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

@@ -13,6 +13,7 @@
                 "${workspaceFolder}/tests/resources",
                 "${workspaceFolder}/output.csv",
                 "-r",
+                "-n",
                 "-p",
                 "group_num:group(\\d)-\\w-\\d+\\.txt",
                 "group(\\d)-(?P<sect>\\w)-(?P<patid>\\d+)\\.txt",

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") {
@@ -17,7 +17,7 @@ pipeline {
                 sh "python -m build"
             }
         }
-        stage("test") {
+        stage("test installation") {
             steps {
                 sh "pip install dist/*.whl"
                 sh "csvbyname -h"
@@ -25,7 +25,7 @@ pipeline {
         }
         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") {
@@ -33,7 +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

@@ -63,12 +63,13 @@ 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 "
+        "the base name of the path instead of the entire path. This is not guaranteed "
         "to be unique.",
         default=False,
         required=False,

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(
-                [
-                    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)
             )
+            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 = 0.0.4
+version = 0.0.6
 author = Harrison
 
 [options]