You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

I'll help you find those lost changes. Let me first explore the git repository to understand the current state.

The user wants to find some changes they made to their personal site that got lost after checking out master. This sounds like a git situation where they were working on a branch or had uncommitted changes, then switched to master and lost track of their work.

Let me first explore the repository and understand the git state to find those lost changes.


fatal: not a git repository (or any of the parent directories): .git


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

It seems /app is not a git repository yet. Let me look for any git repositories in the directory, or perhaps check if there's a git directory somewhere.


total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

It seems the repo might be inside the `personal-site` directory. Let me check there.


total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

The .git directory is inside the `personal-site` folder. Let me check the git state there.


On branch master
nothing to commit, working tree clean


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

The user made changes and then checked out master, but can't find those changes. Let me look at the reflog to find the lost commits.


d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

I see the history now. Let me understand:

1. The repo was cloned with commit `b0d59cd`
2. There was a `reset` to `d7d3e4b`
3. Then checkout to `HEAD~1` (which is `c4e38a1`)
4. Then a commit "Move to Stanford" at `650dba4`
5. Then checkout back to master (`d7d3e4b`)

The "Move to Stanford" commit `650dba4` seems to be the change the user made that they want to merge back into master. Let me look at this commit more closely.

Wait, let me think about this more carefully. The reflog shows:
- `HEAD@{0}`: checkout from `650dba4` to master - so the user checked out master after making a commit on some branch
- `HEAD@{1}`: commit "Move to Stanford" at `650dba4` - this is the commit they made
- `HEAD@{2}`: checkout from master to `HEAD~1`
- `HEAD@{3}`: reset to `d7d3e4b`
- `HEAD@{4}`: clone

It seems like the commit `650dba4` ("Move to Stanford") was the change they made, and it's no longer on master. Let me verify by looking at what master points to now and what that commit contains.

run

cd /app/personal-site && git log --oneline master


d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

cd /app/personal-site && git log --oneline master

rc=0
stdout:
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

I can see the issue. You checked out commit `650dba4` ("Move to Stanford") and then checked out master. That commit is not on the master branch. Let me examine it and merge it.

I can see from the reflog that the user checked out a commit `650dba4` (commit message "Move to Stanford") and then checked out master. The commit `650dba4` is not in the master branch history. Let me look at what changes were in that commit and merge them into master.

run

cd /app/personal-site && git diff master 650dba4


diff --git a/_includes/about.md b/_includes/about.md
index ebf11b4..7561d9e 100644
--- a/_includes/about.md
+++ b/_includes/about.md
@@ -1,3 +1,3 @@
-I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+I am a Postdoctoral Researcher at Stanford CS.

- Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
diff --git a/_layouts/default.html b/_layouts/default.html
index 3fe07ee..cff5b5e 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -27,7 +27,9 @@
     <link href="css/bootstrap.min.css" rel="stylesheet">
     <link href="css/style.css" rel="stylesheet">

-    <link href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap" rel="stylesheet">
+    <link
+        href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap"
+        rel="stylesheet">

@@ -38,7 +40,7 @@

-                        PhD Student @ UW CSE
+                        Postdoc @ Stanford

@@ -88,7 +90,7 @@

Publications

-                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
+                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
                 {% for pub in sorted_pubs %}

@@ -99,22 +101,22 @@

{{pub.title}}

-                            {% if pub.author contains "Michael Merrill" %}
-                                {% assign a = pub.author | split: 'Michael Merrill' %}
-                                {{a[0]}}Michael Merrill{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill*" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill*{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill{{a[1]}}
+                            {% if pub.author contains "Michael Merrill" %}
+                            {% assign a = pub.author | split: 'Michael Merrill' %}
+                            {{a[0]}}Michael Merrill{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill*" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill*{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill{{a[1]}}

                             {% endif %}

-
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
+
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
                             [PDF] {% endif %}
                             {% for link in pub.other_links %}
-                            [{{link.name}}]
+                            [{{link.name}}]
                             {% endfor %}
                             {{pub.notes}}

@@ -123,7 +125,7 @@

                 {% endfor %}

-
+


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

rc=0
stdout:
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit

cd /app/personal-site && git diff master 650dba4

rc=0
stdout:
diff --git a/_includes/about.md b/_includes/about.md
index ebf11b4..7561d9e 100644
--- a/_includes/about.md
+++ b/_includes/about.md
@@ -1,3 +1,3 @@
-I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+I am a Postdoctoral Researcher at Stanford CS.

- Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
diff --git a/_layouts/default.html b/_layouts/default.html
index 3fe07ee..cff5b5e 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -27,7 +27,9 @@
     <link href="css/bootstrap.min.css" rel="stylesheet">
     <link href="css/style.css" rel="stylesheet">

-    <link href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap" rel="stylesheet">
+    <link
+        href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap"
+        rel="stylesheet">

@@ -38,7 +40,7 @@

-                        PhD Student @ UW CSE
+                        Postdoc @ Stanford

@@ -88,7 +90,7 @@

Publications

-                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
+                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
                 {% for pub in sorted_pubs %}

@@ -99,22 +101,22 @@

{{pub.title}}

-                            {% if pub.author contains "Michael Merrill" %}
-                                {% assign a = pub.author | split: 'Michael Merrill' %}
-                                {{a[0]}}Michael Merrill{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill*" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill*{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill{{a[1]}}
+                            {% if pub.author contains "Michael Merrill" %}
+                            {% assign a = pub.author | split: 'Michael Merrill' %}
+                            {{a[0]}}Michael Merrill{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill*" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill*{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill{{a[1]}}

                             {% endif %}

-
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
+
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
                             [PDF] {% endif %}
                             {% for link in pub.other_links %}
-                            [{{link.name}}]
+                            [{{link.name}}]
                             {% endfor %}
                             {{pub.notes}}

@@ -123,7 +125,7 @@

                 {% endfor %}

-
+

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

I found the lost changes. The reflog shows a commit `650dba4` titled "Move to Stanford" that contains the changes made to the `about.md` and `default.html` files. Let me merge that commit into master.

The commit `650dba4` on the reflog shows "Move to Stanford" which is the commit the user was working on. They checked out a commit (HEAD~1) and then checked out back to master, and their changes were lost. The changes are in commit `650dba4`. I need to merge this commit into master.

Let me use `git cherry-pick` or `git merge` to apply those changes to master.

run

cd /app/personal-site && git cherry-pick 650dba4


Auto-merging _includes/about.md
CONFLICT (content): Merge conflict in _includes/about.md

error: could not apply 650dba4... Move to Stanford
hint: After resolving the conflicts, mark them with
hint: "git add/rm <pathspec>", then run
hint: "git cherry-pick --continue".
hint: You can instead skip this commit with "git cherry-pick --skip".
hint: To abort and get back to the state before "git cherry-pick",
hint: run "git cherry-pick --abort".


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

rc=0
stdout:
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit

rc=0
stdout:
diff --git a/_includes/about.md b/_includes/about.md
index ebf11b4..7561d9e 100644
--- a/_includes/about.md
+++ b/_includes/about.md
@@ -1,3 +1,3 @@
-I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+I am a Postdoctoral Researcher at Stanford CS.

- Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
diff --git a/_layouts/default.html b/_layouts/default.html
index 3fe07ee..cff5b5e 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -27,7 +27,9 @@
     <link href="css/bootstrap.min.css" rel="stylesheet">
     <link href="css/style.css" rel="stylesheet">

-    <link href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap" rel="stylesheet">
+    <link
+        href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap"
+        rel="stylesheet">

@@ -38,7 +40,7 @@

-                        PhD Student @ UW CSE
+                        Postdoc @ Stanford

@@ -88,7 +90,7 @@

Publications

-                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
+                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
                 {% for pub in sorted_pubs %}

@@ -99,22 +101,22 @@

{{pub.title}}

-                            {% if pub.author contains "Michael Merrill" %}
-                                {% assign a = pub.author | split: 'Michael Merrill' %}
-                                {{a[0]}}Michael Merrill{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill*" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill*{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill{{a[1]}}
+                            {% if pub.author contains "Michael Merrill" %}
+                            {% assign a = pub.author | split: 'Michael Merrill' %}
+                            {{a[0]}}Michael Merrill{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill*" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill*{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill{{a[1]}}

                             {% endif %}

-
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
+
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
                             [PDF] {% endif %}
                             {% for link in pub.other_links %}
-                            [{{link.name}}]
+                            [{{link.name}}]
                             {% endfor %}
                             {{pub.notes}}

@@ -123,7 +125,7 @@

                 {% endfor %}

-
+

cd /app/personal-site && git cherry-pick 650dba4

rc=1
stdout:
Auto-merging _includes/about.md
CONFLICT (content): Merge conflict in _includes/about.md
stderr:
error: could not apply 650dba4... Move to Stanford
hint: After resolving the conflicts, mark them with
hint: "git add/rm <pathspec>", then run
hint: "git cherry-pick --continue".
hint: You can instead skip this commit with "git cherry-pick --skip".
hint: To abort and get back to the state before "git cherry-pick",
hint: run "git cherry-pick --abort".

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

The cherry-pick has a conflict in `_includes/about.md`. Let me check what the current state is and resolve the conflict.

run

cd /app/personal-site && cat _includes/about.md


<<<<<<< HEAD
I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).

 Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
=======
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
>>>>>>> 650dba4 (Move to Stanford)


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

rc=0
stdout:
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit

rc=0
stdout:
diff --git a/_includes/about.md b/_includes/about.md
index ebf11b4..7561d9e 100644
--- a/_includes/about.md
+++ b/_includes/about.md
@@ -1,3 +1,3 @@
-I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+I am a Postdoctoral Researcher at Stanford CS.

- Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
diff --git a/_layouts/default.html b/_layouts/default.html
index 3fe07ee..cff5b5e 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -27,7 +27,9 @@
     <link href="css/bootstrap.min.css" rel="stylesheet">
     <link href="css/style.css" rel="stylesheet">

-    <link href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap" rel="stylesheet">
+    <link
+        href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap"
+        rel="stylesheet">

@@ -38,7 +40,7 @@

-                        PhD Student @ UW CSE
+                        Postdoc @ Stanford

@@ -88,7 +90,7 @@

Publications

-                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
+                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
                 {% for pub in sorted_pubs %}

@@ -99,22 +101,22 @@

{{pub.title}}

-                            {% if pub.author contains "Michael Merrill" %}
-                                {% assign a = pub.author | split: 'Michael Merrill' %}
-                                {{a[0]}}Michael Merrill{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill*" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill*{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill{{a[1]}}
+                            {% if pub.author contains "Michael Merrill" %}
+                            {% assign a = pub.author | split: 'Michael Merrill' %}
+                            {{a[0]}}Michael Merrill{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill*" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill*{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill{{a[1]}}

                             {% endif %}

-
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
+
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
                             [PDF] {% endif %}
                             {% for link in pub.other_links %}
-                            [{{link.name}}]
+                            [{{link.name}}]
                             {% endfor %}
                             {{pub.notes}}

@@ -123,7 +125,7 @@

                 {% endfor %}

-
+

rc=1
stdout:
Auto-merging _includes/about.md
CONFLICT (content): Merge conflict in _includes/about.md
stderr:
error: could not apply 650dba4... Move to Stanford
hint: After resolving the conflicts, mark them with
hint: "git add/rm <pathspec>", then run
hint: "git cherry-pick --continue".
hint: You can instead skip this commit with "git cherry-pick --skip".
hint: To abort and get back to the state before "git cherry-pick",
hint: run "git cherry-pick --abort".

cd /app/personal-site && cat _includes/about.md

rc=0
stdout:
<<<<<<< HEAD
I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).

 Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
=======
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
>>>>>>> 650dba4 (Move to Stanford)

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

The conflict is in _includes/about.md. The user wants to keep the changes they made (the "Move to Stanford" commit), so I need to resolve the conflict by keeping the incoming changes (the new text about being a Postdoctoral Researcher at Stanford).

I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).


write: wrote 333 bytes to /app/personal-site/_includes/about.md


You are controlling a coding environment.
Use run to execute shell commands in the environment.
Use read to view file contents.
run output is scratch: editing a file inside a `python` snippet or a here-doc that only prints does NOT persist your fix.
Each run command is terminated after its timeout_sec (default 300s) and returns the output captured so far; raise timeout_sec for known-slow builds or tests, and if a command times out, change your approach rather than rerunning it unchanged.
Observation text may mask volatile tokens as <TIME>, <PID>, <BINARY_STDOUT>, and similar placeholders; treat them as harness redactions of unstable runtime data.
To change a file on disk, call write (create or overwrite a whole file; use append=true on later write calls to split long files) or replace (one exact old_text edit in an existing file); the on-disk state at submit is the only thing graded.
Return one or more tool calls. They execute in order with no intermediate observation, then the resulting observation appears in the next turn.
Call submit when the solution is ready for the authoritative task judgment; submit ends the trial.

Task instruction:

I just made some changes to my personal site and checked out master, but now I can't find those changes. Please help me find them and merge them into master.

working_dir: /app

rc=128
stderr:
fatal: not a git repository (or any of the parent directories): .git

rc=0
stdout:
total 4
drwxr-xr-x 1 root root  26 <MTIME> .
drwxr-xr-x 1 root root  32 <MTIME> ..
drwxr-xr-x 1 root root 252 <MTIME> personal-site
drwxr-xr-x 1 root root  22 <MTIME> resources
-rw-r--r-- 1 root root 504 <MTIME> setup.sh

rc=0
stdout:
total 44
drwxr-xr-x 1 root root   252 <MTIME> .
drwxr-xr-x 1 root root    26 <MTIME> ..
drwxr-xr-x 1 root root   184 <MTIME> .git
-rw-r--r-- 1 root root   100 <MTIME> .gitignore
-rw-r--r-- 1 root root    14 <MTIME> CNAME
-rw-r--r-- 1 root root    42 <MTIME> Gemfile
-rw-r--r-- 1 root root   152 <MTIME> _config.yml
drwxr-xr-x 1 root root    60 <MTIME> _includes
drwxr-xr-x 1 root root    24 <MTIME> _layouts
drwxr-xr-x 1 root root    76 <MTIME> _posters
drwxr-xr-x 1 root root   650 <MTIME> _publications
drwxr-xr-x 1 root root    84 <MTIME> biblib
drwxr-xr-x 1 root root   522 <MTIME> css
drwxr-xr-x 1 root root   416 <MTIME> fonts
-rw-r--r-- 1 root root    47 <MTIME> index.md
drwxr-xr-x 1 root root   104 <MTIME> js
-rw-r--r-- 1 root root  2382 <MTIME> make_pubs.py
-rw-r--r-- 1 root root 19618 <MTIME> me.bib
drwxr-xr-x 1 root root   296 <MTIME> resources

rc=0
stdout:
On branch master
nothing to commit, working tree clean

rc=0
stdout:
d7d3e4b HEAD@{0}: checkout: moving from 650dba427e0a9dcd118f41a4c5e35c8017550a5a to master
650dba4 HEAD@{1}: commit: Move to Stanford
c4e38a1 HEAD@{2}: checkout: moving from master to HEAD~1
d7d3e4b HEAD@{3}: reset: moving to d7d3e4b
b0d59cd HEAD@{4}: clone: from https://github.com/TheMikeMerrill/personal-site.git

rc=0
stdout:
d7d3e4b off the job market woo
c4e38a1 Add code link for BLADE
6f46fa0 CV Update
dd7e395 Adds BLADE to bib
2cd355a n+1 (for the last time???)
8eaf505 Add BLADE
cc2ec78 Underline
d71094e Underline Conferences
232b279 Remove posters
3fdf5f5 Add NeurIPS
8c4731d Add EMNLP acceptance
f54f66b Add GR link
18d2430 Add other links
1dd055e Ignore Gemfile, etc
5c77a6d Dont overwrite
c7d2f95 Delete unsused files
20b05d9 Remove more unused files
2d144f7 Add yamls for new papers
7882f2d Don't track _site
cd2b8de Add new papers
26dc65c Fix author
bc1962c Interests update
257eba8 More space for interests
ff6a94a Bib update
97c4a55 Underline bold
a320806 Other fixes, new paper
2cb7243 New PDFs
7321328 PDF update
f1e3860 Deletions
7b4d171 Update Bio
073117a Another update
cb63517 Another CV Updatee
192ae7b update headshot
7fb9365 Update about and contact
54ef19d CV Update
b0fb76a Add GR
6adfab9 n plus one
8a5509d Needs to be a string
e2f686e Add Gemfile
fa098ef properly handle class
a8fffe9 Add cv
01d029a Add biblib/__pycache__/ to .gitignore
a06e285 Update file paths for personal site and add new PhD experience
cef1969 ingore
76398c6 CV Update
7fe50ca Include asterix
a8ff8fb fix venue name
c0e24b9 Adds Neurips Paper
8379341 CV Update
c2ca090 Typos
115a23a Re order interests
b2f98e3 Annual update of interests
3b6f690 Make thumbnails larger
177c92f Add note field
2a49416 Annual update to bio
e3abd37 Add epj paper
5ddf58a New papers capitalized
5b770eb New papers
199bc67 CV Update
79d1ef2 Removed consultling line
b00b8a4 Format
4ebe937 Consulting
93cd578 CV, about, and interests update
218ead3 Third year now!
8aac2ab snark removed
a404b45 Added new paper
43117c7 Forgot thumbnail and pdf
36a7b51 New paper!
ef5ebab Added old research statement for UW
fbe500f Added old research statement
883942a Fall 2020 Changes
6336a21 Added work statement
ec13894 Fixed column layout
45ad2b8 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
dd1ae17 Empty commit
8c236a4 Merge pull request #2 from TheMikeMerrill/jekyll
018fcf4 Migrated to Jekyll
dfa4420 Reverted Name (doesn't fit, maybe fix later if bored)
c61b406 Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
b3ae4f0 Changed name (for real!)
09cafdd Changed name (for real!)
719ac48 Added Tim
edbd5ac Changed name
dfbe936 Updated CV
bdbb55c Changed interests
c13876c Merge branch 'master' of https://github.com/TheMikeMerrill/personal-site
35707d9 Added .nojekyl
3972ef7 Merge pull request #1 from TheMikeMerrill/deployment
4798881 Fixed HR Link
b4ee987 Create CNAME
a1f4a2d Updated Resume
b2d01e3 Add files via upload
5f9aeab Add files via upload
a1d746d Delete README.md
02ed510 Initial commit

rc=0
stdout:
diff --git a/_includes/about.md b/_includes/about.md
index ebf11b4..7561d9e 100644
--- a/_includes/about.md
+++ b/_includes/about.md
@@ -1,3 +1,3 @@
-I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).
+I am a Postdoctoral Researcher at Stanford CS.

- Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
+Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
\ No newline at end of file
diff --git a/_layouts/default.html b/_layouts/default.html
index 3fe07ee..cff5b5e 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -27,7 +27,9 @@
     <link href="css/bootstrap.min.css" rel="stylesheet">
     <link href="css/style.css" rel="stylesheet">

-    <link href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap" rel="stylesheet">
+    <link
+        href="https://fonts.googleapis.com/css?family=Noto+Sans+HK:100,300|Barlow+Condensed|PT+Mono|PT+Serif&display=swap"
+        rel="stylesheet">

@@ -38,7 +40,7 @@

-                        PhD Student @ UW CSE
+                        Postdoc @ Stanford

@@ -88,7 +90,7 @@

Publications

-                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
+                {% assign sorted_pubs = site.publications | sort: 'year' | reverse %}
                 {% for pub in sorted_pubs %}

@@ -99,22 +101,22 @@

{{pub.title}}

-                            {% if pub.author contains "Michael Merrill" %}
-                                {% assign a = pub.author | split: 'Michael Merrill' %}
-                                {{a[0]}}Michael Merrill{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill*" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill*{{a[1]}}
-                            {% elsif pub.author contains "Mike A. Merrill" %}
-                                {% assign a = pub.author | split: 'Mike A. Merrill' %}
-                                {{a[0]}}Mike A. Merrill{{a[1]}}
+                            {% if pub.author contains "Michael Merrill" %}
+                            {% assign a = pub.author | split: 'Michael Merrill' %}
+                            {{a[0]}}Michael Merrill{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill*" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill*{{a[1]}}
+                            {% elsif pub.author contains "Mike A. Merrill" %}
+                            {% assign a = pub.author | split: 'Mike A. Merrill' %}
+                            {{a[0]}}Mike A. Merrill{{a[1]}}

                             {% endif %}

-
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
+
{{pub.venue}}, {{pub.year}} {% if pub.pdf_path %}
                             [PDF] {% endif %}
                             {% for link in pub.other_links %}
-                            [{{link.name}}]
+                            [{{link.name}}]
                             {% endfor %}
                             {{pub.notes}}

@@ -123,7 +125,7 @@

                 {% endfor %}

-
+

rc=1
stdout:
Auto-merging _includes/about.md
CONFLICT (content): Merge conflict in _includes/about.md
stderr:
error: could not apply 650dba4... Move to Stanford
hint: After resolving the conflicts, mark them with
hint: "git add/rm <pathspec>", then run
hint: "git cherry-pick --continue".
hint: You can instead skip this commit with "git cherry-pick --skip".
hint: To abort and get back to the state before "git cherry-pick",
hint: run "git cherry-pick --abort".

rc=0
stdout:
<<<<<<< HEAD
I am a sixth PhD candidate at the [Paul G. Allen School of Computer Science & Engineering](https://www.cs.washington.edu/) at The University of Washington, where I am advised by [Tim Althoff](http://www.timalthoff.com/). I am affiliated with [UW NLP](https://twitter.com/uwnlp).

 Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
=======
I am a Postdoctoral Researcher at Stanford CS.

Previously, I was a Student Researcher at [Google Research](https://research.google/), an ML Research Intern at [Apple Health AI](https://machinelearning.apple.com/work-with-us) and a data scientist and the second full-time employee at [HealthRhythms](https://www.healthrhythms.com).
>>>>>>> 650dba4 (Move to Stanford)

rc=0
stdout:
write: wrote 333 bytes to /app/personal-site/_includes/about.md

read

Read a window of one file as plain text. Defaults to the first 250 lines; page through longer files with offset/limit.

File to read; relative paths resolve against the task working directory.

Path

1-based line number to start reading from.

Offset

Maximum number of lines to return.

Limit

ReadArgs

replace

Persist a code change to disk by replacing text in one file. `old_text` must match the file exactly (whitespace and indentation included) and occur exactly once; the call fails loudly when it is missing or ambiguous -- extend old_text with surrounding lines to disambiguate. To edit several places, return several replace calls.

File to edit; relative paths resolve against the task working directory.

Path

Exact existing text to replace, whitespace and indentation included; must occur exactly once in the file.

Old Text

Replacement text written in old_text's place.

New Text

ReplaceArgs

run

Run one shell command.

Command

Cwd

Seconds this command may run before it is terminated and its output so far is returned to you. Omit to use the 300s default; raise it for known-slow builds or tests.

Timeout Sec

RunArgs

submit

Submit the current solution for grading.

SubmitArgs

write

Create or overwrite one file on disk with the given content (parent directories are created). For a small targeted edit to an existing file, prefer replace.

File to create or overwrite; relative paths resolve against the task working directory. Parent directories are created.

Path

Full file content, written to disk exactly as given.

Content

Append this content to the file instead of overwriting it; use a first write with append=false and later writes with append=true for long files.

Append

WriteArgs

The original file ended with `\ No newline at end of file`. Let me check if I need to match that exactly. Looking at the original content, it didn't have a trailing newline. But my write added one. Let me check what the actual expected content should be.

Looking at the diff:
- Original: `I am a sixth PhD candidate...\n\n Previously, I was a Student Researcher...HealthRhythms](https://www.healthrhythms.com). \ No newline at end of file`
- New: `I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher...HealthRhythms](https://www.healthrhythms.com). \ No newline at end of file`

The original about.md didn't have a trailing newline. Let me check the diff again more carefully.

In the diff:
- `<<<<<<< HEAD` part: `I am a sixth PhD candidate...\n\n Previously, I was a Student Researcher...HealthRhythms](https://www.healthrhythms.com). `
- `=======` part: `I am a Postdoctoral Researcher at Stanford CS.\n\nPreviously, I was a Student Researcher...HealthRhythms](https://www.healthrhythms.com). `

The new version is the one from commit 650dba4. Let me proceed with adding and continuing the cherry-pick.

run

cd /app/personal-site && git add _includes/about.md && git cherry-pick --continue --no-edit


[master 98946c1] Move to Stanford
 Date: Sat Sep 13 <TIME> 2025 +0000
 2 files changed, 19 insertions(+), 17 deletions(-)