Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Sun, 30 Mar 2025 22:05:02 UTC
Severity: normal
Tags: patch
Done: Andreas Enge <andreas <at> enge.fr>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: David Elsing <david.elsing <at> posteo.net> To: 77394 <at> debbugs.gnu.org Cc: David Elsing <david.elsing <at> posteo.net> Subject: [bug#77394] [PATCH 1/5] gnu: inchi: Update to 1.07.3. Date: Sun, 30 Mar 2025 22:06:54 +0000
* gnu/packages/chemistry.scm (inchi): Update to 1.07.3.
[source]: Switch to git-fetch.
[arguments]: Use gexps. Adjust chdir-to-build-directory, build and install
phases. Enable parallel building.
[native-inputs]: Remove input label.
[license]: Change to Expat license.
---
gnu/packages/chemistry.scm | 122 ++++++++++++++++++-------------------
1 file changed, 59 insertions(+), 63 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..df5048d22e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -146,68 +146,66 @@ (define-public inchi
(package
(name "inchi")
;; Update the inchi-doc native input when updating inchi.
- (version "1.06")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://www.inchi-trust.org/download/"
- (string-join (string-split version #\.) "")
- "/INCHI-1-SRC.zip"))
- (sha256
- (base32
- "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28"))
- (file-name (string-append name "-" version ".zip"))))
+ (version "1.07.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/IUPAC-InChI/InChI")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0r32f6i5d8ir96ic3nvqb5lywxrznwrkk6hnz1q0a4bgsw5pmk0n"))
+ (modules '((guix build utils)))
+ (snippet '(delete-file-recursively "INCHI-1-BIN"))))
(build-system gnu-build-system)
(arguments
- '(#:tests? #f ; no check target
- #:phases
- (modify-phases %standard-phases
- (delete 'configure) ; no configure script
- (add-before 'build 'chdir-to-build-directory
- (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t))
- (add-after 'build 'build-library
- (lambda _
- (chdir "../../../INCHI_API/libinchi/gcc")
- (invoke "make")))
- (replace 'install
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin"))
- (doc (string-append out "/share/doc/inchi"))
- (include-dir (string-append out "/include/inchi"))
- (lib (string-append out "/lib/inchi"))
- (inchi-doc (assoc-ref inputs "inchi-doc"))
- (unzip (search-input-file inputs "/bin/unzip")))
- (chdir "../../..")
- ;; Install binary.
- (with-directory-excursion "INCHI_EXE/bin/Linux"
- (rename-file "inchi-1" "inchi")
- (install-file "inchi" bin))
- ;; Install libraries.
- (with-directory-excursion "INCHI_API/bin/Linux"
- (for-each (lambda (file)
- (install-file file lib))
- (find-files "." "libinchi\\.so\\.1\\.*")))
- ;; Install header files.
- (with-directory-excursion "INCHI_BASE/src"
- (for-each (lambda (file)
- (install-file file include-dir))
- (find-files "." "\\.h$")))
- ;; Install documentation.
- (mkdir-p doc)
- (invoke unzip "-j" "-d" doc inchi-doc)
- #t))))))
- (native-inputs
- `(("unzip" ,unzip)
- ("inchi-doc"
- ,(origin
- (method url-fetch)
- (uri (string-append "http://www.inchi-trust.org/download/"
- (string-join (string-split version #\.) "")
- "/INCHI-1-DOC.zip"))
- (sha256
- (base32
- "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f"))
- (file-name (string-append name "-" version ".zip"))))))
+ (list
+ #:tests? #f ; no check target
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-after 'unpack 'chdir-to-build-directory
+ (lambda _ (chdir "INCHI-1-SRC/INCHI_EXE/inchi-1/gcc")))
+ (add-after 'build 'build-library
+ (lambda* (#:key parallel-build? #:allow-other-keys)
+ (chdir "../../../INCHI_API/libinchi/gcc")
+ (invoke "make" "-j" (if parallel-build?
+ (number->string (parallel-job-count))
+ "1"))))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((bin (string-append #$output "/bin"))
+ (doc (string-append #$output "/share/doc/inchi"))
+ (include-dir (string-append #$output "/include/inchi"))
+ (lib (string-append #$output "/lib/inchi")))
+ (chdir "../../..")
+ ;; Install binary.
+ (with-directory-excursion "INCHI_EXE/bin/Linux"
+ (rename-file "inchi-1" "inchi")
+ (install-file "inchi" bin))
+ ;; Install library.
+ (with-directory-excursion "INCHI_API/bin/Linux"
+ (let ((libname (basename
+ (car
+ (find-files "." "libinchi\\.so\\.1\\.*")))))
+ (install-file libname lib)
+ (with-directory-excursion lib
+ (symlink libname "libinchi.so.1")
+ (symlink "libinchi.so.1" "libinchi.so"))))
+ ;; Install header files.
+ (with-directory-excursion "INCHI_BASE/src"
+ (for-each (lambda (file)
+ (install-file file include-dir))
+ (find-files "." "\\.h$")))
+ ;; Install documentation.
+ (with-directory-excursion "../INCHI-1-DOC"
+ (for-each
+ (lambda (file)
+ (install-file file doc))
+ (find-files "." "\\.pdf$")))))))))
+ (native-inputs (list unzip))
(home-page "https://www.inchi-trust.org")
(synopsis "Utility for manipulating machine-readable chemical structures")
(description
@@ -216,9 +214,7 @@ (define-public inchi
unique to the compound they describe and can encode absolute stereochemistry
making chemicals and chemistry machine-readable and discoverable. A simple
analogy is that InChI is the bar-code for chemistry and chemical structures.")
- (license (license:non-copyleft
- "file://LICENCE"
- "See LICENCE in the distribution."))))
+ (license license:expat)))
(define-public libmsym
(package
--
2.48.1
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.