Installed software in folder

This page is generated from the code and must not be edited by hand.

A folder is recognized as an installed program, such as a copy of Fiji or a Python environment, from the parts it holds, a name ending .app, its program-style subfolders or a majority of program files; its files are still indexed and read, and rules about experiments leave them alone.

installed_software_in_folder version 3

• Kind of rule: What is raised for attention (flags). Raises something for a person’s attention without concluding anything.

• What it concludes: a finding

• Reasoning: defeasible. A conclusion is usually right, and is retracted when a rule it names concludes against it.

• What it reads: one folder at a time

Is it available in this version?

Yes. The engine runs it.

What would defeat it

It names no rule whose conclusion would defeat it.

This rule is named as what would defeat:

• acquisition_stage_from_format

• analysis_stage_from_derived_sense

• archive_link_copy_of_a_file

• binding_is_ambiguous_outside_programs

• broken_addresses_in_folder

• claim_class_a_person_answered

• clocks_disagree

• content_contradicts_extension

• content_says_do_not_analyse

• content_unreadable

• copied_in_bulk

• copies_a_person_answered

• date_neighbourhood_of_a_file

• date_neighbourhood_of_a_folder

• declared_attribute_to_clarify

• declared_copy_window_exceeded

• derivation_by_a_scripts_calls

• derivation_named_by_a_describing_file

• derivation_named_for_an_acquisition

• derivation_of_one_name_in_sibling_folders

• derivation_summarising_a_series

• derivation_within_name_identity

• domain_pack_would_read_this_pool

• doubt_in_a_folder_name

• doubt_to_confirm_in_a_folder_name

• duplicate_candidate_unverified

• empty_replicate_is_no_data_point

• experiment_folder_from_contents

• experiment_folder_from_dated_name

• experiments_approved_together

• experiments_may_belong_together

• file_role_unless_program

• folder_copied_by_declared_clocks

• folder_copied_in_bulk

• format_built_on_a_container

• group_incomplete_against_workflow

• group_resolution_deviation

• group_resolved_across_experiments

• group_resolved_within_experiment

• group_series_across_experiments

• identical_by_declared_digest

• identical_by_declared_sha256

• indexed_label_may_mark_replicates

• miscellaneous_files_approved

• miscellaneous_files_to_approve

• name_family_without_stages

• named_for_a_series

• named_for_an_acquisition

• note_written_as_a_file_name

• one_name_in_sibling_folders

• pipeline_stage_from_name

• references_a_mentioned_file

• related_by_a_describing_file

• related_by_one_name_in_sibling_folders

• related_within_name_identity

• replicate_from_indexed_label

• replicates_of_one_condition

• replication_below_expected

• repudiated_by_name

• roi_archive_from_members

• roi_archive_named_but_unlisted

• same_name_identity

• same_name_identity_within_experiment

• same_observed_metadata_outside_programs

• software_outside_the_catalogue

• stage_disagrees_with_a_derivation

• stated_count_may_mark_replicates

• unbound_word_in_a_kinds_place

• vocabulary_unread_in_folder_outside_programs

Parameters

Parameter	Shipped value	May be	What it does
archive_suffixes	[".zip", ".tar.gz", ".tgz", ".tar.bz2", ".tar.xz", ".tar"]	list of text	Endings of an archive’s name, compared without case: a folder of code with an archive of its own name beside it (dapi.zip, dapi-0.3.tar.gz) was shared as that archive.
minimum_code_share	0.5	number, from 0 to 1	The share of a folder’s files that must be one kind’s code for the archive beside it to make it a package.
bundle_name_suffixes	[".app"]	list of text	Endings of a folder’s own name that packaging gives an application: a macOS application is a folder so named, and Fiji keeps the name on every platform. Raised as an application bundle where no known program’s parts name it.
layout_folder_names	["bin", "sbin", "lib", "lib64", "libexec", "include", "share", "site-packages", "dist-packages", "Frameworks", "__pycache__", "node_modules"]	list of text	Folder names packaging conventions give an installed program’s parts, compared without case. Two of them side by side is a layout; one alone is a word a laboratory might use.
minimum_layout_folders	2	whole number, from 1 to 20	How many of those folders the folder must hold directly.
program_extensions	["h", "hpp", "so", "dylib", "dll", "a", "o", "lib", "pyc", "pyd", "class", "jar", "exe"]	list of text	Extensions of compiled objects, libraries and headers, which a program carries and a laboratory’s analysis does not. A laboratory’s own scripts are left out on purpose: code a person wrote is not an installed program.
minimum_program_files	20	whole number, from 1 to 100000	How many such files the folder must hold directly, so a folder with a stray header is not a program’s.
minimum_program_share	0.5	number, from 0 to 1	The share of the folder’s files they must make up.
manifest_names	["setup.py", "setup.cfg", "pyproject.toml", "package.json", "CMakeLists.txt", "Makefile", "configure", "Cargo.toml"]	list of text	Packaging files, compared without case: cited where a layout signal raises the folder, and never enough alone.