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authorEfraim Flashner2022-01-27 11:20:08 +0200
committerEfraim Flashner2022-01-27 11:21:03 +0200
commitd1b682348601d968dd5ed3beb0049e7f51bb2c61 (patch)
treeb4264b1203c88a331206acb447303341bbccbcb7 /gn
parentafd77f2276ca79f6fe92ce36a2eb8eb45040cd93 (diff)
downloadguix-bioinformatics-d1b682348601d968dd5ed3beb0049e7f51bb2c61.tar.gz
julia package cleanup
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/julia.scm49
1 files changed, 18 insertions, 31 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 276a21a..ff1d7aa 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -46,8 +46,7 @@
(chmod "runpluto.sh" #o555) ; it starts as #o444
(substitute* "runpluto.sh"
;; The arguments don't pass through the wrapper so we hardcode the port.
- (("\\$\\{1\\}") "4343"))
- #t))
+ (("\\$\\{1\\}") "4343"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@@ -61,8 +60,7 @@
"runpluto.sh"
"notebooks"
"Project.toml"
- "Manifest.toml"))
- #t)))
+ "Manifest.toml")))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@@ -70,12 +68,10 @@
(wrap-script (string-append out "/runpluto.sh")
`("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin")
,(string-append (assoc-ref inputs "coreutils") "/bin")))
- `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH"))))
- #t)))
+ `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))))))
(replace 'precompile
(lambda _
- (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\"")
- #t)))))
+ (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\""))))))
(propagated-inputs
`(;; from setup.py
("python-jupyter-server-proxy"
@@ -226,8 +222,7 @@ distributed computing.")
(add-after 'link-depot 'hardcode-conda-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Conda.jl"
- (("bin_dir\\(ROOTENV\\), \"conda\"") (string-append "\"" (assoc-ref inputs "conda") "/bin/\", \"conda\"")))
- #t))
+ (("bin_dir\\(ROOTENV\\), \"conda\"") (string-append "\"" (assoc-ref inputs "conda") "/bin/\", \"conda\"")))))
(add-before 'check 'pre-check
(lambda* (#:key inputs #:allow-other-keys)
;(setenv "CONDA_JL_HOME" (string-append (assoc-ref inputs "conda") ))
@@ -324,7 +319,8 @@ properties
(base32 "0bv281n999kmjlp9p3vl4vv4phdl17z4gdpvkjzxsyk6dvcg2nrf"))))
(build-system julia-build-system)
(arguments
- `(#:tests? #f)) ; TODO: Fix test
+ `(#:tests? #f ; TODO: Fix test
+ ))
(propagated-inputs
`(("julia-compat" ,julia-compat)
("julia-fillarrays" ,julia-fillarrays)
@@ -428,14 +424,12 @@ optimization of functions.")
(add-after 'link-depot 'dont-check-for-upgrades
(lambda _
(substitute* "frontend/components/Welcome.js"
- (("local_index !== -1") "false"))
- #t))
+ (("local_index !== -1") "false"))))
(add-after 'link-depot 'skip-network-tests
(lambda _
(substitute* "test/runtests.jl"
;; Attempts to update the package registry.
- ((".*Basic.jl.*") ""))
- #t)))))
+ ((".*Basic.jl.*") "")))))))
(propagated-inputs
`(("julia-configurations" ,julia-configurations)
("julia-fuzzycompletions" ,julia-fuzzycompletions)
@@ -502,8 +496,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(add-after 'link-depot 'adjust-test-suite
(lambda _
(substitute* "test/misc.jl"
- (("test logmvbeta\\(1") "test_nowarn logmvbeta(1"))
- #t)))))
+ (("test logmvbeta\\(1") "test_nowarn logmvbeta(1")))))))
(propagated-inputs
`(("julia-logexpfunctions" ,julia-logexpfunctions)
("julia-rmath" ,julia-rmath)
@@ -542,16 +535,14 @@ and numerical functions for statistical computing.")
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
- (invoke "julia" "test.jl"))
- #t))
+ (invoke "julia" "test.jl"))))
(add-before 'install 'build
(lambda _
(invoke "make")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (install-file "src/libRmath-julia.so" (string-append out "/lib"))
- #t))))))
+ (install-file "src/libRmath-julia.so" (string-append out "/lib"))))))))
(home-page "https://github.com/JuliaStats/Rmath-julia")
(synopsis "Rmath library from R")
(description "This is a slightly modified version of the standalone Rmath
@@ -586,8 +577,7 @@ functions.")
(let* ((rmath (assoc-ref inputs "rmath"))
(librmath (string-append rmath "/lib/libRmath-julia.so")))
(substitute* "src/Rmath.jl"
- (("libRmath\\)") (string-append "\"" librmath "\")")))
- #t))))))
+ (("libRmath\\)") (string-append "\"" librmath "\")")))))))))
(propagated-inputs
`(("julia-rmath-jll" ,julia-rmath-jll)))
(inputs
@@ -663,8 +653,7 @@ R's d-p-q-r functions for probability distributions. It is a wrapper around
(substitute* "test/examples.jl"
;; Prevent a cycle with Optim.jl.
(("^ SKIPFILE.*") "")
- (("^ #SKIPFILE") " SKIPFILE"))
- #t)))))
+ (("^ #SKIPFILE") " SKIPFILE")))))))
(propagated-inputs
`(("julia-nlsolversbase" ,julia-nlsolversbase)
("julia-nanmath" ,julia-nanmath)
@@ -892,7 +881,7 @@ that still support Julia versions older than 1.6.")
;; https://github.com/JuliaPackaging/Yggdrasil/tree/7e9ec714d786c4c841a80bdf75b84570c5bda7a1/E/EarCut
(define-public julia-earcut-jll
- ;; Only release tag contains just a license file.
+ ;; The only release tag contains just a license file.
(let ((commit "b234ae0c064af12eb5482c7474a64af8be0f511e")
(revision "1"))
(package
@@ -921,9 +910,8 @@ that still support Julia versions older than 1.6.")
(string-append
"generate_wrapper_header(\"EarCut\", \""
(assoc-ref inputs "earcut") "\")\n"))))
- ;; There's a Julia file for each platform, override them all
- (find-files "src/wrappers/" "\\.jl$"))
- #t)))))
+ ;; There's a Julia file for each platform, override them all.
+ (find-files "src/wrappers/" "\\.jl$")))))))
(inputs ;required by artifacts
`(("earcut" ,earcut-for-julia-earcut-jll)))
(propagated-inputs
@@ -950,8 +938,7 @@ that still support Julia versions older than 1.6.")
(snippet
'(begin
(substitute* "CMakeLists.txt"
- ((".*add_subdirectory.*") ""))
- #t))))
+ ((".*add_subdirectory.*") ""))))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))