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WIP: Update_packaging #732

Merged
merged 48 commits into from
Jan 4, 2025
Merged

WIP: Update_packaging #732

merged 48 commits into from
Jan 4, 2025

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Adamtaranto
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Work in progress, do not merge.

Migrating from setuptools to Hatch as the build system.

Currently stuck on getting hatch-cython to build only "jcvi_assembly_chic" and "jcvi_formats_cblast".

@Adamtaranto
Do not try to set usetex=False or resave
8e4c872 
if savefig fails. Instead just return error msg.
@Adamtaranto
Replace check_call with check_out in sh()
8029175 
Allows collection of outputs.
Added redirect_error arg so stderr can be
redirected to stdout and user in error logging.
@Adamtaranto
Collect stderr msgs from lastal for use in
a5225ec 
informative logging.
@Adamtaranto
Log suggestion to use --notex if savefig fails
3f7ad6d
@Adamtaranto
Add cleanup empty pdf before exit if savefig fails
00ff793
@Adamtaranto
Merge branch 'main' of https://github.com/tanghaibao/jcvi
6b986bb
@Adamtaranto
Add logging to clarify why latex is
e378e6f 
deactivated.
@Adamtaranto
Merge branch 'main' of https://github.com/tanghaibao/jcvi
2daf3dc
@Adamtaranto
Merge remote-tracking branch 'upstream/main'
ae7c0ef
@Adamtaranto
Merge branch 'tanghaibao:main' into main
c70602a
@Adamtaranto
ignore version and cython files
afb75ef
@Adamtaranto
mv exclude to pyproject
4029d67
@Adamtaranto
use hatch for build
6a5359e
@Adamtaranto
use hatch-vcs version
eff4eb6
@Adamtaranto
log error when no cblast
b77c309
@Adamtaranto
mv pkg into src
39b70d7
@Adamtaranto
ignore version
60ec604
@Adamtaranto
init env yml
98752a8
@Adamtaranto
rm version, switch to dynamic vcs version
011d467
@Adamtaranto
WIP: migrating to hatch
ed97aa1
@Adamtaranto
rm cblast.c from tracking
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@Adamtaranto
ignore dev files
b203b88
@Adamtaranto
Use setuptools for cython modules
e5be700
@Adamtaranto
automate run setup.py for cython build
a640776
@Adamtaranto
setup_magick_home() assumes ImageMagick always installed with homebre…
e6a722b 
…w on MacOS, change error to warning if homebrew path not found.
@Adamtaranto
install non-pip deps using conda. Install libmagic without homebrew.
c6d1140
@tanghaibao tanghaibao marked this pull request as draft January 3, 2025 04:51
@Adamtaranto Adamtaranto self-assigned this Jan 4, 2025
@Adamtaranto
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Adamtaranto commented Jan 4, 2025 •
edited
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  • Use Hatch for majority of build and install tasks (kept setuptools for build Cython modules)
  • Move all practical config content into pyproject.toml
  • Add conda env YAMLs to handle install of non-python deps (i.e. bedtools and imagemagick) - no more manual install steps or requirements for homebrew on MacOS.
  • Updated install instructions to include conda env YAMLs
  • Moved package modules into src dir in line with modern package structure
  • Use hatch-vcs to dynamically set version based on git tags (add a new tag prefixed with "v" before creating new releases)
  • Build with one step hatch build and upload to pypi as normal.
  • I haven't tested the environment.yml setup on a linux machine yet

Bug fixes:

@Adamtaranto Adamtaranto marked this pull request as ready for review January 4, 2025 04:28
@Adamtaranto Adamtaranto requested a review from tanghaibao January 4, 2025 04:29
@tanghaibao tanghaibao merged commit ea05c58 into tanghaibao:main Jan 4, 2025
7 checks passed
@Adamtaranto Adamtaranto deleted the update_packaging branch January 4, 2025 05:31
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@tanghaibao tanghaibao tanghaibao approved these changes

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@Adamtaranto @tanghaibao