From 2ac16b43ad46d6e2c077497fb61b7acfcb88dea4 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 10 Nov 2021 11:39:40 +0530 Subject: Use git-predicate in guix.scm. * guix.scm: Do not import (srfi srfi-1), (srfi srfi-26), (ice-9 match), (ice-9 popen) and (ice-9 rdelim). Use git-predicate instead of git-file?. (git-file?): Delete function. --- guix.scm | 23 +---------------------- 1 file changed, 1 insertion(+), 22 deletions(-) (limited to 'guix.scm') diff --git a/guix.scm b/guix.scm index 81e8389..aae7576 100644 --- a/guix.scm +++ b/guix.scm @@ -29,11 +29,6 @@ ;; env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm (use-modules - (srfi srfi-1) - (srfi srfi-26) - (ice-9 match) - (ice-9 popen) - (ice-9 rdelim) (gn packages gemma) (gn packages python) (gnu packages base) @@ -60,29 +55,13 @@ (define %source-dir (dirname (current-filename))) -(define git-file? - (let* ((pipe (with-directory-excursion %source-dir - (open-pipe* OPEN_READ "git" "ls-files"))) - (files (let loop ((lines '())) - (match (read-line pipe) - ((? eof-object?) - (reverse lines)) - (line - (loop (cons line lines)))))) - (status (close-pipe pipe))) - (lambda (file stat) - (match (stat:type stat) - ('directory #t) - ((or 'regular 'symlink) - (any (cut string-suffix? <> file) files)) - (_ #f))))) (package (name "genenetwork3.git") (version "0.0.1") (source (local-file %source-dir #:recursive? #t - #:select? git-file?)) + #:select? (git-predicate %source-dir))) (propagated-inputs `(("coreutils" ,coreutils) ("gemma-wrapper" ,gemma-wrapper) ("gunicorn" ,gunicorn) -- cgit v1.2.3 From b0ec075228abd721644bf65b7df7b5fa7b5aadea Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 10 Nov 2021 11:41:31 +0530 Subject: Name source checkout in the store. * guix.scm: Name source checkout in the store to "genenetwork3-checkout". --- guix.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'guix.scm') diff --git a/guix.scm b/guix.scm index aae7576..418e2a3 100644 --- a/guix.scm +++ b/guix.scm @@ -59,7 +59,7 @@ (package (name "genenetwork3.git") (version "0.0.1") - (source (local-file %source-dir + (source (local-file %source-dir "genenetwork3-checkout" #:recursive? #t #:select? (git-predicate %source-dir))) (propagated-inputs `(("coreutils" ,coreutils) -- cgit v1.2.3 From 8fd78ff74124bb4d247424a26d22482f7c93b8ef Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 10 Nov 2021 11:42:41 +0530 Subject: Set version to 0.1.0. Semantic versioning begins at 0.1.0, not 0.0.1. * guix.scm: Set genenetwork package version to 0.1.0. --- guix.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'guix.scm') diff --git a/guix.scm b/guix.scm index 418e2a3..f15542d 100644 --- a/guix.scm +++ b/guix.scm @@ -58,7 +58,7 @@ (package (name "genenetwork3.git") - (version "0.0.1") + (version "0.1.0") (source (local-file %source-dir "genenetwork3-checkout" #:recursive? #t #:select? (git-predicate %source-dir))) -- cgit v1.2.3 From 5c69ff5abf7ca360c9ead65338f66d8e33b682ae Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 10 Nov 2021 11:50:54 +0530 Subject: Indent guix.scm use-modules better. * guix.scm: Indent use-modules better, the more conventional way. --- guix.scm | 47 +++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 24 deletions(-) (limited to 'guix.scm') diff --git a/guix.scm b/guix.scm index f15542d..bf72b5b 100644 --- a/guix.scm +++ b/guix.scm @@ -28,30 +28,29 @@ ;; ;; env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm -(use-modules - (gn packages gemma) - (gn packages python) - (gnu packages base) - (gnu packages check) - (gnu packages graph) - (gnu packages cran) - (gnu packages databases) - (gnu packages statistics) - (gnu packages bioconductor) - (gnu packages golang) - (gn packages genenetwork) - (gnu packages python) - (gnu packages python-check) - (gnu packages python-crypto) - (gnu packages python-web) - (gnu packages python-xyz) - (gnu packages python-science) - ((guix build utils) #:select (with-directory-excursion)) - (guix build-system python) - (guix gexp) - (guix git-download) - (guix licenses) - (guix packages)) +(use-modules (gn packages gemma) + (gn packages python) + (gnu packages base) + (gnu packages check) + (gnu packages graph) + (gnu packages cran) + (gnu packages databases) + (gnu packages statistics) + (gnu packages bioconductor) + (gnu packages golang) + (gn packages genenetwork) + (gnu packages python) + (gnu packages python-check) + (gnu packages python-crypto) + (gnu packages python-web) + (gnu packages python-xyz) + (gnu packages python-science) + ((guix build utils) #:select (with-directory-excursion)) + (guix build-system python) + (guix gexp) + (guix git-download) + (guix licenses) + (guix packages)) (define %source-dir (dirname (current-filename))) -- cgit v1.2.3 From 189435602e2e5c94d7cb80254242fa68406a132c Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 10 Nov 2021 15:44:45 +0530 Subject: Remove repeated input python-flask-cors. * guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors. --- guix.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'guix.scm') diff --git a/guix.scm b/guix.scm index bf72b5b..a48b05a 100644 --- a/guix.scm +++ b/guix.scm @@ -89,8 +89,7 @@ ("python-plotly" ,python-plotly) ("python-pandas" ,python-pandas) ("python-pingouin" ,python-pingouin) - ("rust-qtlreaper" ,rust-qtlreaper) - ("python-flask-cors" ,python-flask-cors))) + ("rust-qtlreaper" ,rust-qtlreaper))) (build-system python-build-system) (home-page "https://github.com/genenetwork/genenetwork3") (synopsis "GeneNetwork3 API for data science and machine learning.") -- cgit v1.2.3