Bumped package version

.gitignore

@@ -212,3 +212,4 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
+output.csv

.vscode/launch.json

@@ -8,19 +8,20 @@
             "name": "Use Test Resources",
             "type": "python",
             "request": "launch",
-            "program": "${workspaceFolder}/csvbyname/csvbyname.py",
             "console": "integratedTerminal",
             "args": [
                 "${workspaceFolder}/tests/resources",
                 "${workspaceFolder}/output.csv",
                 "-r",
+                "-n",
                 "-p",
                 "group_num:group(\\d)-\\w-\\d+\\.txt",
                 "group(\\d)-(?P<sect>\\w)-(?P<patid>\\d+)\\.txt",
                 "-V",
                 "DEBUG"
             ],
-            "justMyCode": true
+            "justMyCode": true,
+            "module": "csvbyname.cli"
         }
     ]
 }

Jenkinsfile

@@ -20,9 +20,15 @@ pipeline {
         stage("test") {
             steps {
                 sh "pip install dist/*.whl"
+                sh "csvbyname -h"
             }
         }
-        stage("publish") {
+        stage("archive") {
+            steps {
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
+            }
+        }
+        stage("publish package") {
             when {
                 branch '**/main'
             }

csvbyname/cli.py

@@ -0,0 +1,95 @@
+import argparse
+import logging
+
+from csvbyname.generate import collect_files, write_collected_to_csv
+
+
+def run(args):
+    logger.info('Collecting files from "%s"', args.directory)
+    collected, pkeys = collect_files(
+        args.directory,
+        args.include_folders,
+        args.entire_path,
+        args.recursive,
+        args.add_re_property,
+    )
+    write_collected_to_csv(args.output, collected, pkeys, args.output_basename)
+
+
+def main():
+    argparser = argparse.ArgumentParser(
+        "csvbyname",
+        description="Catalogue a directory of files by patterns in their names into a "
+        "CSV.",
+    )
+    argparser.add_argument(
+        "directory",
+        type=str,
+        help="The directory containing the files to obtain catalogue names of",
+        metavar="i",
+    )
+    argparser.add_argument(
+        "output", type=str, help="The path to the catalogued CSVs.", metavar="o"
+    )
+    argparser.add_argument(
+        "-l",
+        "--include-folders",
+        help="Include folders in the cataloguing process",
+        action="store_true",
+        required=False,
+        default=False,
+    )
+    argparser.add_argument(
+        "-e",
+        "--entire-path",
+        help="Include the full path when applying the groupings to find properties",
+        action="store_true",
+        required=False,
+        default=False,
+    )
+    argparser.add_argument(
+        "-r",
+        "--recursive",
+        help="Catalogue recursively",
+        action="store_true",
+        required=False,
+        default=False,
+    )
+    argparser.add_argument(
+        "-p",
+        "--add-re-property",
+        help="Add a property in the resulting CSV obtained from the first capture "
+        "group of the given REGEX in the following format:\n property-name:regex.\n"
+        "Alternatively, use named REGEX groups.",
+        nargs="+",
+        type=str,
+        required=True
+    )
+    argparser.add_argument(
+        "-n",
+        "--output-basename",
+        help='Adds a column called "basename" to the resulting CSV where it is just '
+        "The base name of the path instead of the entire path. This is not guaranteed "
+        "to be unique.",
+        default=False,
+        required=False,
+        action="store_true",
+    )
+    argparser.add_argument(
+        "-V",
+        "--verbosity",
+        help="Set the verbosity of the logging",
+        type=str,
+        required=False,
+        default="INFO",
+    )
+
+    args = argparser.parse_args()
+    logging.basicConfig(level=args.verbosity.upper())
+    global logger
+    logger = logging.getLogger(__name__)
+    run(args)
+
+
+if __name__ == "__main__":
+    main()

csvbyname/generate.py

@@ -1,11 +1,12 @@
-import argparse
 import csv
 import os
 import re
 from typing import Iterable
-import exceptions
+from csvbyname import exceptions
 import logging
 
+logger = logging.getLogger(__name__)
+
 
 def matcher(full_path: str, use_full_path: bool, regex_groups: list[str]):
     captured_properties = {}
@@ -71,100 +72,24 @@ def collect_files(
 
 
 def write_collected_to_csv(
-    output_path: str, collected: dict[str, dict[str, str]], property_keys: Iterable[str]
+    output_path: str,
+    collected: dict[str, dict[str, str]],
+    property_keys: Iterable[str],
+    output_basename: bool,
 ):
-    with open(output_path, "w") as output_fd:
+    with open(output_path, "w", newline="", encoding="utf-8") as output_fd:
         s_property_keys = sorted(property_keys)
-        header = ["path", *s_property_keys]
+        header = ["path"]
+        if output_basename:
+            header.append("basename")
+        header.extend(s_property_keys)
         writer = csv.writer(output_fd)
         writer.writerow(header)
         for full_path, properties in collected.items():
-            writer.writerow(
+            row = [full_path]
-                [
+            if output_basename:
-                    full_path,
+                row.append(os.path.basename(full_path))
-                    *(
+            row.extend(
-                        properties[k] if k in properties else "N/A"
+                (properties[k] if k in properties else "N/A" for k in s_property_keys)
-                        for k in s_property_keys
-                    ),
-                ]
             )
-
+            writer.writerow(row)
-
-def run(args):
-    logger.info('Collecting files from "%s"', args.directory)
-    collected, pkeys = collect_files(
-        args.directory,
-        args.include_folders,
-        args.entire_path,
-        args.recursive,
-        args.add_re_property,
-    )
-    write_collected_to_csv(args.output, collected, pkeys)
-
-
-def main():
-    argparser = argparse.ArgumentParser(
-        "csvbyname",
-        description="Catalogue a directory of files by patterns in their names into a "
-        "CSV.",
-    )
-    argparser.add_argument(
-        "directory",
-        type=str,
-        help="The directory containing the files to obtain catalogue names of",
-        metavar="i",
-    )
-    argparser.add_argument(
-        "output", type=str, help="The path to the catalogued CSVs.", metavar="o"
-    )
-    argparser.add_argument(
-        "-l",
-        "--include-folders",
-        help="Include folders in the cataloguing process",
-        action="store_true",
-        required=False,
-        default=False,
-    )
-    argparser.add_argument(
-        "-e",
-        "--entire-path",
-        help="Include the full path when applying the groupings to find properties",
-        action="store_true",
-        required=False,
-        default=False,
-    )
-    argparser.add_argument(
-        "-r",
-        "--recursive",
-        help="Catalogue recursively",
-        action="store_true",
-        required=False,
-        default=False,
-    )
-    argparser.add_argument(
-        "-p",
-        "--add-re-property",
-        help="Add a property in the resulting CSV obtained from the first capture "
-        "group of the given REGEX in the following format:\n property-name:regex.\n"
-        "Alternatively, use named REGEX groups.",
-        nargs="+",
-        type=str,
-    )
-    argparser.add_argument(
-        "-V",
-        "--verbosity",
-        help="Set the verbosity of the logging",
-        type=str,
-        required=False,
-        default="INFO",
-    )
-
-    args = argparser.parse_args()
-    logging.basicConfig(level=args.verbosity.upper())
-    global logger
-    logger = logging.getLogger(__name__)
-    run(args)
-
-
-if __name__ == "__main__":
-    main()

environment.yml

@@ -5,4 +5,4 @@ dependencies:
   - build=0.7.0
   - pytest=7.2.2
   - twine=4.0.2
-  - python=3.9
+  - python=3.11

setup.cfg

@@ -1,10 +1,11 @@
 [metadata]
 name = csvbyname
-version = 0.0.1
+version = 0.0.6
+author = Harrison
 
 [options]
 packages = csvbyname
 
 [options.entry_points]
 console_scripts =
-    csvbyname = csvbyname.csvbyname:main
+    csvbyname = csvbyname.cli:main