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authorEfraim Flashner2021-05-27 16:52:41 +0300
committerEfraim Flashner2021-05-27 17:00:10 +0300
commite567af106e0ffda08f236c94b3790f0cb776ef64 (patch)
treeac813deecff50e74dffef6a2e737e87830853db8 /gn/packages/python.scm
parent2df25a354555437cfe149f4293adb0ad8cbc5160 (diff)
downloadguix-bioinformatics-e567af106e0ffda08f236c94b3790f0cb776ef64.tar.gz
gn: upstream some libraries
Diffstat (limited to 'gn/packages/python.scm')
-rw-r--r--gn/packages/python.scm54
1 files changed, 14 insertions, 40 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 2146931..03560c2 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1692,17 +1692,12 @@ sorted order.")
"Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like @code{/rstudio} next to others like @code{/lab}. Alongside the python package that provides the main functionality, the JupyterLab extension (@code{@@jupyterlab/server-proxy}) provides buttons in the JupyterLab launcher window to get to RStudio for example.")
(license license:bsd-3)))
-(define-public python-jupyter-server-proxy-1
+(define-public python-jupyter-server-proxy-1 ; bundled javascript?
(package
- (inherit python-jupyter-server-proxy)
(name "python-jupyter-server-proxy")
(version "1.6.0")
(source
(origin
- ;(method url-fetch)
- ;(uri (pypi-uri "jupyter-server-proxy" version))
- ;(sha256
- ; (base32 "0sdiywnymdqsmdddj1gszb8fj1z3p1njy419q0i921ib4rmdc22y"))))
;; Tests not included in release.
(method git-fetch)
(uri (git-reference
@@ -1711,6 +1706,7 @@ sorted order.")
(file-name (git-file-name name version))
(sha256
(base32 "03yry0jz6xlvy28h3w514pw0q9w51lnr1lpcigqmhnf5x7g9bfyy"))))
+ (build-system python-build-system)
(arguments
`(#:tests? #f ; Running the test suite isn't fully documented.
#:phases
@@ -1719,8 +1715,10 @@ sorted order.")
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
+ ;; see .github/workflows/test.yaml and CONTRIBUTING.md
(setenv "JUPYTER_TOKEN" "secret")
(setenv "HOME" (getcwd))
+ (invoke "jupyter" "serverextension" "enable" "jupyter_server_proxy")
(system "jupyter-notebook --config=./tests/resources/jupyter_server_config.py &")
(sleep 5)
(invoke "pytest" "--verbose"))
@@ -1730,41 +1728,17 @@ sorted order.")
("python-notebook" ,python-notebook)
("python-simpervisor" ,python-simpervisor)))
(native-inputs
- `(("python-pytest" ,python-pytest)))))
-
-(define-public python-simpervisor ; upstream ready
- (package
- (name "python-simpervisor")
- (version "0.4")
- (source
- (origin
- ;; Tests not included in release.
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/yuvipanda/simpervisor")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1brsisx7saf4ic0dih1n5y7rbdbwn1ywv9pl32bch3061r46prvv"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f ; Test suite can't find aiohttp.
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "--maxfail" "3" "--verbose"))
- #t)))))
- (native-inputs
- `(("python-aiohttp" ,python-aiohttp)
- ("python-pytest" ,python-pytest)
- ("python-pytest-asyncio" ,python-pytest-asyncio)))
- (home-page "https://github.com/yuvipanda/simpervisor")
- (synopsis "Simple async process supervisor")
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://jupyter-server-proxy.readthedocs.io/")
+ (synopsis "Jupyter server extension to supervise and proxy web services")
(description
- "This package provides a simple async process supervisor in Python.")
+ "Jupyter Server Proxy lets you run arbitrary external processes (such as
+RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your
+notebook server and provide authenticated web access to them using a path like
+@code{/rstudio} next to others like @code{/lab}. Alongside the python package
+that provides the main functionality, the JupyterLab extension
+(@code{@@jupyterlab/server-proxy}) provides buttons in the JupyterLab launcher
+window to get to RStudio for example.")
(license license:bsd-3)))
(define-public python-jupyter-server