interactive computing";
+    changelog = "https://github.com/jupyter/notebook/blob/v${version}/CHANGELOG.md";
+    description = "Web-based notebook environment for interactive computing";
     homepage = "https://github.com/jupyter/notebook";
     license = lib.licenses.bsd3;
-    maintainers = with lib.maintainers; [ fridh ];
+    maintainers = lib.teams.jupyter.members;
     mainProgram = "jupyter-notebook";
   };
 }

pkgs/top-level/python-aliases.nix

@@ -183,6 +183,7 @@ mapAliases ({
   jupyter_client = jupyter-client; # added 2021-10-15
   jupyter_core = jupyter-core; # added 2023-01-05
   jupyter_server = jupyter-server; # added 2023-01-05
+  jupyter-server-ydoc = jupyter-collaboration; # added 2023-07-18
   Kajiki = kajiki; # added 2023-02-19
   Keras = keras; # added 2021-11-25
   ldap = python-ldap; # added 2022-09-16

pkgs/top-level/python-packages.nix

@@ -5183,6 +5183,8 @@ self: super: with self; {
 
   ipydatawidgets = callPackage ../development/python-modules/ipydatawidgets { };
 
+  ipynbname = callPackage ../development/python-modules/ipynbname { };
+
   ipyniivue = callPackage ../development/python-modules/ipyniivue { };
 
   ipykernel = callPackage ../development/python-modules/ipykernel { };
@@ -5489,6 +5491,8 @@ self: super: with self; {
 
   jupyter-client = callPackage ../development/python-modules/jupyter-client { };
 
+  jupyter-collaboration = callPackage ../development/python-modules/jupyter-collaboration { };
+
   jupyter-contrib-core = callPackage ../development/python-modules/jupyter-contrib-core { };
 
   jupyter-contrib-nbextensions = callPackage ../development/python-modules/jupyter-contrib-nbextensions { };
@@ -5511,8 +5515,6 @@ self: super: with self; {
 
   jupyter-server-terminals = callPackage ../development/python-modules/jupyter-server-terminals { };
 
-  jupyter-server-ydoc = callPackage ../development/python-modules/jupyter-server-ydoc { };
-
   jupyter-ui-poll = callPackage ../development/python-modules/jupyter-ui-poll { };
 
   jupyter-ydoc = callPackage ../development/python-modules/jupyter-ydoc { };