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Moved all singularity-related download functions into a new file #3509

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ae0d4dd
Moved all singularity-related download functions into a new file
muffato Mar 25, 2025
bbd297f
Added a helper method to use a temporary file as intermediate output
muffato Mar 25, 2025
a9b2b00
First round of fixing the tests
muffato Mar 25, 2025
dc333b3
downloads.singularity functions should rely on proper parameters, no …
muffato Mar 25, 2025
fbc09ac
Duplicated with the line above
muffato Mar 25, 2025
fee7182
Added tests for utils.intermediate_file and fixed it !
muffato Mar 25, 2025
c507d9e
Simpler implementation
muffato Mar 25, 2025
aba5233
Added helper functions to manage the main task so that callers don't …
muffato Mar 26, 2025
0403a37
No need to build a temp path here
muffato Mar 26, 2025
159c34e
More tests
muffato Mar 26, 2025
693da64
Fixed the symlink_registries tests
muffato Mar 26, 2025
c5379fb
Rewrote to support older versions of Python
muffato Mar 26, 2025
8ee8eed
Added a dest for the main_task-management methods added to DownloadPr…
muffato Mar 26, 2025
71ab538
Added some tests for the DownloadProgress object
muffato Mar 26, 2025
a141820
Turned two methods into functions, simplified testing
muffato Mar 26, 2025
4133c90
Test comments
muffato Mar 26, 2025
2b8fbd6
Theoretically it could be None, so check it really is a string
muffato Mar 26, 2025
7813f30
More type hints
muffato Mar 27, 2025
cb71d42
More tests for get_container_filename
muffato Mar 27, 2025
2d8cb4d
No need to keep a wraper as a method
muffato Mar 27, 2025
4bfb45e
Better comments
muffato Mar 27, 2025
d6b8f6c
New class to support the downloads
muffato Mar 27, 2025
4abd736
Introduced a context manager that creates a new sub task. Useful to g…
muffato Mar 27, 2025
31f5627
Forgot that pytest.raises exists !
muffato Mar 27, 2025
06d3760
Moved the download class to utils
muffato Mar 27, 2025
3857fae
The output path cannot be a directory or a symbolic link
muffato Mar 27, 2025
31fe914
Basic test for FileDownloader.download_file
muffato Mar 27, 2025
02cc2ca
Empty files are not allowed
muffato Mar 27, 2025
b648bc1
Test log.debug too
muffato Mar 27, 2025
467ba3f
Test the kill_with_fire flag
muffato Mar 27, 2025
ea4bc89
Refactored the FileDownloader
muffato Mar 27, 2025
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1 change: 0 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib64/
Expand Down
647 changes: 38 additions & 609 deletions nf_core/pipelines/download.py

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As I mentioned in #3506 (comment), the directory name should be download

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This was my decision to avoid import errors for now. Running git mv is later is pretty quick, I guess.

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