2 Commits

  1. 2
      VERSION
  2. 2
      gn/deploy/machines/myserver.scm
  3. 2
      gn/deploy/octopus.scm
  4. 83
      gn/packages/julia.scm
  5. 2
      gn/services/bh20-seq-resource-container.scm
  6. 2
      gn/services/bnw-container.scm
  7. 2
      gn/services/bxd-power-container.scm
  8. 2
      gn/services/discourse.scm
  9. 2
      gn/services/genecup-container.scm
  10. 2
      gn/services/genenetwork.scm
  11. 2
      gn/services/genome-browser.scm
  12. 2
      gn/services/gitea-container.scm
  13. 2
      gn/services/pluto.scm
  14. 2
      gn/services/ratspub-container.scm
  15. 2
      gn/services/rn6-assembly-container.scm
  16. 2
      gn/services/singlecell-container.scm

2
VERSION

@ -1 +1 @@
dc4c830a37905046ce71a3723be19ef3194f8b8a
2ca982ff41270288913ad6b7d5d9e1cad87b06d9

2
gn/deploy/machines/myserver.scm

@ -17,7 +17,7 @@
;; root file system.
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "/dev/sdX")))
(targets '("/dev/sdX"))))
(file-systems (cons (file-system
(device (file-system-label "my-root"))
(mount-point "/")

2
gn/deploy/octopus.scm

@ -19,7 +19,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "/dev/sda")
(targets '("/dev/sda"))
(terminal-outputs '(console serial))))
(kernel-arguments '("console=tty1" "console=ttyS0,115200n8"))

83
gn/packages/julia.scm

@ -200,36 +200,41 @@ leave-one-chromosome-out}, computation of kinship matrices, and support for
distributed computing.")
(license license:gpl3)))
;; ready to upstream
(define-public julia-pyplot
(package
(name "julia-pyplot")
(version "2.9.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPy/PyPlot.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0lvnraw8i851xnlfyd8d1p1bp8nrr1s9z56fw6znlmakpjjwny39"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f
))
(propagated-inputs
`(
("julia-colors" ,julia-colors)
("julia-latexstrings" ,julia-latexstrings)
("julia-pycall" ,julia-pycall)
("julia-versionparsing" ,julia-versionparsing)
))
(home-page "https://github.com/JuliaPy/PyPlot.jl")
(synopsis "Plotting for Julia based on matplotlib.pyplot")
(description "This module provides a Julia interface to the Matplotlib plotting library from Python, and specifically to the @code{matplotlib.pyplot} module. PyPlot uses the Julia PyCall package to call Matplotlib directly from Julia with little or no overhead (arrays are passed without making a copy).")
(license license:expat)))
;; Test suite was fixed since the last release.
(let ((commit "52a83c88fc10f159d044db5e14563f524562898b")
(revision "1"))
(package
(name "julia-pyplot")
(version (git-version "2.9.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPy/PyPlot.jl")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1nbr9lva4s042l9n67xckak87lhn9q5jpajc18y7vk5r1vr89n5l"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-colors" ,julia-colors)
("julia-latexstrings" ,julia-latexstrings)
("julia-pycall" ,julia-pycall)
("julia-versionparsing" ,julia-versionparsing)
;; python-matplotlib is expected to be available at runtime.
("python-matplotlib" ,(@ (gnu packages python-xyz) python-matplotlib))))
(home-page "https://github.com/JuliaPy/PyPlot.jl")
(synopsis "Plotting for Julia based on matplotlib.pyplot")
(description "This module provides a Julia interface to the Matplotlib
plotting library from Python, and specifically to the @code{matplotlib.pyplot}
module. PyPlot uses the Julia PyCall package to call Matplotlib directly from
Julia with little or no overhead (arrays are passed without making a copy).")
(license license:expat))))
;; ready to upstream
(define-public julia-pycall
(package
(name "julia-pycall")
@ -246,7 +251,12 @@ distributed computing.")
"07r99ni6nkxpyrp3wsb5qg4jxz7i2r08dyqbiffy2zm3g0bn88jq"))))
(build-system julia-build-system)
(arguments
`(#:phases
`(#:imported-modules ((guix build python-build-system)
,@%julia-build-system-modules)
#:modules ((guix build julia-build-system)
(guix build utils)
((guix build python-build-system) #:prefix python:))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-conda
(lambda _
@ -268,13 +278,14 @@ distributed computing.")
(format #t
"const python = \"~a/bin/python3\"~@
const pyprogramname = \"~a/bin/python3\"~@
const libpython = \"~a/lib/libpython3.8.so.1.0\"~@
const PYTHONHOME = \"~a/lib/python3.8\"~@
const libpython = \"~a/lib/libpython~a.so.1.0\"~@
const PYTHONHOME = \"~a\"~@
const pyversion_build = v\"~a\"~@
const conda = false~%"
python
python
python
(python:python-version python)
python
,(package-version python))))
#t)))
@ -289,12 +300,14 @@ distributed computing.")
(inputs
`(("python" ,python)))
(native-inputs
`(("python-numpy" ,(@ (gnu packages python-xyz) python-numpy))
("python-pip" ,(@ (gnu packages python-xyz) python-pip))
("python-virtualenv" ,(@ (gnu packages python-xyz) python-virtualenv))))
`(("python-numpy" ,(@ (gnu packages python-xyz) python-numpy))))
(home-page "https://github.com/JuliaPy/PyCall.jl")
(synopsis "Call Python functions from the Julia language")
(description "This package provides the ability to directly call and fully interoperate with Python from the Julia language. You can import arbitrary Python modules from Julia, call Python functions (with automatic conversion of types between Julia and Python), define Python classes from Julia methods, and share large data structures between Julia and Python without copying them.")
(description "This package provides the ability to directly call and fully
interoperate with Python from the Julia language. You can import arbitrary
Python modules from Julia, call Python functions (with automatic conversion of
types between Julia and Python), define Python classes from Julia methods, and
share large data structures between Julia and Python without copying them.")
(license license:expat)))
(define-public julia-conda

2
gn/services/bh20-seq-resource-container.scm

@ -96,7 +96,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

2
gn/services/bnw-container.scm

@ -77,7 +77,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

2
gn/services/bxd-power-container.scm

@ -11,7 +11,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

2
gn/services/discourse.scm

@ -112,7 +112,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

2
gn/services/genecup-container.scm

@ -104,7 +104,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems (list (file-system
(device "does-not-matter")
(mount-point "/")

2
gn/services/genenetwork.scm

@ -15,7 +15,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs
(firmware '())

2
gn/services/genome-browser.scm

@ -103,7 +103,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs
(firmware '())

2
gn/services/gitea-container.scm

@ -70,7 +70,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs or containers.
(firmware '())

2
gn/services/pluto.scm

@ -76,7 +76,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems (list (file-system
(device "does-not-matter")
(mount-point "/")

2
gn/services/ratspub-container.scm

@ -104,7 +104,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems (list (file-system
(device "does-not-matter")
(mount-point "/")

2
gn/services/rn6-assembly-container.scm

@ -11,7 +11,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

2
gn/services/singlecell-container.scm

@ -14,7 +14,7 @@
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "does-not-matter")))
(targets '("does-not-matter"))))
(file-systems %base-file-systems)
;; No firmware for VMs.
(firmware '())

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