brainforge-cli 1.0.0__tar.gz → 1.0.1__tar.gz

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainforge-cli
-Version: 1.0.0
+Version: 1.0.1
 Summary: Command-line interface for Brainforge
 Author: Daniel Trinh
 Requires-Python: >=3.10

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/brainforge/__init__.py

@@ -2,4 +2,4 @@
 Brainforge CLI Package
 """
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/brainforge/cli.py

@@ -12,7 +12,7 @@ from brainforge.template import generate_yaml_template
 
 
 @click.group()
-@click.version_option(version="1.0.0")
+@click.version_option(version="1.0.1")
 def main():
     """
     BrainForge CLI: The premier interface for executing neuroimaging analyses.
@@ -26,7 +26,7 @@ def main():
 @main.command()
 def info():
     """Display information about Brainforge CLI and its current version."""
-    click.echo("Welcome to the Brainforge CLI v1.0.0")
+    click.echo("Welcome to the Brainforge CLI v1.0.1")
     click.echo("Run 'brainforge --help' to see all available commands.")
 
 
@@ -137,15 +137,6 @@ def logs(job_id, log_type, follow):
 
 
 @job.command(name="generate")
-@click.option(
-    '--type',
-    '-t',
-    'job_type',  # map back to variable name
-    prompt='Select job template type',
-    type=click.Choice(['single', 'multiple']),
-    default='single',
-    help="Type of job template (single or multiple).",
-)
 @click.option(
     '--name',
     '-n',
@@ -153,15 +144,15 @@ def logs(job_id, log_type, follow):
     default='template.yaml',
     help="Output filename for the generated template.",
 )
-def generate_cmd(job_type, name):
+def generate_cmd(name):
     """
     Generate a working YAML template for a BrainForge SLURM job.
 
     Creates a boilerplate .yaml file pre-filled with all required
     variables (`SINGULARITY_IMAGE`, `HOST_INPUT_DIR`, etc.) to run
-    either a `single` job or an array job over `multiple` participants.
+    an array job over one or more `participants`.
     """
-    generate_yaml_template(job_type, name)
+    generate_yaml_template(name)
 
 
 if __name__ == "__main__":

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/brainforge/run.py

@@ -99,38 +99,21 @@ def validate_spec(spec):
             sys.exit(1)
 
     participants = execution.get('participants')
-    participant = execution.get('participant')
 
-    if participants is not None and participant is not None:
+    if participants is None:
         click.secho(
-            "Error: Cannot specify both 'participant' and 'participants'. Choose one.",
+            "Error: You must specify 'participants' as a list of identifiers.",
             fg="red",
         )
         sys.exit(1)
 
-    if participants is None and participant is None:
+    if not isinstance(participants, list) or len(participants) == 0:
         click.secho(
-            "Error: You must specify either 'participant' (for single jobs) or 'participants' (for array jobs).",
+            "Error: 'participants' must be a non-empty list of subject identifiers.",
             fg="red",
         )
         sys.exit(1)
 
-    if participants is not None:
-        if not isinstance(participants, list) or len(participants) == 0:
-            click.secho(
-                "Error: 'participants' must be a non-empty list of subject identifiers.",
-                fg="red",
-            )
-            sys.exit(1)
-
-    if participant is not None:
-        # Checking if it's truthy handles empty strings intuitively (e.g. "")
-        if not str(participant).strip():
-            click.secho(
-                "Error: 'participant' must be a valid, non-empty identifier.", fg="red"
-            )
-            sys.exit(1)
-
 
 def generate_sbatch_script(spec):
     lines = ["#!/bin/bash"]
@@ -159,21 +142,15 @@ def generate_sbatch_script(spec):
     lines.append("# --- Auto-generated by BrainForge CLI ---")
     lines.append("")
 
-    # 3. Handle array item mapping or single participant mapping
+    # 3. Handle array item mapping
     if participants:
-        lines.append('BFG_PARTICIPANTS=(')
+        lines.append('PARTICIPANTS=(')
         for item in participants:
             # Safely quote items
             lines.append(f'  "{item}"')
         lines.append(')')
-        lines.append('BFG_PARTICIPANT=${BFG_PARTICIPANTS[$SLURM_ARRAY_TASK_ID]}')
-        lines.append('echo "BrainForge Task running for participant: $BFG_PARTICIPANT"')
-        lines.append("")
-    elif 'participant' in execution:
-        # Singular participant definition
-        val = execution['participant']
-        lines.append(f'BFG_PARTICIPANT="{val}"')
-        lines.append('echo "BrainForge Task running for participant: $BFG_PARTICIPANT"')
+        lines.append('PARTICIPANT=${PARTICIPANTS[$SLURM_ARRAY_TASK_ID]}')
+        lines.append('echo "BrainForge Task running for participant: $PARTICIPANT"')
         lines.append("")
 
     # 4. Modules loading

brainforge_cli-1.0.1/brainforge/template.py

@@ -0,0 +1,44 @@
+import os
+
+import click
+
+JOB_TEMPLATE = """# Job Template for BrainForge CLI
+slurm:
+  job-name: "name"
+  partition: "partition"
+  account: "account"
+  nodes: 1
+  ntasks: 1
+  mem: "8G"
+  cpus-per-task: 4
+  output: "logs/job_%A_%a.out"
+  error: "logs/job_%A_%a.err"
+
+execution:
+  modules:
+    - singularity
+  env:
+    SINGULARITY_IMAGE: "/path/to/container.sif"
+    HOST_INPUT_DIR: "/path/to/input"
+    HOST_OUTPUT_DIR: "/path/to/output"
+  participants:
+    - "sub-01"
+    - "sub-02"
+    - "sub-03"
+  command: "singularity run --bind $HOST_INPUT_DIR:/input --bind $HOST_OUTPUT_DIR:/output $SINGULARITY_IMAGE --participant $PARTICIPANT"
+"""
+
+
+def generate_yaml_template(output_name):
+    # Ensure we don't accidentally overwrite without warning, though
+    # for simplicity we'll just open and write.
+    # If file exists, click.confirm could be used, but let's keep it simple first.
+    if os.path.exists(output_name):
+        click.confirm(f"File '{output_name}' already exists. Overwrite?", abort=True)
+
+    with open(output_name, 'w') as f:
+        f.write(JOB_TEMPLATE)
+
+    click.secho(
+        f"Successfully generated template: {output_name}", fg="green"
+    )

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/brainforge_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brainforge-cli
-Version: 1.0.0
+Version: 1.0.1
 Summary: Command-line interface for Brainforge
 Author: Daniel Trinh
 Requires-Python: >=3.10

{brainforge_cli-1.0.0 → brainforge_cli-1.0.1}/setup.py

@@ -3,7 +3,7 @@ from setuptools import setup
 
 setup(
     name="brainforge-cli",
-    version="1.0.0",
+    version="1.0.1",
     description="Command-line interface for Brainforge",
     author="Daniel Trinh",
     packages=find_packages(),

brainforge_cli-1.0.0/brainforge/template.py

@@ -1,72 +0,0 @@
-import os
-
-import click
-
-SINGLE_JOB_TEMPLATE = """# Single Job Template for BrainForge CLI
-slurm:
-  job-name: "name"
-  partition: "partition"
-  account: "account"
-  nodes: 1
-  ntasks: 1
-  mem: "8G"
-  cpus-per-task: 4
-  output: "logs/job_%j.out"
-  error: "logs/job_%j.err"
-
-execution:
-  modules:
-    - singularity
-  env:
-    SINGULARITY_IMAGE: "/path/to/container.sif"
-    HOST_INPUT_DIR: "/path/to/input"
-    HOST_OUTPUT_DIR: "/path/to/output"
-  participant: "sub-01"
-  command: "echo 'Running Single Job for item $BFG_PARTICIPANT'"
-"""
-
-MULTIPLE_JOB_TEMPLATE = """# Multiple Job Template for BrainForge CLI
-slurm:
-  job-name: "name"
-  partition: "partition"
-  account: "account"
-  nodes: 1
-  ntasks: 1
-  mem: "8G"
-  cpus-per-task: 4
-  output: "logs/job_%A_%a.out"
-  error: "logs/job_%A_%a.err"
-
-execution:
-  modules:
-    - singularity
-  env:
-    SINGULARITY_IMAGE: "/path/to/container.sif"
-    HOST_INPUT_DIR: "/path/to/input"
-    HOST_OUTPUT_DIR: "/path/to/output"
-  participants:
-    - "sub-01"
-    - "sub-02"
-    - "sub-03"
-  command: "echo 'Running Multiple Job for item $BFG_PARTICIPANT'"
-"""
-
-
-def generate_yaml_template(job_type, output_name):
-    if job_type == 'multiple':
-        content = MULTIPLE_JOB_TEMPLATE
-    else:
-        content = SINGLE_JOB_TEMPLATE
-
-    # Ensure we don't accidentally overwrite without warning, though
-    # for simplicity we'll just open and write.
-    # If file exists, click.confirm could be used, but let's keep it simple first.
-    if os.path.exists(output_name):
-        click.confirm(f"File '{output_name}' already exists. Overwrite?", abort=True)
-
-    with open(output_name, 'w') as f:
-        f.write(content)
-
-    click.secho(
-        f"Successfully generated {job_type} template: {output_name}", fg="green"
-    )