Incompatible with docker-desktop

[twiecki]

Installed (on arm64) successfully, then running:

>>python run.py --model_name gpt4   --data_path https://github.com/pymc-devs/pymc/issues/7223 --config_file config/default_from_url.yaml
Parsing command file: config/commands/defaults.sh
Parsing command file: config/commands/search.sh
Parsing command file: config/commands/edit_linting.sh
Parsing command file: config/commands/_split_string.py
Parsing command file: config/commands/defaults.sh
Parsing command file: config/commands/search.sh
Parsing command file: config/commands/edit_linting.sh
Parsing command file: config/commands/_split_string.py
INFO     📙 Arguments: agent:
           config:
             _commands:
             - arguments:
                 line_number:
                   description: the line number to move the window to (if not provided, the
                     window will start at the top of the file)
                   required: false
                   type: integer
                 path:
                   description: the path to the file to open
                   required: true
                   type: string
               code: 'open() {    if [ -z "$1" ]    then        echo "Usage: open <file>"        return    fi    #
                 Check if the second argument is provided    if [ -n "$2" ]; then        #
                 Check if the provided argument is a valid number        if ! [[ $2 =~ ^[0-9]+$
                 ]]; then            echo "Usage: open <file> [<line_number>]"            echo
                 "Error: <line_number> must be a number"            return  # Exit if the line
                 number is not valid        fi        local max_line=$(awk ''END {print NR}''
                 $1)        if [ $2 -gt $max_line ]; then            echo "Warning: <line_number>
                 ($2) is greater than the number of lines in the file ($max_line)"            echo
                 "Warning: Setting <line_number> to $max_line"            local line_number=$(jq
                 -n "$max_line")  # Set line number to max if greater than max        elif
                 [ $2 -lt 1 ]; then            echo "Warning: <line_number> ($2) is less than
                 1"            echo "Warning: Setting <line_number> to 1"            local
                 line_number=$(jq -n "1")  # Set line number to 1 if less than 1        else            local
                 OFFSET=$(jq -n "$WINDOW/6" | jq ''floor'')            local line_number=$(jq
                 -n "[$2 + $WINDOW/2 - $OFFSET, 1] | max | floor")        fi    else        local
                 line_number=$(jq -n "$WINDOW/2")  # Set default line number if not provided    fi    if
                 [ -f "$1" ]; then        export CURRENT_FILE=$(realpath $1)        export
                 CURRENT_LINE=$line_number        _constrain_line        _print    elif [ -d
                 "$1" ]; then        echo "Error: $1 is a directory. You can only open files.
                 Use cd or ls to navigate directories."    else        echo "File $1 not found"    fi}'
               docstring: opens the file at the given path in the editor. If line_number is
                 provided, the window will be move to include that line
               end_name: null
               name: open
               signature: open <path> [<line_number>]
             - arguments:
                 line_number:
                   description: the line number to move the window to
                   required: true
                   type: integer
               code: 'goto() {    if [ $# -gt 1 ]; then        echo "goto allows only one line
                 number at a time."        return    fi    if [ -z "$CURRENT_FILE" ]    then        echo
                 "No file open. Use the open command first."        return    fi    if [ -z
                 "$1" ]    then        echo "Usage: goto <line>"        return    fi    if
                 ! [[ $1 =~ ^[0-9]+$ ]]    then        echo "Usage: goto <line>"        echo
                 "Error: <line> must be a number"        return    fi    local max_line=$(awk
                 ''END {print NR}'' $CURRENT_FILE)    if [ $1 -gt $max_line ]    then        echo
                 "Error: <line> must be less than or equal to $max_line"        return    fi    local
                 OFFSET=$(jq -n "$WINDOW/6" | jq ''floor'')    export CURRENT_LINE=$(jq -n
                 "[$1 + $WINDOW/2 - $OFFSET, 1] | max | floor")    _constrain_line    _print}'
               docstring: moves the window to show <line_number>
               end_name: null
               name: goto
               signature: goto <line_number>
             - arguments: null
               code: scroll_down() {    if [ -z "$CURRENT_FILE" ]    then        echo "No file
                 open. Use the open command first."        return    fi    export CURRENT_LINE=$(jq
                 -n "$CURRENT_LINE + $WINDOW - $OVERLAP")    _constrain_line    _print}
               docstring: moves the window down {WINDOW} lines
               end_name: null
               name: scroll_down
               signature: scroll_down
             - arguments: null
               code: scroll_up() {    if [ -z "$CURRENT_FILE" ]    then        echo "No file
                 open. Use the open command first."        return    fi    export CURRENT_LINE=$(jq
                 -n "$CURRENT_LINE - $WINDOW + $OVERLAP")    _constrain_line    _print}
               docstring: moves the window down {WINDOW} lines
               end_name: null
               name: scroll_up
               signature: scroll_down
             - arguments:
                 filename:
                   description: the name of the file to create
                   required: true
                   type: string
               code: "create() {    if [ -z \"$1\" ]; then        echo \"Usage: create <filename>\"\
                 \        return    fi    # Check if the file already exists    if [ -e \"\
                 $1\" ]; then        echo \"Error: File '$1' already exists.\"\t\topen \"$1\"\
                 \        return    fi    # Create the file an empty new line    printf \"\\\
                 n\" > \"$1\"    # Use the existing open command to open the created file \
                 \   open \"$1\"}"
               docstring: creates and opens a new file with the given name
               end_name: null
               name: create
               signature: create <filename>
             - arguments: null
               code: 'submit() {    cd $ROOT    # Check if the patch file exists and is non-empty    if
                 [ -s "/root/test.patch" ]; then        # Apply the patch in reverse        git
                 apply -R < "/root/test.patch"    fi    git add -A    git diff --cached > model.patch    echo
                 "<<SUBMISSION||"    cat model.patch    echo "||SUBMISSION>>"}'
               docstring: submits your current code and terminates the session
               end_name: null
               name: submit
               signature: submit
             - arguments:
                 dir:
                   description: the directory to search in (if not provided, searches in the
                     current directory)
                   required: false
                   type: string
                 search_term:
                   description: the term to search for
                   required: true
                   type: string
               code: 'search_dir() {    if [ $# -eq 1 ]; then        local search_term="$1"        local
                 dir="./"    elif [ $# -eq 2 ]; then        local search_term="$1"        if
                 [ -d "$2" ]; then            local dir="$2"        else            echo "Directory
                 $2 not found"            return        fi    else        echo "Usage: search_dir
                 <search_term> [<dir>]"        return    fi    dir=$(realpath "$dir")    local
                 matches=$(find "$dir" -type f ! -path ''*/.*'' -exec grep -nIH "$search_term"
                 {} + | cut -d: -f1 | sort | uniq -c)    # if no matches, return    if [ -z
                 "$matches" ]; then        echo "No matches found for \"$search_term\" in $dir"        return    fi    #
                 Calculate total number of matches    local num_matches=$(echo "$matches" |
                 awk ''{sum+=$1} END {print sum}'')    # calculate total number of files matched    local
                 num_files=$(echo "$matches" | wc -l | awk ''{$1=$1; print $0}'')    # if num_files
                 is > 100, print an error    if [ $num_files -gt 100 ]; then        echo "More
                 than $num_files files matched for \"$search_term\" in $dir. Please narrow
                 your search."        return    fi        echo "Found $num_matches matches
                 for \"$search_term\" in $dir:"    echo "$matches" | awk ''{$2=$2; gsub(/^\.+\/+/,
                 "./", $2); print $2 " ("$1" matches)"}''    echo "End of matches for \"$search_term\"
                 in $dir"}'
               docstring: searches for search_term in all files in dir. If dir is not provided,
                 searches in the current directory
               end_name: null
               name: search_dir
               signature: search_dir <search_term> [<dir>]
             - arguments:
                 file:
                   description: the file to search in (if not provided, searches in the current
                     open file)
                   required: false
                   type: string
                 search_term:
                   description: the term to search for
                   required: true
                   type: string
               code: 'search_file() {    # Check if the first argument is provided    if [
                 -z "$1" ]; then        echo "Usage: search_file <search_term> [<file>]"        return    fi    #
                 Check if the second argument is provided    if [ -n "$2" ]; then        #
                 Check if the provided argument is a valid file        if [ -f "$2" ]; then            local
                 file="$2"  # Set file if valid        else            echo "Usage: search_file
                 <search_term> [<file>]"            echo "Error: File name $2 not found. Please
                 provide a valid file name."            return  # Exit if the file is not valid        fi    else        #
                 Check if a file is open        if [ -z "$CURRENT_FILE" ]; then            echo
                 "No file open. Use the open command first."            return  # Exit if no
                 file is open        fi        local file="$CURRENT_FILE"  # Set file to the
                 current open file    fi    local search_term="$1"    file=$(realpath "$file")    #
                 Use grep to directly get the desired formatted output    local matches=$(grep
                 -nH "$search_term" "$file")    # Check if no matches were found    if [ -z
                 "$matches" ]; then        echo "No matches found for \"$search_term\" in $file"        return    fi    #
                 Calculate total number of matches    local num_matches=$(echo "$matches" |
                 wc -l | awk ''{$1=$1; print $0}'')        # calculate total number of lines
                 matched    local num_lines=$(echo "$matches" | cut -d: -f1 | sort | uniq |
                 wc -l | awk ''{$1=$1; print $0}'')    # if num_lines is > 100, print an error    if
                 [ $num_lines -gt 100 ]; then        echo "More than $num_lines lines matched
                 for \"$search_term\" in $file. Please narrow your search."        return    fi    #
                 Print the total number of matches and the matches themselves    echo "Found
                 $num_matches matches for \"$search_term\" in $file:"    echo "$matches" |
                 cut -d: -f1-2 | sort -u -t: -k2,2n | while IFS=: read -r filename line_number;
                 do        echo "Line $line_number:$(sed -n "${line_number}p" "$file")"    done    echo
                 "End of matches for \"$search_term\" in $file"}'
               docstring: searches for search_term in file. If file is not provided, searches
                 in the current open file
               end_name: null
               name: search_file
               signature: search_file <search_term> [<file>]
             - arguments:
                 dir:
                   description: the directory to search in (if not provided, searches in the
                     current directory)
                   required: false
                   type: string
                 file_name:
                   description: the name of the file to search for
                   required: true
                   type: string
               code: 'find_file() {    if [ $# -eq 1 ]; then        local file_name="$1"        local
                 dir="./"    elif [ $# -eq 2 ]; then        local file_name="$1"        if
                 [ -d "$2" ]; then            local dir="$2"        else            echo "Directory
                 $2 not found"            return        fi    else        echo "Usage: find_file
                 <file_name> [<dir>]"        return    fi    dir=$(realpath "$dir")    local
                 matches=$(find "$dir" -type f -name "$file_name")    # if no matches, return    if
                 [ -z "$matches" ]; then        echo "No matches found for \"$file_name\" in
                 $dir"        return    fi    # Calculate total number of matches    local
                 num_matches=$(echo "$matches" | wc -l | awk ''{$1=$1; print $0}'')    echo
                 "Found $num_matches matches for \"$file_name\" in $dir:"    echo "$matches"
                 | awk ''{print $0}''}'
               docstring: finds all files with the given name in dir. If dir is not provided,
                 searches in the current directory
               end_name: null
               name: find_file
               signature: find_file <file_name> [<dir>]
             - arguments:
                 end_line:
                   description: the line number to end the edit at (inclusive)
                   required: true
                   type: integer
                 replacement_text:
                   description: the text to replace the current selection with
                   required: true
                   type: string
                 start_line:
                   description: the line number to start the edit at
                   required: true
                   type: integer
               code: 'edit() {    if [ -z "$CURRENT_FILE" ]    then        echo ''No file open.
                 Use the `open` command first.''        return    fi    local start_line="$(echo
                 $1: | cut -d: -f1)"    local end_line="$(echo $1: | cut -d: -f2)"    if [
                 -z "$start_line" ] || [ -z "$end_line" ]    then        echo "Usage: edit
                 <start_line>:<end_line>"        return    fi    local re=''^[0-9]+$''    if
                 ! [[ $start_line =~ $re ]]; then        echo "Usage: edit <start_line>:<end_line>"        echo
                 "Error: start_line must be a number"        return    fi    if ! [[ $end_line
                 =~ $re ]]; then        echo "Usage: edit <start_line>:<end_line>"        echo
                 "Error: end_line must be a number"        return    fi    # Bash array starts
                 at 0, so let''s adjust    local start_line=$((start_line - 1))    local end_line=$((end_line))    local
                 line_count=0    local replacement=()    while IFS= read -r line    do        replacement+=("$line")        ((line_count++))    done    #
                 Create a backup of the current file    cp "$CURRENT_FILE" "/root/$(basename
                 "$CURRENT_FILE")_backup"    # Read the file line by line into an array    mapfile
                 -t lines < "$CURRENT_FILE"    local new_lines=("${lines[@]:0:$start_line}"
                 "${replacement[@]}" "${lines[@]:$((end_line))}")    # Write the new stuff
                 directly back into the original file    printf "%s\n" "${new_lines[@]}" >|
                 "$CURRENT_FILE"        # Run linter    if [[ $CURRENT_FILE == *.py ]]; then        lint_output=$(flake8
                 --select=F821,F822,F831,E111,E112,E113,E999,E902 "$CURRENT_FILE" 2>&1)    else        #
                 do nothing        lint_output=""    fi    # if there is no output, then the
                 file is good    if [ -z "$lint_output" ]; then        export CURRENT_LINE=$start_line        _constrain_line        _print        echo
                 "File updated. Please review the changes and make sure they are correct (correct
                 indentation, no duplicate lines, etc). Edit the file again if necessary."    else        echo
                 "Your proposed edit has introduced new syntax error(s). Please understand
                 the fixes and retry your edit commmand."        echo ""        echo "ERRORS:"        _split_string
                 "$lint_output"        echo ""        # Save original values        original_current_line=$CURRENT_LINE        original_window=$WINDOW        #
                 Update values        export CURRENT_LINE=$(( (line_count / 2) + start_line
                 )) # Set to "center" of edit        export WINDOW=$((line_count + 10)) # Show
                 +/- 5 lines around edit        echo "This is how your edit would have looked
                 if applied"        echo "-------------------------------------------------"        _constrain_line        _print        echo
                 "-------------------------------------------------"        echo ""        #
                 Restoring CURRENT_FILE to original contents.        cp "/root/$(basename "$CURRENT_FILE")_backup"
                 "$CURRENT_FILE"        export CURRENT_LINE=$(( ((end_line - start_line + 1)
                 / 2) + start_line ))        export WINDOW=$((end_line - start_line + 10))        echo
                 "This is the original code before your edit"        echo "-------------------------------------------------"        _constrain_line        _print        echo
                 "-------------------------------------------------"        # Restore original
                 values        export CURRENT_LINE=$original_current_line        export WINDOW=$original_window        echo
                 "Your changes have NOT been applied. Please fix your edit command and try
                 again."        echo "You either need to 1) Specify the correct start/end line
                 arguments or 2) Correct your edit code."        echo "DO NOT re-run the same
                 failed edit command. Running it again will lead to the same error."    fi    #
                 Remove backup file    rm -f "/root/$(basename "$CURRENT_FILE")_backup"}'
               docstring: replaces lines <start_line> through <end_line> (inclusive) with the
                 given text in the open file. The replacement text is terminated by a line
                 with only end_of_edit on it. All of the <replacement text> will be entered,
                 so make sure your indentation is formatted properly. Python files will be
                 checked for syntax errors after the edit. If the system detects a syntax error,
                 the edit will not be executed. Simply try to edit the file again, but make
                 sure to read the error message and modify the edit command you issue accordingly.
                 Issuing the same command a second time will just lead to the same error message
                 again.
               end_name: end_of_edit
               name: edit
               signature: |-
                 edit <start_line>:<end_line>
                 <replacement_text>
                 end_of_edit
             _subroutines: {}
             blocklist:
             - vim
             - vi
             - emacs
             - nano
             - nohup
             - git
             blocklist_error_template: Interactive operation '{name}' is not supported by this
               environment
             blocklist_standalone:
             - python
             - python3
             - ipython
             - bash
             - sh
             - exit
             - /bin/bash
             - /bin/sh
             - nohup
             - vi
             - vim
             - emacs
             - nano
             command_docs: |+
               open:
                 docstring: opens the file at the given path in the editor. If line_number is provided, the window will be move to include that line
                 signature: open <path> [<line_number>]
                 arguments:
                   - path (string) [required]: the path to the file to open
                   - line_number (integer) [optional]: the line number to move the window to (if not provided, the window will start at the top of the file)

               goto:
                 docstring: moves the window to show <line_number>
                 signature: goto <line_number>
                 arguments:
                   - line_number (integer) [required]: the line number to move the window to

               scroll_down:
                 docstring: moves the window down {WINDOW} lines
                 signature: scroll_down

               scroll_up:
                 docstring: moves the window down {WINDOW} lines
                 signature: scroll_down

               create:
                 docstring: creates and opens a new file with the given name
                 signature: create <filename>
                 arguments:
                   - filename (string) [required]: the name of the file to create

               submit:
                 docstring: submits your current code and terminates the session
                 signature: submit

               search_dir:
                 docstring: searches for search_term in all files in dir. If dir is not provided, searches in the current directory
                 signature: search_dir <search_term> [<dir>]
                 arguments:
                   - search_term (string) [required]: the term to search for
                   - dir (string) [optional]: the directory to search in (if not provided, searches in the current directory)

               search_file:
                 docstring: searches for search_term in file. If file is not provided, searches in the current open file
                 signature: search_file <search_term> [<file>]
                 arguments:
                   - search_term (string) [required]: the term to search for
                   - file (string) [optional]: the file to search in (if not provided, searches in the current open file)

               find_file:
                 docstring: finds all files with the given name in dir. If dir is not provided, searches in the current directory
                 signature: find_file <file_name> [<dir>]
                 arguments:
                   - file_name (string) [required]: the name of the file to search for
                   - dir (string) [optional]: the directory to search in (if not provided, searches in the current directory)

               edit:
                 docstring: replaces lines <start_line> through <end_line> (inclusive) with the given text in the open file. The replacement text is terminated by a line with only end_of_edit on it. All
         of the <replacement text> will be entered, so make sure your indentation is formatted properly. Python files will be checked for syntax errors after the edit. If the system detects a syntax
         error, the edit will not be executed. Simply try to edit the file again, but make sure to read the error message and modify the edit command you issue accordingly. Issuing the same command a
         second time will just lead to the same error message again.
                 signature: edit <start_line>:<end_line>
               <replacement_text>
               end_of_edit
                 arguments:
                   - start_line (integer) [required]: the line number to start the edit at
                   - end_line (integer) [required]: the line number to end the edit at (inclusive)
                   - replacement_text (string) [required]: the text to replace the current selection with

             command_files:
             - config/commands/defaults.sh
             - config/commands/search.sh
             - config/commands/edit_linting.sh
             - config/commands/_split_string.py
             demonstration_template: |
               Here is a demonstration of how to correctly accomplish this task.
               It is included to show you how to correctly use the interface.
               You do not need to follow exactly what is done in the demonstration.
               --- DEMONSTRATION ---
               {demonstration}
               --- END OF DEMONSTRATION ---
             demonstrations:
             - trajectories/demonstrations/replay__marshmallow-code__marshmallow-1867__default__t-0.20__p-0.95__c-2.00__install-1___install_from_source/marshmallow-code__marshmallow-1867.traj
             env_variables:
               CURRENT_FILE: ''
               CURRENT_LINE: '0'
               OVERLAP: '2'
               SEARCH_FILES: ()
               SEARCH_INDEX: '0'
               SEARCH_RESULTS: ()
               WINDOW: '100'
             format_error_template: |
               Your output was not formatted correctly. You must always include one discussion and one command as part of your response. Make sure you do not have multiple discussion/command tags.
               Please make sure your output precisely matches the following format:
               DISCUSSION
               Discuss here with yourself about what your planning and what you're going to do in this step.

               ```
               command(s) that you're going to run
               ```
             history_processor: {}
             history_processor_args: {}
             instance_template: "We're currently solving the following issue within our repository.\
               \ Here's the issue text:\nISSUE:\n{issue}\n\nINSTRUCTIONS:\nNow, you're going\
               \ to solve this issue on your own. Your terminal session has started and you're\
               \ in the repository's root directory. You can use any bash commands or the special\
               \ interface to help you. Edit all the files you need to and run any checks or\
               \ tests that you want. \nRemember, YOU CAN ONLY ENTER ONE COMMAND AT A TIME.\
               \ You should always wait for feedback after every command. \nWhen you're satisfied\
               \ with all of the changes you've made, you can submit your changes to the code\
               \ base by simply running the submit command.\nNote however that you cannot use\
               \ any interactive session commands (e.g. python, vim) in this environment, but\
               \ you can write scripts and run them. E.g. you can write a python script and\
               \ then run it with `python <script_name>.py`.\n\nNOTE ABOUT THE EDIT COMMAND:\
               \ Indentation really matters! When editing a file, make sure to insert appropriate\
               \ indentation before each line! \n\nIMPORTANT TIPS:\n1. Always start by trying\
               \ to replicate the bug that the issues discusses. \n   If the issue includes\
               \ code for reproducing the bug, we recommend that you re-implement that in your\
               \ environment, and run it to make sure you can reproduce the bug.\n   Then start\
               \ trying to fix it.\n   When you think you've fixed the bug, re-run the bug\
               \ reproduction script to make sure that the bug has indeed been fixed.\n   \n\
               \   If the bug reproduction script does not print anything when it succesfully\
               \ runs, we recommend adding a print(\"Script completed successfully, no errors.\"\
               ) command at the end of the file,\n   so that you can be sure that the script\
               \ indeed ran fine all the way through. \n\n2. If you run a command and it doesn't\
               \ work, try running a different command. A command that did not work once will\
               \ not work the second time unless you modify it!\n\n3. If you open a file and\
               \ need to get to an area around a specific line that is not in the first 100\
               \ lines, say line 583, don't just use the scroll_down command multiple times.\
               \ Instead, use the goto 583 command. It's much quicker. \n   \n4. If the bug\
               \ reproduction script requires inputting/reading a specific file, such as buggy-input.png,\
               \ and you'd like to understand how to input that file, conduct a search in the\
               \ existing repo code, to see whether someone else has already done that. Do\
               \ this by running the command: find_file \"buggy-input.png\" If that doensn't\
               \ work, use the linux 'find' command. \n\n5. Always make sure to look at the\
               \ currently open file and the current working directory (which appears right\
               \ after the currently open file). The currently open file might be in a different\
               \ directory than the working directory! Note that some commands, such as 'create',\
               \ open files, so they might change the current  open file.\n\n6. When editing\
               \ files, it is easy to accidentally specify a wrong line number or to write\
               \ code with incorrect indentation. Always check the code after you issue an\
               \ edit to make sure that it reflects what you wanted to accomplish. If it didn't,\
               \ issue another command to fix it.\n\n7. It may be necessary to install the\
               \ repository from source before you can run code. Please think about how to\
               \ install the environment from the repository directory if you need to do so.\n\
               \   \n\n(Open file: {open_file})\n(Current directory: {working_dir})\nbash-$"
             next_step_no_output_template: |-
               Your command ran successfully and did not produce any output.
               (Open file: {open_file})
               (Current directory: {working_dir})
               bash-$
             next_step_template: |-
               {observation}
               (Open file: {open_file})
               (Current directory: {working_dir})
               bash-$
             parse_command: {}
             parse_function: {}
             put_demos_in_history: false
             state_command:
               arguments: null
               code: |
                 state() {
                   local working_dir="$PWD";
                   if [ -z $CURRENT_FILE ]; then
                       echo '{"open_file": "n/a", "working_dir": "'$working_dir'"}';
                   else
                       echo '{"open_file": "'$(realpath $CURRENT_FILE)'", "working_dir": "'$working_dir'"}';
                   fi
                 };
               docstring: null
               end_name: null
               name: state
               signature: null
             strategy_template: null
             submit_command: submit
             subroutine_types: []
             system_template: "SETTING: You are an autonomous programmer, and you're working\
               \ directly in the command line with a special interface.\n\nThe special interface\
               \ consists of a file editor that shows you {WINDOW} lines of a file at a time.\n\
               In addition to typical bash commands, you can also use the following commands\
               \ to help you navigate and edit files.\n\nCOMMANDS:\n{command_docs}\n\nPlease\
               \ note that THE EDIT COMMAND REQUIRES PROPER INDENTATION. \nIf you'd like to\
               \ add the line '        print(x)' you must fully write that out, with all those\
               \ spaces before the code! Indentation is important and code that is not indented\
               \ correctly will fail and require fixing before it can be run.\n\nRESPONSE FORMAT:\n\
               Your shell prompt is formatted as follows:\n(Open file: <path>) <cwd> $\n\n\
               You need to format your output using two fields; discussion and command.\nYour\
               \ output should always include _one_ discussion and _one_ command field EXACTLY\
               \ as in the following example:\nDISCUSSION\nFirst I'll start by using ls to\
               \ see what files are in the current directory. Then maybe we can look at some\
               \ relevant files to see what they look like.\n```\nls -a\n```\n\nYou should\
               \ only include a *SINGLE* command in the command section and then wait for a\
               \ response from the shell before continuing with more discussion and commands.\
               \ Everything you include in the DISCUSSION section will be saved for future\
               \ reference.\nIf you'd like to issue two commands at once, PLEASE DO NOT DO\
               \ THAT! Please instead first submit just the first command, and then after receiving\
               \ a response you'll be able to issue the second command. \nYou're free to use\
               \ any other bash commands you want (e.g. find, grep, cat, ls, cd) in addition\
               \ to the special commands listed above.\nHowever, the environment does NOT support\
               \ interactive session commands (e.g. python, vim), so please do not invoke them."
             util_functions:
             - arguments: null
               code: '_print() {    local total_lines=$(awk ''END {print NR}'' $CURRENT_FILE)    echo
                 "[File: $(realpath $CURRENT_FILE) ($total_lines lines total)]"    lines_above=$(jq
                 -n "$CURRENT_LINE - $WINDOW/2" | jq ''[0, .] | max | floor'')    lines_below=$(jq
                 -n "$total_lines - $CURRENT_LINE - $WINDOW/2" | jq ''[0, .] | max | round'')    if
                 [ $lines_above -gt 0 ]; then        echo "($lines_above more lines above)"    fi    cat
                 $CURRENT_FILE | grep -n $ | head -n $(jq -n "[$CURRENT_LINE + $WINDOW/2, $WINDOW/2]
                 | max | floor") | tail -n $(jq -n "$WINDOW")    if [ $lines_below -gt 0 ];
                 then        echo "($lines_below more lines below)"    fi}'
               docstring: null
               end_name: null
               name: _print
               signature: _print
             - arguments: null
               code: _constrain_line() {    if [ -z "$CURRENT_FILE" ]    then        echo "No
                 file open. Use the open command first."        return    fi    local max_line=$(awk
                 'END {print NR}' $CURRENT_FILE)    local half_window=$(jq -n "$WINDOW/2" |
                 jq 'floor')    export CURRENT_LINE=$(jq -n "[$CURRENT_LINE, $max_line - $half_window]
                 | min")    export CURRENT_LINE=$(jq -n "[$CURRENT_LINE, $half_window] | max")}
               docstring: null
               end_name: null
               name: _constrain_line
               signature: _constrain_line
           config_file: config/default_from_url.yaml
           model:
             host_url: localhost:11434
             model_name: gpt4
             per_instance_cost_limit: 2.0
             replay_path: null
             temperature: 0.2
             top_p: 0.95
             total_cost_limit: 0.0
         environment:
           base_commit: null
           container_name: null
           data_path: https://github.com/pymc-devs/pymc/issues/7223
           image_name: swe-agent
           install_environment: true
           no_mirror: false
           split: dev
           timeout: 35
           verbose: true
         instance_filter: .*
         skip_existing: true
         suffix: ''

INFO     💽 Loaded dataset from https://github.com/pymc-devs/pymc/issues/7223
Traceback (most recent call last):
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connectionpool.py", line 793, in urlopen
    response = self._make_request(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connectionpool.py", line 496, in _make_request
    conn.request(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connection.py", line 400, in request
    self.endheaders()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 1280, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 1040, in _send_output
    self.send(msg)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 980, in send
    self.connect()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/transport/unixconn.py", line 27, in connect
    sock.connect(self.unix_socket)
FileNotFoundError: [Errno 2] No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/adapters.py", line 486, in send
    resp = conn.urlopen(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connectionpool.py", line 847, in urlopen
    retries = retries.increment(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/util/retry.py", line 470, in increment
    raise reraise(type(error), error, _stacktrace)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/util/util.py", line 38, in reraise
    raise value.with_traceback(tb)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connectionpool.py", line 793, in urlopen
    response = self._make_request(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connectionpool.py", line 496, in _make_request
    conn.request(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/urllib3/connection.py", line 400, in request
    self.endheaders()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 1280, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 1040, in _send_output
    self.send(msg)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/http/client.py", line 980, in send
    self.connect()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/transport/unixconn.py", line 27, in connect
    sock.connect(self.unix_socket)
urllib3.exceptions.ProtocolError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 213, in _retrieve_server_version
    return self.version(api_version=False)["ApiVersion"]
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/daemon.py", line 181, in version
    return self._result(self._get(url), json=True)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/utils/decorators.py", line 44, in inner
    return f(self, *args, **kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 236, in _get
    return self.get(url, **self._set_request_timeout(kwargs))
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/sessions.py", line 602, in get
    return self.request("GET", url, **kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/adapters.py", line 501, in send
    raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/twiecki/projects/SWE-agent/run.py", line 223, in <module>
    main(args)
  File "/Users/twiecki/projects/SWE-agent/run.py", line 66, in main
    env = SWEEnv(args.environment)
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 101, in __init__
    self._reset_container()
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 349, in _reset_container
    self._init_container()
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 371, in _init_container
    client = docker.from_env()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/client.py", line 94, in from_env
    return cls(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/client.py", line 45, in __init__
    self.api = APIClient(*args, **kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 197, in __init__
    self._version = self._retrieve_server_version()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 220, in _retrieve_server_version
    raise DockerException(
docker.errors.DockerException: Error while fetching server API version: ('Connection aborted.', FileNotFoundError(2, 'No such file or directory'))

It also didn't seem to find keys.cfg, I had to set GITHUB_TOKEN as an env variable.

[bishopZ]

I have the same result. I'm on a m1 mac.

At first it complains that there is no GITHUB_TOKEN, even though it's in the keys.cfg file.

If I export GITHUB_TOKEN as an env variable, I get the error shown above.

[twiecki]

Then it's probably arm64 related.

[klieret]

Regarding GITHUB_TOKEN, this should be fixed soon with #31

[klieret]

I'm on a M1 and cannot reproduce this. This is silly, but did you double check that your docker daemon is running?

[klieret]

I can reproduce this by killing docker and rerunning the command.

So the fix is simply: Make sure that docker is running.

I agree that the error handling could be improved. I'll open a PR for that.

[timothycarambat]

Ensure docker is running
Docker desktop > Settings > Advanced > Allow the default Docker socket to be used (requires password) needs to be enabled.

[klieret]

Feel free to reopen if issue persists.

[twiecki]

I'm positive that Docker is running (docker run works). So it must be something else. I can't reopen the issue.

[entuerem]

Ensure docker is running Docker desktop > Settings > Advanced > Allow the default Docker socket to be used (requires password) needs to be enabled.

I'm seeing this issue with Docker Desktop (the recommended way of installing docker according to the docker docs) on Ubuntu 23. This setup uses a different location for the default Docker socket which probably causes the FileNotFoundError thrown by the docker python library. Creating a symlink at the expected location with the following command fixes it:

sudo ln -s -f /home/<user>/.docker/desktop/docker.sock /var/run/docker.sock

[twiecki]

Thanks @entuerem, that solved that problem. Now I'm getting:

ERROR    Unexpected container setup output: Unable to find image 'swe-agent:latest' locally
         docker: Error response from daemon: pull access denied for swe-agent, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
         See 'docker run --help'.

Traceback (most recent call last):
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 265, in _raise_for_status
    response.raise_for_status()
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/requests/models.py", line 1021, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: http+docker://localhost/v1.43/containers/swe-agent-515b31641c/json

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/twiecki/projects/SWE-agent/run.py", line 223, in <module>
    main(args)
  File "/Users/twiecki/projects/SWE-agent/run.py", line 66, in main
    env = SWEEnv(args.environment)
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 101, in __init__
    self._reset_container()
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 349, in _reset_container
    self._init_container()
  File "/Users/twiecki/projects/SWE-agent/sweagent/environment/swe_env.py", line 378, in _init_container
    self.container_obj = client.containers.get(self.container_name)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/models/containers.py", line 951, in get
    resp = self.client.api.inspect_container(container_id)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/utils/decorators.py", line 19, in wrapped
    return f(self, resource_id, *args, **kwargs)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/container.py", line 792, in inspect_container
    return self._result(
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 271, in _result
    self._raise_for_status(response)
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/api/client.py", line 267, in _raise_for_status
    raise create_api_error_from_http_exception(e) from e
  File "/Users/twiecki/micromamba/envs/swe-agent/lib/python3.9/site-packages/docker/errors.py", line 39, in create_api_error_from_http_exception
    raise cls(e, response=response, explanation=explanation) from e
docker.errors.NotFound: 404 Client Error for http+docker://localhost/v1.43/containers/swe-agent-515b31641c/json: Not Found ("No such container: swe-agent-515b31641c")

Running docker login successfully didn't fix it.

[klieret]

Hi @twiecki : Sorry for missing your commend last week! (and I didn't know that you couldn't re-open the issue!)

Thanks for following up with detailed logs.

@timothycarambat @entuerem This is only for using the fully containerized version of the software, right? (i.e., when you mount the docker socket)

@twiecki Could it be that you didn't build/pull the swe-agent container? (step 2 of the express setup instructions or running setup.sh with the conda instructions)

[klieret]

Also note that we have updated the images to support arm64 as well as amd64 :)

[entuerem]

Hi @twiecki : Sorry for missing your commend last week! (and I didn't know that you couldn't re-open the issue!)

Thanks for following up with detailed logs.

@timothycarambat @entuerem This is only for using the fully containerized version of the software, right? (i.e., when you mount the docker socket)

@twiecki Could it be that you didn't pull the swe-agent container (step 2 of the express setup instructions)

No. This happened when I followed the "Setup with conda (development version)" instructions. On Ubuntu 23 this is the only issue I encountered. After creating the symlink it worked. Thx for this. Currently analyzing how you guys wrote this thing :)

[Amon1412]

The message below is the same problem I'm having when executing commands in Windows docker desctop, is it the same problem? How can i solve it.

Traceback (most recent call last):
  File "/app/run.py", line 108, in main
    observation, info = env.reset(index)
  File "/app/sweagent/environment/swe_env.py", line 216, in reset
    self.communicate_with_handling(
  File "/app/sweagent/environment/swe_env.py", line 485, in communicate_with_handling
    logs = self.communicate(input, timeout_duration=timeout_duration)
  File "/app/sweagent/environment/swe_env.py", line 468, in communicate
    output = self._communicate(
  File "/app/sweagent/environment/swe_env.py", line 437, in _communicate
    raise e
  File "/app/sweagent/environment/swe_env.py", line 430, in _communicate
    buffer = read_with_timeout(self.container, self.get_pids, timeout_duration)
  File "/app/sweagent/environment/utils.py", line 128, in read_with_timeout
    raise TimeoutError("Timeout reached while reading from subprocess.\nCurrent buffer: {}\nRunning PIDs: {}".format(buffer.decode(), pids))
TimeoutError: Timeout reached while reading from subprocess.
Current buffer:
Running PIDs: [['1994', 'pip']]

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/app/run.py", line 321, in <module>
    main(args)
  File "/app/run.py", line 157, in main
    env.reset_container()
  File "/app/sweagent/environment/swe_env.py", line 362, in reset_container
    self._reset_container()
  File "/app/sweagent/environment/swe_env.py", line 356, in _reset_container
    self._init_scripts()
  File "/app/sweagent/environment/swe_env.py", line 403, in _init_scripts
    self.communicate_with_handling(
  File "/app/sweagent/environment/swe_env.py", line 485, in communicate_with_handling
    logs = self.communicate(input, timeout_duration=timeout_duration)
  File "/app/sweagent/environment/swe_env.py", line 468, in communicate
    output = self._communicate(
  File "/app/sweagent/environment/swe_env.py", line 437, in _communicate
    raise e
  File "/app/sweagent/environment/swe_env.py", line 434, in _communicate
    exit_code = read_with_timeout(self.container, self.get_pids, 5).strip()
  File "/app/sweagent/environment/utils.py", line 128, in read_with_timeout
    raise TimeoutError("Timeout reached while reading from subprocess.\nCurrent buffer: {}\nRunning PIDs: {}".format(buffer.decode(), pids))
TimeoutError: Timeout reached while reading from subprocess.
Current buffer: 0

Running PIDs: []

[klieret]

@Amon1412 Please open a separate bug report.

[klieret]

Could it be that you didn't build/pull the swe-agent container? (step 2 of the express setup instructions or running setup.sh with the conda instructions)

@twiecki

[twiecki]

Yes, that was indeed the problem and pulling fixed. I now have a different problem for which I'll open a new issue. thanks!