add( rich click to cg) (#3975) (patch)

# Description

add rich click

cg/apps/demultiplex/sample_sheet/api.py

@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.apps.demultiplex.sample_sheet.read_sample_sheet import get_samples_from_content
 from cg.apps.demultiplex.sample_sheet.sample_models import IlluminaSampleIndexSetting

cg/cli/add.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS, is_case_name_allowed
 from cg.constants import DataDelivery, Priority, Workflow

cg/cli/archive.py

@@ -1,4 +1,4 @@
-import click
+import rich_click as click
 from click.core import ParameterSource
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS

cg/cli/backup.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Iterable
 
-import click
+import rich_click as click
 import housekeeper.store.models as hk_models
 
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/base.py

@@ -4,7 +4,7 @@
 import sys
 from pathlib import Path
 
-import click
+import rich_click as click
 import coloredlogs
 from sqlalchemy.orm import scoped_session
 

cg/cli/clean.py

@@ -4,7 +4,7 @@
 from datetime import datetime, timedelta
 from pathlib import Path
 
-import click
+import rich_click as click
 from housekeeper.store.models import File, Version
 
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/compress/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.compress.fastq import (
     clean_fastq,

cg/cli/compress/fastq.py

@@ -3,7 +3,7 @@
 import logging
 from typing import Iterable
 
-import click
+import rich_click as click
 
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.cli.compress.helpers import (

cg/cli/delete/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.delete.case import delete_case
 from cg.cli.delete.cases import delete_cases

cg/cli/delete/case.py

@@ -3,7 +3,7 @@
 import datetime
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.get import get_case as print_case
 from cg.constants.cli_options import DRY_RUN, SKIP_CONFIRMATION

cg/cli/delete/cases.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.delete.case import delete_case
 from cg.constants.cli_options import DRY_RUN

cg/cli/delete/illumina_sequencing_run.py

@@ -1,4 +1,4 @@
-import click
+import rich_click as click
 
 from cg.constants.cli_options import DRY_RUN
 from cg.services.illumina.post_processing.housekeeper_storage import (

cg/cli/delete/observations.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 from sqlalchemy.orm import Query
 
 from cg.cli.upload.observations.utils import get_observations_api

cg/cli/deliver/base.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.apps.tb import TrailblazerAPI
 from cg.cli.deliver.utils import deliver_raw_data_for_analyses

cg/cli/demultiplex/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.cli.demultiplex.demux import (

cg/cli/demultiplex/demux.py

@@ -2,7 +2,7 @@
 from glob import glob
 from pathlib import Path
 
-import click
+import rich_click as click
 from pydantic import ValidationError
 
 from cg.apps.demultiplex.demultiplex_api import DemultiplexingAPI

cg/cli/demultiplex/finish.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN, FORCE

cg/cli/demultiplex/sample_sheet.py

@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 from pydantic import ValidationError
 
 from cg.apps.demultiplex.sample_sheet.api import IlluminaSampleSheetService

cg/cli/downsample.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Tuple
 
-import click
+import rich_click as click
 
 from cg.apps.downsample.downsample import DownsampleAPI
 from cg.apps.downsample.utils import store_downsampled_sample_bundle

cg/cli/generate/base.py

@@ -1,6 +1,6 @@
 """Common CLI file generation functions"""
 
-import click
+import rich_click as click
 
 from cg.cli.generate.delivery_report.base import (
     generate_available_delivery_reports,

cg/cli/generate/delivery_report/base.py

@@ -5,7 +5,7 @@
 from datetime import datetime
 from pathlib import Path
 
-import click
+import rich_click as click
 from housekeeper.store.models import Version
 
 from cg.cli.generate.delivery_report.options import (

cg/cli/generate/delivery_report/options.py

@@ -1,6 +1,6 @@
 """Delivery report specific command options."""
 
-import click
+import rich_click as click
 
 from cg.constants import REPORT_SUPPORTED_WORKFLOW
 

cg/cli/generate/delivery_report/utils.py

@@ -3,7 +3,7 @@
 import logging
 from datetime import datetime
 
-import click
+import rich_click as click
 
 from cg.constants import REPORT_SUPPORTED_DATA_DELIVERY, REPORT_SUPPORTED_WORKFLOW, Workflow
 from cg.meta.delivery_report.balsamic import BalsamicDeliveryReportAPI

cg/cli/get.py

@@ -2,7 +2,7 @@
 import re
 from typing import Iterable
 
-import click
+import rich_click as click
 from tabulate import tabulate
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS

cg/cli/post_process/post_process.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.post_process.utils import (
     UnprocessedRunInfo,

cg/cli/sequencing_qc/sequencing_qc.py

@@ -1,5 +1,5 @@
 import logging
-import click
+import rich_click as click
 
 from cg.models.cg_config import CGConfig
 from cg.services.sequencing_qc_service.sequencing_qc_service import SequencingQCService

cg/cli/set/base.py

@@ -5,7 +5,7 @@
 import logging
 from typing import Iterable
 
-import click
+import rich_click as click
 
 from cg.cli.set.case import set_case
 from cg.cli.set.cases import set_cases

cg/cli/set/case.py

@@ -3,7 +3,7 @@
 import logging
 from typing import Callable
 
-import click
+import rich_click as click
 
 from cg.constants import DataDelivery, Priority, Workflow
 from cg.constants.constants import CaseActions

cg/cli/set/cases.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.set.case import set_case
 from cg.constants import Priority

cg/cli/store/base.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.apps.crunchy.crunchy import CrunchyAPI
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/store/store.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Iterable
 
-import click
+import rich_click as click
 from housekeeper.store.models import File
 
 from cg.apps.crunchy.files import update_metadata_paths

cg/cli/transfer.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.apps.lims import LimsAPI
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS

cg/cli/upload/base.py

@@ -4,7 +4,7 @@
 import sys
 import traceback
 
-import click
+import rich_click as click
 
 from cg.cli.upload.coverage import upload_coverage
 from cg.cli.upload.delivery_report import upload_delivery_report_to_scout

cg/cli/upload/coverage.py

@@ -1,6 +1,6 @@
 """Code for uploading coverage reports via CLI"""
 
-import click
+import rich_click as click
 
 from cg.meta.upload.coverage import UploadCoverageApi
 from cg.models.cg_config import CGConfig

cg/cli/upload/delivery_report.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 from housekeeper.store.models import Version
 
 from cg.cli.generate.delivery_report.options import ARGUMENT_CASE_ID

cg/cli/upload/fohm.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN

cg/cli/upload/genotype.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.apps.gt import GenotypeAPI
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/upload/gens.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 from housekeeper.store.models import File
 
 from cg.apps.gens import GensAPI

cg/cli/upload/gisaid.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.meta.upload.gisaid import GisaidAPI
 from cg.models.cg_config import CGConfig

cg/cli/upload/mutacc.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.apps.mutacc_auto import MutaccAutoAPI
 from cg.apps.scout.scout_export import ScoutExportCase

cg/cli/upload/nipt/base.py

@@ -3,7 +3,7 @@
 import logging
 import traceback
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN, FORCE

cg/cli/upload/nipt/ftp.py

@@ -1,7 +1,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN, FORCE

cg/cli/upload/nipt/statina.py

@@ -1,6 +1,6 @@
 import logging
 
-import click
+import rich_click as click
 
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants.cli_options import DRY_RUN, FORCE

cg/cli/upload/observations/observations.py

@@ -3,7 +3,7 @@
 import logging
 from datetime import datetime
 
-import click
+import rich_click as click
 from sqlalchemy.orm import Query
 
 from cg.cli.upload.observations.utils import get_observations_api

cg/cli/upload/scout.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import click
+import rich_click as click
 from housekeeper.store.models import File, Version
 
 from cg.apps.housekeeper.hk import HousekeeperAPI

cg/cli/upload/utils.py

@@ -2,7 +2,7 @@
 
 import logging
 
-import click
+import rich_click as click
 
 from cg.constants import Workflow
 from cg.constants.constants import MAX_ITEMS_TO_RETRIEVE