Problems with dependency version specifiers when uploading to Tool Shed

[Tristan Croll]

Just trying to upload a new ISOLDE build to the Tool Shed (to correct a bug in its handling of known ligands), after taking on board Conrad's suggestion in #2214 for specifying the Clipper dependency version. Unfortunately it's currently blocking every attempt. My first try at uploading yielded:

The file you submitted problem with dependencies: unsupport version operator: "==".

... which some trial-and-error revealed was due to my using "==1.0" for the ChimeraX-Atomic dependency rather than ">=". I think this is a new behaviour? Would be great if the Tool Shed could print the name of the offending dependency.

After fixing that, with

<Dependency name="ChimeraX-Clipper" version="==0.9.*"/>

in bundle_info.xml, the message I got from the Tool Shed was:

The file you submitted problem with dependencies: Unsupported version format: "0.9.*".

I then tried:

<Dependency name="ChimeraX-Clipper" version=">=0.9.12, &lt;0.10"/>

... which gave me:

The file you submitted problem with dependencies: Unsupported version format: "0.10,>=0.9.12".

Checking the METADATA file from the build, the "<" is there:

Requires-Dist: ChimeraX-Clipper (<0.10,>=0.9.12)

... so looks like it's getting dropped by Django. Anyway, will fall back to the simple ">=0.9.12" for now.

[Tristan Croll]

This will block the suggested solution to #2214, making it fairly urgent that it's fixed before 0.91 is released.

[Conrad Huang]

My previous proposal for using Bundle==x.y.* has not been deployed on the production site yet. The first cut at implementation is on the preview site (​https://cxtoolshed-preview.rbvi.ucsf.edu/). Can you try submitting there and see what errors you get? To test installing bundles from the preview site in ChimeraX, use the commands:

toolshed url https://cxtoolshed-preview.rbvi.ucsf.edu
toolshed reload available

To return to using the production toolshed, use

toolshed url https://cxtoolshed.rbvi.ucsf.edu
toolshed reload available

Thanks.

[Tristan Croll]

I can't currently submit new releases to the preview site because of the 
old versions of Clipper and ISOLDE there - it seems somehow I've been 
de-registered as their owner, so I don't have permission to 
change/update them.

On 2019-12-05 19:17, ChimeraX wrote:

[Conrad Huang]

I must have been the one to upload those the first time. I've updated the list of editors to include your email, so you should be able to upload them now.

[Tristan Croll]

OK. Will try tomorrow. By the way, the Clipper and ISOLDE bundles are now on GitHub at github.com/tristanic/chimerax-clipper and github.com/tristanic/isolde, in case you ever want to urgently test something.
 

 

[Tristan Croll]

OK - Just successfully uploaded Mac builds of Clipper and ISOLDE to the 
preview ToolShed. Seems to install fine too - but could you double-check 
on a naive machine?

On 2019-12-05 19:17, ChimeraX wrote:

[Tristan Croll]

Ho hum... if you *do* install that particular version, be aware that it 
won't actually run simulations. I'm still learning how to use git-lfs, 
and consequently the build is missing a zip file full of ligand 
definitions.

On 2019-12-18 18:18, ChimeraX wrote:

[Conrad Huang]

I tried installing ISOLDE using ChimeraX 0.91 and it seems to pick up the right versions of ISOLDE and Clipper. Installing with 0.9 still fails, displaying:

chimerax-clipper 0.10.0 has requirement ChimeraX-Core==0.91, but you'll have chimerax-core 0.9 which is incompatible.

0.92 properly reports that there are no available bundles for ISOLDE.

Assuming that using the ==0.91.* version fix works, we have a few options, one of which is to remove the 0.9-compatible versions of ISOLDE and Clipper, and just tell users to get 0.91. Is that a reasonable solution?

[Tristan Croll]

I’m OK with that.

 
 

 

[Conrad Huang]

Ticket retargeted after milestone closed

[Greg Couch]

All of those version specifiers are now accepted.