Document a few dependencies more clearly in the README, and also work on fixing the build #555
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
fedarko
changed the title
fedarko
changed the title
fedarko
changed the title
fedarko
added a commit
to kwcantrell/empress
that referenced
this pull request
May 20, 2022
The build will still fail to dependency issues (documented in biocore#555), but when those are fixed it should at least pass.
|
@fedarko, while the issue in IOW is sorted out, would we be able to pin the version requirement? |
|
@ElDeveloper Just pinned the iow version requirement to 0.1.3 for now. This fixes the build (McHelper is broken which causes the "Main CI + McHelper" build to fail, but all of the installations / tests pass). I think 0.1.3 is the only iow version that will work with EMPress (see https://pypi.org/project/iow/#history): earlier versions of iow will not have the updates Erfan added in 2020, and later versions of iow will have the problematic linear-tree check. Thanks! 🌲 🌳 🎄 |
|
Thanks so much @fedarko |
|
Thanks @ElDeveloper!!!
…On Mon, May 23, 2022, 7:39 AM Yoshiki Vázquez Baeza < ***@***.***> wrote:
Merged #555 <#555> into master.
—
Reply to this email directly, view it on GitHub
<#555 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/AA736P2XCPARQAMPTYB34V3VLOKAHANCNFSM5T2RMXXQ>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR adds an "installation troubleshooting" section to the README; this addresses #550 and #553. It also adds two short places indicating where users can get support (opening an issue / via the Q2 forum).
Update: Multiple tests in the build are failing due to changes in the dependencies' behavior:
One of the failures is due to
biom-formatnow explicitly raising errors whenTable.update_ids()is called with a dict containing non-string values (as done in this test). This PR fixes this test. I've also submitted a PR tobiom-formatwhich clarifies this behavior.Another issue (causing two failing tests) is due to our use of "linear" trees causing problems with iow. This time, the problem is not on our side but on iow's, and I contend that we should keep the linear trees in the tests (if only to make sure that these sort of trees remain explicitly supported). I have submitted a PR to iow which fixes the relevant problem.
Even though this build is currently failing, I imagine that it's probably better to merge this PR in sooner rather than later (I'm aware this is me being a hypocrite considering the backlog of things I need to review, sorry...) -- having the installation documentation up-to-date will prevent user confusion.
Thanks!