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authorEfraim Flashner2019-11-06 06:53:51 -0600
committerEfraim Flashner2019-11-06 06:53:51 -0600
commit1f7e1da5ba030572b1ef1f1d5c17ef85ff93ab38 (patch)
treea0a5dd8cd66a67b9c23b364011286f594e4af111 /gn/packages
parentc71951c24a3c4d7428ada6e350a326daa07790e1 (diff)
downloadguix-bioinformatics-1f7e1da5ba030572b1ef1f1d5c17ef85ff93ab38.tar.gz
gn: Add jupyterhub, the-littlest-jupyterhub
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/jupyterhub.scm480
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diff --git a/gn/packages/jupyterhub.scm b/gn/packages/jupyterhub.scm
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+(define-module (gn packages jupyterhub)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages)
+ #:use-module (guix download)
+ #:use-module (guix git-download)
+ #:use-module (guix build-system python)
+ #:use-module (gnu packages check)
+ #:use-module (gnu packages databases)
+ #:use-module (gnu packages libffi)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages monitoring)
+ #:use-module (gnu packages openstack)
+ #:use-module (gnu packages protobuf)
+ #:use-module (gnu packages python-crypto)
+ #:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages serialization)
+ #:use-module (gnu packages time)
+ )
+
+(define-public jupyterhub
+ (package
+ (name "jupyterhub")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jupyterhub" version))
+ (sha256
+ (base32
+ "0zx6gw9yhgki05j21p6x1x2sf5a2mg2c2mx0ii8rl6q4b98ilm1k"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f ; Tests require a webserver, postgresql database and npm.
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (;; From .travis.yml
+ (invoke "initdb" "main")
+ (invoke "pg_ctl" "-D" "main" "start")
+ (invoke "psql" "--list")
+ ;; From ci/init-db.sh
+ (invoke "psql" "-d" "postgres" "-c"
+ "CREATE DATABASE jupyterhub_upgrade_072;")
+ (invoke "psql" "-d" "postgres" "-c"
+ "CREATE DATABASE jupyterhub_upgrade_081;")
+ (invoke "psql" "-d" "postgres" "-c"
+ "CREATE DATABASE jupyterhub_upgrade_094;")
+ (invoke "pytest" "-v" "--maxfail=2" "jupyterhub/tests"))
+ #t))))))
+ (propagated-inputs
+ `(("python-alembic" ,python-alembic)
+ ("python-async-generator" ,python-async-generator)
+ ("python-certipy" ,python-certipy)
+ ("python-dateutil" ,python-dateutil)
+ ("python-entrypoints" ,python-entrypoints)
+ ("python-jinja2" ,python-jinja2)
+ ("python-oauthlib" ,python-oauthlib)
+ ("python-pamela" ,python-pamela)
+ ("python-prometheus-client" ,python-prometheus-client)
+ ("python-requests" ,python-requests)
+ ("python-sqlalchemy" ,python-sqlalchemy)
+ ("python-tornado" ,python-tornado)
+ ("python-traitlets" ,python-traitlets)))
+ (native-inputs
+ `(
+ ;("postgresql" ,postgresql)
+ ;("python-psycopg2" ,python-psycopg2)
+
+ ("python-beautifulsoup4" ,python-beautifulsoup4)
+ ("python-jupyter-client" ,python-jupyter-client)
+ ("python-notebook" ,python-notebook)
+ ("python-pytest" ,python-pytest)
+ ("python-pyzmq" ,python-pyzmq)
+ ("python-requests-mock" ,python-requests-mock)))
+ (home-page "https://jupyter.org")
+ (synopsis "Multi-user server for Jupyter notebooks")
+ (description
+ "JupyterHub is the best way to serve Jupyter notebook for multiple users.
+It can be used in a classes of students, a corporate data science group or
+scientific research group. It is a multi-user Hub that spawns, manages, and
+proxies multiple instances of the single-user Jupyter notebook server.")
+ (license license:bsd-3)))
+
+(define-public the-littlest-jupyterhub
+ (let ((commit "770b95027951c1e191690b0f65d3e2e2d72ba05f") ; Oct 30, 2019
+ (revision "1"))
+ (package
+ (name "the-littlest-jupyterhub")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jupyterhub/the-littlest-jupyterhub.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0dnin2rwrqr8nzf7gj6sjqchvdi24kd0sgjh655c4zq1hdbpsmc6"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'loosen-input-requirements
+ (lambda _
+ (substitute* "setup.py"
+ (("==.*'") "'"))
+ #t))
+ (add-after 'unpack 'patch-some-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((python (assoc-ref inputs "python")))
+ ;; Delete some tests that we're not going to run.
+ (delete-file "tests/test_conda.py")
+ (delete-file "tests/test_user.py")
+ (delete-file "tests/test_utils.py")
+ ;; No need to make node available for the test suite.
+ (substitute* "tests/test_installer.py"
+ (("installer.ensure_node.*") "")
+ (("/usr/bin/node") (string-append python "/bin/python")))
+ ;; Don't download traefik.
+ (substitute* "tests/test_traefik.py"
+ (("traefik.ensure_traefik_binary")
+ "#traefik.ensure_traefik_binary")
+ (("assert traefik") "#assert traefik")
+ (("assert \\(traefik") "#assert (traefik"))
+ #t)))
+ (replace 'check
+ (lambda _
+ (invoke "python3" "-m" "pytest" "-v" "tests/"))))))
+ (propagated-inputs
+ `(("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-jinja2" ,python-jinja2)
+ ("python-pluggy" ,python-pluggy)
+ ("python-passlib" ,python-passlib)
+ ("python-backoff" ,python-backoff)
+ ("python-requests" ,python-requests)
+ ("python-jupyterhub-traefik-proxy" ,python-jupyterhub-traefic-proxy)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-pytoml" ,python-pytoml)))
+ (home-page "https://the-littlest-jupyterhub.readthedocs.io/en/latest/")
+ (synopsis "JupyterHub server for a single server")
+ (description
+ "The Littlest JupyterHub (TLJH) distribution helps you provide Jupyter
+Notebooks to 1-50 users on a single server. Administrators who do not consider
+themselves 'system administrators' but would like to provide hosted Jupyter
+Notebooks for their students / users are the primary audience. All users are
+provided with the same environment, and administrators can easily install
+libraries into this environment without any specialized knowledge.")
+ (license license:bsd-3))))
+
+(define-public python-backoff
+ (package
+ (name "python-backoff")
+ (version "1.8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "backoff" version))
+ (sha256
+ (base32
+ "0g2s4p34ml8dnldbj5qkg7ni5bwsq492nhry2inc2pn66qyx47iz"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/litl/backoff")
+ (synopsis "Function decoration for backoff and retry")
+ (description
+ "Function decoration for backoff and retry")
+ (license license:expat)))
+
+(define-public python-jupyterhub-traefic-proxy
+ (package
+ (name "python-jupyterhub-traefic-proxy")
+ (version "0.1.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jupyterhub/traefik-proxy.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "021lqll3b84qmyw417wj15wpvs8ckvabx8ygm4fjy9bdllaxmmag"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("jupyterhub" ,jupyterhub)
+ ("python-etcd3" ,python-etcd3)
+ ("python-aiohttp" ,python-aiohttp)
+ ("python-passlib" ,python-passlib)
+ ("python-consul" ,python-consul)
+ ("python-toml" ,python-toml)
+ ("python-escapism" ,python-escapism)))
+ (native-inputs
+ `(("python-jupyter-client" ,python-jupyter-client)
+ ("python-notebook" ,python-notebook)
+ ("python-numpy" ,python-numpy)
+ ("python-pyzmq" ,python-pyzmq)
+ ("python-websockets" ,python-websockets)))
+ (home-page "https://jupyterhub-traefik-proxy.readthedocs.io/")
+ (synopsis "JupyterHub proxy implementation with traefik")
+ (description "An implementation of the JupyterHub proxy api with traefik: an
+extremely lightweight, portable reverse proxy implementation, that supports load
+balancing and can configure itself automatically and dynamically.")
+ (license license:bsd-3)))
+
+(define-public python-etcd3
+ (package
+ (name "python-etcd3")
+ (version "0.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "etcd3" version))
+ (sha256
+ (base32
+ "11qf9v69h5gx212p9hv3m8z290gagn834x89y0gn7iijy2wj9995"))))
+ (build-system python-build-system)
+ (arguments '(#:tests? #f)) ; Tests require running etcd.
+ (propagated-inputs
+ `(("python-grpcio" ,python-grpcio)
+ ("python-protobuf" ,python-protobuf)
+ ("python-tenacity" ,python-tenacity)))
+ (home-page "https://github.com/kragniz/python-etcd3")
+ (synopsis "Python client for the etcd3 API")
+ (description "Python client for the etcd3 API")
+ (license license:asl2.0)))
+
+(define-public python-escapism
+ (package
+ (name "python-escapism")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "escapism" version))
+ (sha256
+ (base32
+ "11lv1kqlk2brx1i2yczajga4c657z184f6fsnf2mnpx90kxc272z"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/minrk/escapism")
+ (synopsis "Simple, generic API for escaping strings")
+ (description
+ "Simple, generic API for escaping strings.")
+ (license license:expat)))
+
+(define-public python-tenacity
+ (package
+ (name "python-tenacity")
+ (version "6.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "tenacity" version))
+ (sha256
+ (base32
+ "0w9miqmmi63yqp9lw7p6nf6gh5pa57vg60v6f94f11qqpg19gwvj"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "pytest"))))))
+ (propagated-inputs
+ `(("python-six" ,python-six)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-setuptools-scm" ,python-setuptools-scm)
+ ("python-tornado" ,python-tornado)))
+ (home-page "https://github.com/jd/tenacity")
+ (synopsis "Retry code until it succeeeds")
+ (description "Tenacity is a general-purpose retrying library to simplify the
+task of adding retry behavior to just about anything.")
+ (license license:asl2.0)))
+
+(define-public python-certipy
+ (package
+ (name "python-certipy")
+ (version "0.1.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "certipy" version))
+ (sha256
+ (base32
+ "0n980gqpzh0fm58h3i4mi2i10wgj606lscm1r5sk60vbf6vh8mv9"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-pyopenssl" ,python-pyopenssl)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/LLNL/certipy")
+ (synopsis "Utility to create and sign CAs and certificates")
+ (description
+ "Utility to create and sign CAs and certificates")
+ (license license:bsd-3)))
+
+(define-public python-pamela
+ (package
+ (name "python-pamela")
+ (version "1.0.0")
+ (source
+ (origin
+ ;; Tests not distributed in pypi release.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/minrk/pamela.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0cg3w6np1fbjpvzhv54xg567hpf38szwp2d4gvzb9r736nxbv0vr"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f ; Tests aren't designed to be run inside a container.
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'hardcode-pam.so
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((pam (assoc-ref inputs "linux-pam")))
+ (substitute* "pamela.py"
+ ; (("\"pam\"") (string-append "\"" pam "/lib/libpam.so\"")))
+ (("find_library\\(\"pam\")") (string-append "'" pam "/lib/libpam.so'")))
+ ; (("LIBPAM =.*") (string-append "LIBPAM = \"" pam "/lib\"\n")))
+ #t)))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (if (file-exists? "test_pamela.py")
+ (invoke "py.test" "--assert=plain" "test_pamela.py")
+ (invoke "python" "-m" "pamela" "-a" "`whoami`"))
+ #t))))))
+ (inputs
+ `(("linux-pam" ,linux-pam)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/minrk/pamela")
+ (synopsis "PAM interface using ctypes")
+ (description "PAM interface using ctypes")
+ (license license:expat)))
+
+(define-public python-pifpaf
+ (package
+ (name "python-pifpaf")
+ (version "2.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pifpaf" version))
+ (sha256
+ (base32
+ "09xixb4ddjp15spbm2788yq6rjr5fzy1p8dzcqyzp6pbkv7vwxvg"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "python" "setup.py" "testr" "--slowest"
+ "--testr-args=until-failure"))))))
+ (propagated-inputs
+ `(("python-click" ,python-click)
+ ("python-daiquiri" ,python-daiquiri)
+ ("python-fixtures" ,python-fixtures)
+ ("python-jinja2" ,python-jinja2)
+ ("python-pbr" ,python-pbr)
+ ("python-psutil" ,python-psutil)
+ ("python-six" ,python-six)
+ ("python-xattr" ,python-xattr)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-os-testr" ,python-os-testr)
+ ("python-requests" ,python-requests)
+ ("python-testrepository" ,python-testrepository)
+ ("python-testtools" ,python-testtools)))
+ (home-page "https://github.com/jd/pifpaf")
+ (synopsis
+ "Suite of tools and fixtures to manage daemons for testing")
+ (description
+ "Suite of tools and fixtures to manage daemons for testing")
+ (license license:asl2.0)))
+
+(define-public python-daiquiri
+ (package
+ (name "python-daiquiri")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "daiquiri" version))
+ (sha256
+ (base32
+ "1hclvhfm3ix40g3m7g14w0nz2qawb7gp3fjba7d6xzxhh9mj6fn1"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-json-logger" ,python-json-logger)
+ ("python-pbr" ,python-pbr)
+ ("python-pytest" ,python-pytest)
+ ("python-six" ,python-six)))
+ (home-page "https://github.com/jd/daiquiri")
+ (synopsis "Library to configure Python logging easily")
+ (description
+ "Library to configure Python logging easily")
+ (license license:asl2.0)))
+
+(define-public python-xattr
+ (package
+ (name "python-xattr")
+ (version "0.9.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "xattr" version))
+ (sha256
+ (base32
+ "0n3llkk488bjywzifgyhyxcfdz22851k3s2h8g69kzmlxa7b5cbw"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-cffi" ,python-cffi)))
+ (home-page "https://github.com/xattr/xattr")
+ (synopsis "Python wrapper for extended filesystem attributes")
+ (description
+ "Python wrapper for extended filesystem attributes")
+ (license license:expat)))
+
+(define-public python-json-logger
+ (package
+ (name "python-json-logger")
+ (version "0.1.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "python-json-logger" version))
+ (sha256
+ (base32
+ "10g2ya6nsvn5vxzvq2wb8q4d43i3d7756i5rxyjna6d0y9i138xp"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/madzak/python-json-logger")
+ (synopsis "Python library adding a json log formatter")
+ (description
+ "A python library adding a json log formatter")
+ (license license:bsd-3)))
+
+(define-public python-websockets
+ (package
+ (name "python-websockets")
+ (version "8.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "websockets" version))
+ (sha256
+ (base32
+ "03s3ml6sbki24aajllf8aily0xzrn929zxi84p50zkkbikdd4raw"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/aaugustin/websockets")
+ (synopsis "Implementation of the WebSocket Protocol")
+ (description
+ "An implementation of the WebSocket Protocol (RFC 6455 & 7692).")
+ (license license:bsd-3)))
+
+(define-public python-pytoml
+ (package
+ (name "python-pytoml")
+ (version "0.1.21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytoml" version))
+ (sha256
+ (base32
+ "1rv1byiw82k7mj6aprcrqi2vdabs801y97xhfnrz7kxds34ggv4f"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/avakar/pytoml")
+ (synopsis "A parser for TOML-0.4.0")
+ (description "A parser for TOML-0.4.0")
+ (license license:expat)))