Let npx run the CLI without installing it

[bmesuere]

This pull request makes npx unipept-cli work, and releases it as 4.2.2.

npx runs the binary named after the package, and only falls back to the sole binary when a package ships exactly one. This package ships four, none of them called unipept-cli, so the obvious invocation failed:

$ npx unipept-cli --version
npm error could not determine executable to run

The natural second guess is worse. npx unipept looks for a package called unipept, which does not exist on npm and returns a 404 that points nowhere useful. That was the name of the old Ruby gem, so it is exactly what someone coming from the old documentation would type.

Adding unipept-cli as an alias for the unipept binary makes the obvious form work, while the other three commands stay reachable with -p, which is the normal way to run a named binary out of a package:

$ npx unipept-cli pept2lca AALTER
peptide,cutoff_used,taxon_id,taxon_name,taxon_rank
AALTER,1,1,root,no rank

$ echo "AALTERSVKAAPKR" | npx -p unipept-cli prot2pept
AALTER
SVK
AAPK
R

Why this is worth more than convenience. Pinning a version through npx makes an analysis reproducible without asking anyone to install anything, which is a better thing to put in a methods section than "we used the Unipept CLI":

$ npx unipept-cli@4.2.2 --version
4.2.2 (UniProt 2026.02)

Patch rather than minor. The alias points at the same script as unipept and adds no capability: the command was already reachable through npx -p unipept-cli unipept, so nothing a user could do before changes. The counter argument is that bin is public surface and the documentation now says the short form needs a given version, but that gate is on an alias rather than on anything the tool can do.

Manual testing instructions

• npx unipept-cli pept2lca AALTER returns the usual CSV
• npx -p unipept-cli prot2pept, peptfilter and uniprot still work
• A global install still provides unipept, peptfilter, prot2pept and uniprot unchanged
• unipept-cli --help reports its own name in the usage line, since npm's shim path is what commander reads

Verification run

Verified against a packed tarball installed into a scratch project, rather than from source, so the bin wiring is the real thing:

node_modules/.bin: peptfilter prot2pept unipept unipept-cli uniprot

$ npx unipept-cli --version
4.2.2 (UniProt 2026.02)
$ npx unipept-cli pept2lca AALTER
peptide,cutoff_used,taxon_id,taxon_name,taxon_rank
AALTER,1,1,root,no rank

The version pinned form npx unipept-cli@4.2.2 cannot be exercised until this is published, but the equivalent npx -p unipept-cli@4.2.0 unipept --version was confirmed to print 4.2.0, so version resolution itself works.

Test Files  25 passed (25)
     Tests  111 passed (111)

Lint, typecheck and build pass.

Checklist

• Tests: two added, checking that every declared bin has a source file and that a bin exists matching the package name, which is the condition npx depends on
• Docs: README gains a "Running without installing" section; the website docs get the same in Bring the CLI documentation up to date with 4.2.2 unipept#1872
• Announcement: 🚀 The CLI can now be run without installing it, with npx unipept-cli
• AI: Claude Code found that npx did not work, then made the change, the tests and the docs

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