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Modernize repo #2

Closed
30 tasks done
genehack opened this issue May 23, 2024 · 0 comments · Fixed by #20
Closed
30 tasks done

Modernize repo #2

genehack opened this issue May 23, 2024 · 0 comments · Fixed by #20
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@genehack
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enhancement New feature or request

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genehack commented May 23, 2024 •
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Rough plan of attack:
@genehack genehack added enhancement New feature or request source: office hours Issue mentioned during office hours labels May 23, 2024
@genehack genehack self-assigned this May 23, 2024
@genehack genehack removed the source: office hours Issue mentioned during office hours label May 23, 2024
genehack added a commit that referenced this issue May 23, 2024
@genehack
Archive previous contents under _LEGACY [#2]
f139941 
Once the repo modernization is complete, these files will be deleted;
for the moment this allows them to be easily accessed.
genehack added a commit that referenced this issue May 23, 2024
@genehack
Strip out old README; scaffold new one [#2]
2a8574c
genehack added a commit that referenced this issue May 23, 2024
@genehack
Add pre-commit-config.yaml and supporting files [#2]
df1a6dd 
Exclude the _LEGACY tree because there's no point in cleaning that
stuff up; leave a comment so I remember to go back and remove it when
`_LEGACY` goes away.
genehack added a commit that referenced this issue May 23, 2024
@genehack
Pull ingest and phylogenetic workflows from guide repo [#2]
3a2acd2 
Also apply pre-commit cleanup
@genehack genehack mentioned this issue May 23, 2024
Merged
genehack added a commit that referenced this issue May 24, 2024
@genehack
Update snakefmt pre-commit action [#2]
c25d878
genehack added a commit that referenced this issue May 29, 2024
@genehack
Sync with "standard" pre-commit-config [#2]
d823917 
Remove unused configuration files
This was referenced May 30, 2024
Merged
Closed
genehack added a commit that referenced this issue Jun 27, 2024
@genehack
Update .gitignore to match seasonal-cov [#2]
cdbd7f6
genehack added a commit that referenced this issue Jun 27, 2024
@genehack
Update ingest and make it work [#2]
f0e18fe 
* sync `ingest/README` with `seasonal-cov` version
* move from `defaults` to `config` for config files
* strip fetch-from-entrez stuff from config and rules files
* add `ncbi_taxon_id` to config
* strip guidance comments, light reformat of Snakemake and rules files
  for readability
* add benchmarks where missing
* remove unused nextclade bits
genehack added a commit that referenced this issue Jul 11, 2024
@genehack
Update ingest and make it work [#2]
f6795e7 
* sync `ingest/README` with `seasonal-cov` version
* move from `defaults` to `config` for config files
* strip fetch-from-entrez stuff from config and rules files
* add `ncbi_taxon_id` to config
* strip guidance comments, light reformat of Snakemake and rules files
  for readability
* add benchmarks where missing
* remove unused nextclade bits
* add "clean" convenience rule
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Phylogenetic workflow modernization [#2]
e6a0b1b 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Remove _LEGACY [#2]
093674c 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Misc cleanups and formatting [#2]
19a9f43 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Add .snakemake to clean rules [#2]
44d66ae
genehack added a commit that referenced this issue Jul 18, 2024
@genehack
Note why we're wildcarding a single thing [#2]
6578df9
@genehack genehack mentioned this issue Jul 18, 2024
Merged
1 task
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Phylogenetic workflow modernization [#2]
e6f2a81 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Remove _LEGACY [#2]
e535265 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Misc cleanups and formatting [#2]
044dd08 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Add .snakemake to clean rules [#2]
c473611
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Note why we're wildcarding a single thing [#2]
31c1ab7
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Phylogenetic workflow modernization [#2]
2b98ab2 
* Update template files to remove instructions and placeholders
* Add Genbank and GFF references
* Bring in phylo workflow from pathogen-repo-guide and modify to work
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Remove _LEGACY [#2]
a9e739b 
Also remove exclusion from .pre-commit-config.yaml
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Misc cleanups and formatting [#2]
be791e3 
* Drop to Python 3.11 in GitHub pre-commit CI, to match actual
  development practice
* Clean up formatting of several files
* Convert all Markdown links to use reference dictionary at end of
  file
* Add `log` and `benchmark` to all Snakemake rules that didn't have
  them
* Remove `dump_ncbi_dataset_report` rule
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Download Nextclade dataset during ingest... [#2]
272d4c6 
...instead of depending on having one built locally.

Also corrects nextclade dataset name in the config.
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Add / tweak bits to allow upload of ingested files to S3 [#2]
5f61500
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Convert nextclade workflow to download inputs from S3 [#2]
12865fc
genehack added a commit that referenced this issue Nov 16, 2024
@genehack
Convert phylogenetic workflow to download inputs from S3 [#2]
52f3da5
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
We have a gene-specific build so we don't need this comment [#2]
55daabf
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Set explicit clock rate of 2e-04 ± 1e-05 [#2]
967c4e7
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Only run timetree on genome build [#2]
8f9dc75
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Put params in order of use [#2]
5c62c7c
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Swap 'authors' -> 'full_authors' and 'abbr_authors' -> 'authors' [#2]
e953108 
This makes the metadata annotations in the Auspice visualization look
much nicer.
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add frequencies panel [#2]
8bef86e 
This is _largely_ copy-pasta-ed from the `measles` repo; the one
significant change is I enabled the frequencies on both the whole
genome and prM-E builds, and I set the `min_date` param to
`2017-01-01`, because virtually all of the post-1927 samples are dated
2017 and later.
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Filter out Chinese travel cases from 2016-ish outbreak [#2]
0557dac
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Copypasta assign-colors.py and associated data from dengue [#2]
6625d78
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Remove old colors file; update config [#2]
84fea9b
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Update color_orderings for YFV [#2]
2ac2f54 
Also small script tweak
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Build colors.tsv dynamically during phylo build {#2}
59999fb
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add CI workflow and configs [#2]
ef81bc9
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add example data [#2]
13a56ae 
This is the full NCBI yellow-fever dataset (taxon ID 11089) as
downloaded on 21 Nov 2024.

CI _could_ work just fine without embedding this data in the repo, but
having a hard-coded example-data file means that we don't depend on
NCBI for successful CI runs.
@genehack genehack mentioned this issue Nov 21, 2024
Merged
1 task
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Add ingest-to-phylo Github workflow [#2]
917d07c
@genehack genehack mentioned this issue Nov 21, 2024
Merged
1 task
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Update README [#2]
f3dad1a
genehack added a commit that referenced this issue Nov 21, 2024
@genehack
Clean up old cruft in nextclade workflow [#2]
f1a35a6
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Update color_orderings for YFV [#2]
a1ec892 
Also small script tweak
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Build colors.tsv dynamically during phylo build {#2}
bc41b40
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Add CI workflow and configs for ingest and phylogeny workflows [#2]
bbd653e 
Also add custom rule import bits to phylogenetic/Snakefile
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Add example data for ingest and phylogenetic CI workflows [#2]
fd22561 
This is the full NCBI yellow-fever dataset (taxon ID 11089) as
downloaded on 21 Nov 2024, and the ingested sequences and metadata as
downloaded from Nextstrain on 21 Nov 2024.

CI _could_ work just fine without embedding this data in the repo, but
having a hard-coded example-data file means that we don't depend on
NCBI or Nextstrain.org for successful CI runs.
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Add ingest-to-phylo Github workflow [#2]
9d2aadb
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Update README [#2]
729a60f
genehack added a commit that referenced this issue Nov 26, 2024
@genehack
Clean up old cruft in nextclade workflow [#2]
04b92ca
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Finish modernization nextstrain/yellow-fever
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