Adding JFruit2 skeleton

Author: JBris

.gitignore

@@ -168,6 +168,6 @@ slurm-*.out
 .python-version
 sbi-logs
 catboost_info
-
+jfruit2.log
 # TEgenomeSimulator output
 workshop/tegenomesimulator/demo_m0

poetry.lock

@@ -15,12 +15,10 @@ package-mode = false
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.13"
-calisim = {extras = ["hydra", "torchx"], version = "^0.6.0"}
-tegenomesimulator = {git = "https://git@github.com/Plant-Food-Research-Open/TEgenomeSimulator.git", rev = "v1.0.0"}
+calisim = {extras = ["hydra", "torchx"], version = "^0.6.1"}
+tegenomesimulator = {git = "https://git@github.com/Plant-Food-Research-Open/TEgenomeSimulator.git", rev = "290baade3d2a802949b36bffc756b6a1fef3955c"}
 mesa = {version = "<3.1.1", extras = ["rec", "network", "viz"]}
-mmh3 = "^5.1.0"
-screed = "^1.1.3"
-sourmash = "<4.9.3"
+
 
 [tool.poetry.group.docs.dependencies]
 sphinx-rtd-theme = "^3.0.1"