Move CLI to click

[ElDeveloper]

It would be awesome if the CLI could be moved to click, are there any current technical limitations?

[wasade]

No, just dev effort and agree. I think there might already be an open issue?

[ElDeveloper]

Got it, couldn't find it, I only found mentions of click in the issues.

On (Apr-23-15|17:36), Daniel McDonald wrote:

No, just dev effort and agree. I think there might already be an open issue?

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#631 (comment)

[wasade]

ah, well you take the 🍰 :)

[josenavas]

If we move the CLI to click means that is a major release? Just checking cause it think I won't be backwards compatible, or am I missing something?

[wasade]

yes

On Thu, Apr 23, 2015 at 8:44 PM, josenavas notifications@github.com wrote:

If we move the CLI to click means that is a major release? Just checking
cause I think I won't be backwards compatible, or am I missing something?

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#631 (comment).

[ElDeveloper]

3.0, here we go!

On (Apr-23-15|19:49), Daniel McDonald wrote:

yes

On Thu, Apr 23, 2015 at 8:44 PM, josenavas notifications@github.com wrote:

If we move the CLI to click means that is a major release? Just checking
cause I think I won't be backwards compatible, or am I missing something?

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#631 (comment).

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#631 (comment)

[wasade]

we could do a minor release i suppose

On Thu, Apr 23, 2015 at 8:51 PM, Yoshiki Vázquez Baeza <
notifications@github.com> wrote:

3.0, here we go!

On (Apr-23-15|19:49), Daniel McDonald wrote:

yes

On Thu, Apr 23, 2015 at 8:44 PM, josenavas notifications@github.com
wrote:

If we move the CLI to click means that is a major release? Just
checking
cause I think I won't be backwards compatible, or am I missing
something?

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<
https://github.com/biocore/biom-format/issues/631#issuecomment-95780259>.

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#631 (comment)

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#631 (comment).

[gregcaporaso]

Just remember that backward compatibility is needed for biom-format >= 2.1.3, < 2.2.0 - that's what QIIME depends on.

[wasade]

Ya, so I was thinking 2.2 instead of 3.0

On Thu, Apr 23, 2015 at 9:15 PM, Greg Caporaso notifications@github.com
wrote:

Just remember that backward compatibility is needed for biom-format >=
2.1.3, < 2.2.0 - that's what QIIME depends on.

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#631 (comment).

[gregcaporaso]

Ok, perfect.

[ebolyen]

• add-metadata Add metadata to a BIOM table (@gregcaporaso) - note that failure to write biom table with latest version #530 has been present since 2.1.3, and it's still present
• convert Convert to/from the BIOM table format (@gregcaporaso)
  • adding observation metadata doesn't work, but it seems like it didn't work in 2.1.4 either (and maybe we don't need to fix this, b/c that's what add-metadata is for)
  • add unit tests
  • test the examples listed on the web biom docs
• normalize-table Normalize a BIOM table (@wasade)
• show-install-info Provide information about the biom-format installation (@jairideout)
• subset-table Subset a BIOM table (@jairideout)
• summarize-table Summarize sample or observation data in a BIOM table (@ebolyen)
• validate-table Validate a BIOM-formatted file (@ebolyen)
• head
from-uc (@gregcaporaso or @jairideout)

[gregcaporaso]

I've tested all of the commands presented on the website, and they're working as they did in 2.1.4. Closing this.

[ElDeveloper]

🎆