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Modernize repo #2

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25 of 30 tasks
genehack opened this issue May 23, 2024 · 0 comments
Open
25 of 30 tasks

Modernize repo #2

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

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@genehack
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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 Jul 19, 2024
@genehack
Add .snakemake to clean rules [#2]
555b11b
genehack added a commit that referenced this issue Jul 19, 2024
@genehack
Note why we're wildcarding a single thing [#2]
9a03a26
genehack added a commit that referenced this issue Jul 24, 2024
@genehack
add a TODO based on PR feedback [#2]
6f2158b
genehack added a commit that referenced this issue Jul 24, 2024
@genehack
Refinements to phylogenetic build [#2]
ddcf049 
* Switch Auspice to default color-by=region
* Remove extra `metadata_columns` (and associated config) when calling
  `augur export v2`
* Move `--columns` arg of `augur traits` into config
* Add `--metadata-id-columns` arg to `augur traits` invocation --
  fixes issue where traits were being improperly inferred
* Use a mid-point tree rooting
genehack added a commit that referenced this issue Jul 24, 2024
@genehack
Refinements to phylogenetic build [#2]
19d398a 
* Switch Auspice to default color-by=region
* Remove extra `metadata_columns` (and associated config) when calling
  `augur export v2`
* Move `--columns` arg of `augur traits` into config
* Add `--metadata-id-columns` arg to `augur traits` invocation --
  fixes issue where traits were being improperly inferred
* Use a mid-point tree rooting
genehack added a commit that referenced this issue Jul 31, 2024
@genehack
Refinements to phylogenetic build [#2]
ebf1fde 
* Switch Auspice to default color-by=region
* Remove extra `metadata_columns` (and associated config) when calling
  `augur export v2`
* Move `--columns` arg of `augur traits` into config
* Add `--metadata-id-columns` arg to `augur traits` invocation --
  fixes issue where traits were being improperly inferred
* Use a mid-point tree rooting
genehack added a commit that referenced this issue Jul 31, 2024
@genehack
Merge pull request #9 from nextstrain/phylogenetic-2
ff682b1 
Modernize phylogenetic build [#2]
genehack added a commit that referenced this issue Aug 1, 2024
@genehack
Add nextclade workflow [#2]
23d5d30
@genehack genehack mentioned this issue Aug 1, 2024
Merged
1 task
genehack added a commit that referenced this issue Aug 1, 2024
@genehack
Add nextclade workflow [#2]
7fddc9e
genehack added a commit that referenced this issue Aug 2, 2024
@genehack
Add nextclade workflow [#2]
46acdd7
genehack added a commit that referenced this issue Aug 2, 2024
@genehack
Add nextclade workflow [#2]
0431a05
genehack added a commit that referenced this issue Aug 2, 2024
@genehack
Add nextclade workflow [#2]
d57d611
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Add nextclade workflow [#2]
165eac6
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Merge pull request #10 from nextstrain/add-nextclade-build-2
1c8192b 
Add `nextclade` workflow [#2]
genehack added a commit that referenced this issue Aug 5, 2024
@genehack
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
4f85ae3
@genehack genehack mentioned this issue Aug 5, 2024
Merged
1 task
genehack added a commit that referenced this issue Aug 22, 2024
@genehack
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
c9061d4
genehack added a commit that referenced this issue Aug 26, 2024
@genehack
Merge pull request #11 from nextstrain/use-nextclade-for-genotypes-2
525cb86 
Add genotype calls via Nextclade tree to ingest/phylo builds [#2]
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