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authorpjotrp2020-02-10 12:21:33 -0600
committerpjotrp2020-02-10 12:21:33 -0600
commit5df680178c01cd7db0f1d4a766a868dc08317e4b (patch)
treee16e4ac62a5422ef83f9ef59397df0458d58063a /gn/packages/python.scm
parentf7b75fe1730e6e5e77768d332f9f3946b5218c8c (diff)
parent5a69fb0666a2bf53b13ab9490b3ed44e5dc944b4 (diff)
downloadguix-bioinformatics-5df680178c01cd7db0f1d4a766a868dc08317e4b.tar.gz
Update
Diffstat (limited to 'gn/packages/python.scm')
-rw-r--r--gn/packages/python.scm153
1 files changed, 101 insertions, 52 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index b69dd91..60558a2 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -488,58 +488,107 @@ Python 3 support.")
 ; pinned QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG recursively
 
 (define-public python2-htmlgen-gn ; guix obsolete
-(package
-  (name "python2-htmlgen-gn")
-  (version "2.2.2")
-  (source (origin
-           (method url-fetch)
-           ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
-           (uri (string-append
-                 "http://ipfs.genenetwork.org/ipfs/QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG/htmlgen-" version "-gn.tar.gz"))
-           (sha256
-            (base32
-             "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
-           ;;(patches (list
-           ;;          (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
-           ;;          (search-patch "python2-htmlgen-Fix-test-for-random.patch")
-            ))
-  (build-system python-build-system)
-  (outputs '("out"))
-  (native-inputs
-   `(("make" ,gnu-make)
-     ))
-  (propagated-inputs
-   `(("python2" ,python-2)))
-  (arguments
-   `(#:phases (modify-phases %standard-phases
-     (replace 'build
-              (lambda _
-                (system* "python2" "-m" "compileall" ".")))
-     (replace 'install
-              (lambda* (#:key outputs #:allow-other-keys)
-                       (let* ((out (assoc-ref outputs "out"))
-                              (include (string-append out "/include"))
-                              (lib2 (string-append out "/lib/htmlgen"))
-                              (lib (string-append (assoc-ref %outputs "out") "/lib/python2.7/site-packages/htmlgen"))
-                              (pkgconfig (string-append out "/lib/pkgconfig"))
-                              (doc (string-append out "/share/doc")))
-                         ;; Install libs and headers.
-                         ;; (copy-file "HTMLgen.pyc" "HTMLgen2.pyc")
-                         (install-file "HTMLgen.pyc" lib)
-                         (install-file "HTMLgen2.pyc" lib)
-                         (install-file "imgsize.pyc" lib)
-                         (install-file "ImageH.pyc" lib)
-                         (install-file "ImagePaletteH.pyc" lib)
-                         (install-file "__init__.pyc" lib)
-              ))) ; install
-     ) ; phases
-     #:tests? #f))
-  (home-page
-    "https://packages.debian.org/unstable/python/python-htmlgen")
-  (synopsis "Genenetwork version of Python2 HTMLgen (defunkt
-project)")
-  (description #f)
-  (license #f)))
+  (package
+    (name "python2-htmlgen-gn")
+    (version "2.2.2")
+    (source (origin
+              (method url-fetch)
+              ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
+              (uri (string-append
+                     "http://ipfs.genenetwork.org/ipfs/QmZLWsPHLFTU3hWAfdTwj3RXFrS8Ma7KEixne1suWuYqeG/htmlgen-" version "-gn.tar.gz"))
+              (sha256
+               (base32
+                "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
+              ;;(patches (list
+              ;;          (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
+              ;;          (search-patch "python2-htmlgen-Fix-test-for-random.patch")
+              ))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'modernize-imports
+           (lambda _
+             (substitute* "HTMLgen.py"
+               (("whrandom") "random"))
+             (substitute* "HTMLcalendar.py"
+               (("import regex") "import re as regex"))
+             (substitute* "HTMLutil.py"
+               (("import string, regex") "import re as regex\nimport string"))
+             (substitute* "HTMLtest.py"
+               (("import string, regex, regsub") "import re as regex\nimport string")
+               (("regsub.split") "re.split"))
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "python" "-m" "compileall" ".")))
+         (replace 'check
+           (lambda* (#:key (tests? '()) #:allow-other-keys)
+             (if tests?
+               (invoke "python" "HTMLtest.py")
+               #t)))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
+               ;; Install libs and headers.
+               (for-each (lambda (file)
+                           (install-file file lib))
+                         (find-files "." "\\.py[c]?$"))
+               #t))))))
+    (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
+    (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
+    (description #f)
+    (license #f)))
+
+(define-public python2-htmlgen-2.2
+  (package
+    (name "python2-htmlgen-2.2")
+    (version "2.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://debian/pool/main/h/htmlgen/htmlgen_" version ".orig.tar.gz"))
+              (sha256
+               (base32
+                 "186kb434q6z84g31ysvzi4kcfcvl3pmm57k4jlng4ccgls94x6wb"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'modernize-imports
+           (lambda _
+             (substitute* "HTMLgen.py"
+               (("whrandom") "random"))
+             (substitute* "HTMLcalendar.py"
+               (("import regex") "import re as regex"))
+             (substitute* "HTMLutil.py"
+               (("import string, regex") "import re as regex\nimport string"))
+             (substitute* "HTMLtest.py"
+               (("import string, regex, regsub") "import re as regex\nimport string")
+               (("regsub.split") "re.split"))
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "python" "-m" "compileall" ".")))
+         (replace 'check
+           (lambda _
+             (invoke "python" "HTMLtest.py")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib/python2.7/site-packages/htmlgen/")))
+               ;; Install libs and headers.
+               (for-each (lambda (file)
+                           (install-file file lib))
+                         (find-files "." "\\.py[c]?$"))
+               #t))))))
+    (home-page "https://packages.debian.org/unstable/python/python-htmlgen")
+    (synopsis "Genenetwork version of Python2 HTMLgen (defunkt project)")
+    (description #f)
+    (license #f)))
 
 ; penguin2:~/tmp$ env IPFS_PATH=/export/ipfs/ ipfs add -r Imaging/
 ; added QmV8Rew1re8gBTLsaqMU4bd7euFUPEpjiD572mtoz6KhPn Imaging/Imaging-1.1.6-gn.tar.gz