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"
+}

.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
+    agent {
+        kubernetes {
+            cloud 'rsys-devel'
+            defaultContainer 'pip'
+            inheritFrom 'pip'
+        }
+    }
     stages {
-        stage("clean") {
-            steps {
-                sh 'rm -rf ./dist/*'
-            }
-        }
         stage("install") {
             steps {
-                sh 'mamba env update --file environment.yml'
+                sh 'pip install -r requirements.txt'
-                sh 'echo "mamba activate csvbyname" >> ~/.bashrc'
             }
         }
         stage("build") {
@@ -17,14 +17,15 @@ pipeline {
                 sh "python -m build"
             }
         }
-        stage("test") {
+        stage("test installation") {
             steps {
                 sh "pip install dist/*.whl"
+                sh "csvbyname -h"
             }
         }
         stage("archive") {
             steps {
-                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl'
+                archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
             }
         }
         stage("publish package") {
@@ -32,7 +33,7 @@ pipeline {
                 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

@@ -13,7 +13,7 @@ def run(args):
         args.recursive,
         args.add_re_property,
     )
-    write_collected_to_csv(args.output, collected, pkeys)
+    write_collected_to_csv(args.output, collected, pkeys, args.output_basename)
 
 
 def main():
@@ -63,6 +63,17 @@ def main():
         "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",

csvbyname/generate.py

@@ -72,20 +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)

environment.yml

@@ -6,3 +6,4 @@ dependencies:
   - pytest=7.2.2
   - twine=4.0.2
   - python=3.11
+prefix: ./env

requirements.txt

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

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = csvbyname
-version = 0.0.3
+version = 0.0.6
 author = Harrison
 
 [options]