v3.0.0

3.0.0

Added

• --ignore to ignore MD5 checksums

Changed

• (BREAKING) the --force flag now overwrites existing files, but will check the MD5
  checksums of the downloaded files. Previously, it would force download the file, but
  ignore the MD5 as well. See #21 (comment)
  for more details. Use the newly added --ignore flag to ignore MD5 checksums too.
• require Python >=3.9
• updated depends and poetry lock file
• began reorganizing code for better maintainability

v2.0.4

2.0.4

Fixed

• mismatch in --version output

v2.0.3

2.0.3

Added

• Explicit setting of SRA Lite or SRA Normalized (default) downloads
• --sra-lite to prefer SRA Lite downloads from SRA
• print usage on empty options

v2.0.2

2.0.2

Added

• --only-download-metadata to skip FASTQ downloads, and retrieve only the associated metadata @alienzj
• fallback on SRA for metadata retrieval @gtonkinhill
• include prefetchfor SRA downloads @gtonkinhill
• added --force to overwrite existing downloads @gtonkinhill
• update github actions

v2.0.1

2.0.1

Fixed

• Invalid fieldName(s) in ENA query @mbhall88
• gitpod dependency and setup
• dependabot PR

v2.0.0

2.0.0

Added

• Shorthand option -m for --max-attempts and -v for --verbose
• If metadata is unavailable from ENA, try fetching metadata from SRA using pysradb
• Provided query is validated against accession regular expressions
• Support for Biosample/Sample accessions
• Rich click, logging support, type hints
• Support for Gitpod
• Query must now be passed as --accession/-a
• Packaging with poetry
• README improvements

Removed

• Deprecated --sra_only parameter is now removed
• --ftp_only no longer required without Aspera support
• Non-functioning --debug option
• Uneeded logging levels

v1.2.0

• remove support for Aspera
• remove manual vdb-config (no longer required in sra-tools>=3.0.1)
• use accession in pigz command

v1.1.1

Handle experiment accessions with duplicate run accessions

Example: https://www.ebi.ac.uk/ena/browser/view/ERX012546?show=reads

v1.1.0

Big thanks to @mbhall88 for submitting #5 with the following improvements!

Added

• -o shorthand option for --outdir
• a flag -F/--only-provider, which supercedes --sra_only. I left --sra_only in there for backwards compatibility and added a deprecation notice in the help description for it.
• Conda environment file
• Dockerfile. Feel free to try out an image from my quay.io repo here.

Changed

• Move everything into a main function to avoid variable shadowing
• Provider is now optional and defaults to ena. I've also made the option case insensitive, rather than listing the cased versions of the available providers
• If ENA download fails, try SRA
• Reduced a bunch of execute calls which were mostly operations easily dealt with by pathlib.Path
• Changed md5sum to use hashlib.md5 instead of executing a subprocess call to md5sum
• Moved a bunch of import statements out of function bodies to the top of the file

Removed

• Docstring at top of file as this is a mirror of argparse's help menu and creates needless maintenance

Explicit use of ftp for ENA downloads

Includes fix for #3 which requires "ftp://" be added to the beginning of URL for ENA downloads.