Pipeline error!

[alexsweeten]

Most recent commit has broken our pipeline.

Traceback (most recent call last): File "/home/alex/anaconda3/bin/snacc", line 11, in load_entry_point('snacc', 'console_scripts', 'snacc')() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 484, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2707, in load_entry_point return ep.load() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2325, in load return self.resolve() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2331, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/alex/Documents/bioncd-hackseq/snacc/cli.py", line 88, in help="Whether to automatically open the log in the browser if log type is html. Defaults to True.") File "/home/alex/anaconda3/lib/python3.7/site-packages/click/decorators.py", line 170, in decorator _param_memo(f, OptionClass(param_decls, attrs)) File "/home/alex/anaconda3/lib/python3.7/site-packages/click/core.py", line 1460, in init Parameter.init(self, param_decls, type=type, attrs)

[Benjamin-Lee]

Ah! On it.

On Oct 22, 2018, at 2:26 PM, Alex Sweeten notifications@github.com wrote:

Most recent commit has broken our pipeline.

Traceback (most recent call last): File "/home/alex/anaconda3/bin/snacc", line 11, in load_entry_point('snacc', 'console_scripts', 'snacc')() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 484, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2707, in load_entry_point return ep.load() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2325, in load return self.resolve() File "/home/alex/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 2331, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/alex/Documents/bioncd-hackseq/snacc/cli.py", line 88, in help="Whether to automatically open the log in the browser if log type is html. Defaults to True.") File "/home/alex/anaconda3/lib/python3.7/site-packages/click/decorators.py", line 170, in decorator _param_memo(f, OptionClass(param_decls, attrs)) File "/home/alex/anaconda3/lib/python3.7/site-packages/click/core.py", line 1460, in init Parameter.init(self, param_decls, type=type, attrs)

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[Benjamin-Lee]

Can you give me more context as to what caused the error? Is that the full traceback?

[alexsweeten]

That's the full traceback. Did we remove -d and -f as command line arguments?

[Benjamin-Lee]

They should still be usable, just deprecated. You should now be able to pass in directories and files directly to snacc, but it should work either way.

On Oct 22, 2018, at 2:41 PM, Alex Sweeten notifications@github.com wrote:

That's the full traceback. Did we remove -d and -f as command line arguments?

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[Benjamin-Lee]

Can you send the exact command you used to generate the issue?

[alexsweeten]

From snacc home directory: snacc -d ../test_dataset/ -o lzma_test.csv

[Benjamin-Lee]

Well, two things: I'm not getting an error but it isn't working with -d and second, it does work when you just pass the dataset without the flag:

snacc ../test_dataset/ -o lzma_test.csv

Will get on fix, but for now, just make sure to do a pip install -e . in the main directory and omit the -d flag

[alexsweeten]

Thanks!

I'm still getting the error even with omitting the -d flag. It might be an Anaconda issue.

[Benjamin-Lee]

Fixed. See #81.

[alexsweeten]

Unfortunately I'm still getting the same error. I'll try running it on a Conda-free environment to see if that's the issue.

For now, reverting back to e90c26bf5f50f9e2e083cdb657c4967851b61365 allows it to work.

[Benjamin-Lee]

Let me know if the newest version works without Conda - the newest version is running fine for me

[Benjamin-Lee]

(env) Benjamins-MacBook-Pro-9:snacc BenjaminLee$ snacc -d ../test_dataset/ -o lzma_test.csv
Warning: the -f and -d flags are deprecated and will be removed before release. Please pass files and paths directly witho
ut the flags.
Compressing individual files...
  0%|                                                                                               | 0/9 [00:00<?, ?it/s]

[alexsweeten]

Figured out it's a click issue: removing the hidden option makes it work. This is probably due to a less recent version of click installed on my machine.

[souravsingh]

This means we might need to pin a minimum version for click to make the project work.

[Benjamin-Lee]

With 3bddfb63ca7e7de8fab70b30b7def390f0aa4ac6 pinning to click==7.0, I think we can call this issue resolved (hopefully).