Merge pull request #5 from yibeichan/main

standardize naming and packaging

Author: yibeichan

Dockerfile

@@ -78,7 +78,7 @@ ENV TEMP=/work
 ENV TMP=/work
 
 # Create entrypoint script with proper permissions
-RUN echo '#!/bin/bash\nexec ants-nidm-bidsapp "$@"' > /entrypoint.sh && \
+RUN echo '#!/bin/bash\nexec ants-nidm "$@"' > /entrypoint.sh && \
     chmod 755 /entrypoint.sh
 
 # Ensure all installed binaries are executable

README.md

@@ -41,18 +41,18 @@ This BIDS App follows standard BIDS Apps practices with a Dockerfile as the prim
 python setup.py docker
 
 # Or directly with Docker
-docker build -t ants-nidm-bidsapp:latest .
+docker build -t ants-nidm_bidsapp:latest .
 
 # Save for transfer to HPC (if needed)
-docker save ants-nidm-bidsapp:latest -o ants-nidm-bidsapp.tar
+docker save ants-nidm_bidsapp:latest -o ants-nidm_bidsapp.tar
 ```
 
 #### Building with Singularity/Apptainer (for HPC environments)
 
 ```bash
 # Direct build from Singularity definition file
 # The --fakeroot flag is required on HPC systems without root access
-apptainer build --fakeroot ants-nidm-bidsapp.sif Singularity
+apptainer build --fakeroot ants-nidm_bidsapp.sif Singularity
 
 # Or using the setup.py helper
 python setup.py singularity
@@ -64,25 +64,25 @@ If you have a Docker image (either built locally or from a tar file):
 
 ```bash
 # From a saved Docker tar file
-singularity build ants-nidm-bidsapp.sif docker-archive://ants-nidm-bidsapp.tar
+singularity build ants-nidm_bidsapp.sif docker-archive://ants-nidm_bidsapp.tar
 
 # From local Docker daemon (requires Docker)
-singularity build ants-nidm-bidsapp.sif docker-daemon://ants-nidm-bidsapp:latest
+singularity build ants-nidm_bidsapp.sif docker-daemon://ants-nidm_bidsapp:latest
 ```
 
 ## Usage
 
 ### Basic Usage
 
 ```bash
-ants-nidm-bidsapp bids_dir output_dir participant --participant-label 01
+ants-nidm bids_dir output_dir participant --participant-label 01
 ```
 
 ### Advanced Options
 
 ```bash
 # Full pipeline with all options
-ants-nidm-bidsapp bids_dir output_dir participant \
+ants-nidm bids_dir output_dir participant \
   --participant-label 01 \
   --session-label pre \
   --modality T1w \
@@ -98,7 +98,7 @@ If you have already run ANTs segmentation and only want to generate NIDM outputs
 
 ```bash
 # Run only NIDM conversion using existing ANTs results
-ants-nidm-bidsapp bids_dir output_dir participant \
+ants-nidm bids_dir output_dir participant \
   --participant-label 01 \
   --skip-ants \
   --ants-input /path/to/existing/ants-seg \

Singularity

@@ -130,4 +130,4 @@ From: ubuntu:22.04
       singularity run [container] [input_dir] [output_dir] participant [options]
 
     Example:
-      singularity run ants-nidm-bidsapp.sif $PWD/inputs/data/BIDS $PWD/outputs/ants participant --participant-label 01 02 03 --session-label 01 --modality T1w
+      singularity run ants-nidm_bidsapp.sif $PWD/inputs/data/BIDS $PWD/outputs/ants participant --participant-label 01 02 03 --session-label 01 --modality T1w

examples/README.md

@@ -22,7 +22,7 @@ examples/
 To run the ANTs BIDS App on this example data:
 
 ```bash
-ants-bidsapp examples output participant --participant-label 01 02
+ants-nidm examples output participant --participant-label 01 02
 ```
 
 ## Note

setup.py

@@ -5,24 +5,31 @@
 from setuptools import setup, find_namespace_packages
 
 
+# Container image constants - single source of truth for image names
+DOCKER_IMAGE_NAME = "ants-nidm_bidsapp"
+DOCKER_IMAGE_TAG = "latest"
+DOCKER_IMAGE = f"{DOCKER_IMAGE_NAME}:{DOCKER_IMAGE_TAG}"
+SINGULARITY_IMAGE_NAME = f"{DOCKER_IMAGE_NAME}.sif"
+
+
 def build_docker():
     """Build Docker container"""
     print("Building Docker image...")
     try:
-        subprocess.run(["docker", "build", "-t", "ants-nidm-bidsapp:latest", "."], check=True)
-        print("Docker image built successfully: ants-nidm-bidsapp:latest")
+        subprocess.run(["docker", "build", "-t", DOCKER_IMAGE, "."], check=True)
+        print(f"Docker image built successfully: {DOCKER_IMAGE}")
     except subprocess.CalledProcessError as e:
         print(f"Docker build failed: {e}")
         return False
     return True
 
 
-def docker_to_singularity(docker_image="ants-nidm-bidsapp:latest", output_path=None):
+def docker_to_singularity(docker_image=DOCKER_IMAGE, output_path=None):
     """Convert Docker image to Singularity container"""
     print(f"Converting Docker image {docker_image} to Singularity...")
 
     # Use custom output path if provided, otherwise use default
-    output_file = output_path if output_path else "ants-nidm-bidsapp.sif"
+    output_file = output_path if output_path else SINGULARITY_IMAGE_NAME
     output_file = str(Path(output_file).resolve())
 
     try:
@@ -59,7 +66,7 @@ def build_singularity(output_path=None):
         ):
             print("\nDetected Apptainer on cluster environment.")
             print("For cluster environments, please build directly with apptainer:")
-            print("apptainer build --fakeroot ants-nidm-bidsapp.sif Singularity\n")
+            print(f"apptainer build --fakeroot {SINGULARITY_IMAGE_NAME} Singularity\n")
             return False
         elif (
             subprocess.run(["which", "singularity"], capture_output=True).returncode == 0
@@ -70,7 +77,7 @@ def build_singularity(output_path=None):
             return False
 
         # Use custom output path if provided, otherwise use default
-        output_file = output_path if output_path else "ants-nidm-bidsapp.sif"
+        output_file = output_path if output_path else SINGULARITY_IMAGE_NAME
         output_file = str(Path(output_file).resolve())
 
         # Build command
@@ -92,9 +99,9 @@ def build_singularity(output_path=None):
     except subprocess.CalledProcessError as e:
         print(f"Build failed: {e}")
         print("\nFor cluster environments, please build directly with apptainer:")
-        print("apptainer build --remote ants-nidm-bidsapp.sif Singularity")
+        print(f"apptainer build --remote {SINGULARITY_IMAGE_NAME} Singularity")
         print("or")
-        print("apptainer build --fakeroot ants-nidm-bidsapp.sif Singularity")
+        print(f"apptainer build --fakeroot {SINGULARITY_IMAGE_NAME} Singularity")
         return False
 
 
@@ -126,7 +133,7 @@ def print_usage():
     print("\nOther Commands:")
     print("  python setup.py --init-git       - Initialize git submodules")
     print("\nNote: For HPC environments without Docker, use 'singularity' command directly:")
-    print("  apptainer build --fakeroot ants-nidm-bidsapp.sif Singularity")
+    print(f"  apptainer build --fakeroot {SINGULARITY_IMAGE_NAME} Singularity")
     print("\nFor more information, run: python setup.py --help")
 
 
@@ -242,7 +249,7 @@ def install_antspyx():
     print("  python -m pip install -e .")
 
 setup(
-    name="ants-nidm_bidsapp",
+    name="ants-nidm",
     version="0.1.0",
     description="BIDS App for ANTs Segmentation with NIDM Output",
     author="ReproNim",
@@ -263,7 +270,7 @@ def install_antspyx():
     ],
     entry_points={
         "console_scripts": [
-            "ants-nidm-bidsapp=src.run:main",
+            "ants-nidm=src.run:main",
         ],
     },
     python_requires=">=3.9",

src/antspy/wrapper.py

@@ -99,7 +99,7 @@ def __init__(self,
         self.verbose = verbose
 
         # Set up logging
-        self.logger = logging.getLogger('ants_bidsapp.segmentation')
+        self.logger = logging.getLogger('ants-nidm.segmentation')
 
         # Validate required directories
         if not self.bids_dir or not self.bids_dir.exists():

src/run.py

@@ -29,7 +29,7 @@ def setup_logger(log_dir, verbose=False):
     """Set up logging configuration."""
     os.makedirs(log_dir, exist_ok=True)
     timestamp = datetime.now().strftime("%Y%m%d-%H%M%S")
-    log_file = os.path.join(log_dir, f"ants-nidm_bidsapp-{timestamp}.log")
+    log_file = os.path.join(log_dir, f"ants-nidm-{timestamp}.log")
 
     # Configure logging
     log_level = logging.DEBUG if verbose else logging.INFO
@@ -41,7 +41,7 @@ def setup_logger(log_dir, verbose=False):
             logging.StreamHandler()
         ]
     )
-    return logging.getLogger('ants-nidm_bidsapp')
+    return logging.getLogger('ants-nidm')
 
 def find_nidm_input_file(nidm_input_dir, subject_id, session_id=None):
     """Search for NIDM input file in standard locations.