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authorEfraim Flashner2022-04-20 16:14:32 +0300
committerEfraim Flashner2022-04-20 16:15:04 +0300
commit027827b9606a41edf5c778b98639b0f015f56cc9 (patch)
tree110d3f375738e15f86e378139df37f2dc116aaba
parent23cf83df7482c5e0ed185eb8532d4eacf2ad7241 (diff)
downloadguix-bioinformatics-027827b9606a41edf5c778b98639b0f015f56cc9.tar.gz
Remove upstreamed packages
-rw-r--r--gn/packages/jupyterhub.scm19
-rw-r--r--gn/packages/python.scm82
2 files changed, 0 insertions, 101 deletions
diff --git a/gn/packages/jupyterhub.scm b/gn/packages/jupyterhub.scm
index 838412b..322999b 100644
--- a/gn/packages/jupyterhub.scm
+++ b/gn/packages/jupyterhub.scm
@@ -267,25 +267,6 @@ balancing and can configure itself automatically and dynamically.")
"Simple, generic API for escaping strings.")
(license license:expat)))
-;; This package is deprecated upstream.
-;; Author suggests using python-toml
-(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)))
-
(define-public python-jupyter-repo2docker
(package
(name "python-jupyter-repo2docker")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index a689b1c..61c5133 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -32,28 +32,6 @@
#:use-module (guix build-system python)
#:use-module (srfi srfi-1))
-(define-public python-pyvcf
- (package
- (name "python-pyvcf")
- (version "0.6.8")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pyvcf" version))
- (sha256
- (base32
- "1ngryr12d3izmhmwplc46xhyj9i7yhrpm90xnsd2578p7m8p5n79"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f))
- (home-page
- "https://github.com/jamescasbon/PyVCF")
- (synopsis
- "Variant Call Format (VCF) parser for Python")
- (description
- "Variant Call Format (VCF) parser for Python")
- (license #f)))
-
(define-public python-rpy2-2.9
(package
(inherit python-rpy2)
@@ -1409,31 +1387,6 @@ sorted order.")
"Easy to use fixtures to write regression tests.")
(license license:expat)))
-(define-public python-pytest-datadir
- (package
- (name "python-pytest-datadir")
- (version "1.3.1")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pytest-datadir" version))
- (sha256
- (base32
- "066bg6wlzgq2pqnjp73dfrcmk8951xw3aqcxa3p1axgqimrixbyk"))))
- (build-system python-build-system)
- (propagated-inputs
- `(("python-pathlib2" ,python-pathlib2)
- ("python-pytest" ,python-pytest)))
- (inputs
- `(("python-setuptools-scm" ,python-setuptools-scm)))
- (home-page
- "http://github.com/gabrielcnr/pytest-datadir")
- (synopsis
- "pytest plugin for test data directories and files")
- (description
- "pytest plugin for test data directories and files")
- (license license:expat)))
-
(define-public python-pre-commit
(package
(name "python-pre-commit")
@@ -1808,41 +1761,6 @@ The goal of the project is to parse everything in the Pip requirement
file format spec.")
(license license:bsd-3)))
-(define-public python-pytest-pudb
- ;; PyPi does not include tests
- (let ((commit "a6b3d2f4d35e558d72bccff472ecde9c9d9c69e5")
- (revision "0"))
- (package
- (name "python-pytest-pudb")
- (version "0.7.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/wronglink/pytest-pudb")
- (commit commit)))
- (file-name (string-append name "-" commit))
- (sha256
- (base32 "1c0pypxx3y8w7s5bz9iy3w3aablnhn81rnhmb0is8hf2qpm6k3w0"))))
- (build-system python-build-system)
- (propagated-inputs (list pudb))
- (native-inputs
- (list python-pytest))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "pytest" "-v")))))))
- (home-page "https://github.com/wronglink/pytest-pudb")
- (synopsis "Pytest PuDB debugger integration")
- (description
- "@code{python-pytest-pudb} provides PuDB debugger integration based on
- pytest PDB integration.")
- (license license:expat))))
-
(define-public python-supervisor
(package
(name "python-supervisor")