feat: enhance CLI reactivity and improve module imports for performance

seqnado/__init__.py

@@ -17,12 +17,27 @@
     Molecule,
     Organism,
     FileType,
-    GenomicCoordinate
 )
 
-from . import data, config, inputs, outputs
+_LAZY_SUBMODULES = {"data", "config", "inputs", "outputs"}
+_LAZY_ATTRS = {"GenomicCoordinate": ("config", "GenomicCoordinate")}
 
 
+def __getattr__(name: str):
+    if name in _LAZY_SUBMODULES:
+        import importlib
+        mod = importlib.import_module(f".{name}", __name__)
+        globals()[name] = mod
+        return mod
+    if name in _LAZY_ATTRS:
+        mod_name, attr = _LAZY_ATTRS[name]
+        import importlib
+        mod = importlib.import_module(f".{mod_name}", __name__)
+        obj = getattr(mod, attr)
+        globals()[name] = obj
+        return obj
+    raise AttributeError(f"module 'seqnado' has no attribute {name!r}")
+
 
 __all__ = [
     "Assay",
@@ -49,5 +64,5 @@
     "Molecule",
     "Organism",
     "FileType",
-    "GenomicCoordinate"
+    "GenomicCoordinate",
 ]

seqnado/cli/autocomplete.py

@@ -8,7 +8,7 @@
 
 def _assay_names() -> List[str]:
     """Get list of available assay names for autocomplete."""
-    from seqnado.inputs import Assay  # local import to keep CLI startup snappy
+    from seqnado.core import Assay
 
     return list(Assay.all_assay_clean_names())
 

seqnado/cli/commands/benchmark.py

@@ -8,16 +8,6 @@
 from loguru import logger
 
 from seqnado.cli.app_instance import app
-from seqnado.cli.benchmark_helpers import (
-    compute_assay_output_sizes,
-    discover_snakemake_logs,
-    format_compact_number,
-    load_benchmark_table,
-    parse_alignment_processing_logs,
-    parse_snakemake_logs_timeline,
-    summarize_benchmarks,
-    write_html_report,
-)
 from seqnado.cli.utils import _configure_logging, cli_print_table, verbose_option
 
 
@@ -101,6 +91,16 @@ def run_benchmark_report(
     verbose: bool = False,
 ) -> None:
     """Generate benchmark outputs from plain Python code without Typer option wrappers."""
+    from seqnado.cli.benchmark_helpers import (
+        compute_assay_output_sizes,
+        discover_snakemake_logs,
+        format_compact_number,
+        load_benchmark_table,
+        parse_alignment_processing_logs,
+        parse_snakemake_logs_timeline,
+        summarize_benchmarks,
+        write_html_report,
+    )
     _configure_logging(verbose)
 
     resolved_benchmark_dir = _resolve_benchmark_dir(benchmark_dir)

seqnado/cli/commands/pipeline.py

@@ -13,7 +13,6 @@
 
 from seqnado.cli.app_instance import app
 from seqnado.cli.autocomplete import assay_autocomplete
-from seqnado.cli.commands.benchmark import run_benchmark_report
 from seqnado.cli.snakemake_builder import SnakemakeCommandBuilder
 from seqnado.cli.utils import (
     _configure_logging,
@@ -26,7 +25,6 @@
     verbose_option,
     preset_option,
 )
-from seqnado.outputs.multiomics import find_assay_config_paths
 from seqnado.utils import (
     resolve_profile_path,
     extract_cores_from_options,
@@ -44,6 +42,7 @@ def _ensure_default_snakemake_flag(options: List[str], flag: str) -> List[str]:
 def _run_benchmark_after_success(verbose: bool) -> None:
     """Best-effort benchmark/report generation after a successful pipeline run."""
     try:
+        from seqnado.cli.commands.benchmark import run_benchmark_report
         run_benchmark_report(benchmark_dir=Path(".benchmark"), verbose=verbose)
     except typer.Exit as exc:
         if exc.exit_code not in (0, None):
@@ -246,6 +245,7 @@ def pipeline(
     require_snakemake()
 
     # Detect multiomics configs early
+    from seqnado.outputs.multiomics import find_assay_config_paths
     config_files = find_assay_config_paths(Path("."))
     use_multiomics = len(config_files) > 1 and not config_file and not assay
 

seqnado/config/__init__.py

@@ -27,6 +27,7 @@
     SNPCallingConfig,
     MCCConfig,
     MethylationConfig,
+    GenomicCoordinate,
 )
 
 from .user_input import (
@@ -75,4 +76,5 @@
     "MultiomicsConfig",
     "build_multiomics_config",
     "render_multiomics_configs",
+    "GenomicCoordinate",
 ]

seqnado/config/configs.py

@@ -15,7 +15,6 @@
 
 from seqnado import (
     Assay,
-    GenomicCoordinate,
     MethylationMethod,
     MotifMethod,
     PCRDuplicateHandling,
@@ -32,6 +31,32 @@
 )
 
 
+class GenomicCoordinate(BaseModel):
+    """Configuration for genomic coordinates."""
+
+    chromosome: str
+    start: int
+    end: int
+
+    @field_validator("start", "end")
+    def validate_coordinates(cls, v: int) -> int:
+        if v < 0:
+            raise ValueError("Genomic coordinates must be non-negative.")
+        return v
+
+    @field_validator("end")
+    def validate_end_greater_than_start(cls, v: int, info) -> int:
+        if "start" in info.data and v < info.data["start"]:
+            raise ValueError("End coordinate must be greater than start coordinate.")
+        return v
+
+    @classmethod
+    def from_string(cls, coord_str: str) -> "GenomicCoordinate":
+        chromosome, positions = coord_str.split(":")
+        start, end = map(int, positions.split("-"))
+        return cls(chromosome=chromosome, start=start, end=end)
+
+
 def none_str_to_none(v):
     if isinstance(v, str) and v.strip().lower() == "none":
         return None

seqnado/core.py

@@ -1,7 +1,5 @@
 from enum import Enum
 
-from pydantic import BaseModel, field_validator
-
 # =============================================================================
 # CONSTANTS
 # =============================================================================
@@ -210,32 +208,3 @@ class LibraryType(Enum):
     PAIRED = "paired-end"
 
 
-class GenomicCoordinate(BaseModel):
-    """Configuration for genomic coordinates."""
-
-    chromosome: str
-    start: int
-    end: int
-
-    @field_validator("start", "end")
-    def validate_coordinates(cls, v: int) -> int:
-        if v < 0:
-            raise ValueError("Genomic coordinates must be non-negative.")
-        return v
-
-    # Check that end is greater than start
-    @field_validator("end")
-    def validate_end_greater_than_start(cls, v: int, info) -> int:
-        # Only validate if start is available (i.e., it passed validation)
-        if "start" in info.data and v < info.data["start"]:
-            raise ValueError("End coordinate must be greater than start coordinate.")
-        return v
-
-    @classmethod
-    def from_string(cls, coord_str: str) -> "GenomicCoordinate":
-        """
-        Create a GenomicCoordinate instance from a string representation.
-        """
-        chromosome, positions = coord_str.split(":")
-        start, end = map(int, positions.split("-"))
-        return cls(chromosome=chromosome, start=start, end=end)

tests/unit/test_core.py

@@ -3,9 +3,9 @@
 import pytest
 from pydantic import ValidationError
 
+from seqnado.config import GenomicCoordinate
 from seqnado.core import (
     Assay,
-    GenomicCoordinate,
     FileType,
     PileupMethod,
     DataScalingTechnique,