8 files changed, 1531 insertions, 0 deletions

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..d3f77b5
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,38 @@
+name: build
+on:
+  push:
+  pull_request:
+  schedule:
+    # weekly builds, making sure everything still works with guix-proper
+    - cron:  '39 3 * * 0'
+jobs:
+  build:
+    name: Build package
+    runs-on: ubuntu-latest
+    strategy:
+      # building independent packages, don’t abort entire build if one fails
+      fail-fast: false
+      matrix:
+        package:
+          # this builds python-notebook as well
+          - python-jupyterlab
+          - rstudio-server
+          - rstudio
+    steps:
+      - name: Guix cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/guix
+          # use a key that (almost) never matches
+          key: guix-cache-${{ github.sha }}
+          restore-keys: |
+            guix-cache-
+      - name: Install Guix
+        uses: PromyLOPh/guix-install-action@v1
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Lint package
+        run: |
+            guix lint -L . ${{ matrix.package }} |& sed -nre 's#(.*):([0-9]+):([0-9]+): (.*)$#::warning file=\1,line=\2,col=\3::\4#gp'
+      - name: Build package
+        run: guix build -L . ${{ matrix.package }}
diff --git a/.guix-channel b/.guix-channel
new file mode 100644
index 0000000..4c0143b
--- /dev/null
+++ b/.guix-channel
@@ -0,0 +1,3 @@
+(channel
+  (version 0)
+  (url "https://github.com/guix-science/guix-science.git"))
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
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+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/README.rst b/README.rst
new file mode 100644
index 0000000..e8ea3a5
--- /dev/null
+++ b/README.rst
@@ -0,0 +1,20 @@
+Guix science packages
+=====================
+
+.. image:: https://github.com/guix-science/guix-science/workflows/build/badge.svg
+
+This GNU Guix_ channel provides recent versions of scientific software, which
+cannot be included upstream. Currently the following software is packaged:
+
+- Jupyter Notebook (``python-notebook``)
+- JupyterLab (``python-jupyterlab``)
+- RStudio Desktop (``rstudio``)
+- RStudio Web (``rstudio-server``)
+
+See `Using a Custom Guix Channel`_ for instructions how to add it to your
+installation. 
+
+.. _Guix: https://guix.gnu.org/
+.. _Using a Custom Guix Channel: https://guix.gnu.org/manual/en/guix.html#Using-a-Custom-Guix-Channel
+
+
diff --git a/guix-science/packages/jupyter.scm b/guix-science/packages/jupyter.scm
new file mode 100644
index 0000000..e07ed73
--- /dev/null
+++ b/guix-science/packages/jupyter.scm
@@ -0,0 +1,484 @@
+;;;
+;;; Copyright © 2019, 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
+;;;
+;;; This program is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; This program is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix-science packages jupyter)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages monitoring)
+  #:use-module (gnu packages node)
+  #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages python-check)
+  #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages time)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix hg-download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system python))
+
+(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)))
+
+(define-public python-nose-exclude
+  (package
+    (name "python-nose-exclude")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nose-exclude" version))
+       (sha256
+        (base32
+         "0123x1lyv5b2p9civcfg8vilj2ga3q7p2ks1hq25z0gb3ssai3zp"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page
+     "https://github.com/kgrandis/nose-exclude")
+    (synopsis
+     "Exclude specific directories from nosetests runs.")
+    (description
+     "Exclude specific directories from nosetests runs.")
+    (license license:lgpl2.0)))
+
+(define-public python-nose-warnings-filters
+  (package
+    (name "python-nose-warnings-filters")
+    (version "0.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nose_warnings_filters" version))
+       (sha256
+        (base32
+         "17dvfqfy2fm7a5cmiffw2dc3064kpx72fn5mlw01skm2rhn5nv25"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "")
+    (synopsis
+     "Allow to inject warning filters during ``nosetest``.")
+    (description
+     "Allow to inject warning filters during ``nosetest``.")
+    (license #f)))
+
+(define python-terminado-0.8.3
+  (package/inherit python-terminado
+    (name "python-terminado")
+    (version "0.8.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "terminado" version))
+       (sha256
+        (base32
+         "1hmjdxpd9w8fl61f0adlmfh1s3rrqn9j2cppk9ynlc02z1saf128"))))))
+
+(define-public python-jupyter-core-4.6
+  (package
+    (name "python-jupyter-core")
+    (version "4.6.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_core" version))
+       (sha256
+        (base32
+         "0zly44i2b22bqxwya62xvsarzqqcl3wbv00qfihqhz3yg3fxakrr"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+            (if tests?
+             (begin
+              ; Some tests write to $HOME.
+              (setenv "HOME" "/tmp")
+              ; Some tests load the installed package.
+              (add-installed-pythonpath inputs outputs)
+              (invoke "pytest" "-vv")))))
+         (add-after 'unpack 'patch-testsuite
+           (lambda _
+             ;; test_not_on_path() and test_path_priority() try to run a test
+             ;; that loads jupyter_core, so we need PYTHONPATH
+             (substitute* "jupyter_core/tests/test_command.py"
+               (("env = \\{'PATH': ''\\}")
+                "env = {'PATH': '', 'PYTHONPATH': os.environ['PYTHONPATH']}")
+               (("env = \\{'PATH':  str\\(b\\)\\}")
+                "env = {'PATH': str(b), 'PYTHONPATH': os.environ['PYTHONPATH']}"))
+             #t)))))
+    (propagated-inputs
+     `(("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-six" ,python-six)
+       ("python-pytest" ,python-pytest)))
+    ;; This package provides the `jupyter` binary and thus, should also export the
+    ;; search paths instead of the jupyter meta-package.
+    (native-search-paths
+     (list (search-path-specification
+            (variable "JUPYTER_PATH")
+            (files '("share/jupyter")))))
+    (home-page "https://jupyter.org")
+    (synopsis
+     "Jupyter core package. A base package on which Jupyter projects rely.")
+    (description
+     "Jupyter core package. A base package on which Jupyter projects rely.")
+    (license license:bsd-3)))
+
+(define-public python-jupyter-client-6.1
+  (package
+    (name "python-jupyter-client")
+    (version "6.1.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_client" version))
+       (sha256
+        (base32
+         "15d5sz2s0pf0dwzpdp4qa28myxfvk1igi4vfcnj7gicbcgaghq5k"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-testsuite
+           (lambda _
+             ;; There is no such argument “encoding”.
+             (substitute* "jupyter_client/tests/test_session.py"
+               (("msgpack.unpackb\\(buf, encoding='utf8'\\)")
+                "msgpack.unpackb(buf)"))
+             ;; Test fails for unknown reason.
+             (substitute* "jupyter_client/tests/test_session.py"
+               (("import hmac" all) (string-append all "\nimport unittest"))
+               (("(.+)(def test_tracking)" all indent def)
+                (string-append indent "@unittest.skip('disabled by guix')\n"
+                               indent def)))
+             #t))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+            (if tests?
+             (begin
+               ;; Some tests try to write to $HOME.
+               (setenv "HOME" "/tmp")
+               (invoke "pytest" "-vv"))))))))
+    (propagated-inputs
+     `(("python-dateutil" ,python-dateutil)
+       ("python-jupyter-core" ,python-jupyter-core-4.6)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-tornado" ,python-tornado)
+       ("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-async-generator"
+        ,python-async-generator)
+       ("python-ipykernel" ,python-ipykernel-5.3-bootstrap)
+       ("python-ipython" ,python-ipython)
+       ("python-mock" ,python-mock)
+       ("python-msgpack" ,python-msgpack)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-asyncio" ,python-pytest-asyncio)
+       ("python-pytest-timeout" ,python-pytest-timeout)))
+    (home-page "https://jupyter.org")
+    (synopsis
+     "Jupyter protocol implementation and client libraries")
+    (description
+     "Jupyter protocol implementation and client libraries")
+    (license license:bsd-3)))
+
+(define python-jupyter-client-6.1-bootstrap
+  (package/inherit python-jupyter-client-6.1
+    (arguments
+     `(#:tests? #f
+       ,@(package-arguments python-jupyter-client-6.1)))
+    ;; Remove loop ipykernel <-> jupyter-client
+    (native-inputs `())))
+
+;; How to deal with packages that are available here, but have older versions
+;; in guix proper:
+;; Rewrite entire graph of packages with local updates. This avoids having
+;; multiple versions of the same package in the graph. Define packages with the
+;; version guix proper provides and then rewrite it.
+
+(define rewrite-ipykernel
+  (package-input-rewriting
+   `((,python-jupyter-client . ,python-jupyter-client-6.1))))
+
+(define-public python-ipykernel-5.3
+  (rewrite-ipykernel (package/inherit python-ipykernel
+    (name "python-ipykernel")
+    (version "5.3.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ipykernel" version))
+       (sha256
+        (base32
+         "17g8pfmvj38kkmfklfacar7m7h0b0wnk0qhw4cdnm6072spm49lv"))))
+    (propagated-inputs
+     `(("python-ipython" ,python-ipython)
+       ("python-jupyter-client" ,python-jupyter-client)
+       ("python-tornado" ,python-tornado)
+       ("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-flaky" ,python-flaky)
+       ("python-nose" ,python-nose)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov))))))
+
+;; Create a bootstrap variant, which can be used in python-jupyter-client-6.1’s
+;; native-arguments
+(define python-ipykernel-5.3-bootstrap
+  ((package-input-rewriting
+    `((,python-jupyter-client-6.1 . ,python-jupyter-client-6.1-bootstrap))) python-ipykernel-5.3))
+
+(define rewrite-notebook
+  (package-input-rewriting
+   `((,python-jupyter-client . ,python-jupyter-client-6.1)
+     (,python-jupyter-core . ,python-jupyter-core-4.6)
+     (,python-ipykernel . ,python-ipykernel-5.3)
+     (,python-terminado . ,python-terminado-0.8.3))))
+
+(define-public python-notebook-6.1
+  (rewrite-notebook (package
+    (name "python-notebook")
+    (version "6.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "notebook" version))
+       (sha256
+        (base32
+         "1mcq2f7bbha4krg06h8wwnkz64cwwjcpalhn8dvnwrw87f7isfa2"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-testsuite
+           (lambda _
+             ;; These tests try to delete a file using gio, which fails for
+             ;; /tmp.
+             (substitute* "notebook/services/contents/tests/test_contents_api.py"
+               ;; Add import, so we can call skip() below.
+               (("import io" all) (string-append all "\nimport unittest"))
+               (("(.+)(def (test_checkpoints_follow_file|test_delete|test_delete_dirs|test_delete_non_empty_dir))" all indent def)
+                (string-append indent "@unittest.skip('disabled by guix')\n"
+                               indent def)))
+             ;; Same here.
+             (substitute* "notebook/services/contents/tests/test_manager.py"
+               ;; Add import, so we can call skip() below.
+               (("import os" all) (string-append all "\nimport unittest"))
+               (("(.+)(def test_delete)" all indent def)
+                (string-append indent "@unittest.skip('disabled by guix')\n"
+                               indent def)))
+             ;; These tests check paths.jupyter_path(). I don’t know what
+             ;; the expected outcome would be for guix.
+             (substitute* "notebook/tests/test_serverextensions.py"
+               ;; Add import, so we can call skip() below.
+               (("import os" all) (string-append all "\nimport unittest"))
+               (("(.+)(def (test_disable|test_enable|test_merge_config|test_load_ordered))" all indent def)
+                (string-append indent "@unittest.skip('disabled by guix')\n"
+                               indent def)))
+             #t))
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+            (if tests?
+             (begin
+               ;; Some tests try to write to $HOME.
+               (setenv "HOME" "/tmp")
+               (add-installed-pythonpath inputs outputs)
+               ;; Some tests call `jupyter-notebook`.
+               (setenv "PATH" (string-append (getenv "PATH") ":" (assoc-ref outputs "out") "/bin"))
+               ;; Python tests.
+               (invoke "nosetests" "-v" "--exclude-dir" "notebook/tests/selenium")
+               ;; Browser tests. Fail with: No module named 'testpath'
+               ;(invoke "pytest" "-sv" "notebook/tests/selenium")
+             )))))))
+    (propagated-inputs
+     `(("python-argon2-cffi" ,python-argon2-cffi)
+       ("python-ipykernel" ,python-ipykernel)
+       ("python-ipython-genutils"
+        ,python-ipython-genutils)
+       ("python-jinja2" ,python-jinja2)
+       ("python-jupyter-client" ,python-jupyter-client)
+       ("python-jupyter-core" ,python-jupyter-core)
+       ("python-nbconvert" ,python-nbconvert)
+       ("python-nbformat" ,python-nbformat)
+       ("python-prometheus-client"
+        ,python-prometheus-client)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-send2trash" ,python-send2trash)
+       ("python-terminado" ,python-terminado)
+       ("python-tornado" ,python-tornado)
+       ("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-coverage" ,python-coverage)
+       ("python-nbval" ,python-nbval)
+       ("python-nose" ,python-nose)
+       ("python-nose-exclude" ,python-nose-exclude)
+       ("python-nose-warnings-filters"
+        ,python-nose-warnings-filters)
+       ("python-requests" ,python-requests)
+       ("python-requests-unixsocket"
+        ,python-requests-unixsocket)))
+    (home-page "http://jupyter.org")
+    (synopsis
+     "A web-based notebook environment for interactive computing")
+    (description
+     "A web-based notebook environment for interactive computing")
+    (license license:bsd-3))))
+
+(define-public python-json5-0.9.4
+  (package
+    (inherit python-json5)
+    (name "python-json5")
+    (version "0.9.4")
+    (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 "14878npsn7f344pwkxcnw40lc0waqgpi8j25akd7qxlwd7nchy40"))))))
+
+(define rewrite-jupyterlab
+  (package-input-rewriting
+   `((,python-jupyter-client . ,python-jupyter-client-6.1)
+     (,python-jupyter-core . ,python-jupyter-core-4.6)
+     (,python-ipykernel . ,python-ipykernel-5.3)
+     (,python-terminado . ,python-terminado-0.8.3)
+     (,python-notebook . ,python-notebook-6.1)
+     (,python-json5 . ,python-json5-0.9.4))))
+
+(define-public python-jupyterlab-server
+  (rewrite-jupyterlab (package
+    (name "python-jupyterlab-server")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyterlab_server" version))
+       (sha256
+        (base32
+         "132xby7531rbrjg9bqvsx86birr1blynjxy8gi5kcnb6x7fxjcal"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-jinja2" ,python-jinja2)
+       ("python-json5" ,python-json5)
+       ("python-jsonschema" ,python-jsonschema)
+       ("python-notebook" ,python-notebook)
+       ("python-requests" ,python-requests)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("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))))
+
+(define-public python-jupyterlab
+  (rewrite-jupyterlab (package
+    (name "python-jupyterlab")
+    (version "2.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyterlab" version))
+       (sha256
+        (base32
+         "0jydvzjvbyxjvdk7fb7jcwksw9shxbakzkcwz86pdxzl3i66rlp9"))
+       (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)
+       ;; Required to rebuild assets.
+       ("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))))
+
diff --git a/guix-science/packages/rstudio.scm b/guix-science/packages/rstudio.scm
new file mode 100644
index 0000000..afcd77d
--- /dev/null
+++ b/guix-science/packages/rstudio.scm
@@ -0,0 +1,225 @@
+;;;
+;;; Copyright © 2019, 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
+;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
+;;;
+;;; This program is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; This program is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+;; RStudio server and its dependencies. Only the first level of dependencies is
+;; built from source right now. Also RStudio itself bundles a lot of external
+;; libraries, some with custom modifications.
+;; 
+;; An older version is available at
+;; https://github.com/BIMSBbioinfo/guix-bimsb/blob/master/bimsb/packages/staging.scm
+
+(define-module (guix-science packages rstudio)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system ant)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages qt)
+  #:use-module (gnu packages base))
+
+(define-public mathjax
+  (package
+    (name "mathjax")
+    (version "2.7.8")
+    ( source (origin
+               (method url-fetch)
+               (uri (string-append "https://github.com/mathjax/MathJax/archive/" version ".tar.gz"))
+               (sha256
+                (base32
+                 "0pfkybf95a3s3v17rfb7cy598hlswkpi2g0lhnpnvlwcbj1z9p11"))))
+    (build-system copy-build-system)
+    (arguments
+     '(#:install-plan
+       '(("." "."))))
+    (synopsis "JavaScript display engine for mathematics")
+    (description
+     "MathJax is an open-source JavaScript display engine for LaTeX, MathML,
+and AsciiMath notation that works in all modern browsers, with built-in support
+for assistive technology like screen readers.")
+    (home-page "https://www.mathjax.org/")
+    (license license:asl2.0)))
+
+(define-public rstudio-server
+  (package
+    (name "rstudio-server")
+    (version "1.3.1093")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rstudio/rstudio.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0zarhsm3cghz4fn4c53y2zy05z3cxqzp87h16ya8v7hyxapaqfy6"))
+              (patches
+               (search-patches "rstudio-server-1.3.959-unbundle.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; de-blob: windows tools
+                  delete-file-recursively "dependencies/windows/tools"
+                  #t))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       '("-DRSTUDIO_TARGET=Server"
+         "-DCMAKE_BUILD_TYPE=Release"
+         ;; auto-detection seems to be broken with boost 1.72
+         "-DRSTUDIO_BOOST_SIGNALS_VERSION=2")
+       #:tests? #f ; no tests exist
+       #:modules ((guix build cmake-build-system)
+                  (guix build utils)
+                  (ice-9 match))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'unpack-dictionary
+           (lambda* (#:key inputs native-inputs #:allow-other-keys)
+             (let ((dict-dir "dependencies/common/dictionaries"))
+               (mkdir dict-dir)
+               (invoke "unzip" "-qd" dict-dir (assoc-ref inputs "dict-source-tarball")))
+             #t))
+         ;; change the default paths for mathjax and pandoc and a hardcoded call to `which`
+         (add-after 'unpack 'patch-paths
+           (lambda* (#:key inputs native-inputs #:allow-other-keys)
+             (substitute* "src/cpp/session/SessionOptions.cpp"
+               (("resources/mathjax-27") (assoc-ref inputs "mathjax")))
+             (substitute* "src/cpp/session/SessionOptions.cpp"
+               (("bin/pandoc") (string-append (assoc-ref inputs "pandoc") "/bin/pandoc")))
+             (substitute* "src/cpp/core/r_util/REnvironmentPosix.cpp"
+               (("runCommand\\(\"which") (string-append "runCommand(\"" (assoc-ref inputs "which") "/bin/which")))
+             (substitute* '("src/cpp/session/SessionConsoleProcess.cpp" "src/cpp/session/modules/SessionTerminalShell.cpp")
+               (("/usr/bin/env") (string-append (assoc-ref inputs "coreutils") "/bin/env")))
+             (substitute* '("src/cpp/session/modules/SessionFiles.R")
+               (("\"zip\"") (string-append "\"" (assoc-ref inputs "zip") "/bin/zip\"")))
+             (substitute* '("src/cpp/session/modules/SessionFiles.cpp")
+               (("\"unzip ") (string-append "\"" (assoc-ref inputs "unzip") "/bin/unzip ")))
+             #t))
+         (add-after 'unpack 'set-JAVA_HOME
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+             ;; set proper version information
+             (match (string-split ,version #\.)
+               ((major minor patch)
+                (setenv "RSTUDIO_VERSION_MAJOR" major)
+                (setenv "RSTUDIO_VERSION_MINOR" minor)
+                (setenv "RSTUDIO_VERSION_PATCH" patch)))
+             (setenv "PACKAGE_OS" "GNU Guix")
+             #t)))))
+    (native-inputs
+     `(("unzip" ,unzip)
+       ;; gwt-components are built using ant
+       ("ant" ,ant)
+       ("jdk" ,icedtea "jdk")))
+    (inputs
+     `(("boost" ,boost)
+       ("zlib" ,zlib)
+       ("linux-pam" ,linux-pam)
+       ("r-minimal" ,r-minimal)
+       ("openssl" ,openssl)
+       ;; for libuuid
+       ("util-linux" ,util-linux "lib")
+       ("pandoc" ,ghc-pandoc)
+       ("which" ,which)
+       ("mathjax" ,mathjax) ; XXX: not sure this is the correct version, but
+       ; any 2.7 patch release should work, right?
+       ;; for `env`
+       ("coreutils" ,coreutils)
+       ;; File panel -> More -> Export
+       ("zip" ,zip)
+       ;; File panel -> Upload -> Upload zip file
+       ("unzip" ,unzip)
+       ("dict-source-tarball"
+        ,(origin
+           (method url-fetch)
+           (uri "https://s3.amazonaws.com/rstudio-buildtools/dictionaries/core-dictionaries.zip")
+           (sha256
+            (base32
+             "153lg3ai97qzbqp6zjg10dh3sfvz80v42cjw45zwz7gv1risjha3"))))
+       ("junit-source-tarball"
+        ,(origin
+           (method url-fetch)
+           (uri "https://s3.amazonaws.com/rstudio-buildtools/junit-4.9b3.jar")
+           (sha256
+            (base32
+             "0l850yfbq0cgycp8n0r0a1b7xznd37pgfd656vzdwim4blznqmnw"))))))
+    (home-page "https://rstudio.com/products/rstudio/#rstudio-server")
+    (synopsis "Integrated development environment (IDE) for R")
+    (description "RStudio is an integrated development environment (IDE) for the R
+programming language. Some of its features include: Customizable workbench
+with all of the tools required to work with R in one place (console, source,
+plots, workspace, help, history, etc.); syntax highlighting editor with code
+completion; execute code directly from the source editor (line, selection, or
+file); full support for authoring Sweave and TeX documents.  RStudio can also
+be run as a server, enabling multiple users to access the RStudio IDE using a
+web browser.")
+    (license license:agpl3)))
+
+(define-public rstudio
+  (package (inherit rstudio-server)
+    (name "rstudio")
+    (arguments
+     (substitute-keyword-arguments (package-arguments rstudio-server)
+       ((#:configure-flags flags)
+        '(list "-DRSTUDIO_TARGET=Desktop"
+               "-DCMAKE_BUILD_TYPE=Release"
+               ;; auto-detection seems to be broken with boost 1.72
+               "-DRSTUDIO_BOOST_SIGNALS_VERSION=2"
+               (string-append "-DQT_QMAKE_EXECUTABLE="
+                              (assoc-ref %build-inputs "qtbase")
+                              "/bin/qmake")))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'relax-qt-version
+             (lambda _
+               (substitute* "src/cpp/desktop/CMakeLists.txt"
+                 (("5\\.4") "5.9"))
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (qtwebengine-path (string-append
+                                         (assoc-ref inputs "qtwebengine")
+                                         "/lib/qt5/libexec/QtWebEngineProcess")))
+                 (wrap-program (string-append bin "/rstudio")
+                   `("QTWEBENGINEPROCESS_PATH" ":" = (,qtwebengine-path))))
+               #t))))))
+    (inputs
+     `(("qtbase" ,qtbase)
+       ("qtdeclarative" ,qtdeclarative)
+       ("qtlocation" ,qtlocation)
+       ("qtsvg" ,qtsvg)
+       ("qtsensors" ,qtsensors)
+       ("qtxmlpatterns" ,qtxmlpatterns)
+       ("qtwebchannel" ,qtwebchannel)
+       ("qtwebengine" ,qtwebengine)
+       ,@(package-inputs rstudio-server)))
+    (synopsis "Integrated development environment (IDE) for R (desktop version)")))
+
diff --git a/python-jupyterlab-copy-nometa.patch b/python-jupyterlab-copy-nometa.patch
new file mode 100644
index 0000000..5e770c0
--- /dev/null
+++ b/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/rstudio-server-1.3.959-unbundle.patch b/rstudio-server-1.3.959-unbundle.patch
new file mode 100644
index 0000000..dd0893d
--- /dev/null
+++ b/rstudio-server-1.3.959-unbundle.patch
@@ -0,0 +1,54 @@
+diff --git a/src/cpp/session/CMakeLists.txt b/src/cpp/session/CMakeLists.txt
+index 8f0daa57ea..f66220fc8b 100644
+--- a/src/cpp/session/CMakeLists.txt
++++ b/src/cpp/session/CMakeLists.txt
+@@ -22,12 +22,12 @@ add_subdirectory(workers)
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
+   message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27")
+-  message(FATAL_ERROR "Mathjax 2.7 not found (re-run install-dependencies script to install)")
+-endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
++#if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27")
++#  message(FATAL_ERROR "Mathjax 2.7 not found (re-run install-dependencies script to install)")
++#endif()
++#if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
++#  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
++#endif()
+ 
+ # verify embedded packages are available
+ foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+@@ -501,8 +501,8 @@ if (NOT RSTUDIO_SESSION_WIN32)
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+    # install mathjax for local html preview
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
++   #install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27"
++   #        DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+    # icons for database connections
+    install(DIRECTORY "resources/connections"
+@@ -517,13 +517,13 @@ if (NOT RSTUDIO_SESSION_WIN32)
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+    # install pandoc
+-   set(PANDOC_VERSION "2.7.3" CACHE INTERNAL "Pandoc version")
++   #set(PANDOC_VERSION "2.7.3" CACHE INTERNAL "Pandoc version")
+ 
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
++   #set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
++   #file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
++   #install(FILES ${PANDOC_FILES}
++   #        PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
++   #        DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+ 
+    # install embedded packages
+    foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})