20261002

pixi.toml

@@ -1,8 +1,7 @@
 [workspace]
 authors = ["IvisTang <me@ivistang.com>"]
 channels = [
-    "https://mirrors4.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/",
-    "https://mirrors4.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/",
+    "https://prefix.dev/julia-forge",
     "conda-forge",
     "bioconda"
 ]
@@ -57,19 +56,29 @@ r-phytools = ">=2.5_2,<3"
 r-argparser = ">=0.7.2,<0.8"
 r-processx = ">=3.8.6,<4"
 
-[feature.beast.dependencies]
-beagle-lib = ">=4.0.1,<5"
-beast = ">=10.5.0,<11"
-
 [feature.genome.dependencies]
 gffread = ">=0.12.9,<0.13"
 orthofinder = ">=3.1.5,<4"
 seqkit = ">=2.13.0,<3"
 tmux = ">=3.7b_,<4"
-numpy = "<2"
+numpy = "<2.5"
+python = "3.12.*"
+biopython = ">=1.87,<2"
+macse = ">=2.7,<3"
+trimal = ">=1.5.1,<2"
+treeshrink = ">=1.4.0,<2"
+raxml-ng = ">=2.0.2,<3"
+modeltest-ng = ">=0.1.7,<0.2"
+mrbayes = ">=3.2.7,<4"
+seqmagick = ">=0.8.6,<0.9"
+aster = ">=1.25,<2"
+julia = ">=1.12.6,<1.13"
+r-ape = ">=5.8_1,<6"
+r-languageserver = ">=0.3.18,<0.4"
+conda = ">=26.7.0,<27"
+minimap2 = ">=2.31,<3"
 
 
 [environments]
-base = ["base"]
-beast = ["beast"]
+# base = ["base"]
 default = ["genome"]