Mark RISC-V packages as obsolete

6 files changed, 0 insertions, 547 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 7c88afa..0b6521e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -23,7 +23,6 @@
   #:use-module (gnu packages)
   #:use-module (gn packages crates-io)
   #:use-module (gn packages datastructures)
-  #:use-module (gn packages java)
   #:use-module (gn packages maths)
   #:use-module (gn packages ocaml)
   #:use-module (gn packages python)
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
deleted file mode 100644
index fe5fcb2..0000000
--- a/gn/packages/cwl.scm
+++ /dev/null
@@ -1,112 +0,0 @@
-(define-module (gn packages cwl)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix packages)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages bioinformatics)
-  #:use-module (gnu packages docker)
-  #:use-module (gnu packages node)
-  #:use-module (gnu packages python-web)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages serialization)
-  #:use-module (gnu packages time)
-  #:use-module (gn packages python))
-
-
-(define-public cwl-runner
-  (package
-    (name "cwl-runner")
-    (version "1.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "cwl_runner" version))
-        (sha256
-         (base32
-          "0011am2xqwchysdznayrmwhg4bfjl4wlq6m4k20z1m7gccyzjgw0"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("cwltool" ,cwltool)))
-    (home-page
-     "https://github.com/common-workflow-language/common-workflow-language")
-    (synopsis "Common workflow language reference implementation")
-    (description
-     "Common workflow language alternate entry point to allow cwl-runner 
-script as an implementation-agnostic script interpreter.") 
-     (license license:asl2.0)))
-
-;; python-toil tightly integrates with cwltool using it as a library. So,
-;; create a library version of cwltool where inputs become propagated inputs.
-(define-public python-cwltool
-  (package
-    (inherit cwltool)
-    (name "python-cwltool")
-    (inputs
-     (list node))
-    (propagated-inputs
-     (modify-inputs (package-inputs cwltool)
-       (delete "node")))))
-
-(define-public python-toil
-  (package
-    (name "python-toil")
-    (version "6.1.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "toil" version))
-              (sha256
-               (base32
-                "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'disable-optional-features
-            (lambda _
-              (substitute* "requirements-cwl.txt"
-                ;; Loosen version restrictions on ruamel.yaml.
-                (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n")
-                ;; Remove optional dependency on galaxy-util and
-                ;; galaxy-tool-util. TODO: Package these and restore these
-                ;; dependencies.
-                (("galaxy-util[^\n]*") "")
-                (("galaxy-tool-util[^\n]*") ""))
-              ;; Disable optional wdl, wes and mesos features. We don't yet
-              ;; have dependencies packaged for them. TODO: Package these
-              ;; dependencies and enable these features.
-              (substitute* "setup.py"
-                (("\"wdl\",") "")
-                (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]")
-                 "toil-cwl-runner = toil.cwl.cwltoil:main")
-                (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "")
-                (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "")
-                (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") "")))))))
-    (propagated-inputs
-     (list python-addict
-           python-cachecontrol
-           python-configargparse
-           python-cwltool
-           python-dateutil
-           python-dill
-           python-docker
-           python-enlighten
-           python-psutil
-           python-pypubsub
-           python-pytz
-           python-pyyaml
-           python-requests
-           python-ruamel.yaml
-           python-typing-extensions-4.10
-           python-urllib3))
-    (home-page "https://github.com/DataBiosphere/toil")
-    (synopsis "Scalable, efficient and cross-platform workflow engine")
-    (description "Toil is a scalable, efficient, cross-platform pipeline
-management system, written entirely in Python, and designed around the
-principles of functional programming.")
-    (license (list license:asl2.0    ;; main license
-                   license:expat)))) ;; src/toil/batchSystems/lsf.py and
-                                     ;; src/toil/batchSystems/lsfHelper.py
diff --git a/gn/packages/fpga.scm b/gn/packages/fpga.scm
deleted file mode 100644
index b8c3537..0000000
--- a/gn/packages/fpga.scm
+++ /dev/null
@@ -1,17 +0,0 @@
-(define-module (gn packages fpga)
-  #:use-module (gnu packages electronics)
-  #:use-module (guix git-download)
-  #:use-module (guix packages))
-
-(define-public verilator-4.110
-  (package
-   (inherit verilator)
-   (version "4.110")
-   (source (origin
-            (method git-fetch)
-            (uri (git-reference
-                  (inherit (origin-uri (package-source verilator)))
-                  (commit (string-append "v" version))))
-            (sha256
-             (base32
-              "1lm2nyn7wzxj5y0ffwazhb4ygnmqf4d61sl937vmnmrpvdihsrrq"))))))
diff --git a/gn/packages/quality-control.scm b/gn/packages/quality-control.scm
deleted file mode 100644
index 692f08b..0000000
--- a/gn/packages/quality-control.scm
+++ /dev/null
@@ -1,172 +0,0 @@
-(define-module (gn packages quality-control)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system asdf)
-  #:use-module (gnu packages lisp-check)
-  #:use-module (gnu packages lisp-xyz)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages check)
-  #:use-module (gnu packages databases)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages python-web)
-  #:use-module (guix build-system python)
-  #:use-module (gnu packages python-check))
-
-(define-public libcsv
-  (let ((commit "b1d5212831842ee5869d99bc208a21837e4037d5")
-        (revision "0"))
-    (package
-      (name "libcsv")
-      (version commit)
-      (source
-       (origin
-         (method git-fetch)
-         (uri
-          (git-reference
-           (url "https://github.com/rgamble/libcsv")
-           (commit commit)))
-         (file-name (git-file-name name commit))
-         (sha256
-          (base32 "0nni9y0prz8lh3dywbha52yfg8qcf3dn0nb7iinfwlrmmamfyzg2"))))
-      (build-system gnu-build-system)
-      (arguments
-        `(#:make-flags
-          (list (string-append "CC=" ,(cc-for-target)))))
-      (home-page "https://github.com/rgamble/libcsv")
-      (synopsis "CSV library written in pure ANSI C")
-      (description
-"CSV library written in pure ANSI C that can read and write CSV data.")
-      (license license:lgpl2.1+))))
-
-(define-public sbcl-qc
-  (let ((commit "a0d8c807fa3f817f977a64f02f5f8936044050ad")
-        (revision "4"))
-    (package
-      (name "sbcl-qc")
-      (version (git-version "20220331" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                (url "https://git.genenetwork.org/jgart/qc")
-                (commit commit)))
-          (sha256
-           (base32 "12i9s1ipqarvq6gsjqycfm8d3ym7dv7vn3nxb5c6214xrd4mmzjj"))
-          (file-name (git-file-name name commit))))
-      (build-system asdf-build-system/sbcl)
-      (arguments
-        `(#:tests? #f)) ; Need to fix tests.
-      (native-inputs
-        (list sbcl-1am))
-      (inputs
-        (list sbcl-alexandria
-              sbcl-split-sequence))
-      (home-page "https://git.genenetwork.org/jgart/qc/")
-      (synopsis "Quality control of delimited files")
-      (description
-"@code{cl-qc} is a Common Lisp library for linting the following in
-delimited text files:
-@itemize
-@item Whitespace
-@item Floating-point number well-formedness
-@item GeneChip Platform ID checks for Affymetrix, Illumina, and others
-@end itemize\n")
-      (license license:unlicense))))
-
-(define-public cl-qc
-  (sbcl-package->cl-source-package sbcl-qc))
-
-;;  The file
-;;  #P"/tmp/guix-build-sbcl-qc-uploads-20220301-0.76f870e.drv-0/source/strains.csv"
-;;  does not exist:
-;;    No such file or directory
-#;(define-public sbcl-qc-uploads
-  (let ((commit "76f870efad964bf680bf633e272094082008e69c")
-        (revision "0"))
-    (package
-      (name "sbcl-qc-uploads")
-      (version (git-version "20220301" revision commit))
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                (url "https://git.genenetwork.org/jgart/qc-uploads")
-                (commit commit)))
-          (sha256
-           (base32 "1nzcdqjwh1xpr92d01fvlmdysxizyklaid10zrxbi12jmdydapil"))
-          (file-name (git-file-name name commit))))
-      (build-system asdf-build-system/sbcl)
-      ;; needs install-file for strains.tsv. This require more testing.
-      ;; todo: see for an example: https://github.com/interactive-ssr/issr-server/blob/master/guix.scm#L46
-      (arguments
-       `(#:tests? #f ; There are no tests yet.
-         #:asd-files '("qc-uploads.asd")))
-      (inputs
-        (list sbcl-alexandria
-              sbcl-ningle
-              sbcl-clack
-              sbcl-cl-css
-              sbcl-cl-who
-              sbcl-cl-fad
-              sbcl-qc ; packaged in guix-bioinformatics
-              sbcl-woo))
-      (home-page "https://git.genenetwork.org/jgart/qc-uploads/")
-      (synopsis "Web UI for qc")
-      (description 
-"@code{qc-uploads} provides a web UI for @code{qc}.")
-      (license license:expat))))
-
-#;(define-public cl-qc-uploads
-  (sbcl-package->cl-source-package sbcl-qc-uploads))
-
-#;(define-public ecl-qc-uploads
-  (sbcl-package->ecl-package sbcl-qc-uploads))
-
-(define-public genenetwork-qc
-  (let ((commit "b735cae93ac8243bc9b07a10549a68330934d9bf")
-	(revision "2"))
-    (package
-      (name "genenetwork-qc")
-      (version (git-version "0.0.1" revision commit))
-      (source
-       (origin
-	 (method git-fetch)
-	 (uri
-	  (git-reference
-	   ;;(url "https://git.genenetwork.org/fredmanglis/gnqc_py.git")
-	   (url "https://gitlab.com/fredmanglis/gnqc_py.git")
-	   (commit commit)))
-	 (sha256
-	  (base32 "0my3zm7kc5ijsp7lmh5qf6z198x1gw1cr17230d20za65pssri3j"))))
-      (build-system python-build-system)
-      (arguments
-       `(#:tests? #f ; Tests requiring redis server fail. Figure out how to start redis
-	 #:phases
-	 (modify-phases %standard-phases
-	   (replace 'check
-	     (lambda* (#:key tests? #:allow-other-keys)
-	       (when tests?
-		 (invoke "pytest")))))))
-      (inputs
-       (list python-mypy
-	     python-pylint
-	     python-pytest
-	     python-hypothesis))
-      (propagated-inputs
-       (list redis
-	     mariadb
-	     gunicorn
-	     python-redis
-	     python-flask
-	     python-jsonpickle
-	     python-mysqlclient))
-      (synopsis "GeneNetwork Quality Control Application")
-      (description
-       "GeneNetwork qc is a quality control application for the data files that
- eventually are used to add to the data in the GeneNetwork project.")
-      (home-page "https://git.genenetwork.org/fredmanglis/gnqc_py")
-      (license license:agpl3+))))
diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm
deleted file mode 100644
index 61fc882..0000000
--- a/gn/packages/riscv.scm
+++ /dev/null
@@ -1,81 +0,0 @@
-;;;
-;;; Commentary:
-;;;
-;;; This module is a temporary staging ground for Guix packages ported
-;;; to RISC-V. They should be contributed upstream at the earliest.
-;;;
-
-;;;
-;;; Code:
-;;;
-
-(define-module (gn packages riscv)
-  #:use-module (gn packages fpga)
-  #:use-module (gnu packages cpp)
-  #:use-module (gnu packages virtualization)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages))
-
-;; Improvements to riscv support have been merged since the last release.
-(define-public cva6
-  (let ((commit "b40bb3264bc0ca0b5b9e9a3eb351cbaaa9b50b62")
-        (revision "1"))
-    (package
-     (name "cva6")
-     (version (git-version "4.2.0" revision commit))
-     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/openhwgroup/cva6")
-                    (commit commit)
-                    (recursive? #t)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "16zyfqfycii25sirh3bm80dws2fn10a02ny8kzijr0p0a1azklmv"))))
-     (build-system gnu-build-system)
-     (arguments
-      (list
-       #:tests? #f
-       #:make-flags #~(list "verilate"
-                            ;; Dummy RISCV to suppress Makefile error.
-                            "RISCV=foo")
-       #:phases
-       #~(modify-phases %standard-phases
-           ;; Patch cva6 to print to stdout correctly. See
-           ;; https://github.com/openhwgroup/cva6/issues/748
-           (add-after 'unpack 'fix-stdout
-             (lambda _
-               (substitute* "corev_apu/tb/rvfi_tracer.sv"
-                 (("rvfi_i\\[i\\].insn == 32'h00000073")
-                  "0"))))
-           (delete 'configure)
-           (replace 'install
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((bin (string-append (assoc-ref outputs "out")
-                                         "/bin")))
-                 (mkdir-p bin)
-                 (copy-file "work-ver/Variane_testharness"
-                            (string-append bin "/ariane"))))))))
-     (inputs
-      (list spike verilator-4.110))
-     (home-page "https://docs.openhwgroup.org/projects/cva6-user-manual/")
-     (synopsis "Application class 6-stage RISC-V CPU")
-     (description "CVA6 is a 6-stage, single issue, in-order CPU which
-implements the 64-bit RISC-V instruction set. It fully implements I,
-M, A and C extensions as specified in Volume I: User-Level ISA V 2.3
-as well as the draft privilege extension 1.10. It implements three
-privilege levels M, S, U to fully support a Unix-like operating
-system. Furthermore it is compliant to the draft external debug spec
-0.13.
-
-It has configurable size, separate TLBs, a hardware PTW and
-branch-prediction (branch target buffer and branch history table). The
-primary design goal was on reducing critical path length.")
-     (license (list license:asl2.0
-                    license:bsd-3
-                    ;; TODO: Add Solderpad Hardware license.
-                    )))))
diff --git a/gn/packages/virtualization.scm b/gn/packages/virtualization.scm
deleted file mode 100644
index b176ec7..0000000
--- a/gn/packages/virtualization.scm
+++ /dev/null
@@ -1,164 +0,0 @@
-(define-module (gn packages virtualization)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix gexp)
-  #:use-module (guix utils)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system scons)
-  #:use-module (gnu packages)
-  #:use-module (gnu packages boost)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpp)
-  #:use-module (gnu packages graphviz)
-  #:use-module (gnu packages image)
-  #:use-module (gnu packages m4)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages protobuf)
-  #:use-module (gnu packages python)
-  #:use-module (gnu packages python-build)
-  #:use-module (gnu packages python-xyz)
-  #:use-module (past packages python27))
-
-(define-public gem5
-  (package
-    (name "gem5")
-    (version "22.1.0.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://gem5.googlesource.com/public/gem5")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1kcdn8rawzhf88lcb2app8m1r1px4ba041kyl7xigslix7qs05k3"))
-        (snippet
-          #~(begin
-              (use-modules (guix build utils))
-              ;; For reproducibility.
-              (substitute* "src/base/date.cc"
-                (("__DATE__") "\"1970-01-01\"")
-                (("__TIME__") "\"00:00:00\""))
-              ;; Remove vendored pybind11.
-              (substitute* "ext/sst/Makefile"
-                (("-I../../ext/pybind11/include/")
-                 "${shell pybind11-config --includes}"))
-              (substitute* "SConstruct"
-                ((".*pybind11.*") ""))
-              (delete-file-recursively "ext/pybind11")))))
-    (build-system scons-build-system)
-    (arguments
-     `(#:scons-flags
-       (list "--verbose")
-       #:build-targets '("build/ARM/gem5.opt"
-                         "build/MIPS/gem5.opt"
-                         "build/NULL/gem5.opt"
-                         "build/POWER/gem5.opt"
-                         "build/RISCV/gem5.opt"
-                         "build/SPARC/gem5.opt"
-                         "build/X86/gem5.opt")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-source
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "SConstruct"
-               ;; Scons does not use the environment variables by default,
-               ;; but this substitution makes it do so.
-               ;(("main = Environment")
-               ; "main = Environment(ENV=os.environ)\nmain = Environment")
-               ;; Force adding missing includes into the environment.
-               (("main\\.Append\\(CPPPATH=\\[Dir\\('" all)
-                (string-append
-                  all (assoc-ref inputs "kernel-headers") "/include')])\n"
-                  all (assoc-ref inputs "libpng") "/include')])\n"
-                  all (assoc-ref inputs "pybind11") "/include')])\n"
-                  all (assoc-ref inputs "zlib") "/include')])\n"
-                  all)))
-             (substitute* "ext/libelf/SConscript"
-               (("m4env\\.Tool" all)
-                (string-append
-                  "m4env.Append(CPPPATH=[Dir('"
-                  (assoc-ref inputs "kernel-headers")
-                  "/include')])\n"
-                  all)))
-             (substitute* "ext/libelf/native-elf-format"
-               (("cc") ,(cc-for-target)))))
-         ;; This uses the cached results from the previous 'build phase.
-         ;; Move to after 'install and delete build dir first?
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys #:rest args)
-             (when tests?
-               (apply (assoc-ref %standard-phases 'build)
-                      #:build-targets '("build/NULL/unittests.opt")
-                      args))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin/")))
-               (mkdir-p bin)
-               (for-each
-                 (lambda (arch)
-                   (when (directory-exists?
-                           (string-append "build/" (string-upcase arch)))
-                     (copy-file
-                       (string-append "build/" (string-upcase arch) "/gem5.opt")
-                       (string-append bin "gem5-" arch ".opt"))
-                     (copy-file
-                       (string-append "build/" (string-upcase arch) "/gem5py")
-                       (string-append bin "gem5py-" arch))
-                     (copy-file
-                       (string-append "build/" (string-upcase arch) "/gem5py_m5")
-                       (string-append bin "gem5py_m5-" arch))))
-                 (list "arm" "mips" "null" "power" "riscv" "sparc" "x86")))))
-         (add-after 'install 'install-configs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out  (assoc-ref outputs "out"))
-                    (dest (string-append out "/share/gem5/configs")))
-               (copy-recursively "configs" dest))))
-         (add-after 'install 'wrap-binaries
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (for-each
-                 (lambda (file)
-                   (wrap-program file
-                     `("GUIX_PYTHONPATH" ":" prefix
-                       (,(getenv "GUIX_PYTHONPATH")))))
-                 (find-files (string-append out "/bin")))))))))
-    (inputs
-     (list gperftools
-           libpng
-           protobuf
-           pybind11
-           python
-           python-pydot
-           python-six
-           zlib))
-    (native-inputs
-     (list boost
-           m4
-           pkg-config))
-    (home-page "http://gem5.org/")
-    (synopsis "Modular platform for computer-system architecture research")
-    (description "The gem5 simulator is a modular platform for computer-system
-architecture research, encompassing system-level architecture as well as
-processor microarchitecture.")
-    (license license:bsd-2)))
-
-(define-public gem5-riscv
-  (package
-    (inherit gem5)
-    (name "gem5-riscv")
-    (arguments
-     (substitute-keyword-arguments (package-arguments gem5)
-       ((#:build-targets _ '())
-        `(list "build/RISCV/gem5.opt"))
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (bin (string-append out "/bin")))
-                 (install-file "build/RISCV/gem5.opt" bin)
-                 (install-file "build/RISCV/gem5py" bin)
-                 (install-file "build/RISCV/gem5py_m5" bin))))))))))