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v1.1.6 unpin python packages #212

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Oct 6, 2023
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v1.1.6 unpin python packages #212

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7b088ef
unpin python packages
vincerubinetti Oct 2, 2023
eb0c16b
Update citations
vincerubinetti Oct 2, 2023
45aaa26
bump to major
vincerubinetti Oct 6, 2023
53036ab
update date
vincerubinetti Oct 6, 2023
940d917
update packages too
vincerubinetti Oct 6, 2023
1ddfe87
update package versions
vincerubinetti Oct 6, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Reference: common-changelog.org

## 1.1.6 - 2023-10-06

- Use latest minor versions of Python packages in auto-cite script.

## 1.1.5 - 2023-05-19

### Changes
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4 changes: 2 additions & 2 deletions CITATION.cff
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# citation metadata for the template itself

title: "Lab Website Template"
version: 1.1.5
date-released: 2023-05-19
version: 1.1.6
date-released: 2023-10-06
url: "https://github.com/greenelab/lab-website-template"
authors:
- family-names: "Rubinetti"
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13 changes: 7 additions & 6 deletions _cite/requirements.txt
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manubot==0.5.5
PyYAML==6.0
diskcache==5.4.0
rich==12.6.0
python-dotenv==0.21.0
google-search-results==2.4.1
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.


22 changes: 22 additions & 0 deletions _data/citations.yaml
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orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1093/gigascience/giad047
title: Hetnet connectivity search provides rapid insights into how biomedical entities
are related
authors:
- Daniel S Himmelstein
- Michael Zietz
- Vincent Rubinetti
- Kyle Kloster
- Benjamin J Heil
- Faisal Alquaddoomi
- Dongbo Hu
- David N Nicholson
- Yun Hao
- Blair D Sullivan
- Michael W Nagle
- Casey S Greene
publisher: GigaScience
date: '2022-12-28'
link: https://doi.org/gsd85n
orcid: 0000-0002-4655-3773
plugin: orcid.py
file: orcid.yaml
- id: doi:10.1186/s13059-020-02021-3
title: Compressing gene expression data using multiple latent space dimensionalities
learns complementary biological representations
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