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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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memote new should accept a relative path to the model #52

Closed phantomas1234 closed 6 years ago

phantomas1234 commented 7 years ago

[2] % memote new ~/Dev We highly recommend keeping your model in a git repository. It allows you to track changes and easily collaborate with others via online platforms such as https://github.com.

full_name [Nikolaus Sonnenschein]: email [niko.sonnenschein@gmail.com]: github_username [phantomas1234]: project_name [Memote model repository]: test_memote_repo project_slug [test_memote_repo]: project_short_description [Create a repository for a genome-scale metabolic model.]: release_date [2017-03-24]: year [2017]: version [0.1.0]: model [model.xml]: /Users/niso/Dev/cameo/tests/data/EcoliCore.xml Traceback (most recent call last): File "/Users/niso/anaconda3/bin/memote", line 11, in load_entry_point('memote', 'console_scripts', 'memote')() File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in call return self.main(args, kwargs) File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main rv = self.invoke(ctx) File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke return callback(args, *kwargs) File "/Users/niso/anaconda3/lib/python3.5/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), args, *kwargs) File "/Users/niso/Dev/memote/memote/suite/runner.py", line 297, in new output_dir=ctx.obj.get("directory", ".")) File "/Users/niso/anaconda3/lib/python3.5/site-packages/cookiecutter/main.py", line 91, in cookiecutter output_dir=output_dir File "/Users/niso/anaconda3/lib/python3.5/site-packages/cookiecutter/generate.py", line 269, in generate_files overwrite_if_exists File "/Users/niso/anaconda3/lib/python3.5/site-packages/cookiecutter/generate.py", line 190, in render_and_create_dir os.path.join(output_dir, rendered_dirname) File "/Users/niso/anaconda3/lib/python3.5/posixpath.py", line 89, in join genericpath._check_arg_types('join', a, p) File "/Users/niso/anaconda3/lib/python3.5/genericpath.py", line 143, in _check_arg_types (funcname, s.class.name)) from None TypeError: join() argument must be str or bytes, not 'NoneType'

Midnighter commented 7 years ago

If you want to give it a directory then it is: memote --directory <path> new.

Midnighter commented 7 years ago

TODO: The cookiecutter should accept relative paths to the model file.