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* [bug#39765] Add package JupyterLab
@ 2020-02-24 10:18 Lars-Dominik Braun
  2020-03-26 22:55 ` Ludovic Courtès
  0 siblings, 1 reply; 5+ messages in thread
From: Lars-Dominik Braun @ 2020-02-24 10:18 UTC (permalink / raw)
  To: 39765

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Hi,

this patch series adds Jupyter’s JupyterLab, which is the new frontend for
Jupyter Notebooks. The software works fine, but there are a few caveats

1) it comes with bundled pre-compiled JavaScript, which cannot be removed until
   we have proper support for importing from NPM
2) it contains an extension manager, that downloads arbitrary packages from NPM
   (`jupyter lab build`). This works, but is less than optimal imo. We should
   figure out how to package extensions in guix.
3) also it is required to install the package `jupyter`, otherwise installed
   kernels cannot be found and the `jupyter` command does not work.

Cheers,
Lars


[-- Attachment #2: 0001-gnu-Add-package-python-pytest-check-links.patch --]
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From 4a5862e2add1d537770a5ea466dbb8a4851afad9 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 7 Feb 2020 08:38:32 +0100
Subject: [PATCH 1/5] gnu: Add package python-pytest-check-links

* gnu/packages/python-xyz.scm (python-pytest-check-links): New variable.
---
 gnu/packages/python-xyz.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 84b70954bd..902ca5030b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17570,3 +17570,31 @@ sequences.")
 
 (define-public python2-fuzzywuzzy
   (package-with-python2 python-fuzzywuzzy))
+
+(define-public python-pytest-check-links
+  (package
+    (name "python-pytest-check-links")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       ;; URI uses underscores
+       (uri (pypi-uri "pytest_check_links" version))
+       (sha256
+        (base32
+         "12x3wmrdzm6wgk0vz02hb769h68nr49q47w5q1pj95pc89hsa34v"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-docutils" ,python-docutils)
+       ("python-html5lib" ,python-html5lib)
+       ("python-nbconvert" ,python-nbconvert)
+       ("python-nbformat" ,python-nbformat)
+       ("python-pytest" ,python-pytest)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-pbr-minimal" ,python-pbr-minimal)))
+    (home-page
+     "https://github.com/minrk/pytest-check-links")
+    (synopsis "Check links in files")
+    (description "Plugin for pytest that checks URLs for HTML-containing files")
+    (license license:bsd-3)))
-- 
2.20.1


[-- Attachment #3: 0002-gnu-Add-package-python-json5.patch --]
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From 690d45cba7d1a21fa6ae97fbe4fec6e1abae3635 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 7 Feb 2020 08:39:55 +0100
Subject: [PATCH 2/5] gnu: Add package python-json5

* gnu/packages/python-xyz.scm (python-json5): New variable.
---
 gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 902ca5030b..ad1cd5fbd4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17598,3 +17598,27 @@ sequences.")
     (synopsis "Check links in files")
     (description "Plugin for pytest that checks URLs for HTML-containing files")
     (license license:bsd-3)))
+
+(define-public python-json5
+  (package
+    (name "python-json5")
+    (version "0.8.5")
+    (source
+     (origin
+       ;; sample.json5 is missing from PyPi source tarball
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dpranke/pyjson5.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0nyngj18jlkgvm1177lc3cj47wm4yh3dqigygvcvw7xkyryafsqn"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/dpranke/pyjson5")
+    (synopsis
+     "Python implementation of the JSON5 data format")
+    (description
+     "JSON5 extends the JSON data interchange format to make it slightly more
+usable as a configuration language.  This Python package implements parsing and
+dumping of JSON5 data structures.")
+    (license license:asl2.0)))
-- 
2.20.1


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From a4535f6002a618444171d5a92146fb7a7e7e8243 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 7 Feb 2020 08:40:41 +0100
Subject: [PATCH 3/5] gnu: Add package python-jupyterlab-server

* gnu/packages/python-xyz.scm (python-jupyterlab-server): New variable.
---
 gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ad1cd5fbd4..92ee53fe6f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17622,3 +17622,37 @@ sequences.")
 usable as a configuration language.  This Python package implements parsing and
 dumping of JSON5 data structures.")
     (license license:asl2.0)))
+
+(define-public python-jupyterlab-server
+  (package
+    (name "python-jupyterlab-server")
+    (version "1.0.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyterlab_server" version))
+       (sha256
+        (base32
+         "1bax8iqwcc5p02h5ysdc48zvx7ll5jfzfsybhb3lfvyfpwkpb5yh"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-jinja2" ,python-jinja2)
+       ("python-json5" ,python-json5)
+       ("python-jsonschema" ,python-jsonschema)
+       ("python-notebook" ,python-notebook)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-requests" ,python-requests)
+       ("python-ipykernel" ,python-ipykernel)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; python setup.py test does not invoke pytest?
+         (replace 'check
+           (lambda _
+             (invoke "pytest" "-vv"))))))
+    (home-page "https://jupyter.org")
+    (synopsis "JupyterLab Server")
+    (description "A set of server components for JupyterLab and JupyterLab like
+applications")
+    (license license:bsd-3)))
-- 
2.20.1


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From c50fc3ec734cb94e78168a4a29c9aff070f4ae9f Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Fri, 7 Feb 2020 08:41:24 +0100
Subject: [PATCH 4/5] gnu: Add package python-jupyterlab

* gnu/packages/python-xyz.scm (python-jupyterlab): New variable.
---
 .../python-jupyterlab-copy-nometa.patch       | 33 +++++++++++
 gnu/packages/python-xyz.scm                   | 55 +++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 gnu/packages/patches/python-jupyterlab-copy-nometa.patch

diff --git a/gnu/packages/patches/python-jupyterlab-copy-nometa.patch b/gnu/packages/patches/python-jupyterlab-copy-nometa.patch
new file mode 100644
index 0000000000..5e770c0f47
--- /dev/null
+++ b/gnu/packages/patches/python-jupyterlab-copy-nometa.patch
@@ -0,0 +1,33 @@
+diff '--exclude=*.swp' -Naur jupyterlab-1.2.6.orig/jupyterlab/commands.py jupyterlab-1.2.6/jupyterlab/commands.py
+--- jupyterlab-1.2.6.orig/jupyterlab/commands.py	2020-01-24 17:25:16.238353500 +0100
++++ jupyterlab-1.2.6/jupyterlab/commands.py	2020-01-31 12:36:10.497375982 +0100
+@@ -1100,7 +1100,7 @@
+                       'webpack.prod.minimize.config.js',
+                       '.yarnrc', 'yarn.js']:
+             target = pjoin(staging, fname)
+-            shutil.copy(pjoin(HERE, 'staging', fname), target)
++            shutil.copyfile(pjoin(HERE, 'staging', fname), target)
+ 
+         # Ensure a clean templates directory
+         templates = pjoin(staging, 'templates')
+@@ -1108,7 +1108,10 @@
+             _rmtree(templates, self.logger)
+ 
+         try:
+-            shutil.copytree(pjoin(HERE, 'staging', 'templates'), templates)
++            shutil.copytree(pjoin(HERE, 'staging', 'templates'), templates,
++                    copy_function=shutil.copyfile)
++            # cannot replace or disable copytree’s call to .copystat
++            os.chmod (templates, 0o755)
+         except shutil.Error as error:
+             # `copytree` throws an error if copying to + from NFS even though
+             # the copy is successful (see https://bugs.python.org/issue24564
+@@ -1178,7 +1181,7 @@
+             with open(lock_path, 'w', encoding='utf-8') as f:
+                 f.write(template)
+         elif not osp.exists(lock_path):
+-            shutil.copy(lock_template, lock_path)
++            shutil.copyfile(lock_template, lock_path)
+ 
+     def _get_package_template(self, silent=False):
+         """Get the template the for staging package.json file.
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 92ee53fe6f..232841ccb1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -126,6 +126,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages networking)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages node)
   #:use-module (gnu packages openstack)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
@@ -17656,3 +17657,57 @@ dumping of JSON5 data structures.")
     (description "A set of server components for JupyterLab and JupyterLab like
 applications")
     (license license:bsd-3)))
+
+(define-public python-jupyterlab
+  (package
+    (name "python-jupyterlab")
+    (version "1.2.6")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "jupyterlab" version))
+        (sha256
+          (base32
+            "0mc3nrj7fc5q2ajr09m261j386jsp8qjljg8anghlh8czc9ln4s2"))
+        (patches (search-patches "python-jupyterlab-copy-nometa.patch"))))
+    (build-system python-build-system)
+    (propagated-inputs
+      `(("python-jinja2" ,python-jinja2)
+        ("python-jupyterlab-server"
+         ,python-jupyterlab-server)
+        ("python-notebook" ,python-notebook)
+        ("python-tornado" ,python-tornado)
+		("node" ,node)))
+    (native-inputs
+      `(("python-pytest" ,python-pytest)
+        ("python-pytest-check-links"
+         ,python-pytest-check-links)
+        ("python-requests" ,python-requests)
+        ("python-ipykernel" ,python-ipykernel)))
+    (arguments
+     ;; testing requires npm, so disabled for now
+     '(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-syspath
+           (lambda* (#:key outputs inputs configure-flags #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out")))
+               (substitute* "jupyterlab/commands.py"
+                 ;; sys.prefix defaults to Python’s prefix in the store, not
+                 ;; jupyterlab’s. Fix that.
+                 (("sys\\.prefix")
+                  (string-append "'" out "'"))))
+             #t))
+         ;; 'build does not respect configure-flags
+         (replace 'build
+           (lambda _
+             (invoke "python" "setup.py" "build" "--skip-npm"))))
+      #:configure-flags (list "--skip-npm")))
+    (home-page "https://jupyter.org")
+    (synopsis
+      "The JupyterLab notebook server extension")
+    (description
+	  "An extensible environment for interactive and reproducible computing,
+based on the Jupyter Notebook and Architecture.")
+    (license license:bsd-3)))
+
-- 
2.20.1


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From a47fd94aa6f3e62b77f3b7208c4e6757e3a9ee08 Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Date: Thu, 12 Dec 2019 08:53:39 +0100
Subject: [PATCH 5/5] gnu: python-notebook: Support UNIX domain sockets

* gnu/packages/python-xyz.scm (python-notebook): Add patch from upstream
https://github.com/jupyter/notebook/pull/4835
(python-requests-unixsocket) New variable
---
 ...pyter-unix-domain-sockets-4835-5.7.4.patch | 591 ++++++++++++++++++
 gnu/packages/python-xyz.scm                   |  35 +-
 2 files changed, 624 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/jupyter-unix-domain-sockets-4835-5.7.4.patch

diff --git a/gnu/packages/patches/jupyter-unix-domain-sockets-4835-5.7.4.patch b/gnu/packages/patches/jupyter-unix-domain-sockets-4835-5.7.4.patch
new file mode 100644
index 0000000000..134d3ad2b8
--- /dev/null
+++ b/gnu/packages/patches/jupyter-unix-domain-sockets-4835-5.7.4.patch
@@ -0,0 +1,591 @@
+diff -Naur notebook-5.7.4/notebook/base/handlers.py notebook-5.7.4.patched/notebook/base/handlers.py
+--- notebook-5.7.4/notebook/base/handlers.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/base/handlers.py	2019-11-18 12:16:58.315065024 +0100
+@@ -40,7 +40,7 @@
+ import notebook
+ from notebook._tz import utcnow
+ from notebook.i18n import combine_translations
+-from notebook.utils import is_hidden, url_path_join, url_is_absolute, url_escape
++from notebook.utils import is_hidden, url_path_join, url_is_absolute, url_escape, urldecode_unix_socket_path
+ from notebook.services.security import csp_report_uri
+ 
+ #-----------------------------------------------------------------------------
+@@ -426,13 +426,18 @@
+             # ip_address only accepts unicode on Python 2
+             host = host.decode('utf8', 'replace')
+ 
+-        try:
+-            addr = ipaddress.ip_address(host)
+-        except ValueError:
+-            # Not an IP address: check against hostnames
+-            allow = host in self.settings.get('local_hostnames', ['localhost'])
++        # UNIX socket handling
++        check_host = urldecode_unix_socket_path(host)
++        if check_host.startswith('/') and os.path.exists(check_host):
++            allow = True
+         else:
+-            allow = addr.is_loopback
++            try:
++                addr = ipaddress.ip_address(host)
++            except ValueError:
++                # Not an IP address: check against hostnames
++                allow = host in self.settings.get('local_hostnames', ['localhost'])
++            else:
++                allow = addr.is_loopback
+ 
+         if not allow:
+             self.log.warning(
+diff -Naur notebook-5.7.4/notebook/__init__.py notebook-5.7.4.patched/notebook/__init__.py
+--- notebook-5.7.4/notebook/__init__.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/__init__.py	2019-11-18 12:16:58.315065024 +0100
+@@ -20,6 +20,8 @@
+     os.path.join(os.path.dirname(__file__), "templates"),
+ ]
+ 
++DEFAULT_NOTEBOOK_PORT = 8888
++
+ del os
+ 
+ from .nbextensions import install_nbextension
+diff -Naur notebook-5.7.4/notebook/notebookapp.py notebook-5.7.4.patched/notebook/notebookapp.py
+--- notebook-5.7.4/notebook/notebookapp.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/notebookapp.py	2019-11-18 12:21:34.975072928 +0100
+@@ -63,8 +63,11 @@
+ from tornado import web
+ from tornado.httputil import url_concat
+ from tornado.log import LogFormatter, app_log, access_log, gen_log
++if not sys.platform.startswith('win'):
++    from tornado.netutil import bind_unix_socket
+ 
+ from notebook import (
++    DEFAULT_NOTEBOOK_PORT,
+     DEFAULT_STATIC_FILES_PATH,
+     DEFAULT_TEMPLATE_PATH_LIST,
+     __version__,
+@@ -108,7 +111,16 @@
+ from notebook._sysinfo import get_sys_info
+ 
+ from ._tz import utcnow, utcfromtimestamp
+-from .utils import url_path_join, check_pid, url_escape, urljoin, pathname2url
++from .utils import (
++    check_pid,
++    pathname2url,
++    url_escape,
++    url_path_join,
++    urldecode_unix_socket_path,
++    urlencode_unix_socket,
++    urlencode_unix_socket_path,
++    urljoin,
++)
+ 
+ #-----------------------------------------------------------------------------
+ # Module globals
+@@ -212,7 +224,7 @@
+             warnings.warn(_("The `ignore_minified_js` flag is deprecated and will be removed in Notebook 6.0"), DeprecationWarning)
+ 
+         now = utcnow()
+-        
++
+         root_dir = contents_manager.root_dir
+         home = os.path.expanduser('~')
+         if root_dir.startswith(home + os.path.sep):
+@@ -385,6 +397,7 @@
+         set_password(config_file=self.config_file)
+         self.log.info("Wrote hashed password to %s" % self.config_file)
+ 
++
+ def shutdown_server(server_info, timeout=5, log=None):
+     """Shutdown a notebook server in a separate process.
+ 
+@@ -397,14 +410,39 @@
+     Returns True if the server was stopped by any means, False if stopping it
+     failed (on Windows).
+     """
+-    from tornado.httpclient import HTTPClient, HTTPRequest
++    from tornado import gen
++    from tornado.httpclient import AsyncHTTPClient, HTTPClient, HTTPRequest
++    from tornado.netutil import bind_unix_socket, Resolver
+     url = server_info['url']
+     pid = server_info['pid']
++    resolver = None
++
++    # UNIX Socket handling.
++    if url.startswith('http+unix://'):
++        # This library doesn't understand our URI form, but it's just HTTP.
++        url = url.replace('http+unix://', 'http://')
++
++        class UnixSocketResolver(Resolver):
++            def initialize(self, resolver):
++                self.resolver = resolver
++
++            def close(self):
++                self.resolver.close()
++
++            @gen.coroutine
++            def resolve(self, host, port, *args, **kwargs):
++                raise gen.Return([
++                    (socket.AF_UNIX, urldecode_unix_socket_path(host))
++                ])
++
++        resolver = UnixSocketResolver(resolver=Resolver())
++
+     req = HTTPRequest(url + 'api/shutdown', method='POST', body=b'', headers={
+         'Authorization': 'token ' + server_info['token']
+     })
+     if log: log.debug("POST request to %sapi/shutdown", url)
+-    HTTPClient().fetch(req)
++    AsyncHTTPClient.configure(None, resolver=resolver)
++    HTTPClient(AsyncHTTPClient).fetch(req)
+ 
+     # Poll to see if it shut down.
+     for _ in range(timeout*10):
+@@ -435,13 +473,20 @@
+     version = __version__
+     description="Stop currently running notebook server for a given port"
+ 
+-    port = Integer(8888, config=True,
+-        help="Port of the server to be killed. Default 8888")
++    port = Integer(DEFAULT_NOTEBOOK_PORT, config=True,
++        help="Port of the server to be killed. Default %s" % DEFAULT_NOTEBOOK_PORT)
++
++    sock = Unicode(u'', config=True,
++        help="UNIX socket of the server to be killed.")
+ 
+     def parse_command_line(self, argv=None):
+         super(NbserverStopApp, self).parse_command_line(argv)
+         if self.extra_args:
+-            self.port=int(self.extra_args[0])
++            try:
++                self.port = int(self.extra_args[0])
++            except ValueError:
++                # self.extra_args[0] was not an int, so it must be a string (unix socket).
++                self.sock = self.extra_args[0]
+ 
+     def shutdown_server(self, server):
+         return shutdown_server(server, log=self.log)
+@@ -451,16 +496,16 @@
+         if not servers:
+             self.exit("There are no running servers")
+         for server in servers:
+-            if server['port'] == self.port:
+-                print("Shutting down server on port", self.port, "...")
++            if server.get('sock') == self.sock or server['port'] == self.port:
++                print("Shutting down server on %s..." % self.sock or self.port)
+                 if not self.shutdown_server(server):
+                     sys.exit("Could not stop server")
+                 return
+         else:
+             print("There is currently no server running on port {}".format(self.port), file=sys.stderr)
+-            print("Ports currently in use:", file=sys.stderr)
++            print("Ports/sockets currently in use:", file=sys.stderr)
+             for server in servers:
+-                print("  - {}".format(server['port']), file=sys.stderr)
++                print("  - {}".format(server.get('sock', server['port'])), file=sys.stderr)
+             self.exit(1)
+ 
+ 
+@@ -540,6 +585,8 @@
+     'ip': 'NotebookApp.ip',
+     'port': 'NotebookApp.port',
+     'port-retries': 'NotebookApp.port_retries',
++    'sock': 'NotebookApp.sock',
++    'sock-umask': 'NotebookApp.sock_umask',
+     'transport': 'KernelManager.transport',
+     'keyfile': 'NotebookApp.keyfile',
+     'certfile': 'NotebookApp.certfile',
+@@ -678,10 +725,18 @@
+         or containerized setups for example).""")
+     )
+ 
+-    port = Integer(8888, config=True,
++    port = Integer(DEFAULT_NOTEBOOK_PORT, config=True,
+         help=_("The port the notebook server will listen on.")
+     )
+ 
++    sock = Unicode(u'', config=True,
++        help=_("The UNIX socket the notebook server will listen on.")
++    )
++
++    sock_umask = Unicode(u'0600', config=True,
++        help=_("The UNIX socket umask to set on creation (default: 0600).")
++    )
++
+     port_retries = Integer(50, config=True,
+         help=_("The number of additional ports to try if the specified port is not available.")
+     )
+@@ -1370,6 +1425,27 @@
+             self.log.critical(_("\t$ python -m notebook.auth password"))
+             sys.exit(1)
+ 
++        # Socket options validation.
++        if self.sock:
++            if self.port != DEFAULT_NOTEBOOK_PORT:
++                self.log.critical(
++                    _('Options --port and --sock are mutually exclusive. Aborting.'),
++                )
++                sys.exit(1)
++
++            if self.open_browser:
++                # If we're bound to a UNIX socket, we can't reliably connect from a browser.
++                self.log.critical(
++                    _('Options --open-browser and --sock are mutually exclusive. Aborting.'),
++                )
++                sys.exit(1)
++
++            if sys.platform.startswith('win'):
++                self.log.critical(
++                    _('Option --sock is not supported on Windows, but got value of %s. Aborting.' % self.sock),
++                )
++                sys.exit(1)
++
+         self.web_app = NotebookWebApplication(
+             self, self.kernel_manager, self.contents_manager,
+             self.session_manager, self.kernel_spec_manager,
+@@ -1401,6 +1477,32 @@
+                                                  max_body_size=self.max_body_size,
+                                                  max_buffer_size=self.max_buffer_size)
+ 
++        success = self._bind_http_server()
++        if not success:
++            self.log.critical(_('ERROR: the notebook server could not be started because '
++                              'no available port could be found.'))
++            self.exit(1)
++
++    def _bind_http_server(self):
++        return self._bind_http_server_unix() if self.sock else self._bind_http_server_tcp()
++
++    def _bind_http_server_unix(self):
++        try:
++            sock = bind_unix_socket(self.sock, mode=int(self.sock_umask.encode(), 8))
++            self.http_server.add_socket(sock)
++        except socket.error as e:
++            if e.errno == errno.EADDRINUSE:
++                self.log.info(_('The socket %s is already in use.') % self.sock)
++                return False
++            elif e.errno in (errno.EACCES, getattr(errno, 'WSAEACCES', errno.EACCES)):
++                self.log.warning(_("Permission to listen on sock %s denied") % self.sock)
++                return False
++            else:
++                raise
++        else:
++            return True
++
++    def _bind_http_server_tcp(self):
+         success = None
+         for port in random_ports(self.port, self.port_retries+1):
+             try:
+@@ -1418,10 +1520,11 @@
+                 self.port = port
+                 success = True
+                 break
+-        if not success:
+-            self.log.critical(_('ERROR: the notebook server could not be started because '
+-                              'no available port could be found.'))
+-            self.exit(1)
++        return success
++
++    def _concat_token(self, url):
++        token = self.token if self._token_generated else '...'
++        return url_concat(url, {'token': token})
+     
+     @property
+     def display_url(self):
+@@ -1429,26 +1532,33 @@
+             url = self.custom_display_url
+             if not url.endswith('/'):
+                 url += '/'
++        elif self.sock:
++            url = self._unix_sock_url()
+         else:
+             if self.ip in ('', '0.0.0.0'):
+                 ip = "(%s or 127.0.0.1)" % socket.gethostname()
+             else:
+                 ip = self.ip
+-            url = self._url(ip)
+-        if self.token:
+-            # Don't log full token if it came from config
+-            token = self.token if self._token_generated else '...'
+-            url = url_concat(url, {'token': token})
++            url = self._tcp_url(ip)
++        if self.token and not self.sock:
++            url = self._concat_token(url)
++            url += '\n or %s' % self._concat_token(self._tcp_url('127.0.0.1'))
+         return url
+ 
+     @property
+     def connection_url(self):
+-        ip = self.ip if self.ip else 'localhost'
+-        return self._url(ip)
++        if self.sock:
++            return self._unix_sock_url()
++        else:
++            ip = self.ip if self.ip else 'localhost'
++            return self._tcp_url(ip)
+ 
+-    def _url(self, ip):
++    def _unix_sock_url(self, token=None):
++        return '%s%s' % (urlencode_unix_socket(self.sock), self.base_url)
++
++    def _tcp_url(self, ip, port=None):
+         proto = 'https' if self.certfile else 'http'
+-        return "%s://%s:%i%s" % (proto, ip, self.port, self.base_url)
++        return "%s://%s:%i%s" % (proto, ip, port or self.port, self.base_url)
+ 
+     def init_terminals(self):
+         if not self.terminals_enabled:
+@@ -1660,6 +1770,7 @@
+         return {'url': self.connection_url,
+                 'hostname': self.ip if self.ip else 'localhost',
+                 'port': self.port,
++                'sock': self.sock,
+                 'secure': bool(self.certfile),
+                 'base_url': self.base_url,
+                 'token': self.token,
+@@ -1780,19 +1891,31 @@
+         self.write_server_info_file()
+         self.write_browser_open_file()
+ 
+-        if self.open_browser or self.file_to_run:
++        if (self.open_browser or self.file_to_run) and not self.sock:
+             self.launch_browser()
+ 
+         if self.token and self._token_generated:
+             # log full URL with generated token, so there's a copy/pasteable link
+             # with auth info.
+-            self.log.critical('\n'.join([
+-                '\n',
+-                'To access the notebook, open this file in a browser:',
+-                '    %s' % urljoin('file:', pathname2url(self.browser_open_file)),
+-                'Or copy and paste one of these URLs:',
+-                '    %s' % self.display_url,
+-            ]))
++            if self.sock:
++                self.log.critical('\n'.join([
++                    '\n',
++                    'Notebook is listening on %s' % self.display_url,
++                    '',
++                    (
++                        'UNIX sockets are not browser-connectable, but you can tunnel to '
++                        'the instance via e.g.`ssh -L 8888:%s -N user@this_host` and then '
++                        'opening e.g. %s in a browser.'
++                    ) % (self.sock, self._concat_token(self._tcp_url('localhost', 8888)))
++                ]))
++            else:
++                self.log.critical('\n'.join([
++                    '\n',
++                    'To access the notebook, open this file in a browser:',
++                    '    %s' % urljoin('file:', pathname2url(self.browser_open_file)),
++                    'Or copy and paste one of these URLs:',
++                    '    %s' % self.display_url,
++                ]))
+ 
+         self.io_loop = ioloop.IOLoop.current()
+         if sys.platform.startswith('win'):
+diff -Naur notebook-5.7.4/notebook/tests/launchnotebook.py notebook-5.7.4.patched/notebook/tests/launchnotebook.py
+--- notebook-5.7.4/notebook/tests/launchnotebook.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/tests/launchnotebook.py	2019-11-18 12:22:25.931074384 +0100
+@@ -19,12 +19,13 @@
+     from mock import patch #py2
+ 
+ import requests
++import requests_unixsocket
+ from tornado.ioloop import IOLoop
+ import zmq
+ 
+ import jupyter_core.paths
+ from traitlets.config import Config
+-from ..notebookapp import NotebookApp
++from ..notebookapp import NotebookApp, urlencode_unix_socket
+ from ..utils import url_path_join
+ from ipython_genutils.tempdir import TemporaryDirectory
+ 
+@@ -55,7 +56,7 @@
+         url = cls.base_url() + 'api/contents'
+         for _ in range(int(MAX_WAITTIME/POLL_INTERVAL)):
+             try:
+-                requests.get(url)
++                cls.fetch_url(url)
+             except Exception as e:
+                 if not cls.notebook_thread.is_alive():
+                     raise RuntimeError("The notebook server failed to start")
+@@ -79,6 +80,10 @@
+             headers['Authorization'] = 'token %s' % cls.token
+         return headers
+ 
++    @staticmethod
++    def fetch_url(url):
++        return requests.get(url)
++
+     @classmethod
+     def request(cls, verb, path, **kwargs):
+         """Send a request to my server
+@@ -93,6 +98,10 @@
+         return response
+     
+     @classmethod
++    def get_bind_args(cls):
++        return dict(port=cls.port)
++
++    @classmethod
+     def setup_class(cls):
+         cls.tmp_dir = TemporaryDirectory()
+         def tmp(*parts):
+@@ -103,7 +112,7 @@
+                 if e.errno != errno.EEXIST:
+                     raise
+             return path
+-        
++
+         cls.home_dir = tmp('home')
+         data_dir = cls.data_dir = tmp('data')
+         config_dir = cls.config_dir = tmp('config')
+@@ -138,8 +147,8 @@
+             if 'asyncio' in sys.modules:
+                 import asyncio
+                 asyncio.set_event_loop(asyncio.new_event_loop())
++            bind_args = cls.get_bind_args()
+             app = cls.notebook = NotebookApp(
+-                port=cls.port,
+                 port_retries=0,
+                 open_browser=False,
+                 config_dir=cls.config_dir,
+@@ -150,6 +159,7 @@
+                 config=config,
+                 allow_root=True,
+                 token=cls.token,
++                **bind_args
+             )
+             # don't register signal handler during tests
+             app.init_signal = lambda : None
+@@ -197,6 +207,25 @@
+         return 'http://localhost:%i%s' % (cls.port, cls.url_prefix)
+ 
+ 
++class UNIXSocketNotebookTestBase(NotebookTestBase):
++    # Rely on `/tmp` to avoid any Linux socket length max buffer
++    # issues. Key on PID for process-wise concurrency.
++    sock = '/tmp/.notebook.%i.sock' % os.getpid()
++
++    @classmethod
++    def get_bind_args(cls):
++        return dict(sock=cls.sock)
++
++    @classmethod
++    def base_url(cls):
++        return '%s%s' % (urlencode_unix_socket(cls.sock), cls.url_prefix)
++
++    @staticmethod
++    def fetch_url(url):
++        with requests_unixsocket.monkeypatch():
++            return requests.get(url)
++
++
+ @contextmanager
+ def assert_http_error(status, msg=None):
+     try:
+diff -Naur notebook-5.7.4/notebook/tests/test_notebookapp_integration.py notebook-5.7.4.patched/notebook/tests/test_notebookapp_integration.py
+--- notebook-5.7.4/notebook/tests/test_notebookapp_integration.py	1970-01-01 01:00:00.000000000 +0100
++++ notebook-5.7.4.patched/notebook/tests/test_notebookapp_integration.py	2019-11-18 12:16:58.319065025 +0100
+@@ -0,0 +1,39 @@
++import os
++import stat
++import subprocess
++import time
++
++from ipython_genutils.testing.decorators import skip_win32
++
++from .launchnotebook import UNIXSocketNotebookTestBase
++from ..utils import urlencode_unix_socket, urlencode_unix_socket_path
++
++
++@skip_win32
++def test_shutdown_sock_server_integration():
++    sock = UNIXSocketNotebookTestBase.sock
++    url = urlencode_unix_socket(sock)
++    encoded_sock_path = urlencode_unix_socket_path(sock)
++
++    p = subprocess.Popen(
++        ['jupyter', 'notebook', '--no-browser', '--sock=%s' % sock],
++        stdout=subprocess.PIPE, stderr=subprocess.PIPE
++    )
++
++    for line in iter(p.stderr.readline, b''):
++        if url.encode() in line:
++            complete = True
++            break
++
++    assert complete, 'did not find socket URL in stdout when launching notebook'
++
++    assert encoded_sock_path.encode() in subprocess.check_output(['jupyter', 'notebook', 'list'])
++
++    # Ensure default umask is properly applied.
++    assert stat.S_IMODE(os.lstat(sock).st_mode) == 0o600
++
++    subprocess.check_output(['jupyter', 'notebook', 'stop', sock])
++
++    assert encoded_sock_path.encode() not in subprocess.check_output(['jupyter', 'notebook', 'list'])
++
++    p.wait()
+diff -Naur notebook-5.7.4/notebook/tests/test_notebookapp.py notebook-5.7.4.patched/notebook/tests/test_notebookapp.py
+--- notebook-5.7.4/notebook/tests/test_notebookapp.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/tests/test_notebookapp.py	2019-11-18 12:16:58.319065025 +0100
+@@ -25,7 +25,7 @@
+ from notebook.auth.security import passwd_check
+ NotebookApp = notebookapp.NotebookApp
+ 
+-from .launchnotebook import NotebookTestBase
++from .launchnotebook import NotebookTestBase, UNIXSocketNotebookTestBase
+ 
+ 
+ def test_help_output():
+@@ -192,3 +192,15 @@
+         servers = list(notebookapp.list_running_servers())
+         assert len(servers) >= 1
+         assert self.port in {info['port'] for info in servers}
++
++
++# UNIX sockets aren't available on Windows.
++if not sys.platform.startswith('win'):
++    class NotebookUnixSocketTests(UNIXSocketNotebookTestBase):
++        def test_run(self):
++            self.fetch_url(self.base_url() + 'api/contents')
++
++        def test_list_running_sock_servers(self):
++            servers = list(notebookapp.list_running_servers())
++            assert len(servers) >= 1
++            assert self.sock in {info['sock'] for info in servers}
+diff -Naur notebook-5.7.4/notebook/utils.py notebook-5.7.4.patched/notebook/utils.py
+--- notebook-5.7.4/notebook/utils.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/notebook/utils.py	2019-11-18 12:23:05.231075507 +0100
+@@ -306,3 +306,18 @@
+     check_pid = _check_pid_win32
+ else:
+     check_pid = _check_pid_posix
++
++def urlencode_unix_socket_path(socket_path):
++    """Encodes a UNIX socket path string from a socket path for the `http+unix` URI form."""
++    return socket_path.replace('/', '%2F')
++
++
++def urldecode_unix_socket_path(socket_path):
++    """Decodes a UNIX sock path string from an encoded sock path for the `http+unix` URI form."""
++    return socket_path.replace('%2F', '/')
++
++
++def urlencode_unix_socket(socket_path):
++    """Encodes a UNIX socket URL from a socket path for the `http+unix` URI form."""
++    return 'http+unix://%s' % urlencode_unix_socket_path(socket_path)
++
+diff -Naur notebook-5.7.4/setup.py notebook-5.7.4.patched/setup.py
+--- notebook-5.7.4/setup.py	2018-12-17 11:01:51.000000000 +0100
++++ notebook-5.7.4.patched/setup.py	2019-11-18 12:23:33.851076325 +0100
+@@ -98,7 +98,8 @@
+         ':python_version == "2.7"': ['ipaddress'],
+         'test:python_version == "2.7"': ['mock'],
+         'test': ['nose', 'coverage', 'requests', 'nose_warnings_filters',
+-                 'nbval', 'nose-exclude', 'selenium'],
++                 'nbval', 'nose-exclude', 'selenium',
++                 'requests-unixsocket'],
+         'test:sys_platform == "win32"': ['nose-exclude'],
+     },
+     entry_points = {
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 232841ccb1..4263a33c6b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7811,7 +7811,8 @@ convert an @code{.ipynb} notebook file into various static formats including:
               (uri (pypi-uri "notebook" version))
               (sha256
                (base32
-                "0jm7324mbxljmn9hgapj66q7swyz5ai92blmr0jpcy0h80x6f26r"))))
+                "0jm7324mbxljmn9hgapj66q7swyz5ai92blmr0jpcy0h80x6f26r"))
+              (patches (search-patches "jupyter-unix-domain-sockets-4835-5.7.4.patch"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -7834,7 +7835,8 @@ convert an @code{.ipynb} notebook file into various static formats including:
        ("python-nbconvert" ,python-nbconvert)
        ("python-prometheus-client" ,python-prometheus-client)
        ("python-send2trash" ,python-send2trash)
-       ("python-terminado" ,python-terminado)))
+       ("python-terminado" ,python-terminado)
+       ("python-requests-unixsocket" ,python-requests-unixsocket)))
     (native-inputs
      `(("python-nose" ,python-nose)
        ("python-sphinx" ,python-sphinx)
@@ -17711,3 +17713,32 @@ applications")
 based on the Jupyter Notebook and Architecture.")
     (license license:bsd-3)))
 
+(define-public python-requests-unixsocket
+  (package
+    (name "python-requests-unixsocket")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "requests-unixsocket" version))
+       (sha256
+        (base32
+         "1sn12y4fw1qki5gxy9wg45gmdrxhrndwfndfjxhpiky3mwh1lp4y"))))
+    (build-system python-build-system)
+    (native-inputs
+     ;; pbr is required for setup only
+     `(("python-pbr" ,python-pbr)))
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-urllib3" ,python-urllib3)))
+    (arguments
+     ;; tests depend on very specific package version, which are not available in guix
+     '(#:tests? #f))
+    (home-page
+     "https://github.com/msabramo/requests-unixsocket")
+    (synopsis
+     "Use requests to talk HTTP via a UNIX domain socket")
+    (description
+     "Use requests to talk HTTP via a UNIX domain socket")
+    (license license:asl2.0)))
+
-- 
2.20.1


^ permalink raw reply related	[flat|nested] 5+ messages in thread
end of thread, other threads:[~2020-03-30  6:12 UTC | newest]

Thread overview: 5+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2020-02-24 10:18 [bug#39765] Add package JupyterLab Lars-Dominik Braun
2020-03-26 22:55 ` Ludovic Courtès
2020-03-27  7:30   ` Lars-Dominik Braun
2020-03-29 14:37     ` Ludovic Courtès
2020-03-30  6:10       ` Lars-Dominik Braun

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