Getting rid of guix-past dependency

guix-bioinformatics is now fully self-contained -- no more guix-past or guix-rust-past-crates dependencies.

4 files changed, 2 insertions, 205 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8b1a2db..3b21e2e 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -88,8 +88,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
-  #:use-module (gnu packages zig)
-  #:use-module (past packages python27))
+  #:use-module (gnu packages zig))
 
 (define-public mbg
   (package
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index d8c83ac..4690ffb 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -603,27 +603,6 @@ GeneNetwork projects.")
                               #:node-type %package-node-type
                               #:backend %d3js-backend))))))))))))))
 
-;(define (computed-genenetwork-graph)
-;  (with-imported-modules '((guix build utils))
-;    (computed-file "genenetwork-graph"
-;      #~(begin
-;          (use-modules (guix build utils))
-;            (call-with-output-file #$output
-;              (lambda (port)
-;                (format
-;                  port "~a"
-;                  #$(call-with-output-string
-;                      (lambda (p)
-;                        (with-output-to-port p
-;                          (lambda ()
-;                            (run-with-store
-;                              (open-connection)
-;                              (export-graph
-;                                (list genenetwork1)
-;                                p
-;                                #:node-type %package-node-type
-;                                #:backend %d3js-backend)))))))))))))
-
 (define (dag-svg-file)
   (with-imported-modules '((guix build utils))
     (gexp->derivation "dag-svg-file"
diff --git a/gn/packages/machine-learning.scm b/gn/packages/machine-learning.scm
index 3799e9b..49039c2 100644
--- a/gn/packages/machine-learning.scm
+++ b/gn/packages/machine-learning.scm
@@ -12,8 +12,7 @@
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages sphinx)
-  #:use-module (gnu packages python-web)
-  #:use-module (past packages python27))
+  #:use-module (gnu packages python-web))
 
 (define-public python-keras-applications
   (package
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index cdd3f06..1aabf8d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -33,7 +33,6 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages time)
-  #:use-module (past packages python27)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -65,51 +64,6 @@
     (license license:gpl2))
 )
 
-(define-public python2-numarray ; guix: obsolete lib
-  (package
-    (name "python2-numarray")
-    (version "1.5.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "mirror://sourceforge/numpy/numarray-" version ".tar.gz"
-             ))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "0x1i4j7yni7k4p9kjxs1lgln1psdmyrz65wp2yr35yn292iw2vbg"))))
-    (build-system python-build-system)
-    (native-inputs
-     `(("python2-setuptools" ,python2-setuptools)))
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'build
-           (lambda* (#:key inputs #:allow-other-keys)
-             (zero? (system* "python" "setup.py" "build"))))
-         (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    ;; Build and install the Python bindings.  The underlying
-                    ;; C++ library is apparently not meant to be installed.
-                    (let ((out (assoc-ref outputs "out")))
-                      (system* "python" "setup.py" "install"
-                               (string-append "--prefix=" out))))))
-       #:tests? #f))   ; no 'setup.py test' really!
-    (home-page "http://www.numpy.org/")
-    (synopsis "Numerical library array processing of numbers, strings, records and objects")
-    (description
-     "Numarray is an (OBSOLETE) array processing package designed to
-efficiently manipulate large multi-dimensional arrays. Numarray is
-modelled after Numeric and features c-code generated from python
-template scripts, the capacity to operate directly on arrays in files,
-and improved type promotions. Numarray provides support for
-manipulating arrays consisting of numbers, strings, records, or
-objects using the same basic infrastructure and syntax.  Numarray is
-now part of the numpy package, though some legacy software still uses
-the older versions.")
-    (license license:gpl2))) ; actualy PyRAF http://www.stsci.edu/resources/software_hardware/pyraf/LICENSE
 
 (define-public python-htmlgen
   (package
@@ -155,140 +109,6 @@ stand-alone manner.")
     (home-page "https://github.com/srittau/python-asserts")
     (license license:expat)))
 
-(define-public python2-pp
-  (package
-    (name "python2-pp")
-    (version "1.6.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (string-append
-             "http://www.parallelpython.com/downloads/pp/pp-" version ".zip"))
-        (sha256
-         (base32
-          "0qkxcyclz3vgwpl6xvsrg76q59dj0wwy8qx15567bafv659ypyb1"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:use-setuptools? #f
-       #:tests? #f)) ; no tests
-    (native-inputs
-     `(("unzip" ,unzip)))
-    (home-page "http://www.parallelpython.com")
-    (synopsis "Parallel and distributed programming for Python")
-    (description "PP is a python module which provides mechanism for parallel
-execution of python code on SMP (systems with multiple processors or cores) and
-clusters (computers connected via network).")
-    (license license:bsd-3)))
-
-(define GN1-thirdparty-sources
-  (origin
-    (method url-fetch/tarbomb)
-    (uri "https://files.genenetwork.org/software/thirdparty.tgz")
-    (file-name "GN1-thirdparty")
-    (sha256
-     (base32
-      "0nnp6g412hjfrcn3k2yrfb14sxv06k0149whc7qmv678nyj5zhfa"))))
-
-(define-public python2-json-GN1
-  (package
-    (name "python2-json-GN1")
-    (version "GN1")
-    (source GN1-thirdparty-sources)
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'build)
-         (delete 'check)
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out     (assoc-ref outputs "out"))
-                    (sitedir (string-append out "/lib/python2.7/site-packages/json/")))
-               (mkdir-p sitedir)
-               (copy-recursively "thirdparty/json" sitedir)
-               #t))))))
-    (home-page "")
-    (synopsis "")
-    (description "")
-    (license license:lgpl2.1+)))
-
-(define-public python2-pyx-GN1
-  (package
-    (name "python2-pyx-GN1")
-    (version "0.8")
-    (source GN1-thirdparty-sources)
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'build)
-         (delete 'check)
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out     (assoc-ref outputs "out"))
-                    (sitedir (string-append out "/lib/python2.7/site-packages/pyx/")))
-               (mkdir-p sitedir)
-               (copy-recursively "thirdparty/pyx" sitedir)
-               #t))))))
-    (home-page "")
-    (synopsis "")
-    (description "")
-    (license license:gpl2+)))
-
-(define-public python2-pyxlwriter
-  (package
-    (name "python2-pyxlwriter")
-    (version "0.4a3")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (string-append "mirror://sourceforge/pyxlwriter/pyxlwriter/"
-                            version "/pyXLWriter-" version ".zip"))
-        (sha256
-         (base32
-          "1kfsi6la9y53rwayszgayfmkjfknpp650v69a0hwd1fcfk1df735"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:use-setuptools? #f
-       #:tests? #f)) ; no tests
-    (native-inputs
-     `(("unzip" ,unzip)))
-    (home-page "https://sourceforge.net/projects/pyxlwriter/")
-    (synopsis "Python library for generating Excel compatible spreadsheets")
-    (description "PyXLWriter is a Python library for generating Excel compatible
-spreadsheets.  It's a port of John McNamara's Perl @code{Spreadsheet::WriteExcel}
-module version 1.01 to Python.  It allows writing of Excel compatible
-spreadsheets without the need for COM objects.")
-    (license license:lgpl2.1+)))
-
-(define-public python2-svg-GN1
-  (package
-    (name "python2-svg-GN1")
-    (version "1.0")
-    (source GN1-thirdparty-sources)
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'build)
-         (delete 'check)
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out     (assoc-ref outputs "out"))
-                    (sitedir (string-append out "/lib/python2.7/site-packages/svg/")))
-               (mkdir-p sitedir)
-               (copy-recursively "thirdparty/svg" sitedir)
-               #t))))))
-    (home-page "")
-    (synopsis "")
-    (description "")
-    (license license:bsd-4)))
-
 (define-public python-admiral
   (package
     (name "python-admiral")