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cff-version: 1.2.0
title: The Software Gardening Almanack
message: >-
  If you use this work in some way, please consider
  citing it using the metadata from this file.

  This work was supported by the Better Scientific Software Fellowship Program,
  a collaborative effort of the U.S. Department of Energy (DOE), Office of
  Advanced Scientific Research via ANL under Contract DE-AC02-06CH11357 and the
  National Nuclear Security Administration Advanced Simulation and Computing
  Program via LLNL under Contract DE-AC52-07NA27344; and by the National Science
  Foundation (NSF) via SHI under Grant No. 2327079.
type: software
authors:
  - given-names: David
    family-names: Bunten
    orcid: "https://orcid.org/0000-0001-6041-3665"
  - given-names: Will
    family-names: Davidson
    orcid: "https://orcid.org/0009-0006-1415-6964"
  - given-names: Faisal
    family-names: Alquaddoomi
    orcid: "https://orcid.org/0000-0003-4297-8747"
  - given-names: Vincent
    family-names: Rubinetti
    orcid: "https://orcid.org/0000-0002-4655-3773"
  - given-names: Gregory
    family-names: Way
    orcid: "https://orcid.org/0000-0002-0503-9348"
repository-code: "https://github.com/software-gardening/almanack"
abstract: |
  An open-source handbook of applied guidance and tools for sustainable software development and maintenance.
keywords:
  - software-gardening
  - software-sustainability
  - open-source
  - guidance
  - book
license: BSD-3-Clause
identifiers:
  - description: Software DOI
    type: doi
    value: "10.5281/zenodo.14765834"
  - description: Introductory Blog Post through BSSw
    type: doi
    value: "10.5281/zenodo.15330702"
  - description: Poster for CU Anschutz DBMI Retreat - August 2025
    type: doi
    value: "10.5281/zenodo.16943577"
references:
  - authors:
      - given-names: David
        family-names: Bunten
      - family-names: Way
        given-names: Gregory P.
    date-published: "2023-08-17"
    title: Long-Term Software Gardening Strategies for Cultivating Scientific Development Ecosystems
    type: article
    url: https://bssw.io/blog_posts/long-term-software-gardening-strategies-for-cultivating-scientific-development-ecosystems
    notes: |
      This blog article is a related resource published through the Better Scientific Software (BSSw)
      organization and serves as inspiration towards related materials.
  - authors:
      - family-names: Hassan
        given-names: Ahmed E.
    date-published: "2009-05-16"
    doi: 10.1109/ICSE.2009.5070510
    location:
      name: Vancouver, BC, Canada
    publisher:
      name: IEEE
    title: Predicting Faults Using the Complexity of Code Changes
    type: article
    url: https://doi.org/10.1109/ICSE.2009.5070510
    notes: |
      This article is a related resource that serves as inspiration in deriving our
      Shannon's information theory entropy calculations to software.
      This appears as output within the Almanack under metrics labeled with "id : name"
      of "SGA-VS-0001 : repo-agg-info-entropy" and "SGA-VS-0002 : repo-file-info-entropy" (and associated methods).
  - title: 'Ecosyste.ms: Repos'
    type: software
    authors:
      - given-names: Andrew
        family-names: Nesbitt
        email: andrew@ecosyste.ms
        orcid: 'https://orcid.org/0009-0007-2710-1118'
    repository-code: 'https://github.com/ecosyste-ms/repos'
    url: 'https://repos.ecosyste.ms'
    abstract: >-
      An open API service providing repository metadata for many open source software ecosystems.
    keywords:
      - open source
      - package management
      - software
    license: AGPL-3.0
    notes: |
      The Ecosyste.ms Repos API is used to source data for use within the Almanack Python package.
  - title: >-
      OpenAlex: A fully-open index of scholarly works, authors, venues, institutions, and concepts
    abstract: |
      OpenAlex is a new, fully-open scientific knowledge graph (SKG), launched to replace the discontinued Microsoft Academic Graph (MAG). It contains metadata for 209M works (journal articles, books, etc); 2013M disambiguated authors; 124k venues (places that host works, such as journals and online repositories); 109k institutions; and 65k Wikidata concepts (linked to works via an automated hierarchical multi-tag classifier). The dataset is fully and freely available via a web-based GUI, a full data dump, and high-volume REST API. The resource is under active development and future work will improve accuracy and coverage of citation information and author/institution parsing and deduplication.
    type: article
    license: CC0-1.0
    copyright: Creative Commons Zero v1.0 Universal
    database: DOI.org (Datacite)
    date-accessed: "2024-12-11"
    url: https://arxiv.org/abs/2205.01833
    keywords:
      - "Digital Libraries (cs.DL)"
      - "FOS: Computer and information sciences"
    authors:
      - family-names: Priem
        given-names: Jason
      - family-names: Piwowar
        given-names: Heather
      - family-names: Orr
        given-names: Richard
    date-published: "2022-05-04"
    identifiers:
      - type: doi
        value: 10.48550/ARXIV.2205.01833
    notes: |
      The OpenAlex API is used to source data for use within the Almanack Python package.
  - title: >-
      Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
    abstract: |
      Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated use cases, and help define improvement areas. However, there are challenges associated with these analyses including distorted or misleading metrics, as well as ethical and security concerns. More attention to the nuances involved in capturing impact across the spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have compelling typical usage metrics. We propose more general guidelines, as well as strategies for more specific types of software. We highlight outstanding issues regarding how communities measure or evaluate software impact. To get a deeper understanding of current practices for software evaluations, we performed a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that developers recognize the utility of analyzing software usage, but struggle to find the time or funding for such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of evaluations of their software.
    type: article
    database: arXiv.org
    date-accessed: "2024-10-02"
    url: http://arxiv.org/abs/2306.03255
    keywords:
      - Computer Science - Software Engineering
      - Quantitative Biology - Other Quantitative Biology
    authors:
      - family-names: Afiaz
        given-names: Awan
      - family-names: Ivanov
        given-names: Andrey
      - family-names: Chamberlin
        given-names: John
      - family-names: Hanauer
        given-names: David
      - family-names: Savonen
        given-names: Candace
      - family-names: Goldman
        given-names: Mary J.
      - family-names: Morgan
        given-names: Martin
      - family-names: Reich
        given-names: Michael
      - family-names: Getka
        given-names: Alexander
      - family-names: Holmes
        given-names: Aaron
      - family-names: Pati
        given-names: Sarthak
      - family-names: Knight
        given-names: Dan
      - family-names: Boutros
        given-names: Paul C.
      - family-names: Bakas
        given-names: Spyridon
      - family-names: Caporaso
        given-names: J. Gregory
      - family-names: Del Fiol
        given-names: Guilherme
      - family-names: Hochheiser
        given-names: Harry
      - family-names: Haas
        given-names: Brian
      - family-names: Schloss
        given-names: Patrick D.
      - family-names: Eddy
        given-names: James A.
      - family-names: Albrecht
        given-names: Jake
      - family-names: Fedorov
        given-names: Andrey
      - family-names: Waldron
        given-names: Levi
      - family-names: Hoffman
        given-names: Ava M.
      - family-names: Bradshaw
        given-names: Richard L.
      - family-names: Leek
        given-names: Jeffrey T.
      - family-names: Wright
        given-names: Carrie
    date-published: "2023-06-05"
    notes: |
      This article was used to help inspire metrics and content found within the Almanack.