bactopia 2.1.2__tar.gz → 2.1.4__tar.gz

{bactopia-2.1.2 → bactopia-2.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bactopia
-Version: 2.1.2
+Version: 2.1.4
 Summary: A Python package for working with Bactopia
 License: MIT
 License-File: LICENSE

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/atb/atb_downloader.py

@@ -6,10 +6,10 @@ import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
 from bactopia.atb import parse_atb_file_list
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.databases.ncbi import is_biosample, taxid2name
 from bactopia.utils import (
     download_url,
@@ -66,7 +66,7 @@ click.rich_click.OPTION_GROUPS = {
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version", "-V")
+@common_options
 @click.option(
     "--query",
     "-q",
@@ -130,8 +130,6 @@ click.rich_click.OPTION_GROUPS = {
     help="The size of the chunks to split the list into",
 )
 @click.option("--force", is_flag=True, help="Overwrite existing files")
-@click.option("--verbose", is_flag=True, help="Increase the verbosity of output")
-@click.option("--silent", is_flag=True, help="Only critical errors will be printed")
 def atb_downloader(
     query,
     outdir,
@@ -148,17 +146,7 @@ def atb_downloader(
     silent,
 ):
     """Download All-the-Bacteria assemblies based on input query"""
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(
-        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
-    )
+    setup_logging(verbose, silent)
 
     # If outdir does not exist, create it
     outdir = mkdir(outdir)

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/atb/atb_formatter.py

@@ -7,10 +7,10 @@ import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
 from bactopia.atb import create_sample_directory, search_path
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.utils import validate_file
 
 # Set up Rich
@@ -43,7 +43,7 @@ click.rich_click.OPTION_GROUPS = {
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version", "-V")
+@common_options
 @click.option(
     "--path",
     "-p",
@@ -75,8 +75,6 @@ click.rich_click.OPTION_GROUPS = {
 @click.option(
     "--recursive", "-r", is_flag=True, help="Traverse recursively through provided path"
 )
-@click.option("--verbose", is_flag=True, help="Increase the verbosity of output")
-@click.option("--silent", is_flag=True, help="Only critical errors will be printed")
 def atb_formatter(
     path,
     bactopia_dir,
@@ -87,17 +85,7 @@ def atb_formatter(
     silent,
 ):
     """Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools"""
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(
-        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
-    )
+    setup_logging(verbose, silent)
 
     # Get absolute path of input
     abspath = validate_file(path)

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/catalog.py

@@ -11,9 +11,9 @@ import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.nf import (
     find_main_nf,
     get_bactopia_version,
@@ -29,6 +29,30 @@ stderr = rich.console.Console(stderr=True)
 rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1)
 click.rich_click.USE_RICH_MARKUP = True
 
+click.rich_click.OPTION_GROUPS = {
+    "bactopia-catalog": [
+        {"name": "Required Options", "options": ["--bactopia-path"]},
+        {
+            "name": "Output Options",
+            "options": [
+                "--output",
+                "--pretty",
+                "--llms-output",
+                "--llms-template",
+            ],
+        },
+        {
+            "name": "Additional Options",
+            "options": [
+                "--verbose",
+                "--silent",
+                "--version",
+                "--help",
+            ],
+        },
+    ]
+}
+
 
 def _extract_description(groovydoc: dict) -> str:
     """Extract the first line description from GroovyDoc raw lines."""
@@ -407,7 +431,7 @@ def render_llms_txt(catalog: dict, template_path: Path) -> str:
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version")
+@common_options
 @click.option(
     "--bactopia-path",
     required=True,
@@ -420,22 +444,21 @@ def render_llms_txt(catalog: dict, template_path: Path) -> str:
     default=None,
     help="Output path for catalog.json (default: stdout)",
 )
-@click.option("--pretty", is_flag=True, help="Pretty-print JSON output.")
+@click.option("--pretty", is_flag=True, help="Pretty-print JSON output")
 @click.option(
     "--llms-output",
     "llms_output_path",
     type=click.Path(),
     default=None,
-    help="Also render llms.txt to this path. Uses the bundled template at bactopia/templates/bactopia/llms.txt.j2 unless --llms-template is provided.",
+    help="Also render llms.txt to this path. Uses the bundled template at bactopia/templates/bactopia/llms.txt.j2 unless --llms-template is provided",
 )
 @click.option(
     "--llms-template",
     "llms_template_path",
     type=click.Path(exists=True, dir_okay=False),
     default=None,
-    help="Jinja2 template for llms.txt. Defaults to the template bundled inside bactopia-py.",
+    help="Jinja2 template for llms.txt. Defaults to the template bundled inside bactopia-py",
 )
-@click.option("--verbose", is_flag=True, help="Print debug related text.")
 def catalog(
     bactopia_path,
     output_path,
@@ -443,6 +466,7 @@ def catalog(
     llms_output_path,
     llms_template_path,
     verbose,
+    silent,
 ):
     """Generate machine-readable catalog of all Bactopia components.
 
@@ -453,15 +477,7 @@ def catalog(
     Optionally also renders llms.txt from a Jinja2 template when
     --llms-output is provided.
     """
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(logging.DEBUG if verbose else logging.WARNING)
+    setup_logging(verbose, silent)
 
     # Validate path
     bp = Path(bactopia_path).absolute().resolve()

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/citations.py

@@ -1,3 +1,5 @@
+"""CLI command for printing and validating Bactopia citations."""
+
 import json
 import sys
 from pathlib import Path
@@ -11,6 +13,7 @@ from rich.markdown import Markdown
 from rich.table import Table
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.lint.citations import validate_citations
 from bactopia.parsers.citations import parse_citations
 from bactopia.utils import validate_file
@@ -20,6 +23,30 @@ stderr = rich.console.Console(stderr=True)
 rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1)
 click.rich_click.USE_RICH_MARKUP = True
 
+click.rich_click.OPTION_GROUPS = {
+    "bactopia-citations": [
+        {"name": "Required Options", "options": ["--bactopia-path"]},
+        {
+            "name": "Output Options",
+            "options": [
+                "--name",
+                "--plain-text",
+                "--validate",
+                "--json",
+            ],
+        },
+        {
+            "name": "Additional Options",
+            "options": [
+                "--verbose",
+                "--silent",
+                "--version",
+                "--help",
+            ],
+        },
+    ]
+}
+
 
 def _render_validation_report(report: dict, silent: bool, plain_text: bool) -> None:
     """Pretty-print a validate_citations() report using Rich tables."""
@@ -84,7 +111,7 @@ def _render_expected_orphans(console: Console, expected_orphans: dict) -> None:
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version", "-V")
+@common_options
 @click.option(
     "--bactopia-path",
     "-b",
@@ -104,17 +131,13 @@ def _render_expected_orphans(console: Console, expected_orphans: dict) -> None:
     is_flag=True,
     help="Emit validation results as JSON (use with --validate)",
 )
-@click.option(
-    "--silent",
-    is_flag=True,
-    help="Suppress non-error output when validation is clean",
-)
 def citations(
     bactopia_path: str,
     name: str,
     plain_text: bool,
     validate: bool,
     as_json: bool,
+    verbose: bool,
     silent: bool,
 ) -> None:
     """Print or validate citations used throughout Bactopia.
@@ -125,6 +148,7 @@ def citations(
     an entry in citations.yml. Module and subworkflow @citation keys are
     validated by bactopia-lint (rules M035 and S019).
     """
+    setup_logging(verbose, silent)
 
     if validate:
         # Validation mode requires the repo root so we can locate

bactopia-2.1.4/bactopia/cli/common.py

@@ -0,0 +1,37 @@
+"""Shared CLI decorators and helpers for Bactopia commands."""
+
+import functools
+import logging
+
+import rich.console
+import rich_click as click
+from rich.logging import RichHandler
+
+import bactopia
+
+
+def common_options(fn):
+    """Add --verbose, --silent, and --version/-V to a click command."""
+
+    @click.version_option(bactopia.__version__, "--version", "-V")
+    @click.option("--verbose", is_flag=True, help="Print debug related text")
+    @click.option("--silent", is_flag=True, help="Only critical errors will be printed")
+    @functools.wraps(fn)
+    def wrapper(*args, **kwargs):
+        return fn(*args, **kwargs)
+
+    return wrapper
+
+
+def setup_logging(verbose: bool, silent: bool) -> None:
+    """Configure root logger with RichHandler at the appropriate level."""
+    logging.basicConfig(
+        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+        handlers=[
+            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
+        ],
+    )
+    logging.getLogger().setLevel(
+        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
+    )

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/datasets.py

@@ -8,9 +8,9 @@ import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.nf import parse_dataset_urls
 from bactopia.utils import execute
 
@@ -75,7 +75,7 @@ def download_file(url, save_path, max_retry=5):
         allow_extra_args=True,
     )
 )
-@click.version_option(bactopia.__version__, "--version")
+@common_options
 # Use underscores in parameters and only --, since Nextflow parameters are passed in
 @click.option(
     "--bactopia-path",
@@ -91,15 +91,13 @@ def download_file(url, save_path, max_retry=5):
 @click.option(
     "--force",
     is_flag=True,
-    help="Force overwrite of existing pre-built environments.",
+    help="Force overwrite of existing pre-built environments",
 )
 @click.option(
     "--max_retry",
     default=3,
     help="Maximum times to attempt creating Conda environment. (Default: 3)",
 )
-@click.option("--verbose", is_flag=True, help="Print debug related text.")
-@click.option("--silent", is_flag=True, help="Only critical errors will be printed.")
 @click.argument("unknown", nargs=-1, type=click.UNPROCESSED)
 def datasets(
     bactopia_path,
@@ -111,17 +109,7 @@ def datasets(
     unknown,
 ):
     """Download optional datasets to supplement your analyses with Bactopia"""
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(
-        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
-    )
+    setup_logging(verbose, silent)
 
     # Install paths
     bactopia_path = str(Path(bactopia_path).absolute())

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/docs.py

@@ -12,6 +12,7 @@ from rich.console import Console
 from rich.table import Table
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.lint.docs import (
     DEFAULT_DOCS_PATH,
     DEFAULT_PATTERNS_FILE,
@@ -22,6 +23,38 @@ stderr = rich.console.Console(stderr=True)
 rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1)
 click.rich_click.USE_RICH_MARKUP = True
 
+click.rich_click.OPTION_GROUPS = {
+    "bactopia-docs": [
+        {"name": "Required Options", "options": ["--bactopia-path"]},
+        {
+            "name": "Validation Options",
+            "options": [
+                "--docs-path",
+                "--patterns-file",
+                "--bactopia-py-path",
+                "--skip-path-check",
+                "--validate",
+            ],
+        },
+        {
+            "name": "Output Options",
+            "options": [
+                "--json",
+                "--plain-text",
+            ],
+        },
+        {
+            "name": "Additional Options",
+            "options": [
+                "--verbose",
+                "--silent",
+                "--version",
+                "--help",
+            ],
+        },
+    ]
+}
+
 
 def _render_report(report: dict, silent: bool, plain_text: bool) -> None:
     """Pretty-print a validate_docs() report using Rich tables."""
@@ -87,7 +120,7 @@ def _render_report(report: dict, silent: bool, plain_text: bool) -> None:
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version", "-V")
+@common_options
 @click.option(
     "--bactopia-path",
     "-b",
@@ -111,7 +144,7 @@ def _render_report(report: dict, silent: bool, plain_text: bool) -> None:
     default=None,
     type=click.Path(file_okay=False, path_type=Path),
     help="Path to bactopia-py repo (for D105 CLI / D106 lint-rule checks). "
-    "Defaults to <bactopia-path>/../bactopia-py.",
+    "Defaults to <bactopia-path>/../bactopia-py",
 )
 @click.option(
     "--skip-path-check",
@@ -121,7 +154,7 @@ def _render_report(report: dict, silent: bool, plain_text: bool) -> None:
 @click.option(
     "--validate",
     is_flag=True,
-    help="Run validation (default action; flag is accepted for parity with bactopia-citations).",
+    help="Run validation (default action; flag is accepted for parity with bactopia-citations)",
 )
 @click.option(
     "--json",
@@ -129,11 +162,6 @@ def _render_report(report: dict, silent: bool, plain_text: bool) -> None:
     is_flag=True,
     help="Emit results as JSON",
 )
-@click.option(
-    "--silent",
-    is_flag=True,
-    help="Suppress non-error output when validation is clean",
-)
 @click.option(
     "--plain-text",
     "-p",
@@ -148,6 +176,7 @@ def docs(
     skip_path_check: bool,
     validate: bool,
     as_json: bool,
+    verbose: bool,
     silent: bool,
     plain_text: bool,
 ) -> None:
@@ -168,6 +197,7 @@ def docs(
 
     Exits 1 if any FAIL is found.
     """
+    setup_logging(verbose, silent)
     repo_root = Path(bactopia_path)
     if not repo_root.is_dir():
         raise click.ClickException(f"--bactopia-path {repo_root} is not a directory.")

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/download.py

@@ -5,13 +5,15 @@ import time
 from datetime import datetime
 from pathlib import Path
 
+"""CLI command for building Bactopia Conda/Docker/Singularity environments."""
+
 import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.nf import parse_module_config, parse_workflows
 from bactopia.utils import execute
 
@@ -343,7 +345,7 @@ def build_singularity_image(
         allow_extra_args=True,
     )
 )
-@click.version_option(bactopia.__version__, "--version")
+@common_options
 # Use underscores in parameters and only --, since Nextflow parameters are passed in
 @click.option(
     "--bactopia-path",
@@ -355,7 +357,7 @@ def build_singularity_image(
     default="conda",
     show_default=True,
     type=click.Choice(["conda", "docker", "singularity", "all"], case_sensitive=False),
-    help="The type of environment to build.",
+    help="The type of environment to build",
 )
 @click.option(
     "--wf",
@@ -383,7 +385,7 @@ def build_singularity_image(
     "--registry",
     default="quay.io",
     show_default=True,
-    help="Registry to pull Docker containers from.",
+    help="Registry to pull Docker containers from",
 )
 @click.option(
     "--singularity_cache",
@@ -399,7 +401,7 @@ def build_singularity_image(
 @click.option(
     "--force_rebuild",
     is_flag=True,
-    help="Force overwrite of existing pre-built environments.",
+    help="Force overwrite of existing pre-built environments",
 )
 @click.option(
     "--max_retry",
@@ -409,10 +411,8 @@ def build_singularity_image(
 @click.option(
     "--dry-run",
     is_flag=True,
-    help="Show environments that would be built, without building them.",
+    help="Show environments that would be built, without building them",
 )
-@click.option("--verbose", is_flag=True, help="Print debug related text.")
-@click.option("--silent", is_flag=True, help="Only critical errors will be printed.")
 @click.argument("unknown", nargs=-1, type=click.UNPROCESSED)
 def download(
     bactopia_path,
@@ -432,17 +432,7 @@ def download(
     unknown,
 ):
     """Builds Bactopia environments for use with Nextflow."""
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(
-        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
-    )
+    setup_logging(verbose, silent)
 
     singularity_exe = "singularity"
     # Check if -profile x is in unknown

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/helpers/merge_schemas.py

@@ -8,10 +8,10 @@ import rich.console
 import rich.traceback
 import rich_click as click
 from jinja2 import Environment, FileSystemLoader
-from rich.logging import RichHandler
 
 import bactopia
 import bactopia.parsers.nextflow as nf_parsers
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.parsers.generic import parse_json
 from bactopia.parsers.workflows import get_modules_by_workflow
 
@@ -75,7 +75,7 @@ click.rich_click.OPTION_GROUPS = {
         allow_extra_args=True,
     )
 )
-@click.version_option(bactopia.__version__, "--version")
+@common_options
 # Use underscores in parameters and only --, since Nextflow parameters are passed in
 @click.option(
     "--bactopia-path",
@@ -85,7 +85,7 @@ click.rich_click.OPTION_GROUPS = {
 @click.option(
     "--wf",
     required=True,
-    help="The workflow to create a nextflow_schema.json for.",
+    help="The workflow to create a nextflow_schema.json for",
 )
 @click.option(
     "--outdir",
@@ -94,8 +94,6 @@ click.rich_click.OPTION_GROUPS = {
     help="Directory to write output files to",
 )
 @click.option("--force", is_flag=True, help="Overwrite existing output files")
-@click.option("--verbose", is_flag=True, help="Print debug related text.")
-@click.option("--silent", is_flag=True, help="Only critical errors will be printed.")
 @click.argument("unknown", nargs=-1, type=click.UNPROCESSED)
 def merge_schemas(
     bactopia_path,
@@ -107,17 +105,7 @@ def merge_schemas(
     unknown,
 ):
     """Builds a Nextflow Schema and/or Nextflow config for a given workflow."""
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(
-        logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
-    )
+    setup_logging(verbose, silent)
 
     # bactopia paths
     bactopia_path = str(Path(bactopia_path).absolute())

{bactopia-2.1.2 → bactopia-2.1.4}/bactopia/cli/lint.py

@@ -9,9 +9,9 @@ import rich
 import rich.console
 import rich.traceback
 import rich_click as click
-from rich.logging import RichHandler
 
 import bactopia
+from bactopia.cli.common import common_options, setup_logging
 from bactopia.lint.runner import run_lint
 
 # Set up Rich
@@ -44,6 +44,7 @@ click.rich_click.OPTION_GROUPS = {
             "name": "Additional Options",
             "options": [
                 "--verbose",
+                "--silent",
                 "--version",
                 "--help",
             ],
@@ -117,7 +118,7 @@ def print_rich(
 
 
 @click.command()
-@click.version_option(bactopia.__version__, "--version")
+@common_options
 @click.option(
     "--bactopia-path",
     required=True,
@@ -160,13 +161,12 @@ def print_rich(
     "-q",
     "--quiet",
     is_flag=True,
-    help="Only show components with warnings or failures.",
+    help="Only show components with warnings or failures",
 )
-@click.option("--json", "use_json", is_flag=True, help="Output as JSON.")
+@click.option("--json", "use_json", is_flag=True, help="Output as JSON")
 @click.option(
-    "--pretty", is_flag=True, help="Pretty-print JSON output (implies --json)."
+    "--pretty", is_flag=True, help="Pretty-print JSON output (implies --json)"
 )
-@click.option("--verbose", is_flag=True, help="Print debug related text.")
 def lint(
     bactopia_path,
     modules,
@@ -179,21 +179,14 @@ def lint(
     use_json,
     pretty,
     verbose,
+    silent,
 ):
     """Lint Bactopia pipeline components against style guidelines.
 
     Checks modules, subworkflows, and workflows for compliance with
     Bactopia's GroovyDoc, structural, and configuration standards.
     """
-    # Setup logs
-    logging.basicConfig(
-        format="%(asctime)s:%(name)s:%(levelname)s - %(message)s",
-        datefmt="%Y-%m-%d %H:%M:%S",
-        handlers=[
-            RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True))
-        ],
-    )
-    logging.getLogger().setLevel(logging.DEBUG if verbose else logging.WARNING)
+    setup_logging(verbose, silent)
 
     # Validate path
     bp = Path(bactopia_path).absolute().resolve()