Added info for conda installation problems #51

Chris-N-K · 2022-11-18T08:51:59Z

Description

As in napari/napari#5345 at the napari main repository discussed I added a small info box for the case that the conda installation does not work propperly.
In this case mamba is a good alternative.

Type of change

Bug-fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

References

@psobolewskiPhD recommended mamba

How has this been tested?

example: the test suite for my feature covers cases x, y, and z
example: all tests pass with my change

Final checklist:

My PR is the minimum possible work for the desired functionality
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
I have added tests that prove my fix is effective or that my feature works
If I included new strings, I have used trans. to make them localizable.
For more information see our translations guide.

@jaimergp

docs/tutorials/fundamentals/installation.md

psobolewskiPhD · 2022-11-18T09:14:23Z

Further down, at line 143 Checking that it worked perhaps lets add a sentence to run:
napari --version and confirm that the proper version was installed (ideally we clearly state the current version that should be expected, see comment above). We've had a couple issues where someone ended up with napari 0.4.12 or 0.4.14 due to solver issues and didn't realize it.

Chris-N-K · 2022-11-19T09:43:50Z

If you state the current version one has to update the doc every time. Or can we add a prompt with the current version tag?

psobolewskiPhD · 2022-11-19T09:46:57Z

If you state the current version one has to update the doc every time. Or can we add a prompt with the current version tag?

Yeah, I posted about that above, but it's resolved now: #51 (comment)
So will add here:
@melissawm is there a tag for the current version of napari in the docs, so we don't need to correct a reference to the version every time, if we want to add something like that here?

psobolewskiPhD · 2022-11-25T17:01:55Z

@ch-n You want to take a stab at versioning the version number, per @melissawm :

Yes - if you have this stable_version variable defined in a myst_substitutions dictionary in the conf.py file, you can print it anywhere in the docs using the following syntax:
{{ stable_version }}
See this commit for an example.

Chris-N-K · 2022-11-26T09:51:45Z

Yes will take a look.

Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

Chris-N-K · 2022-11-26T10:42:55Z

Guess I just don't find it but the best solution I could come up is to us the link to the latest version. This is stable and dynamic but will not display the correct version tag. @melissawm @psobolewskiPhD

@melissawm

Version by @melissawm

psobolewskiPhD · 2022-11-26T15:16:25Z

Hmm, I tried the myst_substitution provided by @melissawm
psobolewskiPhD#2
It doesn't look like you can substitute in code blocks and the version is not the napari version—at least on CI:

Czaki · 2022-11-26T16:05:36Z

this version problem is a well-known problem of tox as tox is not compatible with setuptools_scm.

psobolewskiPhD · 2022-11-26T18:27:58Z

this version problem is a well-known problem of tox as tox is not compatible with setuptools_scm.

Does that mean it's just messed up in PR builds, or does it mean it will be messed up if released?

melissawm · 2022-12-01T12:06:12Z

Hmm, I tried the myst_substitution provided by @melissawm psobolewskiPhD#2 It doesn't look like you can substitute in code blocks and the version is not the napari version—at least on CI:

Indeed - code blocks are supposed to not be interpreted by the parser so that makes sense.

Chris-N-K · 2022-12-02T11:18:20Z

That would leave us with the link to the latest version I guess.

psobolewskiPhD · 2022-12-03T10:45:50Z

@ch-n I made a PR to your fork with some suggestions.
I added the verbiage from Jaime, from the comment:
#51 (comment)
Also I implemented the version substitution.
I got the version number to work by tweaking the build action.
@Czaki @melissawm How does this fix look for y'all? Do the other actions need the same fix?
Finally, I worked around the code block issue somewhat. It's not perfect. Here's what it looks like:

You can see the built docs in my fork PR:
psobolewskiPhD#3

Czaki · 2022-12-03T18:29:26Z

I have added in Chris-N-K#1 (review) the solution to provide napari version

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

psobolewskiPhD · 2022-12-03T19:05:38Z

Awesome @Czaki super clever!! I've merged your changes into the PR to @ch-n PR.

Adding suggestion from Jaime and napari version Note

Chris-N-K · 2022-12-05T08:56:02Z

All merged now, guess it should be ready for a final review.

psobolewskiPhD · 2022-12-06T07:38:08Z

@Chris-N-K @Czaki I made a PR adding python_version to the substitutions:
Chris-N-K#2
To make it work, I needed to also add a substitution for python={python_version} and the code block of conda env instruction, using the clever strategy from above.
You can check out the built docs in my fork:
https://github.com/psobolewskiPhD/napari-docs/actions/runs/3624911741

I also fixed the listing of supported python versions from 3.7 ... to 3.8 ... because we don't support 3.7 anymore.

For me this is not a blocker, so I leave it up to @Czaki and @jaimergp for the final approval.

jaimergp

Just one nit. Can be merged afterwards!

docs/tutorials/fundamentals/installation.md

Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com>

Chris-N-K · 2022-12-20T10:45:22Z

Just one nit. Can be merged afterwards!

Merged it and fixed a conflict with main.
Happy this can go live now :)

jaimergp · 2022-12-20T15:11:30Z

I have added in ch-n#1 (review) the solution to provide napari version

This is unrelated but I noticed that the font (face and size) is different in the numbered list. Is that intentional or a CSS bug?

psobolewskiPhD · 2022-12-20T19:23:42Z

I resolved the conflict if we want the python version set programmatically as suggested by @Czaki Chris-N-K#2
@jaimergp the formatting does look a bit different. I've triggered the CI—not sure why we hadn't before—so we can get the docs built with this branch and take another look. Otherwise, maybe @melissawm has some thoughts on the formatting.

melissawm · 2022-12-23T17:14:49Z

This is unrelated but I noticed that the font (face and size) is different in the numbered list. Is that intentional or a CSS bug?

I believe this is the current napari-sphinx-theme formatting/design choice. cc @codemonkey800 ?

psobolewskiPhD · 2022-12-26T18:05:40Z

@Czaki @Chris-N-K Did y'all have any input on the python version substitution:
Chris-N-K#2
There's another PR in-flight that also refers to python version (https://github.com/napari/docs/pull/72/files#), so I think it's a decent idea to get it in somewhere to standardize.

Chris-N-K · 2022-12-27T01:35:01Z

@Czaki @Chris-N-K Did y'all have any input on the python version substitution:
Chris-N-K#2
There's another PR in-flight that also refers to python version (https://github.com/napari/docs/pull/72/files#), so I think it's a decent idea to get it in somewhere to standardize.

I think the current solution is absolutely reasonable. There might be a slight lag when a new version is unrolled and the docs repo might not have the newest version for a short amount of time, but that should be no real problem.
If it is noted in the guide for doc additions should be fine and easy to use.

Merry Christmas ;)

DragaDoncila · 2023-01-05T02:52:39Z

This is awesome, thanks folks! Merging now 🎉

…ubstitution (#99) # Description See napari/napari#5509 (comment) The docs live on napari.org don't match PR action downloaded docs when doing napari version substitution (#51) This PR updates the deploy action with `fetch-depth: 0` that was added to the PR `build_docs` action. This should make the version metadata be correct (see pypa/setuptools-scm#480) ## Type of change  - [x] Fixes or improves existing content - [ ] Adds new content page(s) - [ ] Fixes or improves workflow, documentation build or deployment # References Adresses issue noted here napari/napari#5509 (comment) ## Final checklist: - [x] My PR is the minimum possible work for the desired functionality

…stitutions (#5557) # Description This PR an an analog to napari/docs#99 The built docs built by this repo PR action have improper napari version substitution (see napari/docs#51) This PR fixes that based on the README of https://github.com/actions/checkout It updates the deploy action with `fetch-depth: 0`. You can see that this was added to the napari/docs PR build_docs action and works correctly. This makes the version metadata be correct (see pypa/setuptools-scm#480) ## Type of change - [x] Bug-fix (non-breaking change which fixes an issue) # References Motivated by napari/docs#51 Analog to napari/docs#99

Added info for conda installation problems

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github-actions bot assigned Chris-N-K Nov 18, 2022

github-actions bot added the documentation Improvements or additions to documentation label Nov 18, 2022

Czaki added the instalation instalation instructions label Nov 18, 2022

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Chris-N-K and others added 2 commits November 26, 2022 11:02

Update docs/tutorials/fundamentals/installation.md

99e9fc6

Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

Update docs/tutorials/fundamentals/installation.md

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Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

psobolewskiPhD added 5 commits November 26, 2022 15:12

Merge remote-tracking branch 'ch-n/main' into napari_version

ec95edc

Conda per @jaimergp

cc5d362

Version by @melissawm

Add note about checking napari version

e50ee52

Add the myst_subs for napari version

af23a88

use python 3.9 in the example, add link to mamba

33f127b

psobolewskiPhD added 5 commits December 2, 2022 22:33

Don't use versions in codeblock

e3d707d

Fix version?

c0351b8

make 0.x.y version string

e23147e

work around no substitution in code blocks

a926f9c

Tweak version Note

decbde5

psobolewskiPhD mentioned this pull request Dec 3, 2022

Adding suggestion from Jaime and napari version Note Chris-N-K/napari-docs#1

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psobolewskiPhD and others added 3 commits December 3, 2022 20:00

@Czaki trick to sub the whole strong

2ec9047

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

@Czaki fix

57e209b

Co-authored-by: Grzegorz Bokota <bokota+github@gmail.com>

tweak wording

935b658

psobolewskiPhD and others added 2 commits December 3, 2022 21:36

fix the non-code version substitution

f34ca36

Merge pull request #1 from psobolewskiPhD/napari_version

d14e8e5

Adding suggestion from Jaime and napari version Note

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Chris-N-K and others added 2 commits December 20, 2022 11:41

Update docs/tutorials/fundamentals/installation.md

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Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com>

Merge branch 'main' into main

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DragaDoncila merged commit 153467c into napari:main Jan 5, 2023

psobolewskiPhD mentioned this pull request Jan 5, 2023

Feature: implement python version substitution in conf.py #84

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This was referenced Jan 27, 2023

Installing with conda fails to solve environment on macOS 13 (x64) napari/napari#5509

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Add mention of libmamba solver for conda #96

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Update deploy_docs.yml to use metadata to use proper napari version substitution #99

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psobolewskiPhD mentioned this pull request Feb 11, 2023

Bugfix: PR build of docs doesn't use proper napari versioning for substitutions napari/napari#5557

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psobolewskiPhD added this to the 0.4.18 milestone Jun 22, 2023

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Added info for conda installation problems #51

Added info for conda installation problems #51

Chris-N-K commented Nov 18, 2022 •

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Added info for conda installation problems #51

Added info for conda installation problems #51

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Description

Type of change

References

How has this been tested?

Final checklist:

psobolewskiPhD commented Nov 18, 2022

Chris-N-K commented Nov 19, 2022

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