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joverlee521/git-subrepo-pull-conflicts.md

Created September 20, 2023 20:48
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git subrepo pull conflicts in monkeypox
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git-subrepo-pull-conflicts.md

In walking through git subrepo pull with @j23414 for nextstrain/mpox#182, we ran into unexpected merge conflicts.

$ git subrepo pull ingest/vendored -dv
>>> git rev-parse --verify HEAD
* Assert that working copy is clean: /Users/jlee2346/Repos/nextstrain/monkeypox
* Check for worktree with branch subrepo/ingest/vendored
  * Fetch the upstream: https://github.com/nextstrain/ingest (main).
>>> git fetch --no-tags --quiet https://github.com/nextstrain/ingest main
  * Get the upstream subrepo HEAD commit.
>>> git rev-parse FETCH_HEAD^0
  * Create ref 'refs/subrepo/ingest/vendored/fetch'.
>>> git update-ref refs/subrepo/ingest/vendored/fetch c02fa8120edc3a831d5c9ab16a119f1866c300e3
* Deleting old 'subrepo/ingest/vendored' branch.
* Remove worktree: 
>>> git branch -D subrepo/ingest/vendored
* Create subrepo branch 'subrepo/ingest/vendored'.
  * Check if the 'subrepo/ingest/vendored' branch already exists.
  * Subrepo parent: fb8175010a16294954d4d4a499edc137bede8265
  * Create new commits with parents into the subrepo fetch
>>> git rev-list --reverse --ancestry-path --topo-order fb8175010a16294954d4d4a499edc137bede8265..HEAD
  * Working on 00f324e078a1e343ca9e537200808ae40f4c4a1b
>>> git config --blob 00f324e078a1e343ca9e537200808ae40f4c4a1b:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: 1eb8b30428d5f66adac201f0a246a7ab4bdc9792
  * Check for rebase
  * Find parents
  * Create a new commit  -p 1eb8b30428d5f66adac201f0a246a7ab4bdc9792
>>> git cat-file -e 00f324e078a1e343ca9e537200808ae40f4c4a1b:ingest/vendored
  * Create with content
  * Working on f96fa0665ae7712bbd5298a3b80e4bbab1904f1c
>>> git config --blob f96fa0665ae7712bbd5298a3b80e4bbab1904f1c:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: 1eb8b30428d5f66adac201f0a246a7ab4bdc9792
  * is child: fb8175010a16294954d4d4a499edc137bede8265 00f324e078a1e343ca9e537200808ae40f4c4a1b
  * Check for rebase
  * Find parents
  * Create a new commit -p a30c924e1349608457d7fa95196d260d2546f49c 
>>> git cat-file -e f96fa0665ae7712bbd5298a3b80e4bbab1904f1c:ingest/vendored
  * Create with content
  * Working on afeec9cb2887a66c3538f393b13a561e0b6177fb
>>> git config --blob afeec9cb2887a66c3538f393b13a561e0b6177fb:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 
  * Ignore afeec9cb2887a66c3538f393b13a561e0b6177fb, it's not in the selected path
  * Working on 871817bc5fc60f021549cee96792ff7c52a71c31
>>> git config --blob 871817bc5fc60f021549cee96792ff7c52a71c31:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 
  * Ignore 871817bc5fc60f021549cee96792ff7c52a71c31, it's not in the selected path
  * Working on b7664989c511a82f7c5f3143421f40472a69a939
>>> git config --blob b7664989c511a82f7c5f3143421f40472a69a939:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: f96fa0665ae7712bbd5298a3b80e4bbab1904f1c 871817bc5fc60f021549cee96792ff7c52a71c31
  * Check for rebase
  * Find parents
  * Create a new commit -p 2294575bdb3fb2a9fa3732dedd53992a7bd040d0 -p c97df238518171c2b1574bec0349a55855d1e7a7
>>> git cat-file -e b7664989c511a82f7c5f3143421f40472a69a939:ingest/vendored
  * Create with content
  * Working on 82ace30abd07bec140c7e14aee29a46c7bfb28a8
>>> git config --blob 82ace30abd07bec140c7e14aee29a46c7bfb28a8:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: b7664989c511a82f7c5f3143421f40472a69a939
  * Check for rebase
  * Find parents
  * Create a new commit -p 3252511d8c1975263639d2eefeb2a83f5e5b3302 
>>> git cat-file -e 82ace30abd07bec140c7e14aee29a46c7bfb28a8:ingest/vendored
  * Create with content
  * Working on 32eab02293ecb438307e1afcf688d6dc5f83be79
>>> git config --blob 32eab02293ecb438307e1afcf688d6dc5f83be79:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 82ace30abd07bec140c7e14aee29a46c7bfb28a8
  * Check for rebase
  * Find parents
  * Create a new commit -p 7c5a6cf49819fb9ae1f8080b5b1311b73cebb54d 
>>> git cat-file -e 32eab02293ecb438307e1afcf688d6dc5f83be79:ingest/vendored
  * Create with content
  * Working on fb0d318c2a2cd42ebcd79a6ce8954197d5cf27c2
>>> git config --blob fb0d318c2a2cd42ebcd79a6ce8954197d5cf27c2:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: b7664989c511a82f7c5f3143421f40472a69a939 32eab02293ecb438307e1afcf688d6dc5f83be79
  * Check for rebase
  * Find parents
  * Create a new commit -p 39e8ab7ae4be44d3c3a17ed880bf6104303ea56b 
>>> git cat-file -e fb0d318c2a2cd42ebcd79a6ce8954197d5cf27c2:ingest/vendored
  * Create with content
  * Working on 5969604dfe426745b789746427b580c69d484790
>>> git config --blob 5969604dfe426745b789746427b580c69d484790:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: fb0d318c2a2cd42ebcd79a6ce8954197d5cf27c2
  * Check for rebase
  * Find parents
  * Create a new commit -p c7bb426483b59be76481e9fdf3d00f07b857d7ea 
>>> git cat-file -e 5969604dfe426745b789746427b580c69d484790:ingest/vendored
  * Create with content
  * Working on 68190a02294fc7e880453f345034d5937576e9b3
>>> git config --blob 68190a02294fc7e880453f345034d5937576e9b3:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 5969604dfe426745b789746427b580c69d484790
  * Check for rebase
  * Find parents
  * Create a new commit -p ebe684d18b307c8ef2004ba942d75c182f47bee6 
>>> git cat-file -e 68190a02294fc7e880453f345034d5937576e9b3:ingest/vendored
  * Create with content
  * Working on 942c1d00dd163ed837062828ad2869be2822a9ac
>>> git config --blob 942c1d00dd163ed837062828ad2869be2822a9ac:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 5969604dfe426745b789746427b580c69d484790 68190a02294fc7e880453f345034d5937576e9b3
  * Check for rebase
  * Find parents
  * Create a new commit -p e5b6b8028521ff49421ffcd329bee78c268ec1b6 
>>> git cat-file -e 942c1d00dd163ed837062828ad2869be2822a9ac:ingest/vendored
  * Create with content
  * Working on bd3bd3d87b0e6f5fcfc69754cda091e33929f6e1
>>> git config --blob bd3bd3d87b0e6f5fcfc69754cda091e33929f6e1:ingest/vendored/.gitrepo subrepo.commit
  * .gitrepo reference commit: c97df238518171c2b1574bec0349a55855d1e7a7
  * is child: 942c1d00dd163ed837062828ad2869be2822a9ac
  * Check for rebase
  * Find parents
  * Create a new commit -p 9a378a53ea67dffb4001e6d4fdf8b3340ca8aab1 
>>> git cat-file -e bd3bd3d87b0e6f5fcfc69754cda091e33929f6e1:ingest/vendored
  * Create with content
  * Create branch 'subrepo/ingest/vendored' for this new commit set 2a77b3b60ca0e49484a0e4fdc3ce0b23f1e11de5.
>>> git branch subrepo/ingest/vendored 2a77b3b60ca0e49484a0e4fdc3ce0b23f1e11de5
  * Remove the .gitrepo file from 1eb8b30428d5f66adac201f0a246a7ab4bdc9792..subrepo/ingest/vendored
>>> git filter-branch -f --prune-empty --tree-filter rm -f .gitrepo 1eb8b30428d5f66adac201f0a246a7ab4bdc9792..subrepo/ingest/vendored
>>> git worktree add .git/tmp/subrepo/ingest/vendored subrepo/ingest/vendored
  * Create ref 'refs/subrepo/ingest/vendored/branch'.
>>> git update-ref refs/subrepo/ingest/vendored/branch 26507ae0847d8951603f488597491b3dcfe59132
* Merge in changes from refs/subrepo/ingest/vendored/fetch
>>> git merge refs/subrepo/ingest/vendored/fetch
The "git merge" command failed:

  Auto-merging .github/workflows/ci.yaml
  CONFLICT (content): Merge conflict in .github/workflows/ci.yaml
  Auto-merging README.md
  CONFLICT (content): Merge conflict in README.md
  Automatic merge failed; fix conflicts and then commit the result.

You will need to finish the pull by hand. A new working tree has been
created at .git/tmp/subrepo/ingest/vendored so that you can resolve the conflicts
shown in the output above.

This is the common conflict resolution workflow:

  1. cd .git/tmp/subrepo/ingest/vendored
  2. Resolve the conflicts (see "git status").
  3. "git add" the resolved files.
  4. git commit
  5. If there are more conflicts, restart at step 2.
  6. cd /Users/jlee2346/Repos/nextstrain/monkeypox
  7. git subrepo commit ingest/vendored
See "git help merge" for details.

Alternatively, you can abort the pull and reset back to where you started:

  1. git subrepo clean ingest/vendored

See "git help subrepo" for more help.

$ cd .git/tmp/subrepo/ingest/vendored/
$ git diff
diff --cc .github/workflows/ci.yaml
index bbf40f7,c6a218a..0000000
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@@ -18,4 -20,4 +20,8 @@@ jobs
        - uses: actions/checkout@v3
        - uses: actions/setup-python@v4
        - run: pip install cram
 -      - run: cram tests/
++<<<<<<< HEAD
 +      - run: cram tests/
++=======
++      - run: cram tests/
++>>>>>>> refs/subrepo/ingest/vendored/fetch
diff --cc README.md
index 533b39a,008ec43..0000000
--- a/README.md
+++ b/README.md
@@@ -72,10 -90,9 +90,16 @@@ Scripts for supporting ingest workflow 
  NCBI interaction scripts that are useful for fetching public metadata and sequences.
  
  - [fetch-from-ncbi-entrez](fetch-from-ncbi-entrez) - Fetch metadata and nucleotide sequences from [NCBI Entrez](https://www.ncbi.nlm.nih.gov/books/NBK25501/) and output to a GenBank file.
++<<<<<<< HEAD
 +  Useful for pathogens with metadata and annotations in custom fields that are not part of the standard [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/) or [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) outputs.
 +- [fetch-from-ncbi-virus](fetch-from-ncbi-virus) - Fetch metadata and nucleotide sequences from [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/) and output NDJSON records to stdout.
 +- [ncbi-virus-url](ncbi-virus-url) - Generates the URL to download metadata and sequences from NCBI Virus as a single CSV file.
 +- [csv-to-ndjson](csv-to-ndjson) - Converts CSV file to NDJSON file with a hard-coded 200MiB field size limit to accommodate sequences in the NCBI Virus download.
++=======
+   Useful for pathogens with metadata and annotations in custom fields that are not part of the standard [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) outputs.
+ 
+ Historically, some pathogen repos used the undocumented NCBI Virus API through [fetch-from-ncbi-virus](https://github.com/nextstrain/ingest/blob/c97df238518171c2b1574bec0349a55855d1e7a7/fetch-from-ncbi-virus) to fetch data. However we've opted to drop the NCBI Virus scr
++>>>>>>> refs/subrepo/ingest/vendored/fetch
  
  Potential Nextstrain CLI scripts
  
@@@ -97,6 -114,7 +121,10 @@@ Potential augur curate script
  - [transform-authors](transform-authors) - Abbreviates full author lists to '<first author> et al.'
  - [transform-field-names](transform-field-names) - Rename fields of NDJSON records
  - [transform-genbank-location](transform-genbank-location) - Parses `location` field with the expected pattern `"<country_value>[:<region>][, <locality>]"` based on [GenBank's country field](https://www.ncbi.nlm.nih.gov/genbank/collab/country/)
++<<<<<<< HEAD
++=======
+ - [transform-strain-names](transform-strain-names) - Ordered search for strain names across several fields.
++>>>>>>> refs/subrepo/ingest/vendored/fetch
  
  ## Software requirements
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