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v1.1.6 unpin python packages #212

Merged
merged 6 commits into from
Oct 6, 2023
Merged

v1.1.6 unpin python packages #212

merged 6 commits into from
Oct 6, 2023

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vincerubinetti
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@vincerubinetti vincerubinetti commented Oct 2, 2023

Unpins all cite process python packages from their exact versions, pins them to major versions. This ensures users will be on the latest versions of packages, without breaking changes (assuming the packages follow semver properly), and without having to constantly update their template version (which can be a pain).

Closes #210
Addresses #211

FOR THE TEMPLATE MAINTAINER(S)

New template version checklist:

  • I have updated CITATION and CHANGELOG as appropriate.
  • I have updated lab-website-template-docs as appropriate.
  • I have checked the testbed as appropriate.

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PR Preview Action v1.4.4
🚀 Deployed preview to https://greenelab.github.io/lab-website-template/preview/pr-212/
on branch gh-pages at 2023-10-06 19:18 UTC

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@vincerubinetti vincerubinetti changed the title unpin python packages v1.1.6 unpin python packages Oct 2, 2023
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@falquaddoomi falquaddoomi left a comment

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I left a comment, but I'll go ahead and approve since you may already be aware of what I'm saying there.

Comment on lines 1 to 6
manubot==0.*
PyYAML==6.*
diskcache==5.*
rich==12.*
python-dotenv==0.*
google-search-results==2.*
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I apologize if you already know this and have a good reason for specifying them as you have, but anyway...

What you have here will typically select the most recent minor version, but I could imagine a few reasons for keeping the explicit minor version around:

  • minor version changes can introduce new functions which you or another package you're using might rely on, and adding a new package with older dependencies could cause your existing versions to slip back to a prior minor release
  • it's helpful to know from looking at the file that you at least got it to work at the versions specified there

The ~= specifies that the version can be at or after the least significant field, i.e. ~=1.1.5 would allow anything >= 1.1.5 but <1.2.0 (i.e. all patches >= current), and ~=1.1 would allow anything >=1.1 but <2.0 (i.e. all minor versions >= current).

Suggested change
manubot==0.*
PyYAML==6.*
diskcache==5.*
rich==12.*
python-dotenv==0.*
google-search-results==2.*
manubot~=0.5
PyYAML~=6.0
diskcache~=5.4
rich~=12.6
python-dotenv~=0.21
google-search-results~=2.4

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Yeah good idea. I'm not sure if I'm using any functions from any of the previous minor versions, but it's better to be safe. I just wanted to make sure the user is always on the latest non-major version without having to update, and this will satisfy that.

I'm also going to take to opportunity to update to the latest versions of all of them, and test that the citation process still works.

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@vincerubinetti vincerubinetti Oct 6, 2023

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Just tested greenelab.com locally with the new packages, both from scratch and with cached. Various orcid and id types (300+ citations), so probably the best stress test.

Only major version jump was for "rich", and their changelog doesn't mention any breaking changes that would affect us. dotenv has a major version upgrade, but apparently it drops support for python 3.7 and that's something I'd like to still provide.

@vincerubinetti vincerubinetti merged commit 93122f8 into main Oct 6, 2023
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@vincerubinetti vincerubinetti deleted the py-versions branch October 6, 2023 19:26
justincorrigible pushed a commit to courtotlab/courtotlab.github.io that referenced this pull request Jan 5, 2024
Unpins all cite process python packages from their exact versions, pins
them to **major versions**. This ensures users will be on the latest
versions of packages, without breaking changes (assuming the packages
follow semver properly), and without having to constantly update their
template version (which can be a pain).

Closes greenelab#210
Addresses greenelab#211

FOR THE TEMPLATE MAINTAINER(S)

New template version checklist:

- [x] I have updated CITATION and CHANGELOG as appropriate.
- [x] I have updated lab-website-template-docs as appropriate.
- [x] I have checked the testbed as appropriate.
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Pubmed citations do not generate properly
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