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Merge new doc in dev #153

Merged
merged 138 commits into from
Dec 14, 2023
Merged

Merge new doc in dev #153

merged 138 commits into from
Dec 14, 2023

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JeanMainguy
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This PR encompasses a comprehensive reorganization of the documentation structure.

Key Changes:

  1. Documentation Restructuring:

  2. GitHub Action Addition:

    • Implemented a new GitHub Action to validate the successful build of the documentation.

  3. CI Enhancement:

    • Refinement in the main GitHub Action for CI purposes:
      • Manual triggering of the main CI action is now possible.
      • The main CI action triggers automatically only within the context of a PR, preventing unintended launches.

JeanMainguy and others added 30 commits October 4, 2023 16:09
@JeanMainguy
replace panorama with ppangolin and build cmd
a60f65c
@JeanMainguy
Merge remote-tracking branch 'origin/dev' into update_doc
1517235
@JeanMainguy
Create check_doc.yml
40b4a85
@JeanMainguy
add custom build cmd
b72fff7
@JeanMainguy
fix artificat path
f642d24
@JeanMainguy
Update check_doc.yml
abccd12
@jpjarnoux
Reduce welcome page
4d00b96
@jpjarnoux
Add first tutorial pages
8349dd8
@jpjarnoux
Add preparing environment in tutorial
f53d564
@jpjarnoux
Change title for genome download
66a40af
@jpjarnoux
Add projection API doc
238d5bb
@jpjarnoux
Add workflow tutorial and some output
8404437
@jpjarnoux
Begin RGP analyses tutorial
dde306c
@jpjarnoux
Add org stat in tutorial
ff20f32
@jpjarnoux
Change documentation structure
3930321
@jpjarnoux
Paste and enhance installation old doc
a163969
@jpjarnoux
Paste introduction old content
1b990e8
@jpjarnoux
First version of quick usage
8cee54a
@jpjarnoux
Add practical information
2eae3ec
@jpjarnoux
Split pangenome analyses
4e89016
@jpjarnoux
Add todo warning in argparse
bb7384d
@jpjarnoux
Copy paste old outputs content for pangenome analyses
8026a2b
@JeanMainguy
complete doc file within new doc structure
d34cc9b
@JeanMainguy
fix md links
148d9a0
@JeanMainguy
Merge branch 'update_doc' of github.com:labgem/PPanGGOLiN into update…
54f9fb4 
…_doc
@jpjarnoux
Add MMseqs2 options
becd4a5
@jpjarnoux
Reformat workflow pangenome analyses
e956bb0
@JeanMainguy
improve conda install in gh action
a69328c
@JeanMainguy
update conda install run
01584c9
@JeanMainguy
fix bokeh version
58494dd
axbazin and others added 23 commits December 12, 2023 16:19
@axbazin
Merge pull request #151 from labgem/axbazin-pangenome-doc-review
5351103 
PangenomeAnalyses doc
@acalteau
Update writeGenomes.md
2823384 
typos
@acalteau
Update align.md
4d17f32
@acalteau
Update align.md
b98b50c
@acalteau
Update align.md
32d0c6b
@ggautreau
Update index.md
b42af88
@ggautreau
Update quickOutputs.md
66f832f
@JeanMainguy
fix bug in panmodule argument management
f394e3f
@JeanMainguy
remove module info in metrics command
3aff346
@JeanMainguy
Move info format to yaml and improve key names
7b1c765
@JeanMainguy
convert status output to yaml
33d86d3
@JeanMainguy
harmonise yaml output and default of info is to diplay all
5b2942a
@JeanMainguy
remove fix_partitioned fct
82330ab
@JeanMainguy
deal with empty config file
7ce05e3
@JeanMainguy
add the possibility to recompute the fluidity
079bf87
@JeanMainguy
update the workflow
339d817
@JeanMainguy
fix md internal link
41044c1
@JeanMainguy
update description of module stat of cmd info
aa5cfcc
@JeanMainguy
update doc with change in info and metrics command
2de0f03
@JeanMainguy
reorganise the main help with subcommands description
9a269cd
@acalteau
Update projection.md
1f0d53a 
minor corrections
@acalteau
Update projection.md
7fac0e9 
minor corrections
@jpjarnoux
Merge pull request #152 from labgem/metrics
6b91098 
Improve metrics and info command
@jpjarnoux jpjarnoux self-requested a review December 13, 2023 15:19
jpjarnoux
jpjarnoux reviewed Dec 13, 2023
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Cumulative changes from other branches that were already validated.

@jpjarnoux jpjarnoux merged commit ff23a53 into dev Dec 14, 2023
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5 participants
@JeanMainguy @jpjarnoux @acalteau @axbazin @ggautreau