Merge branch 'partial-correlations'

1 files changed, 35 insertions, 62 deletions

diff --git a/guix.scm b/guix.scm
index 9b8f399..9bf23c8 100644
--- a/guix.scm
+++ b/guix.scm
@@ -17,72 +17,47 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/.
 
-;; To use this file to build HEAD of gemma:
-;;
-;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix build -f guix.scm
-;;
-;; After checking out the git repo
-;;   cd ~ ; git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
+;; Make sure you have the
+;; https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics channel
+;; set up.
 ;;
 ;; To get a development container (e.g., run in emacs shell).
 ;;
-;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm
+;;   guix shell -C -Df 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)
- (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)))
 
-(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
+  (version "0.1.0")
+  (source (local-file %source-dir "genenetwork3-checkout"
                       #:recursive? #t
-                      #:select? git-file?))
+                      #:select? (git-predicate %source-dir)))
   (propagated-inputs `(("coreutils" ,coreutils)
                        ("gemma-wrapper" ,gemma-wrapper)
                        ("gunicorn" ,gunicorn)
@@ -90,27 +65,25 @@
                        ("python-bcrypt" ,python-bcrypt)
                        ("python-flask" ,python-flask)
                        ("python-flask-cors" ,python-flask-cors)
+                       ("python-flask-socketio" ,python-flask-socketio)
                        ("python-ipfshttpclient" ,python-ipfshttpclient)
                        ("python-mypy" ,python-mypy)
                        ("python-mypy-extensions" ,python-mypy-extensions)
                        ("python-mysqlclient" ,python-mysqlclient)
                        ("python-numpy" ,python-numpy)
+                       ("python-pandas" ,python-pandas)
+                       ("python-pingouin" ,python-pingouin)
                        ("python-plotly" ,python-plotly)
                        ("python-pylint" ,python-pylint)
                        ("python-redis" ,python-redis)
                        ("python-requests" ,python-requests)
                        ("python-scipy" ,python-scipy)
-                       ("python-sqlalchemy-stubs"
-                        ,python-sqlalchemy-stubs)
                        ("r-optparse" ,r-optparse)
                        ("r-qtl" ,r-qtl)
+                       ("r-rjson" ,r-rjson)
                        ("r-stringi" ,r-stringi)
                        ("r-wgcna" ,r-wgcna)
-                       ("r-rjson" ,r-rjson)
-                       ("python-plotly" ,python-plotly)
-                       ("python-pandas" ,python-pandas)
-                       ("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.")