Add zst (Zstandard) compression support for input files

[Copilot]

Zstandard compressed files (.zst) are now supported as input format, matching existing gzip (.gz) functionality.

Changes

• Core I/O (singlem/biolib_lite/seq_io.py): Added zstandard.open() handling for .zst files in read_fasta() and read_fasta_seq(). Uses text mode 'rt' (unlike gzip's 'rb') as binary mode doesn't support readlines().

• Archive tables (singlem/otu_table_collection.py, singlem/main.py, singlem/summariser.py): Auto-detect .zst files in archive table lists via extension check. Added add_zst_archive_otu_table_file() to StreamingOtuTableCollection.

• File utilities: Updated extension stripping in FastaNameToSampleName.fasta_to_name(), genome handling in prodigal_biolib.py, and ORF checker to use zstdcat for .zst files.

• Dependencies: Added zstandard = "*" to pixi.toml.

• Tests: Added test_zst_good() and test_zst_archive_to_otu_table_conversion() with corresponding test data.

Example

# Both formats now work identically
read_fasta("sequences.fasta.gz")   # existing
read_fasta("sequences.fasta.zst")  # new

# Archive tables auto-detect format by extension
singlem summarise --input-gzip-archive-otu-table-list tables.txt  # handles both .gz and .zst

No new CLI arguments needed—format detection is automatic via file extension.

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Original prompt

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This section details on the original issue you should resolve

<issue_title>zst format should be supported as an input format</issue_title>
<issue_description>like gz is.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes zst format should be supported as an input format #275

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