write tree and df objects with dill for parse_tree

ktmeaton · Feb 23, 2021 · 541b953 · 541b953
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diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,4 @@ workflow/notebooks/__pycache__/
 results/data/local/testlocal1/
 results/data/local/testlocal2/
 docs/results/latest/test/
+*.obj
diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -1,4 +1,4 @@
-# Release v0.2.2
+# Development
 
 1. Add entropy to augur.
 1. Add mugration models to augur.
@@ -11,3 +11,9 @@
 1. Confirm pruning consistency between tree, dataframe, and alignment (n=247).
 1. Plot tree comparison.
 1. Checkpoint before clock modelling in BEAST.
+
+## TO DO
+
+1. Think about snippy_dir in rule ```eager```...
+1. Use pickle to save objects of Jupyter notebooks?
+1. Timetree alters the topology, perhaps run that first?
diff --git a/docs/results/latest/parse_tree/parse_tree.nwk_trimmed_list_X_100 b/docs/results/latest/parse_tree/parse_tree.nwk_trimmed_list_X_100
diff --git a/docs/results/latest/parse_tree/parse_tree.nwk_trimmed_tree_X_100 b/docs/results/latest/parse_tree/parse_tree.nwk_trimmed_tree_X_100