removing script stubs where possible

Author: Mike Lee

CHANGELOG.md

@@ -26,6 +26,7 @@
   - downloads only happen in http now, no more ftp, so the -P flag to specify http has been removed
   - added optional output dir
 - no longer keeping stubs in scripts/, instead keeping a ton of entry points in pyproject.toml
+- `bit-filter-seqs-by-length` renamed to `bit-filter-fasta-by-length` to be more specific (prior retained for now)
 
 
 

bit/modules/general.py

@@ -119,3 +119,24 @@ def attempt_to_make_dir(dir_path):
         os.makedirs(dir_path, exist_ok=True)
     except Exception as e:
         report_failure(f"Failed to create directory '{dir_path}' with the following error:\n{e}")
+
+
+def report_version():
+
+    from datetime import datetime
+    from importlib.metadata import version
+
+    ver = f"v{version('bit')}"
+    print()
+    print(f"{' ' * 22} Bioinformatics Tools (bit) {color_text(ver, 'green')}")
+    print(f"{' ' * 25} github.com/AstrobioMike/bit\n")
+
+    print("    If you happen to find this toolset useful in your work, please be sure to")
+    print("    cite it :)\n")
+
+    print("  Lee M. bit: a multipurpose collection of bioinformatics tools. F1000Research 2022, 11:122")
+    print("  https://doi.org/10.12688/f1000research.79530.1\n")
+
+    today = datetime.today().strftime('%A')
+    signoff = f"Happy {today} :)"
+    print(f"                                                   {color_text(signoff,'green')}\n")

bit/scripts/bit-version

@@ -27,11 +27,6 @@ def pytest_sessionstart(session):
     not_modularized = []
 
     for file in script_files:
-        # pseudo-ignoring bit-version for this purpose
-        if file.name == "bit-version":
-            python_scripts.append(file)
-            modularized.append(file)
-            continue
 
         # checking if helper script
         if file.name.startswith("helper-bit-"):
@@ -55,23 +50,25 @@ def pytest_sessionstart(session):
 
         if 'if __name__ == "__main__"' in first_ten:
             modularized.append(file)
-            print(file)
         else:
             not_modularized.append(file)
 
     print("\n  ====================================================================================================")
     print("  ================================= Progress on modularizing scripts =================================")
     print("  ====================================================================================================\n")
 
-    print(f"    Legacy script files remaining: {len(script_files)}\n")
+    print(f"    Legacy-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"        Python scripts modularized: {len(modularized)}")
+    # print(f"        Python scripts not yet modularized: {len(not_modularized)}\n")
+
+    # if not_modularized:
+    #     print("        Files not yet modularized:\n")
+    #     print_two_columns(not_modularized)
 
-    if not_modularized:
-        print("        Files not yet modularized:\n")
-        print_two_columns(not_modularized)
+    print("\n        Remainig legacy scripts:\n")
+    print_two_columns(script_files)
 
     print("\n  ====================================================================================================\n")

bit/tests/conftest.py

@@ -20,6 +20,8 @@ include-package-data = true
 bit = ["tests/data/*", "smk/*.smk", "smk/envs/*"]
 
 [project.scripts]
+bit-version = "bit.modules.general:report_version"
+
 ## ncbi-related ##
 bit-dl-ncbi-assemblies = "bit.cli.dl_ncbi_assemblies:main"
 get-ncbi-assembly-tables = "bit.modules.ncbi.get_ncbi_assembly_tables:main"