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Implement ensembl-py logging #214

Merged
merged 30 commits into from
Nov 21, 2023
Merged

Implement ensembl-py logging #214

merged 30 commits into from
Nov 21, 2023

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ens-LCampbell
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@ens-LCampbell ens-LCampbell commented Nov 15, 2023 •
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Implement use of ens-py logging for ensembl.io. modules:

genomio.assembly.download
genomio.events.dump
genomio.events.load
genomio.genome_stats.compare
genomio.manifest.check_integrity
genomio.metadata.dump

  • Module updated to use ensembl-py.utilis.logging
  • Nextflow modules set to use --verbose as default

ens-LCampbell and others added 3 commits November 15, 2023 17:46
@ens-LCampbell @JAlvarezJarreta
Add else clause for successful execute
f1ca04c 
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
@ens-LCampbell @JAlvarezJarreta
Update import formatting
ee7ada7 
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
@ens-LCampbell
Implement ensembl-py logging events module
0273e04
ens-LCampbell and others added 4 commits November 16, 2023 10:27
@ens-LCampbell ens-LCampbell changed the title genome_stats.compare implement ensembl-py logging Implement ensembl-py logging Nov 16, 2023
ens-LCampbell and others added 16 commits November 16, 2023 13:44
@ens-LCampbell
genome_metadata logging + restructure nxf modules
70dad00
@ens-LCampbell
Merge pull request #218 from Ensembl/lcampbell/genome_metadata
6261425 
Ensembl-py Logging genome_metadata module
@ens-LCampbell
Add missing license header mkdocs gen script
4514a11
@ens-LCampbell
Fix banner name Ensembl GenomIO
5b9b23e
@ens-LCampbell
Include ensembl genomio pages URL to toml
0bd56ad
@ens-LCampbell
Merge pull request #219 from Ensembl/lcampbell/genome_metadata
174b9dc 
Lcampbell/genome metadata
@ens-LCampbell
ens-py logging manifest integrity check
0d2a796
@ens-LCampbell
remove comment line
93790ef
@ens-LCampbell
Merge pull request #221 from Ensembl/lcampbell/manifest
1509230 
Merging into parent branch: ens-py logging manifest integrity
@ens-LCampbell
Update NXF module logging to verbose not debug
769ae78
@ens-LCampbell
Add license header to mkdoc config yaml
388bffa
@ens-LCampbell
Merge branch 'main' into lcampbell/genome_stats_compare
bde2d8d
@ens-LCampbell
Rename and add license to mkdocs workflow yml
28e6972
@ens-LCampbell
Run black across code changes
a632088
@ens-LCampbell
Remove unused sys import
b21850b
@ens-LCampbell
Remove site logo, update URLs
9d5e570
MatBarba
MatBarba requested changes Nov 20, 2023
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Nice overall, though there should be no need to catch exceptions just to log them

src/python/ensembl/brc4/runnable/core_server.py Outdated Show resolved Hide resolved
src/python/ensembl/io/genomio/assembly/download.py Show resolved Hide resolved
JAlvarezJarreta
JAlvarezJarreta requested changes Nov 20, 2023
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@JAlvarezJarreta JAlvarezJarreta left a comment •
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Looks good to me. It has also helped raise a couple of questions regarding how we want to set the default system + Exception handling that should be discussed in the next software development meeting.

docs/gen_ref_pages.py Outdated Show resolved Hide resolved
pipelines/nextflow/modules/download/download_asm_data.nf Show resolved Hide resolved
src/python/ensembl/brc4/runnable/core_server.py Outdated Show resolved Hide resolved
src/python/ensembl/brc4/runnable/core_server.py Outdated Show resolved Hide resolved
ens-LCampbell and others added 2 commits November 21, 2023 15:08
@ens-LCampbell @JAlvarezJarreta
Update docs/gen_ref_pages.py
0fa6c30 
Co-authored-by: J. Alvarez-Jarreta <jalvarez@ebi.ac.uk>
@JAlvarezJarreta
Apply suggestions from code review
3e95dfc
@JAlvarezJarreta JAlvarezJarreta merged commit 6985344 into main Nov 21, 2023
@ens-LCampbell ens-LCampbell deleted the lcampbell/genome_stats_compare branch November 21, 2023 17:01
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@MatBarba MatBarba MatBarba approved these changes

@JAlvarezJarreta JAlvarezJarreta JAlvarezJarreta approved these changes

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@ens-LCampbell @JAlvarezJarreta @MatBarba