Add q2-annotate Integration Tests

[VinzentRisch]

Several registered actions in q2-annotate currently exercise only mocked external dependency paths. These actions should get integration tests that actually invoke the relevant external CLI, network/API path, or plugin action path where feasible.

Parent issue: rachis-org/roadmap#73

When a registered pipeline wraps a lower-level registered action that reaches the same external dependency, add the integration test for the pipeline and do not add a duplicate integration test for the lower-level action.

Slow Integration Test Marks

If an integration test is too slow or resource-heavy for the normal pull request test suite, mark it so it can run on a less frequent schedule:

• weekly: integration tests that should run only on weekly builds.
• release: integration tests that should run only before a release.

Actions Needing External Integration Tests

• q2_annotate.kraken2.bracken.estimate_bracken
• q2_annotate.eggnog.build_custom_diamond_db
• q2_annotate.eggnog.build_eggnog_diamond_db
• q2_annotate.eggnog.search_orthologs_hmmer
• q2_annotate.prodigal.predict_genes_prodigal
• q2_annotate.kaiju.classify_kaiju
• q2_annotate.filtering.construct_human_pangenome_index
• q2_annotate.filtering.filter_reads_human_pangenome

Plugin	Registered action function	External dependency or plugin call
q2-annotate	q2_annotate.kraken2.bracken.estimate_bracken	bracken CLI.
q2-annotate	q2_annotate.eggnog.build_custom_diamond_db	diamond makedb CLI.
q2-annotate	q2_annotate.eggnog.build_eggnog_diamond_db	create_dbs.py external script.
q2-annotate	q2_annotate.eggnog.search_orthologs_hmmer	Plugin actions; reaches emapper.py through _eggnog_hmmer_search.
q2-annotate	q2_annotate.prodigal.predict_genes_prodigal	prodigal CLI.
q2-annotate	q2_annotate.kaiju.classify_kaiju	Plugin actions for partitioning and feature_table merge/merge_taxa; reaches Kaiju through _classify_kaiju.
q2-annotate	q2_annotate.filtering.construct_human_pangenome_index	wget, gunzip, gfatools, seqtk; plugin actions rescript.get_ncbi_genomes and quality_control.bowtie2_build.
q2-annotate	q2_annotate.filtering.filter_reads_human_pangenome	Plugin actions quality_control.filter_reads and optionally annotate.construct_human_pangenome_index.

Fetch Actions

These actions should get two levels of integration coverage for the download/database path:

• weekly: a lightweight URL or remote availability check that verifies the configured download location is reachable.

• release: a full database download test that verifies the action can fetch and prepare the database before release.

• q2_annotate.kraken2.build_kraken_db

• q2_annotate.eggnog.fetch_eggnog_db

• q2_annotate.eggnog.fetch_diamond_db

• q2_annotate.eggnog.fetch_eggnog_proteins

• q2_annotate.eggnog.fetch_ncbi_taxonomy

• q2_annotate.eggnog.fetch_eggnog_hmmer_db

• q2_annotate.kaiju.fetch_kaiju_db

Plugin	Registered action function	How current tests work
q2-annotate	q2_annotate.kraken2.build_kraken_db	Mocked. Tests patch requests.get, tar extraction, _fetch_prebuilt_dbs, _build_dbs_from_seqs, and Kraken/Bracken helper functions; they verify command/request construction and mocked response handling.
q2-annotate	q2_annotate.eggnog.fetch_eggnog_db	Completely mocked. Tests patch subprocess.run for wget, gunzip, and tar, plus file removal.
q2-annotate	q2_annotate.eggnog.fetch_diamond_db	Completely mocked. Tests patch subprocess.run for wget and gunzip.
q2-annotate	q2_annotate.eggnog.fetch_eggnog_proteins	Completely mocked. Tests patch subprocess.run for both wget calls.
q2-annotate	q2_annotate.eggnog.fetch_ncbi_taxonomy	Completely mocked. Tests patch subprocess.run, MD5 collection/checking, and file removal.
q2-annotate	q2_annotate.eggnog.fetch_eggnog_hmmer_db	Mocked. The top-level action test patches validation and download/build helpers; helper tests patch urllib.request.urlopen with fake HTML and patch subprocess.run for wget, tar, and hmmpress.
q2-annotate	q2_annotate.kaiju.fetch_kaiju_db	Mocked. Tests patch requests.get with static HTML and patch _fetch_and_extract_db; download/extract helper tests also patch requests.get, tar extraction, progress bar, and file removal.