New arch

.Rbuildignore

@@ -5,3 +5,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^\.positai$
+^\.claude$

.gitignore

@@ -3,3 +3,4 @@ inst/doc
 docs
 save.txt
 .Rhistory
+.positai

DESCRIPTION

@@ -1,28 +1,26 @@
 Package: treepplr
 Title: R Interface to TreePPL
-Version: 0.11.0
+Version: 0.14.0
 Authors@R: 
     person("Mariana", "P Braga", , "mpiresbr@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1253-2536"))
 Description: This package in an interface for using TreePPL programs.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 URL: https://github.com/treeppl/treepplr,
     http://treeppl.org/treepplr/
 BugReports: https://github.com/treeppl/treepplr/issues
 Depends:
     R (>= 4.1.0)
 Imports: 
     assertthat,
+    digest,
     methods,
     jsonlite,
     tidytree,
     utils,
-    gh,
     curl,
-    cli,
     bnpsd,
     rlang,
     phangorn
@@ -38,6 +36,7 @@ Suggests:
     evolnets (>= 0.0.0.9000),
     treeio (>= 1.32.0),
     rmarkdown,
+    readr,
     pandoc,
     dplyr
 VignetteBuilder: knitr
@@ -46,3 +45,4 @@ Remotes:
     github::maribraga/evolnets,
     bioc::ggtree,
     bioc::treeio
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,18 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
+export(TPPLC_VERSION)
 export(tp_compile)
 export(tp_data)
-export(tp_expected_input)
+export(tp_installing_treeppl)
 export(tp_json_to_phylo)
+export(tp_list)
 export(tp_map_tree)
-export(tp_model)
 export(tp_model_library)
 export(tp_parse_host_rep)
 export(tp_parse_mcmc)
 export(tp_parse_smc)
 export(tp_phylo_to_tpjson)
 export(tp_run)
-export(tp_run_options)
 export(tp_smc_convergence)
 export(tp_tempdir)
 export(tp_treeppl_json)