Updated CI config to match server CI

.devcontainer/devcontainer.json

@@ -0,0 +1,22 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye"
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "pip3 install --user -r requirements.txt",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.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

@@ -1,15 +1,15 @@
 pipeline {
-    agent any
-    stages {
-        stage("clean") {
-            steps {
-                sh 'rm -rf ./dist/*'
-            }
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
         }
+    }
+    stages {
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml'
-                sh 'echo "mamba activate csvbyname" >> ~/.bashrc'
+                sh 'pip install -r requirements.txt'
             }
         }
         stage("build") {
@@ -17,17 +17,23 @@ pipeline {
                 sh "python -m build"
             }
         }
-        stage("test") {
+        stage("test installation") {
             steps {
                 sh "pip install dist/*.whl"
+                sh "csvbyname -h"
             }
         }
-        stage("publish") {
+        stage("archive") {
+            steps {
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
+            }
+        }
+        stage("publish package") {
             when {
                 branch '**/main'
             }
             steps {
-                withCredentials([usernamePassword(credentialsId: 'rs-git-package-registry-ydeng', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
+                withCredentials([usernamePassword(credentialsId: '4d6f64be-d26d-4f95-8de3-b6a9b0beb311', passwordVariable: 'PASS', usernameVariable: 'USER')]) {
                     sh "python -m twine upload --repository-url https://git.reslate.systems/api/packages/${USER}/pypi -u ${USER} -p ${PASS} --non-interactive --disable-progress-bar --verbose dist/*"
                 }
             }

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(
-                [
-                    full_path,
-                    *(
-                        properties[k] if k in properties else "N/A"
-                        for k in s_property_keys
-                    ),
-                ]
+            row = [full_path]
+            if output_basename:
+                row.append(os.path.basename(full_path))
+            row.extend(
+                (properties[k] if k in properties else "N/A" for k in s_property_keys)
             )
-
-
-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()
+            writer.writerow(row)

environment.yml

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

requirements.txt

@@ -0,0 +1,3 @@
+build
+pytest
+twine

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