diff options
| -rw-r--r-- | doc/guix.texi | 8 | ||||
| -rw-r--r-- | guix/import/cran.scm | 254 | ||||
| -rw-r--r-- | guix/import/utils.scm | 5 | ||||
| -rw-r--r-- | guix/scripts/import.scm | 4 |
4 files changed, 198 insertions, 73 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index 5a64b89086..a87a8a3d9a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8638,6 +8638,14 @@ R package: guix import cran --archive=bioconductor GenomicRanges @end example +Finally, you can also import R packages that have not yet been published on +CRAN or Bioconductor as long as they are in a git repository. Use +@code{--archive=git} followed by the URL of the git repository: + +@example +guix import cran --archive=git https://github.com/immunogenomics/harmony +@end example + @item texlive @cindex TeX Live @cindex CTAN diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 9c964701b1..51c7ea7b2f 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -24,6 +24,7 @@ #:use-module ((ice-9 rdelim) #:select (read-string read-line)) #:use-module (srfi srfi-1) #:use-module (srfi srfi-2) + #:use-module (srfi srfi-11) #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (ice-9 receive) @@ -32,11 +33,13 @@ #:use-module (guix http-client) #:use-module (gcrypt hash) #:use-module (guix store) + #:use-module ((guix serialization) #:select (write-file)) #:use-module (guix base32) #:use-module ((guix download) #:select (download-to-store)) #:use-module (guix import utils) #:use-module ((guix build utils) #:select (find-files)) #:use-module (guix utils) + #:use-module (guix git) #:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri)) #:use-module (guix upstream) #:use-module (guix packages) @@ -166,11 +169,25 @@ bioconductor package NAME, or #F if the package is unknown." (bioconductor-packages-list type)) (cut assoc-ref <> "Version"))) +;; XXX taken from (guix scripts hash) +(define (vcs-file? file stat) + (case (stat:type stat) + ((directory) + (member (basename file) '(".bzr" ".git" ".hg" ".svn" "CVS"))) + ((regular) + ;; Git sub-modules have a '.git' file that is a regular text file. + (string=? (basename file) ".git")) + (else + #f))) + ;; Little helper to download URLs only once. (define download (memoize - (lambda (url) - (with-store store (download-to-store store url))))) + (lambda* (url #:optional git) + (with-store store + (if git + (latest-repository-commit store url) + (download-to-store store url)))))) (define (fetch-description repository name) "Return an alist of the contents of the DESCRIPTION file for the R package @@ -211,7 +228,18 @@ from ~s: ~a (~s)~%" (string-append dir "/DESCRIPTION") read-string)) (lambda (meta) (if (boolean? type) meta - (cons `(bioconductor-type . ,type) meta)))))))))))) + (cons `(bioconductor-type . ,type) meta)))))))))) + ((git) + ;; Download the git repository at "NAME" + (call-with-values + (lambda () (download name #t)) + (lambda (dir commit) + (and=> (description->alist (with-input-from-file + (string-append dir "/DESCRIPTION") read-string)) + (lambda (meta) + (cons* `(git . ,name) + `(git-commit . ,commit) + meta)))))))) (define (listify meta field) "Look up FIELD in the alist META. If FIELD contains a comma-separated @@ -256,7 +284,7 @@ empty list when the FIELD cannot be found." (define cran-guix-name (cut guix-name "r-" <>)) -(define (needs-fortran? tarball) +(define (tarball-needs-fortran? tarball) "Check if the TARBALL contains Fortran source files." (define (check pattern) (parameterize ((current-error-port (%make-void-port "rw+")) @@ -266,69 +294,127 @@ empty list when the FIELD cannot be found." (check "*.f95") (check "*.f"))) +(define (directory-needs-fortran? dir) + "Check if the directory DIR contains Fortran source files." + (match (find-files dir "\\.f(90|95)?") + (() #f) + (_ #t))) + +(define (needs-fortran? thing tarball?) + "Check if the THING contains Fortran source files." + (if tarball? + (tarball-needs-fortran? thing) + (directory-needs-fortran? thing))) + +(define (files-match-pattern? directory regexp . file-patterns) + "Return #T if any of the files matching FILE-PATTERNS in the DIRECTORY match +the given REGEXP." + (let ((pattern (make-regexp regexp))) + (any (lambda (file) + (call-with-input-file file + (lambda (port) + (let loop () + (let ((line (read-line port))) + (cond + ((eof-object? line) #f) + ((regexp-exec pattern line) #t) + (else (loop)))))))) + (apply find-files directory file-patterns)))) + (define (tarball-files-match-pattern? tarball regexp . file-patterns) "Return #T if any of the files represented by FILE-PATTERNS in the TARBALL match the given REGEXP." (call-with-temporary-directory (lambda (dir) - (let ((pattern (make-regexp regexp))) - (parameterize ((current-error-port (%make-void-port "rw+"))) - (apply system* "tar" - "xf" tarball "-C" dir - `("--wildcards" ,@file-patterns))) - (any (lambda (file) - (call-with-input-file file - (lambda (port) - (let loop () - (let ((line (read-line port))) - (cond - ((eof-object? line) #f) - ((regexp-exec pattern line) #t) - (else (loop)))))))) - (find-files dir)))))) - -(define (needs-zlib? tarball) + (parameterize ((current-error-port (%make-void-port "rw+"))) + (apply system* "tar" + "xf" tarball "-C" dir + `("--wildcards" ,@file-patterns))) + (files-match-pattern? dir regexp)))) + +(define (directory-needs-zlib? dir) + "Return #T if any of the Makevars files in the src directory DIR contain a +zlib linker flag." + (files-match-pattern? dir "-lz" "(Makevars.*|configure.*)")) + +(define (tarball-needs-zlib? tarball) "Return #T if any of the Makevars files in the src directory of the TARBALL contain a zlib linker flag." (tarball-files-match-pattern? tarball "-lz" "*/src/Makevars*" "*/src/configure*" "*/configure*")) -(define (needs-pkg-config? tarball) +(define (needs-zlib? thing tarball?) + "Check if the THING contains files indicating a dependency on zlib." + (if tarball? + (tarball-needs-zlib? thing) + (directory-needs-zlib? thing))) + +(define (directory-needs-pkg-config? dir) + "Return #T if any of the Makevars files in the src directory DIR reference +the pkg-config tool." + (files-match-pattern? dir "pkg-config" + "(Makevars.*|configure.*)")) + +(define (tarball-needs-pkg-config? tarball) "Return #T if any of the Makevars files in the src directory of the TARBALL reference the pkg-config tool." (tarball-files-match-pattern? tarball "pkg-config" "*/src/Makevars*" "*/src/configure*" "*/configure*")) +(define (needs-pkg-config? thing tarball?) + "Check if the THING contains files indicating a dependency on pkg-config." + (if tarball? + (tarball-needs-pkg-config? thing) + (directory-needs-pkg-config? thing))) + +;; XXX adapted from (guix scripts hash) +(define (file-hash file select? recursive?) + ;; Compute the hash of FILE. + (if recursive? + (let-values (((port get-hash) (open-sha256-port))) + (write-file file port #:select? select?) + (force-output port) + (get-hash)) + (call-with-input-file file port-sha256))) + (define (description->package repository meta) "Return the `package' s-expression for an R package published on REPOSITORY from the alist META, which was derived from the R package's DESCRIPTION file." (let* ((base-url (case repository ((cran) %cran-url) - ((bioconductor) %bioconductor-url))) + ((bioconductor) %bioconductor-url) + ((git) #f))) (uri-helper (case repository ((cran) cran-uri) - ((bioconductor) bioconductor-uri))) + ((bioconductor) bioconductor-uri) + ((git) #f))) (name (assoc-ref meta "Package")) (synopsis (assoc-ref meta "Title")) (version (assoc-ref meta "Version")) (license (string->license (assoc-ref meta "License"))) ;; Some packages have multiple home pages. Some have none. - (home-page (match (listify meta "URL") - ((url rest ...) url) - (_ (string-append base-url name)))) - (source-url (match (apply uri-helper name version - (case repository - ((bioconductor) - (list (assoc-ref meta 'bioconductor-type))) - (else '()))) - ((url rest ...) url) - ((? string? url) url) - (_ #f))) - (tarball (download source-url)) + (home-page (case repository + ((git) (assoc-ref meta 'git)) + (else (match (listify meta "URL") + ((url rest ...) url) + (_ (string-append base-url name)))))) + (source-url (case repository + ((git) (assoc-ref meta 'git)) + (else + (match (apply uri-helper name version + (case repository + ((bioconductor) + (list (assoc-ref meta 'bioconductor-type))) + (else '()))) + ((url rest ...) url) + ((? string? url) url) + (_ #f))))) + (git? (assoc-ref meta 'git)) + (source (download source-url git?)) (sysdepends (append - (if (needs-zlib? tarball) '("zlib") '()) + (if (needs-zlib? source (not git?)) '("zlib") '()) (filter (lambda (name) (not (member name invalid-packages))) (map string-downcase (listify meta "SystemRequirements"))))) @@ -339,41 +425,67 @@ from the alist META, which was derived from the R package's DESCRIPTION file." (listify meta "Imports") (listify meta "LinkingTo") (delete "R" - (listify meta "Depends")))))) + (listify meta "Depends"))))) + (package + `(package + (name ,(cran-guix-name name)) + (version ,(case repository + ((git) + `(git-version ,version revision commit)) + (else version))) + (source (origin + (method ,(if git? + 'git-fetch + 'url-fetch)) + (uri ,(case repository + ((git) + `(git-reference + (url ,(assoc-ref meta 'git)) + (commit commit))) + (else + `(,(procedure-name uri-helper) ,name version + ,@(or (and=> (assoc-ref meta 'bioconductor-type) + (lambda (type) + (list (list 'quote type)))) + '()))))) + ,@(if git? + '((file-name (git-file-name name version))) + '()) + (sha256 + (base32 + ,(bytevector->nix-base32-string + (case repository + ((git) + (file-hash source (negate vcs-file?) #t)) + (else (file-sha256 source)))))))) + ,@(if (not (and git? + (equal? (string-append "r-" name) + (cran-guix-name name)))) + `((properties ,`(,'quasiquote ((,'upstream-name . ,name))))) + '()) + (build-system r-build-system) + ,@(maybe-inputs sysdepends) + ,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs) + ,@(maybe-inputs + `(,@(if (needs-fortran? source (not git?)) + '("gfortran") '()) + ,@(if (needs-pkg-config? source (not git?)) + '("pkg-config") '())) + 'native-inputs) + (home-page ,(if (string-null? home-page) + (string-append base-url name) + home-page)) + (synopsis ,synopsis) + (description ,(beautify-description (or (assoc-ref meta "Description") + ""))) + (license ,license)))) (values - `(package - (name ,(cran-guix-name name)) - (version ,version) - (source (origin - (method url-fetch) - (uri (,(procedure-name uri-helper) ,name version - ,@(or (and=> (assoc-ref meta 'bioconductor-type) - (lambda (type) - (list (list 'quote type)))) - '()))) - (sha256 - (base32 - ,(bytevector->nix-base32-string (file-sha256 tarball)))))) - ,@(if (not (equal? (string-append "r-" name) - (cran-guix-name name))) - `((properties ,`(,'quasiquote ((,'upstream-name . ,name))))) - '()) - (build-system r-build-system) - ,@(maybe-inputs sysdepends) - ,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs) - ,@(maybe-inputs - `(,@(if (needs-fortran? tarball) - '("gfortran") '()) - ,@(if (needs-pkg-config? tarball) - '("pkg-config") '())) - 'native-inputs) - (home-page ,(if (string-null? home-page) - (string-append base-url name) - home-page)) - (synopsis ,synopsis) - (description ,(beautify-description (or (assoc-ref meta "Description") - ""))) - (license ,license)) + (case repository + ((git) + `(let ((commit ,(assoc-ref meta 'git-commit)) + (revision "1")) + ,package)) + (else package)) propagate))) (define cran->guix-package diff --git a/guix/import/utils.scm b/guix/import/utils.scm index 2a3b7341fb..252875eeab 100644 --- a/guix/import/utils.scm +++ b/guix/import/utils.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2012, 2013, 2018, 2019 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org> ;;; Copyright © 2016 David Craven <david@craven.ch> -;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2017, 2019 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2019 Robert Vollmert <rob@vllmrt.net> ;;; @@ -252,6 +252,9 @@ package definition." (match guix-package (('package ('name (? string? name)) _ ...) `(define-public ,(string->symbol name) + ,guix-package)) + (('let anything ('package ('name (? string? name)) _ ...)) + `(define-public ,(string->symbol name) ,guix-package)))) (define (build-system-modules) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index 0b326e1049..c6cc93fad8 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014 David Thompson <davet@gnu.org> ;;; Copyright © 2018 Kyle Meyer <kyle@kyleam.com> +;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -113,7 +114,8 @@ Run IMPORTER with ARGS.\n")) (pretty-print expr (newline-rewriting-port (current-output-port)))))) (match (apply (resolve-importer importer) args) - ((and expr ('package _ ...)) + ((and expr (or ('package _ ...) + ('let _ ...))) (print expr)) ((? list? expressions) (for-each (lambda (expr) |