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Release 2#39

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hallucigenia-sparsa merged 791 commits into
msysbio:mainfrom
AndrewRadev:release-2
Jun 29, 2026
Merged

Release 2#39
hallucigenia-sparsa merged 791 commits into
msysbio:mainfrom
AndrewRadev:release-2

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@AndrewRadev

@AndrewRadev AndrewRadev commented Dec 8, 2025

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This PR is intended to bring the main repository up to date with the deployed code, and there's been a lot of changes since the last one, #33. I will list high-level changes on the basis of PRs, though there's probably more changes in the "various improvements" categories:

This should make things much simpler instead of juggling the session.
Probably still need to fix some things, though.
Simplifies a lot of other things if we just pin what study (existing or
new) the form is focused on and we can't change it halfway through.
* main:
  Use non-deprecated logging method
  Allow filtering page visits by path in the admin
  Track API visits separately from web ones
  Record time measurements as WARN logs
  Record time measurements as DEBUG logs
  Measure how long it takes to track page visits
* main:
  Allow building documentation from this branch
  Documentation for the "isAverage" field
  Return a flag about whether the bioreplicate is an "averaged" one
  Add redis to the github actions setup
  Pin more specific python version for tests
  Move maxminddb out to separate initializer, remove timing information
  Record page visits through a background job
@hallucigenia-sparsa

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Approved

@hariszaf hariszaf left a comment

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This is a massive PR most of which has been already reviewer, within @AndrewRadev fork.

I guess it's more than good to go, since it has been already tested in production mode.

list and the title of a study.
"""
def __init__(self, doi):
self.doi = doi

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Consider having something like:
doi.strip('https://doi.org/') just in case ? except if you re making sure of that somewhere else

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The crossref API works fine if the DOI given is a URL starting with https://doi.org, so this works in practice. Though weirdly enough, I can't quite tell where requests is escaping it, so maybe I'll add an explicit quoting function just in case.

@hallucigenia-sparsa
hallucigenia-sparsa merged commit 1a6fbda into msysbio:main Jun 29, 2026
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3 participants