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authorEfraim Flashner2022-01-31 12:43:42 +0200
committerEfraim Flashner2022-01-31 12:43:42 +0200
commit5ff6f54f4682bf1dd62318136072b6b38c0d41a9 (patch)
tree0c0c0b5b534ac9bfca752c7909b0232c4d938649
parent40dfce43b467e1ac99b85e003070d5107660dce4 (diff)
downloadguix-bioinformatics-5ff6f54f4682bf1dd62318136072b6b38c0d41a9.tar.gz
gn: julia package updates
-rw-r--r--gn/packages/julia.scm92
1 files changed, 36 insertions, 56 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index f6856e0..34a7a35 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -509,11 +509,11 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(substitute* "test/misc.jl"
(("test logmvbeta\\(1") "test_nowarn logmvbeta(1")))))))
(propagated-inputs
- `(("julia-logexpfunctions" ,julia-logexpfunctions)
- ("julia-rmath" ,julia-rmath)
- ("julia-specialfunctions" ,julia-specialfunctions)))
+ (list julia-logexpfunctions
+ julia-rmath
+ julia-specialfunctions))
(native-inputs
- `(("julia-forwarddiff" ,julia-forwarddiff)))
+ (list julia-forwarddiff))
(home-page "https://github.com/JuliaStats/StatsFuns.jl")
(synopsis "Mathematical functions related to statistics")
(description "This package provides a collection of mathematical constants
@@ -664,13 +664,20 @@ 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")))))))
+ (("^ #SKIPFILE") " SKIPFILE"))))
+ (add-after 'link-depot 'skip-doublefloats-tests
+ (lambda _
+ (substitute* "test/runtests.jl"
+ (("using DoubleFloats.*") "")
+ ((".*arbitrary_precision\\.jl.*") "")))))))
(propagated-inputs
(list julia-nlsolversbase
julia-nanmath
julia-parameters))
(native-inputs
- (list julia-doublefloats
+ ;; DoubleFloats.jl transitively depends on TimeZones.jl, which is currently
+ ;; unpackageable due to its oversized Artifacts.toml.
+ (list ;julia-doublefloats
julia-optimtestproblems))
(home-page "https://github.com/JuliaNLSolvers/LineSearches.jl")
(synopsis "Line search methods for optimization and root-finding")
@@ -710,6 +717,7 @@ floats and complex types.")
(license license:expat)))
;; ready to upstream
+;; This package depends on TimeZones.jl.
(define-public julia-polynomials
(package
(name "julia-polynomials")
@@ -758,15 +766,16 @@ polynomials.")
(arguments
`(#:tests? #f)) ; TODO: Fix! broken with timezone stuff
(propagated-inputs
- `(("julia-recipesbase" ,julia-recipesbase)
- ("julia-timezones" ,julia-timezones)))
+ (list julia-infinity
+ julia-recipesbase
+ julia-timezones))
(native-inputs
- `(("julia-documenter" ,julia-documenter)
- ;("julia-imagemagick" ,julia-imagemagick)
- ;("julia-infinity" ,julia-infinity)
- ;("julia-plots" ,julia-plots)
- ;("julia-visualregressiontests" ,julia-visualregressiontests)
- ))
+ (list julia-documenter
+ julia-imagemagick
+ julia-infinity
+ ;julia-plots
+ ;julia-visualregressiontests
+ ))
(home-page "https://github.com/invenia/Intervals.jl")
(synopsis "Non-iterable ranges")
(description "This package defines:
@@ -774,13 +783,15 @@ polynomials.")
AbstractInterval, along with its subtypes Interval and AnchoredInterval, and also Bound.")
(license license:expat)))
-;; TODO: Keep this in sync with tzdata in base.scm
-;; Package can use more work
-;; Need to figure out how to generate Artifacts.toml from tzdata package
+;; TODO: There is talk upstream about separating out the timezone data into a
+;; separate package which can allow this to actually be packaged in a sane way.
+;; As of 1.7.1 there are 257 items in Artifact.toml
+;; https://github.com/JuliaTime/TimeZones.jl/issues/359
+;; Versions after 1.5.x introduce a dependency on julia-inlinestrings, which needs help with its test suite.
(define-public julia-timezones
(package
(name "julia-timezones")
- (version "1.7.1")
+ (version "1.5.9")
(source
(origin
(method git-fetch)
@@ -789,49 +800,18 @@ polynomials.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0sqckna9sivwxrhr7h7rmzmjxz3496q9yhd816y5z3b7vpv3gbqi"))))
+ (base32 "1r6vnhfykw4zmpq1nahv9zflsd4gnpdj84admnhd0pnbrfwv8prw"))))
(build-system julia-build-system)
(arguments
(list
- #:tests? #f ; Tests attempt to download timezone information
- ;#:phases
- ;#~(modify-phases %standard-phases
- ; (add-after 'link-depot 'patch-tzdata
- ; (lambda* (#:key inputs #:allow-other-keys)
- ; ;(substitute* "src/tzdata/TZData.jl"
- ; ; (("(COMPILED_DIR = ).*" _ key)
- ; ; (string-append key "\"" (assoc-ref inputs "tzdata") "/share/zoneinfo\"")))
- ; (substitute* "test/runtests.jl"
- ; (("2016j") "2021a")
- ; ((".*download.jl.*") "")
- ; )
- ; (make-file-writable "Artifacts.toml")
- ; (with-output-to-file "Artifacts.toml"
- ; (lambda _
- ; (format #t "[tzdata2021a]~@
- ; git-tree-sha1 = \"6d94ada27957590cbd0d7678f5ae711232a4d714\"~@
- ; lazy = true~@
- ; ~@
- ; [[tzdata2021a.download]]~@
- ; sha256 = \"39e7d2ba08c68cbaefc8de3227aab0dec2521be8042cf56855f7dc3a9fb14e08\"~@
- ; url = \"file://~a\"~%"
- ; (assoc-ref inputs "tzdata-src"))))
- ; #t))
- ; )
- ))
+ ;; Tests attempt to download timezone information
+ ;; In its current form this is basically a source-only package.
+ #:tests? #f))
(propagated-inputs
(list
- julia-inlinestrings
+ ;julia-inlinestrings
julia-mocking
julia-recipesbase))
- (native-inputs
- `(
- ;("julia-compat" ,julia-compat)
- ;("julia-timezones" ,julia-timezones)
- ;("curl" ,(@ (gnu packages curl) curl-minimal))
- ;("tzdata" ,(@ (gnu packages base) tzdata))
- ;("tzdata-src" ,(package-source (@ (gnu packages base) tzdata)))
- ))
(home-page "https://github.com/JuliaTime/TimeZones.jl")
(synopsis "IANA time zone database access for Julia")
(description "IANA time zone database access for the Julia programming
@@ -842,7 +822,7 @@ include a new time zone aware @code{TimeType: ZonedDateTime}.")
(define-public julia-inlinestrings
(package
(name "julia-inlinestrings")
- (version "1.1.1")
+ (version "1.1.2")
(source
(origin
(method git-fetch)
@@ -851,7 +831,7 @@ include a new time zone aware @code{TimeType: ZonedDateTime}.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0vr0hdig2vmgpnkxwhiw4wcl8pv69xyk0wpfig08sd6m8dg5wq4c"))))
+ (base32 "1fwbnjrsig0fbi9vjn8apbn186xvzhk7vnw3g661q3g8f2j0snp9"))))
(build-system julia-build-system)
(arguments
(list