added __init__ and __main__ to orthohmm

.github/workflows/ci.yml

@@ -35,6 +35,7 @@ jobs:
         cd ..
     - name: Run tests
       run: |
+        PATH=$PATH:$HOME/local/bin
         make test.fast
   test-full:
     runs-on: macos-latest
@@ -57,7 +58,6 @@ jobs:
     - name: Install HMMER
       run: |
         brew install hmmer
-        phmmer --version
     - name: Install MCL
       run: |
         mkdir installmcl

orthohmm/__main__.py

@@ -0,0 +1,6 @@
+"""orthohmm.__main__: executed when orthohmm is called as script"""
+import sys
+
+from .orthohmm import main
+
+main(sys.argv[1:])

orthohmm/parser.py

@@ -134,9 +134,10 @@ def create_parser() -> ArgumentParser:
         
         orthohmm_single_copy_orthogroups
             A directory of FASTA files wherein each file is a single-copy ortholog.
-            Headers are modified to have taxon names come before the gene identifier. Taxon names are the file name
-            excluding the extension. Taxon name and gene identifier are separated by a pipe symbol "|".
-            This aims to help streamline phylogenomic workflows wherein sequences will be concatenated downstream
+            Headers are modified to have taxon names come before the gene identifier.
+            Taxon names are the file name excluding the extension. Taxon name and gene
+            identifier are separated by a pipe symbol "|". This aims to help streamline
+            phylogenomic workflows wherein sequences will be concatenated downstream
             based on taxon names.
         """  # noqa
         ),