removing legacy, adding quiet mode with custom logger, coloured print…

… outs
cov-lineages · Feb 8, 2021 · d1ec054 · d1ec054
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Showing 20 changed files with 605 additions and 1,694 deletions.
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@
   * [SNPs associated with a given lineage](#snps-associated-with-a-given-lineage)
   * [Source data](#source-data)
   * [Authors](#authors)
-  * [Citing <strong>pangolin</strong>](#citing-pangolin)
+  * [Citing pangolin](#citing-pangolin)
   * [References](#references)
 
 

diff --git a/environment.yml b/environment.yml
@@ -1,20 +1,15 @@
-name: pangolin
+name: pangolin2
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - biopython=1.74
-  - iqtree<2
-  - mafft
   - minimap2
   - pip=19.3.1
   - python=3.7
   - snakemake-minimal=5.13
   - pip:
     - pandas==1.0.1
-    - pytools==2020.1
-    - dendropy>=4.4.0
     - git+https://github.com/cov-ert/datafunk.git
     - git+https://github.com/cov-lineages/pangoLEARN.git
-    - git+https://github.com/cov-lineages/lineages.git@2020-05-19-2 
diff --git a/pangolin/__init__.py b/pangolin/__init__.py
@@ -1,2 +1,2 @@
 _program = "pangolin"
-__version__ = "2.1.11"
+__version__ = "2.2.0"
diff --git a/pangolin/command.py b/pangolin/command.py
diff --git a/pangolin/scripts/Snakefile b/pangolin/scripts/Snakefile
diff --git a/pangolin/scripts/assign_lineage.py b/pangolin/scripts/assign_lineage.py
diff --git a/pangolin/scripts/assign_query_file.smk b/pangolin/scripts/assign_query_file.smk