modularizing bit-dl-ncbi-assemblies

Author: Mike Lee

bit/cli/dl_ncbi_assemblies.py

@@ -13,7 +13,7 @@ def main():
 
     parser = argparse.ArgumentParser(
         description=desc,
-        epilog="Ex. usage: `bit-dl-ncbi-assemblies -w wanted-accessions.txt -f fasta -j 4`",
+        epilog="Ex. usage: `bit-dl-ncbi-assemblies -w wanted-accessions.txt`",
         formatter_class=CustomRichHelpFormatter,
         add_help=False
     )
@@ -25,7 +25,7 @@ def main():
         "-w",
         "--wanted-accessions",
         metavar="<FILE>",
-        help='Input file with wanted accessions',
+        help='Input file with wanted accessions, one per line',
         required=True,
     )
 

bit/scripts/bit-dl-ncbi-assemblies

@@ -62,13 +62,12 @@ def pytest_sessionstart(session):
     print("  ================================= Progress on modularizing scripts =================================")
     print("  ====================================================================================================\n")
 
-    print(f"    Total script files: {len(script_files)}\n")
+    print(f"    Base script files remaining: {len(script_files)}\n")
     print(f"    Total helper scripts: {len(helper_scripts)}")
     print(f"    Total bash scripts: {len(bash_scripts)}")
     print(f"    Total python scripts: {len(python_scripts)}")
     print(f"        Python scripts modularized: {len(modularized)}")
     print(f"        Python scripts not yet modularized: {len(not_modularized)}\n")
-    print(f"    Percent of python modularized: {round(len(modularized) / len(python_scripts) * 100, 2)}%\n")
 
     if not_modularized:
         print("        Files not yet modularized:\n")

bit/tests/conftest.py

@@ -8,7 +8,9 @@ if [ "${CONDA_DEFAULT_ENV}" != "bit-dev" ]; then
     exit 1
 fi
 
-pip install -e .
+rm -rf build/ bit.egg-info/
+
+pip install --no-build-isolation -e .
 
 BIN_DIR=$(dirname $(which python))
 

dev-setup.sh

@@ -20,5 +20,16 @@ include-package-data = true
 bit = ["tests/data/*", "smk/*.smk", "smk/envs/*"]
 
 [project.scripts]
+## ncbi-related ##
+bit-dl-ncbi-assemblies = "bit.cli.dl_ncbi_assemblies:main"
 get-ncbi-assembly-tables = "bit.modules.ncbi.get_ncbi_assembly_tables:main"
 get-ncbi-tax-data = "bit.modules.ncbi.get_ncbi_tax_data:main"
+
+
+## gtdb-related ##
+
+
+## coverage / mapping ##
+
+
+## sequence utilities ##

pyproject.toml

@@ -1,6 +1,12 @@
 from setuptools import setup
 import glob
 
+# scripts ported to pyproject.toml [project.scripts] entry points
+# exclude them from the glob so they don't conflict
+ported = {
+    "bit/scripts/bit-dl-ncbi-assemblies",
+}
+
 setup(
-    scripts=glob.glob("bit/scripts/*")
+    scripts=[s for s in glob.glob("bit/scripts/*") if s not in ported]
 )