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Download: Refactor CLI commands and introduce --download-configs as well as --container-library. #2336

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merged 14 commits into from
Jun 27, 2023
Merged

Download: Refactor CLI commands and introduce --download-configs as well as --container-library. #2336

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a542152
Refactor CLI commands of nf-core download.
MatthiasZepper Jun 13, 2023
ee39770
Enable pulling from multiple container image libraries (registries).
MatthiasZepper Jun 13, 2023
f06772a
Adapt the tests.
MatthiasZepper Jun 13, 2023
9485e22
Fix the CLI test with regard to the revised CLI.
MatthiasZepper Jun 19, 2023
130ce36
Create a ContainerError class with several specific sub-errors.
MatthiasZepper Jun 19, 2023
cdbe6d1
More extensive tests for the Singularity ContainerErrors.
MatthiasZepper Jun 21, 2023
2845e5c
Handle the Singularity exceptions in get_singularity_images().
MatthiasZepper Jun 21, 2023
82df716
Run issort, README and CHANGELOG updates.
MatthiasZepper Jun 22, 2023
6e836c3
Add a test for the wrapper around singularity_pull_image() in get_si…
MatthiasZepper Jun 22, 2023
2e678e6
Fix the test for get_singularity_images()
MatthiasZepper Jun 22, 2023
9fe1236
Replaced all 'sys.exit(1)' from the code. Hopefully this does not aff…
MatthiasZepper Jun 26, 2023
ee4a09a
Create a custom exception for intended program terminations. This can…
MatthiasZepper Jun 26, 2023
2c93bd8
Custom excepthook broke rich.traceback coloring. Fixed now.
MatthiasZepper Jun 26, 2023
9041d93
Some Click versions may pass `container_library` as empty tuple when …
MatthiasZepper Jun 27, 2023
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10 changes: 5 additions & 5 deletions nf_core/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@
import rich_click as click

from nf_core import __version__
from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE
from nf_core.download import DownloadError
from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE
from nf_core.utils import check_if_outdated, rich_force_colors, setup_nfcore_dir

# Set up logging as the root logger
Expand Down Expand Up @@ -71,13 +71,13 @@

# Define exceptions for which no traceback should be printed,
# because they are actually preliminary, but intended program terminations.
# (cleaner than `sys.exit(1)`, which we were using before)
# (Custom exceptions are cleaner than `sys.exit(1)`, which we used before)
def selective_traceback_hook(exctype, value, traceback):
if exctype in {DownloadError}: # extend as needed
if exctype in {DownloadError}: # extend set as needed
log.error(value)
else:
# for all other exceptions, print the full traceback
sys.__excepthook__(exctype, value, traceback)
# print the colored traceback for all other exceptions with rich as usual
stderr.print(rich.traceback.Traceback.from_exception(exctype, value, traceback))
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sys.excepthook = selective_traceback_hook
Expand Down