Build modernization #54

bethac07 · 2023-12-21T19:05:42Z

See #53 for motivations

I changed the embedding of the images and figures to be compatible with markdown text. Simplified small images in single file panels.

I deleted the last part because the cited notebook was not available anymore

I pulled the most recent version of Beginner Segmentation as a base for the simplified version

unify common button image names accors tutorials make hierarchical titles for markdown fix images in markdown

Unify button images accros tutorials fix markdown images fix title hierarchy

I used the modernized version of Beginner Segmentation as base

allows inline images when geenrating html

- add new figures and images - modify the entire text - modify the pipeline accordingly

…ication

…fication Beginner segmentation simplification

…fication minor text changes

…fication Beginner segmentation simplification final

bethac07 · 2024-03-15T14:43:05Z

@emiglietta and @PaulaLlanos, where do we stand with this?

My open q's/things I'd like to see before we pull (sooooo close, nice work!)

Has the code to update the POs been run( see eventually block here, and have updated POs been pushed here?
Can we add the instructions about that step to the instructions md (and also give it a typo check, I found a few)?
Do we want to keep both BS and BS_S? Or should your new one replace the old BS? If we're going to keep both, maybe this is me but "Beginner_Simplified" starts getting towards the point where i wonder if we're getting accidentally insulting - maybe something like Intro to Segmentation? I don't have super strong feelings here I just wanted to raise it.

I think that's it but I reserve the right to realize I've forgotten something lol

….com/CellProfiler/tutorials into Beginner_segmentation_simplification

…ersion

- add SaveImages module - remove Costes threshold measurement to speed up - add comments to pipelines - updated html, toc and pdf files

…ication

…fication final merge of this branch so the whole Build Modernization can be merged indo Master to update the Beginner tutorial before workshop

bethac07 and others added 30 commits December 21, 2023 13:30

build modernization

edbb73f

fix malformed PO file

73caa37

Fix conf, now building

13309a4

Fix bad align flag

78faaa6

Delete spurious file

c230401

Allow for us to provide our own frontpage/sidebar titles

4ae6db0

Merge branch 'master' into build_modernization

cd7bf04

Formatted hierarchic titles

9cf55a7

Adapt Translocation tutorial to Markdown

a7a4b78

I changed the embedding of the images and figures to be compatible with markdown text. Simplified small images in single file panels.

Updated fig1

68595e7

Update CPbeginner_Segmentation.md

1ea15d8

create new simplified folder and update original tutorial

a7f8591

correct title hierarchy

fe34b78

fix title hierarchy

c822253

3D nuclei tutorial modernization

d77aca3

I deleted the last part because the cited notebook was not available anymore

Update Advanced Segmentation according to modernization

f54f46c

Update Translocation.md

7be9f0d

add Beginner Segmentation_simplified to source for editing

dfbe526

I pulled the most recent version of Beginner Segmentation as a base for the simplified version

update tutorials

67e1038

unify common button image names accors tutorials make hierarchical titles for markdown fix images in markdown

Update tutorial

ff59d60

Unify button images accros tutorials fix markdown images fix title hierarchy

update UnmixColors tutorial

4b26abb

update QC tutorial

cf46df1

unify aesthetic of modules

500773b

start simplified beginner segmentation tutorial

99f1e55

I used the modernized version of Beginner Segmentation as base

start simplified beginner segmentation tutorial

0454be1

I used the modernized version of Beginner Segmentation as base

fix H1 to H3 transition

864905e

fix inconsistencies in commits

5d93397

include new image names

8a96981

add missing fig files

9e58704

change intro and fig1

5cf9a0b

emiglietta and others added 17 commits March 5, 2024 09:20

add html_image to conf file

954fe88

allows inline images when geenrating html

Update Fig1.png

bc5f211

Update Fig1.png

b0b0d92

fix Titles in index file and in each md file

dddcae6

renamed tutorial image files

c163ed4

Update figs up to 5

c9ca3e7

Finish Simplification

97b07d5

- add new figures and images - modify the entire text - modify the pipeline accordingly

update building instructions

10ccafa

update index to include Simplified Beginner Segmentation

32a4a01

Merge branch 'build_modernization' into Beginner_segmentation_simplif…

88058b4

…ication

Merge pull request #73 from CellProfiler/Beginner_segmentation_simpli…

6f32309

…fication Beginner segmentation simplification

add index modification instructions

3ceae84

Update CPbeginner_Segmentation_simplified.md

097cf78

Merge pull request #74 from CellProfiler/Beginner_segmentation_simpli…

c36cc5d

…fication minor text changes

Paula Comments

df989f7

update instructions, generate pdf for simplified beginner sgem

b4f699b

Merge pull request #75 from CellProfiler/Beginner_segmentation_simpli…

109291f

…fication Beginner segmentation simplification final

PaulaLlanos and others added 9 commits March 15, 2024 10:55

Update Fig2.png

1d556a7

Merge branch 'Beginner_segmentation_simplification' of https://github…

45c5e0d

….com/CellProfiler/tutorials into Beginner_segmentation_simplification

Esteban and Paula names were added

787da90

Remove old Beginner segmentation and replace it with the simplified v…

5987109

…ersion

update toc files and instructions

0aae2bd

Update Beginner segmentation and organelle analysis.pdf

b1b8c4d

Update simplified beginner tutorial

3c2b295

- add SaveImages module - remove Costes threshold measurement to speed up - add comments to pipelines - updated html, toc and pdf files

Merge branch 'build_modernization' into Beginner_segmentation_simplif…

402e0bb

…ication

Merge pull request #76 from CellProfiler/Beginner_segmentation_simpli…

75ad557

…fication final merge of this branch so the whole Build Modernization can be merged indo Master to update the Beginner tutorial before workshop

emiglietta merged commit d35290a into master Mar 15, 2024

emiglietta deleted the build_modernization branch March 19, 2024 17:08

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Build modernization #54

Build modernization #54

bethac07 commented Dec 21, 2023

bethac07 commented Mar 15, 2024 •

edited by emiglietta

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Build modernization #54

Build modernization #54

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