Add update instructions

[ericpre]

Closes #2618.

Progress of the PR

• Add update instruction in the user guide,
• add entry to CHANGES.rst,
• ready for review.

[codecov]

Codecov Report

Merging #2621 (750e73d) into RELEASE_next_patch (8b56d91) will increase coverage by 0.02%.
The diff coverage is n/a.

@@                  Coverage Diff                   @@
##           RELEASE_next_patch    #2621      +/-   ##
======================================================
+ Coverage               76.30%   76.33%   +0.02%     
======================================================
  Files                     202      202              
  Lines                   29603    29640      +37     
  Branches                 6461     6469       +8     
======================================================
+ Hits                    22590    22625      +35     
- Misses                   5236     5237       +1     
- Partials                 1777     1778       +1     

Impacted Files	Coverage Δ
hyperspy/io.py	82.85% <0.00%> (-0.07%)	⬇️
hyperspy/io_plugins/digital_micrograph.py	66.85% <0.00%> (-0.07%)	⬇️
hyperspy/io_plugins/image.py	83.33% <0.00%> (ø)
hyperspy/signal.py	75.88% <0.00%> (+0.04%)	⬆️
hyperspy/io_plugins/protochips.py	95.41% <0.00%> (+0.07%)	⬆️
hyperspy/_components/gaussian.py	97.36% <0.00%> (+0.26%)	⬆️
hyperspy/_components/lorentzian.py	97.40% <0.00%> (+0.34%)	⬆️
hyperspy/_components/skew_normal.py	89.71% <0.00%> (+0.94%)	⬆️

---

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[ericpre]

@NathalieBrun, based on the suggestions your made on gitter, I have updated the installation section of the user. Could you please check the follow page and comment if necessary?

https://hyperspy--2621.org.readthedocs.build/en/2621/user_guide/install.html

[NathalieBrun]

Hello thanks for taking into account my questions. I have other questions that maybe could be useful in the user guide : - if you have an HyperSpy bundle installation can you update it using "conda update ... "? Some people told me to simply uninstall it then reinstall the new version, is it OK to do so? - in my case I had to specify the current version to update, is it a bug in my previous installation (made with Anaconda Navigator, cf 3rd question)? You could indicate in the User Guide that specify the version can solve an issue, even if you want to update with the current version. - is it not recommended to do the installation with Anaconda Navigator (which is very convenient to manage environments and versions of the different packages) ? Best regards Nathalie Brun De: "Eric Prestat" <notifications@github.com> À: "hyperspy/hyperspy" <hyperspy@noreply.github.com> Cc: "Nathalie Brun" <nathalie.brun@u-psud.fr>, "Mention" <mention@noreply.github.com> Envoyé: Mardi 19 Janvier 2021 18:56:40 Objet: Re: [hyperspy/hyperspy] Add update instructions (#2621) [ https://github.com/NathalieBrun | @NathalieBrun ] , based on the suggestions your made on gitter, I have updated the installation section of the user. Could you please check the follow page and comment if necessary? [ https://hyperspy--2621.org.readthedocs.build/en/2621/user_guide/install.html | https://hyperspy--2621.org.readthedocs.build/en/2621/user_guide/install.html ] — You are receiving this because you were mentioned. Reply to this email directly, [ #2621 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AAIXDIBWHKVLT4HXB4YNWKTS2XBVRANCNFSM4WEVWFDA | unsubscribe ] .

[ericpre]

• if you have an HyperSpy bundle installation can you update it using "conda update ... "? Some people told me to simply uninstall it then reinstall the new version, is it OK to do so?

Yes, this should work fine if your hyperspy bundle is not the portable one or <=2019.07.28 - see https://github.com/hyperspy/hyperspy-bundle/releases for details.

Uninstalling and reinstalling will definitively work! In the past, updating was not as easy and trouble free as of today, and I guess this is why people will choose this route!

• in my case I had to specify the current version to update, is it a bug in my previous installation (made with Anaconda Navigator, cf 3rd question)? You could indicate in the User Guide that specify the version can solve an issue, even if you want to update with the current version.

This isn't an expected behaviour but there may be various reasons for this - most likely you had other dependencies in your environment preventing hyperspy to update, but I would imagine that this is a corner case.

• is it not recommended to do the installation with Anaconda Navigator (which is very convenient to manage environments and versions of the different packages) ?

There are "integration issues" with Anaconda navigator: it works well only with the anaconda distribution and it doesn't always work well with conda-forge which is the community and main repository for scientific packages and the one we rely on.
Instead, I think, that we should recommend alternative to the Anaconda navigator, as mentioned in #2618 (comment).

[NathalieBrun]

Thanks a lot I think everything is clear now. Best regards Nathalie Brun De: "Eric Prestat" <notifications@github.com> À: "hyperspy/hyperspy" <hyperspy@noreply.github.com> Cc: "Nathalie Brun" <nathalie.brun@u-psud.fr>, "Mention" <mention@noreply.github.com> Envoyé: Mercredi 20 Janvier 2021 15:30:49 Objet: Re: [hyperspy/hyperspy] Add update instructions (#2621) * if you have an HyperSpy bundle installation can you update it using "conda update ... "? Some people told me to simply uninstall it then reinstall the new version, is it OK to do so? Yes, this should work fine if your hyperspy bundle is not the portable one or <=2019.07.28 - see [ https://github.com/hyperspy/hyperspy-bundle/releases | https://github.com/hyperspy/hyperspy-bundle/releases ] for details. Uninstalling and reinstalling will definitively work! In the past, updating was not as easy and trouble free as of today, and I guess this is why people will choose this route! BQ_BEGIN * in my case I had to specify the current version to update, is it a bug in my previous installation (made with Anaconda Navigator, cf 3rd question)? You could indicate in the User Guide that specify the version can solve an issue, even if you want to update with the current version. BQ_END This isn't an expected behaviour but there may be various reasons for this - most likely you had other dependencies in your environment preventing hyperspy to update, but I would imagine that this is a corner case. BQ_BEGIN * is it not recommended to do the installation with Anaconda Navigator (which is very convenient to manage environments and versions of the different packages) ? BQ_END There are "integration issues" with Anaconda navigator: it works well only with the anaconda distribution and it doesn't always work well with conda-forge which is the community and main repository for scientific packages and the one we rely on. Instead, I think, that we should recommend alternative to the Anaconda navigator, as mentioned in [ #2618 (comment) | #2618 (comment) ] . — You are receiving this because you were mentioned. Reply to this email directly, [ #2621 (comment) | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/AAIXDIEUWLTHURZQOUUXVODS23SJTANCNFSM4WEVWFDA | unsubscribe ] .

[jlaehne]

LGTM