Merge pull request #97 from BIMSBbioinfo/guix

Guix updates

channels.scm

@@ -3,40 +3,40 @@
        (url "https://git.savannah.gnu.org/git/guix.git")
        (branch "master")
        (commit
-        "acb6cdc2990df2373707393d55da6827353862a8")
+        "9fa107c774017e35d2b0f05c2032ba520b9c0218")
        (introduction
         (make-channel-introduction
          "9edb3f66fd807b096b48283debdcddccfea34bad"
          (openpgp-fingerprint
           "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA"))))
       (channel
        (name 'guix-science-nonfree)
-       (url "https://github.com/guix-science/guix-science-nonfree.git")
+       (url "https://codeberg.org/guix-science/guix-science-nonfree")
        (branch "master")
        (commit
-        "5942e5a6370ce1a83872a824ee7056cad40cabd2")
+        "de7cda4027d619bddcecf6dd68be23b040547bc7")
        (introduction
         (make-channel-introduction
          "58661b110325fd5d9b40e6f0177cc486a615817e"
          (openpgp-fingerprint
           "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"))))
       (channel
        (name 'guix-past)
-       (url "https://gitlab.inria.fr/guix-hpc/guix-past")
+       (url "https://codeberg.org/guix-science/guix-past")
        (branch "master")
        (commit
-        "aab6148759476f0270bbe098919a978da45d7a2d")
+        "2d3485b7fd7c1904bc7c1a87fc45048376ff4d3a")
        (introduction
         (make-channel-introduction
          "0c119db2ea86a389769f4d2b9c6f5c41c027e336"
          (openpgp-fingerprint
           "3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"))))
       (channel
        (name 'guix-science)
-       (url "https://github.com/guix-science/guix-science.git")
+       (url "https://codeberg.org/guix-science/guix-science")
        (branch "master")
        (commit
-        "12eba5aa0c5cbf357c476ef7872e0d562d054eff")
+        "aa7f6fec7013363ea62c51c68ea516d6fd4f022d")
        (introduction
         (make-channel-introduction
          "b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"

guix.scm

@@ -15,20 +15,25 @@
 
 (package
   (name "flexynesis")
-  (version "0.1.7")
+  (version "0.2.13")
   (source (git-checkout (url (dirname (current-filename)))))
   (build-system pyproject-build-system)
   (arguments
    (list
     #:phases
     #~(modify-phases %standard-phases
+        (add-after 'unpack 'disable-doctests
+          (lambda _
+            ;; Disable doctests because they are broken.  See
+            ;; https://github.com/BIMSBbioinfo/flexynesis/issues/93
+            (substitute* "pyproject.toml"
+              ((".*--doctest-modules.*") ""))))
         (add-before 'check 'set-numba-cache-dir
           (lambda _
             (setenv "NUMBA_CACHE_DIR" "/tmp")))
         (add-after 'wrap 'isolate-python
           (lambda _
-            (substitute* (list (string-append #$output "/bin/.flexynesis-real")
-                                (string-append #$output "/bin/.flexynesis-cli-real"))
+            (substitute* (string-append #$output "/bin/.flexynesis-real")
               (("/bin/python") "/bin/python -I")))))))
   (propagated-inputs %packages)
   (native-inputs %dev-packages)

manifest.scm

@@ -10,23 +10,26 @@
   (if (getenv "FLEXYNESIS_USE_CPU")
       identity  ;don't do anything
       (let ((cpu-torch (specification->package "python-pytorch"))
-            (gpu-torch (specification->package "python-pytorch-with-cuda11")))
+            (gpu-torch (specification->package "python-pytorch-with-cuda12")))
         (package-input-rewriting `((,cpu-torch . ,gpu-torch))))))
 
 (define %packages
   (map replace-cpu-torch-with-gpu-torch
        (map specification->package
             (list "python-captum"
+                  "python-geomloss"
+                  "python-ipykernel"
                   "python-ipywidgets"
-                  "python-louvain"
                   "python-lifelines"
+                  "python-louvain"
                   "python-matplotlib"
                   "python-numpy"
                   "python-pandas"
                   "python-papermill"
+                  "python-pot"
                   "python-pytorch"
-                  "python-pytorch-lightning"
                   "python-pytorch-geometric"
+                  "python-pytorch-lightning"
                   "python-pyyaml"
                   "python-rich"
                   "python-scikit-optimize"
@@ -35,7 +38,8 @@
                   "python-seaborn"
                   "python-torchvision"
                   "python-tqdm"
-                  "python-umap-learn"))))
+                  "python-umap-learn"
+                  "python-xgboost"))))
 (define %dev-packages
   (map specification->package
        (list "python-pytest")))