Merge pull request #121 from metabarcoding/push-swrrsvqysysz

Release 4.4.46

.gitignore

@@ -21,6 +21,8 @@ xx
 
 .rhistory
 /.vscode
+
+/benchmarck
 /build
 /bugs
 autodoc

.serena/.gitignore

@@ -0,0 +1,2 @@
+/cache
+/project.local.yml

.serena/project.yml

@@ -0,0 +1,133 @@
+# the name by which the project can be referenced within Serena
+project_name: "obitools4"
+
+
+# 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+#   (This list may be outdated.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:
+- go
+
+# 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 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: []
+
+# 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 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:
+
+# 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:
+
+# 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: []

pkg/obiformats/fastseq_obi_header.go

@@ -17,7 +17,7 @@ import (
 )
 
 var __obi_header_value_string_pattern__ = regexp.MustCompile(`^'\s*([^']*'|"[^"]*")\s*;`)
-var __obi_header_value_numeric_pattern__ = regexp.MustCompile(`^\s*([+-]?\.\d+|[+-]?\d+(\.\d*)?([eE][+-]?\d+)?)\s*;`)
+var __obi_header_value_numeric_pattern__ = regexp.MustCompile(`^\s*[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?\s*;`)
 var __obi_header_map_int_key__ = regexp.MustCompile("([{,])([0-9]+):")
 
 func __match__dict__(text []byte) []int {
@@ -316,28 +316,28 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
 						stop = m[1] + 1
 					} else {
 
-					// Generic value
+						// Generic value
 
-					// m = __obi_header_value_general_pattern__.FindIndex(part)
+						// m = __obi_header_value_general_pattern__.FindIndex(part)
-					m = __match__general__(part)
+						m = __match__general__(part)
-					if len(m) > 0 {
+						if len(m) > 0 {
-						bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
+							bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
 
-						if __is_false__(bvalue) {
+							if __is_false__(bvalue) {
-							value = false
+								value = false
-						} else {
-							if __is_true__(bvalue) {
-								value = true
 							} else {
-								value = string(bvalue)
+								if __is_true__(bvalue) {
+									value = true
+								} else {
+									value = string(bvalue)
+								}
 							}
-						}
 
-						stop = m[1] + 1
+							stop = m[1] + 1
-					} else {
+						} else {
-						// no value
+							// no value
-						break
+							break
-					} // End of No value
+						} // End of No value
 					} // End of not array
 				} // End of not dict
 			} // End of not string
@@ -347,6 +347,8 @@ func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
 		case float64:
 			if vt == math.Floor(vt) {
 				annotations[key] = int(vt)
+			} else {
+				annotations[key] = vt
 			}
 		default:
 			annotations[key] = value

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.45"
+var _Version = "Release 4.4.46"
 
 // Version returns the version of the obitools package.
 //

version.txt

@@ -1 +1 @@
-4.4.45
+4.4.46