software-component-identification
Summary
Systematically identify and document named subproject components within a complex research software system by scanning repository structure, configuration files, and documentation. This skill extracts component names, directory paths, functional roles, and interdependencies to produce a structured manifest of the system architecture.
When to use
When you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions. Use this skill when you have access to a source repository (GitHub, GitLab, Zenodo) and need to map logical subprojects to their implementation locations and roles within a larger workflow.
When NOT to use
- Repository is a monolithic single-purpose application with no subproject structure.
- Documentation or README explicitly states that the project is not modular or does not use named subproject components.
- You only need to identify external dependencies (pip, conda, npm packages); this skill is for internal component discovery only.
Inputs
- GitHub repository URL or cloned repository directory
- README.md or similar documentation files
- setup.py, setup.cfg, or pyproject.toml configuration files
- Directory tree structure and subdirectory names
Outputs
- Structured manifest (JSON or CSV) of component names, paths, roles, and interdependencies
- Component registry with entries for each named subproject
- Documented subproject interdependency graph
How to apply
Begin by cloning or accessing the target repository (e.g., https://github.com/NLeSC/MAGMa). Scan the repository root for README files, setup.py, configuration files (setup.cfg, pyproject.toml, docker-compose.yml), and directory structure to identify candidate subproject directories. For each candidate, extract its name (e.g., 'job', 'joblauncher', 'pubchem') and infer its functional role by reading inline documentation, module docstrings, and dependency declarations. Document interdependencies by tracing how subprojects reference or invoke one another (e.g., 'web application starts job calculations via joblauncher webservice'). Compile findings into a structured manifest (JSON or CSV) with columns for component name, directory path, inferred role, and documented dependencies. Cross-reference your findings against the README and any architecture diagrams to validate assignments.
Related tools
- MAGMa (The target system being decomposed into components; acronym for 'Ms Annotation based on in silico Generated Metabolites'.) — https://github.com/NLeSC/MAGMa
Examples
git clone https://github.com/NLeSC/MAGMa && cd MAGMa && git submodule update --init && grep -A 20 '^Subprojects:' README.rst | head -10
Evaluation signals
- All named subproject components mentioned in the README are present in the manifest with assigned directory paths.
- Each component entry includes a role description that aligns with the README's documented purpose (e.g., 'job' → 'Runs MAGMa calculation').
- Interdependencies in the manifest match the documented dependency statements (e.g., 'web application starts job calculations via joblauncher webservice').
- Directory paths in the manifest correspond to actual subdirectories in the cloned repository.
- The manifest is serializable to valid JSON or CSV with consistent schema across all component entries.
Limitations
- Component roles may be inferred rather than explicitly stated; validation against inline code or external documentation may be necessary.
- Submodules (e.g., joblauncher in MAGMa) require explicit initialization (git submodule update --init) and may not be discoverable from the README alone.
- The skill relies on documentation accuracy; if the README is out of sync with the actual codebase, the manifest may be incomplete or incorrect.
- Complex transitive dependencies between components may not be fully resolvable from static analysis of configuration files alone.
Evidence
[readme] Subprojects:
emetabolomics_site - The http://www.emetabolomics.org website
job - Runs MAGMa calculation
joblauncher - Webservice to execute jobs
pubchem - Processing of PubChem database, used to find mass candidates
web - Web application to start jobs and view results: "Subprojects:
emetabolomics_site - The http://www.emetabolomics.org website
job - Runs MAGMa calculation
joblauncher - Webservice to execute jobs
pubchem - Processing of PubChem database,"
[readme] Subproject interdependencies
- The
emetabolomics_site website can be used as starting pages for the web application.
- The
job calculation requires a pubchem lookup database which can be made using the pubchem application.
- The
web application starts job calculations via the joblauncher webservice.: "The web application starts job calculations via the joblauncher webservice."
- [other] The MAGMa system comprises five named subproject components: emetabolomics_site (website), job (calculation engine), joblauncher (webservice for job execution), pubchem (data processing), and magmaweb (results interface).: "The MAGMa system comprises five named subproject components: emetabolomics_site (website), job (calculation engine), joblauncher (webservice for job execution), pubchem (data processing), and"
- [readme] Use following command to initialize and fetch the joblauncher submodule:
.. code-block:: bash
git submodule update --init: "Use following command to initialize and fetch the joblauncher submodule"
1---2name: software-component-identification3description: Use when when you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions.4license: CC-BY-4.05---67# software-component-identification89## Summary1011Systematically identify and document named subproject components within a complex research software system by scanning repository structure, configuration files, and documentation. This skill extracts component names, directory paths, functional roles, and interdependencies to produce a structured manifest of the system architecture.1213## When to use1415When you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions. Use this skill when you have access to a source repository (GitHub, GitLab, Zenodo) and need to map logical subprojects to their implementation locations and roles within a larger workflow.1617## When NOT to use1819- Repository is a monolithic single-purpose application with no subproject structure.20- Documentation or README explicitly states that the project is not modular or does not use named subproject components.21- You only need to identify external dependencies (pip, conda, npm packages); this skill is for internal component discovery only.2223## Inputs2425- GitHub repository URL or cloned repository directory26- README.md or similar documentation files27- setup.py, setup.cfg, or pyproject.toml configuration files28- Directory tree structure and subdirectory names2930## Outputs3132- Structured manifest (JSON or CSV) of component names, paths, roles, and interdependencies33- Component registry with entries for each named subproject34- Documented subproject interdependency graph3536## How to apply3738Begin by cloning or accessing the target repository (e.g., https://github.com/NLeSC/MAGMa). Scan the repository root for README files, setup.py, configuration files (setup.cfg, pyproject.toml, docker-compose.yml), and directory structure to identify candidate subproject directories. For each candidate, extract its name (e.g., 'job', 'joblauncher', 'pubchem') and infer its functional role by reading inline documentation, module docstrings, and dependency declarations. Document interdependencies by tracing how subprojects reference or invoke one another (e.g., 'web application starts job calculations via joblauncher webservice'). Compile findings into a structured manifest (JSON or CSV) with columns for component name, directory path, inferred role, and documented dependencies. Cross-reference your findings against the README and any architecture diagrams to validate assignments.3940## Related tools4142- **MAGMa** (The target system being decomposed into components; acronym for 'Ms Annotation based on in silico Generated Metabolites'.) — https://github.com/NLeSC/MAGMa4344## Examples4546```47git clone https://github.com/NLeSC/MAGMa && cd MAGMa && git submodule update --init && grep -A 20 '^Subprojects:' README.rst | head -1048```4950## Evaluation signals5152- All named subproject components mentioned in the README are present in the manifest with assigned directory paths.53- Each component entry includes a role description that aligns with the README's documented purpose (e.g., 'job' → 'Runs MAGMa calculation').54- Interdependencies in the manifest match the documented dependency statements (e.g., 'web application starts job calculations via joblauncher webservice').55- Directory paths in the manifest correspond to actual subdirectories in the cloned repository.56- The manifest is serializable to valid JSON or CSV with consistent schema across all component entries.5758## Limitations5960- Component roles may be inferred rather than explicitly stated; validation against inline code or external documentation may be necessary.61- Submodules (e.g., joblauncher in MAGMa) require explicit initialization (git submodule update --init) and may not be discoverable from the README alone.62- The skill relies on documentation accuracy; if the README is out of sync with the actual codebase, the manifest may be incomplete or incorrect.63- Complex transitive dependencies between components may not be fully resolvable from static analysis of configuration files alone.6465## Evidence6667- [readme] Subprojects:6869- emetabolomics_site - The http://www.emetabolomics.org website70- job - Runs MAGMa calculation71- joblauncher - Webservice to execute jobs72- pubchem - Processing of PubChem database, used to find mass candidates73- web - Web application to start jobs and view results: "Subprojects:7475- emetabolomics_site - The http://www.emetabolomics.org website76- job - Runs MAGMa calculation77- joblauncher - Webservice to execute jobs78- pubchem - Processing of PubChem database,"79- [readme] Subproject interdependencies80----------------------------8182- The `emetabolomics_site` website can be used as starting pages for the `web` application.83- The `job` calculation requires a pubchem lookup database which can be made using the `pubchem` application.84- The `web` application starts `job` calculations via the `joblauncher` webservice.: "The `web` application starts `job` calculations via the `joblauncher` webservice."85- [other] The MAGMa system comprises five named subproject components: emetabolomics_site (website), job (calculation engine), joblauncher (webservice for job execution), pubchem (data processing), and magmaweb (results interface).: "The MAGMa system comprises five named subproject components: emetabolomics_site (website), job (calculation engine), joblauncher (webservice for job execution), pubchem (data processing), and"86- [readme] Use following command to initialize and fetch the joblauncher submodule:8788.. code-block:: bash8990 git submodule update --init: "Use following command to initialize and fetch the joblauncher submodule"
HolobiomicsLab