Linting and testing

 - update version of python

.github/workflows/main.yaml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8.0'
+          python-version: '3.10.10'
 
       - name: Install Poetry
         uses: snok/install-poetry@v1

cojac/cooc_curate.py

@@ -103,7 +103,7 @@ def listmutations(lineage, extras={}):
     if "variantQuery" in extras.keys():
         # NOTE according to covspectrum: "Please specify the variant either by using the fields pangoLineage, nextstrainClade, gisaidClade, aaMutations and nucMutations, or by using variantQuery - don't use both at the same time."
         return nucmutations(**extras)
-    return nucmutations(**{ lintype: (lineage + "*") }, **extras)
+    return nucmutations(**{lintype: (lineage + "*")}, **extras)
 
 
 def aggregated(**kwargs):
@@ -122,8 +122,7 @@ def aggregated(**kwargs):
 def listsublineages(lineage):
     """list all lineages which are known to be either the variant it self or one of its sub-variants"""
     return set(
-        s[lintype]
-        for s in aggregated(**{ lintype: (lineage + "*") }, fields=lintype)
+        s[lintype] for s in aggregated(**{lintype: (lineage + "*")}, fields=lintype)
     )
 
 
@@ -243,11 +242,11 @@ def curate_muts(
         su = {combined}
     else:
         su = set(sublineages)
-    #print(muts)
+    # print(muts)
     freqs = freqperlineage(muts, alllin)
-    #print(freqs)
+    # print(freqs)
     (s, o, r) = rank(su, freqs, limit=low)
-    #print(s,o,r)
+    # print(s,o,r)
 
     fi = [i for i in freqs.items()]
     # print({p:fi[p-1] for p in [s,o,r]})

cojac/cooc_pubmut.py

@@ -98,7 +98,11 @@
 def cooc_pubmut(
     vocdir, amp, json_fname, yaml_fname, csv_fname, escape, semi, batchname, quiet
 ):
-    escape = ("\\n", csv.QUOTE_NONNUMERIC, "\\") if escape else ("\n", csv.QUOTE_MINIMAL, None)
+    escape = (
+        ("\\n", csv.QUOTE_NONNUMERIC, "\\")
+        if escape
+        else ("\n", csv.QUOTE_MINIMAL, None)
+    )
 
     # TODO make the "header prettification" code more generic and share with colourmut
 

cojac/cooc_tabmut.py

@@ -188,7 +188,6 @@ def cooc_tabmut(
             )  # , inplace=True)
     # rstudio_table_df.index.rename('sample', inplace=True)
 
-
     if not quiet:
         with pd.option_context(
             "display.max_rows", None

cojac/phe2cojac.py

@@ -57,7 +57,7 @@ def phe2cojac(shortname, outname, fname):
     )
 
     for bl in yam["belongs-to-lineage"]:
-        for (s, l) in bl.items():
+        for s, l in bl.items():
             if s == "PANGO":
                 outy["variant"]["pangolin"] = l
             elif s == "nextstrain":
@@ -113,7 +113,7 @@ def phe2cojac(shortname, outname, fname):
     # start writing
     with open(outname, "wt") if outname is not None else sys.stdout as yf:
         print(yaml.dump(outy, sort_keys=False), end="", file=yf)
-        for (t, s) in variants.items():
+        for t, s in variants.items():
             if 0 == len(s):
                 continue
             print(f"{t}:", file=yf)