update docs notes

docs/notes/Notes_Development.md

@@ -1,7 +1 @@
 # Development
-
-1. Cleanup with BFG repo cleaner.
-1. Maybe write a function to condense notebook import/exporting.
-1. Rethink the use of large dill objects that can't be version controlled...
-1. Test bokeh.
-1. How should auspice and narratives folders be managed?

docs/notes/Notes_v0.2.6.md

@@ -1,37 +1,23 @@
 # v0.2.6
 
-1. Put project specific results in different directories:
-    - ```project/test```
-    - ```project/main```
-    - ```project/denmark```
-    - ```project/megapestis```
+1. Put project specific results in seperate repository.
 1. Added 2020 Latvia samples to database, mark as low coverage for now.
 1. Move log directory to within results.
-1. Add jupyter notebooks to snakemake pipeline.
 1. Remove xml tree output from notebooks.
 1. Create scripts to backup, restore, and clean projects.
 1. Remove plot_table rules and script.
 1. Only include visual files into the report.
 1. Put config files inside the associated project directory.
 1. Update function ```identify_local_sample``` to use database.
-1. Environment addition: ugur, cartopy, ffpmeg, snp-dists, bokeh.
+1. Environment addition: augur, cartopy, ffpmeg, snp-dists, bokeh.
 1. Create Pairwise SNP matrix.
 1. Remove results folder from docs.
 1. Create new output folder collect for detect snp density.
-1. Move project specific results to a new repository.
 1. Remove US Kim strain, mark as laboratory manipulation.
-1. Rerun projects: test, megapestis, denmark, main.
 1. Clean snp density files from version control.
-
-## To-Do
-
-1. Migrate projects to new repository.
-    - test
-    - megapestis
-    - denmark
-    - main/global
-1. Clean projects from main repository.
-    - test
-    - megapestis
-    - denmark
-    - main/global
+1. Add country to continent mapping for metadata.
+1. Improvements to plotting missing data and filtering log.
+1. Change all metadata column names to lowercase.
+1. Changed from TreeTime to LSD2.
+1. Included rules to prepare for BEAST.
+1. Jupyter Notebooks pertaining to TreeTime are not used.