diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index dcdeb92f..00000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.gitignore b/.gitignore index 505a3b1c..d3b3107f 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,9 @@ wheels/ # Virtual environments .venv + +# Serena +.serena/ + +# macOS +.DS_Store diff --git a/.serena/.gitignore b/.serena/.gitignore deleted file mode 100644 index 2e510aff..00000000 --- a/.serena/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -/cache -/project.local.yml diff --git a/.serena/project.yml b/.serena/project.yml deleted file mode 100644 index 0e9207aa..00000000 --- a/.serena/project.yml +++ /dev/null @@ -1,141 +0,0 @@ -# the name by which the project can be referenced within Serena -project_name: "prompt_updates_sequential" - - -# list of languages for which language servers are started; choose from: -# al angular ansible bash clojure -# cpp cpp_ccls crystal csharp csharp_omnisharp -# dart elixir elm erlang fortran -# fsharp go groovy haskell haxe -# hlsl html java json julia -# kotlin lean4 lua luau markdown -# matlab msl nix ocaml pascal -# perl php php_phpactor powershell python -# python_jedi python_ty r rego ruby -# ruby_solargraph rust scala scss solidity -# svelte swift systemverilog terraform toml -# typescript typescript_vts vue yaml zig -# (This list may be outdated. For the current list, see values of Language enum here: -# https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py -# For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.) -# Note: -# - For C, use cpp -# - For JavaScript, use typescript -# - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root) -# - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm) -# - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three) -# - For Free Pascal/Lazarus, use pascal -# Special requirements: -# Some languages require additional setup/installations. -# See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers -# When using multiple languages, the first language server that supports a given file will be used for that file. -# The first language is the default language and the respective language server will be used as a fallback. -# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored. -languages: -- python - -# the encoding used by text files in the project -# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings -encoding: "utf-8" - -# line ending convention to use when writing source files. -# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default) -# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings. -line_ending: - -# The language backend to use for this project. -# If not set, the global setting from serena_config.yml is used. -# Valid values: LSP, JetBrains -# Note: the backend is fixed at startup. If a project with a different backend -# is activated post-init, an error will be returned. -language_backend: - -# whether to use project's .gitignore files to ignore files -ignore_all_files_in_gitignore: true - -# advanced configuration option allowing to configure language server-specific options. -# Maps the language key to the options. -# Have a look at the docstring of the constructors of the LS implementations within solidlsp (e.g., for C# or PHP) to see which options are available. -# No documentation on options means no options are available. -ls_specific_settings: {} - -# list of additional paths to ignore in this project. -# Same syntax as gitignore, so you can use * and **. -# Note: global ignored_paths from serena_config.yml are also applied additively. -ignored_paths: [] - -# whether the project is in read-only mode -# If set to true, all editing tools will be disabled and attempts to use them will result in an error -# Added on 2025-04-18 -read_only: false - -# list of tool names to exclude. -# This extends the existing exclusions (e.g. from the global configuration) -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -excluded_tools: [] - -# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default). -# This extends the existing inclusions (e.g. from the global configuration). -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -included_optional_tools: [] - -# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools. -# This cannot be combined with non-empty excluded_tools or included_optional_tools. -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -fixed_tools: [] - -# list of mode names to that are always to be included in the set of active modes -# The full set of modes to be activated is base_modes + default_modes. -# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply. -# Otherwise, this setting overrides the global configuration. -# Set this to [] to disable base modes for this project. -# Set this to a list of mode names to always include the respective modes for this project. -base_modes: - -# list of mode names that are to be activated by default, overriding the setting in the global configuration. -# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes. -# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply. -# Otherwise, this overrides the setting from the global configuration (serena_config.yml). -# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply -# for this project. -# This setting can, in turn, be overridden by CLI parameters (--mode). -# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes -default_modes: - -# initial prompt for the project. It will always be given to the LLM upon activating the project -# (contrary to the memories, which are loaded on demand). -initial_prompt: "" - -# time budget (seconds) per tool call for the retrieval of additional symbol information -# such as docstrings or parameter information. -# This overrides the corresponding setting in the global configuration; see the documentation there. -# If null or missing, use the setting from the global configuration. -symbol_info_budget: - -# list of regex patterns which, when matched, mark a memory entry as read‑only. -# Extends the list from the global configuration, merging the two lists. -read_only_memory_patterns: [] - -# list of regex patterns for memories to completely ignore. -# Matching memories will not appear in list_memories or activate_project output -# and cannot be accessed via read_memory or write_memory. -# To access ignored memory files, use the read_file tool on the raw file path. -# Extends the list from the global configuration, merging the two lists. -# Example: ["_archive/.*", "_episodes/.*"] -ignored_memory_patterns: [] - -# list of mode names to be activated additionally for this project, e.g. ["query-projects"] -# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes. -# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes -added_modes: - -# list of additional workspace folder paths for cross-package reference support (e.g. in monorepos). -# Paths can be absolute or relative to the project root. -# Each folder is registered as an LSP workspace folder, enabling language servers to discover -# symbols and references across package boundaries. -# Currently supported for: TypeScript. -# Example: -# additional_workspace_folders: -# - ../sibling-package -# - ../shared-lib -additional_workspace_folders: [] diff --git a/0. 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-# the name by which the project can be referenced within Serena -project_name: "Case_02_Comparison_Research" - - -# list of languages for which language servers are started; choose from: -# al angular ansible bash clojure -# cpp cpp_ccls crystal csharp csharp_omnisharp -# dart elixir elm erlang fortran -# fsharp go groovy haskell haxe -# hlsl html java json julia -# kotlin lean4 lua luau markdown -# matlab msl nix ocaml pascal -# perl php php_phpactor powershell python -# python_jedi python_ty r rego ruby -# ruby_solargraph rust scala scss solidity -# svelte swift systemverilog terraform toml -# typescript typescript_vts vue yaml zig -# (This list may be outdated. For the current list, see values of Language enum here: -# https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py -# For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.) -# Note: -# - For C, use cpp -# - For JavaScript, use typescript -# - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root) -# - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm) -# - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three) -# - For Free Pascal/Lazarus, use pascal -# Special requirements: -# Some languages require additional setup/installations. -# See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers -# When using multiple languages, the first language server that supports a given file will be used for that file. -# The first language is the default language and the respective language server will be used as a fallback. -# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored. -languages: [] - -# the encoding used by text files in the project -# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings -encoding: "utf-8" - -# line ending convention to use when writing source files. -# Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default) -# This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings. -line_ending: - -# The language backend to use for this project. -# If not set, the global setting from serena_config.yml is used. -# Valid values: LSP, JetBrains -# Note: the backend is fixed at startup. If a project with a different backend -# is activated post-init, an error will be returned. -language_backend: - -# whether to use project's .gitignore files to ignore files -ignore_all_files_in_gitignore: true - -# advanced configuration option allowing to configure language server-specific options. -# Maps the language key to the options. -# The settings are considered only if the project is trusted (see global configuration to define trusted projects). -# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings -ls_specific_settings: {} - -# list of additional paths to ignore in this project. -# Same syntax as gitignore, so you can use * and **. -# Note: global ignored_paths from serena_config.yml are also applied additively. -ignored_paths: [] - -# whether the project is in read-only mode -# If set to true, all editing tools will be disabled and attempts to use them will result in an error -# Added on 2025-04-18 -read_only: false - -# list of tool names to exclude. -# This extends the existing exclusions (e.g. from the global configuration) -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -excluded_tools: [] - -# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default). -# This extends the existing inclusions (e.g. from the global configuration). -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -included_optional_tools: [] - -# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools. -# This cannot be combined with non-empty excluded_tools or included_optional_tools. -# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html -fixed_tools: [] - -# list of mode names to that are always to be included in the set of active modes -# The full set of modes to be activated is base_modes + default_modes. -# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply. -# Otherwise, this setting overrides the global configuration. -# Set this to [] to disable base modes for this project. -# Set this to a list of mode names to always include the respective modes for this project. -base_modes: - -# list of mode names that are to be activated by default, overriding the setting in the global configuration. -# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes. -# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply. -# Otherwise, this overrides the setting from the global configuration (serena_config.yml). -# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply -# for this project. -# This setting can, in turn, be overridden by CLI parameters (--mode). -# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes -default_modes: - -# initial prompt for the project. It will always be given to the LLM upon activating the project -# (contrary to the memories, which are loaded on demand). -initial_prompt: "" - -# time budget (seconds) per tool call for the retrieval of additional symbol information -# such as docstrings or parameter information. -# This overrides the corresponding setting in the global configuration; see the documentation there. -# If null or missing, use the setting from the global configuration. -symbol_info_budget: - -# list of regex patterns which, when matched, mark a memory entry as read‑only. -# Extends the list from the global configuration, merging the two lists. -read_only_memory_patterns: [] - -# list of regex patterns for memories to completely ignore. -# Matching memories will not appear in list_memories or activate_project output -# and cannot be accessed via read_memory or write_memory. -# To access ignored memory files, use the read_file tool on the raw file path. -# Extends the list from the global configuration, merging the two lists. -# Example: ["_archive/.*", "_episodes/.*"] -ignored_memory_patterns: [] - -# list of mode names to be activated additionally for this project, e.g. ["query-projects"] -# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes. -# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes -added_modes: - -# list of additional workspace folder paths for cross-package reference support (e.g. in monorepos). -# Paths can be absolute or relative to the project root. -# Each folder is registered as an LSP workspace folder, enabling language servers to discover -# symbols and references across package boundaries. -# Currently supported for: TypeScript. -# Example: -# additional_workspace_folders: -# - ../sibling-package -# - ../shared-lib -additional_workspace_folders: [] - -# optional shell command to run before the language backend (LSP or JetBrains) is initialised. -# the command runs in the project root directory and is only executed if the project is trusted -# (see trusted_project_path_patterns in the global configuration). -# serena waits for the command to exit: a non-zero exit code is logged as an error but does not -# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety -# backstop for non-terminating commands; on expiry the process is killed and activation continues. -# example: activation_command: "npx nx run-many -t build" -activation_command: - -# maximum time in seconds to wait for activation_command to complete before killing it (default 180s). -# must be a positive number. -activation_command_timeout: 180.0 diff --git a/Case_02_Comparison_Research/Default_Agent_updated/.DS_Store b/Case_02_Comparison_Research/Default_Agent_updated/.DS_Store deleted file mode 100644 index a7e83bad..00000000 Binary files a/Case_02_Comparison_Research/Default_Agent_updated/.DS_Store and /dev/null differ diff --git a/Case_02_Comparison_Research/Results_by_Stage/.DS_Store b/Case_02_Comparison_Research/Results_by_Stage/.DS_Store deleted file mode 100644 index 20d52c28..00000000 Binary files a/Case_02_Comparison_Research/Results_by_Stage/.DS_Store and /dev/null differ diff --git a/Case_02_Comparison_Research/Results_by_Stage/2. 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