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bio2bel / kegg

A Bio2BEL package for integrating pathway-related information from KEGG in BEL
http://bio2bel-kegg.rtfd.io
MIT License
13 stars 4 forks source link

Error: No such command 'export'. #20

Closed kozo2 closed 2 years ago

kozo2 commented 2 years ago

python3 -m bio2bel_kegg export in does not work.

https://github.com/bio2bel/kegg/commit/c93f91e46e351ad0fc53c862076df04963cad34a is the commit I used for this.

(base) C:\Users\hoge>python -m bio2bel_kegg export
Usage: python -m bio2bel_kegg [OPTIONS] COMMAND [ARGS]...
Try 'python -m bio2bel_kegg --help' for help.

Error: No such command 'export'.

(base) C:\Users\hoge>python -m bio2bel_kegg --help
Usage: python -m bio2bel_kegg [OPTIONS] COMMAND [ARGS]...

  Default connection at
  sqlite:///C:/Users/hoge/.data/pybel/pybel_0.14.0_cache.db

  using Bio2BEL v0.4.2

Options:
  -c, --connection TEXT  [default: sqlite:///C:/Users/hoge/.data/pybel/pybel_0
                         .14.0_cache.db]
  --help                 Show this message and exit.

Commands:
  bel               Manage BEL.
  belns             Manage BEL namespace.
  cache             Manage cached data.
  drop              Drop the database.
  export-gene-sets  Export all pathway - gene info to a excel file.
  populate          Populate the database.
  summarize         Summarize the contents of the database.
  web               Run the web app.
kozo2 commented 2 years ago

I sent a PR https://github.com/bio2bel/kegg/pull/21

kozo2 commented 2 years ago

It didn't work without the -f option. https://github.com/bio2bel/kegg/pull/22