From 416ff5c25440636cd19da770e57a184af04f94df Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 11:13:51 +0000 Subject: [PATCH 01/10] convert authors to myst --- AUTHORS.md | 32 ++++++++++++++++++++++++++++++++ AUTHORS.rst | 35 ----------------------------------- 2 files changed, 32 insertions(+), 35 deletions(-) create mode 100644 AUTHORS.md delete mode 100644 AUTHORS.rst diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 0000000..bac446b --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,32 @@ +# Credits + +## Project Coordinators + +- [Eric Hutton](https://github.com/mcflugen) +- [Mark Piper](https://github.com/mdpiper) + +## Contributors + +- Richard Barnes +- Ibrahim Demir +- Greg Ewing +- Michael Galloy +- Sam Harrison +- Julian Hofer +- Rolf Hut +- Eric Hutton +- Allen Lee +- Eric Morway +- Boyana Norris +- Scott Peckham +- Mark Piper +- Carlos Erazo Ramirez +- Mike Taves +- Greg Tucker +- Ashani Vaidya +- Martijn Visser +- Ben van Werkhoven + +If you have contributed to the BMI project and your name is missing, +please send an email to the coordinators, or open a pull request +for this page in the [BMI repository](https://github.com/csdms/bmi). diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index 7256045..0000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,35 +0,0 @@ -======= -Credits -======= - -Project Coordinators --------------------- - -* Eric Hutton -* Mark Piper - -Contributors ------------- - -* Richard Barnes -* Ibrahim Demir -* Greg Ewing -* Michael Galloy -* Sam Harrison -* Julian Hofer -* Eric Hutton -* Allen Lee -* Eric Morway -* Boyana Norris -* Scott Peckham -* Mark Piper -* Carlos Erazo Ramirez -* Mike Taves -* Greg Tucker -* Ashani Vaidya -* Martijn Visser -* Ben van Werkhoven - -If you have contributed to the BMI project and your name is missing, -please send an email to the coordinators, or open a pull request -for this page in the `BMI repository `_. From 521b5332f413aa159725ea15cf844a7ca2c41138 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 11:14:13 +0000 Subject: [PATCH 02/10] convert citation to myst --- CITATION.rst => CITATION.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename CITATION.rst => CITATION.md (98%) diff --git a/CITATION.rst b/CITATION.md similarity index 98% rename from CITATION.rst rename to CITATION.md index e59988d..56f98de 100644 --- a/CITATION.rst +++ b/CITATION.md @@ -1,9 +1,9 @@ -Citation -======== +# Citation If you use the Basic Model Interface for work/research presented in a publication, we ask that you please cite: +```{eval-rst} .. tab-set:: .. tab-item:: APA @@ -50,3 +50,4 @@ presented in a publication, we ask that you please cite: }, journal={Journal of Open Source Software} } +``` From e9c677af2d0c8c7dc99ace127e35d6fca048b8cf Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 11:14:49 +0000 Subject: [PATCH 03/10] convert code of conduct to myst --- CODE-OF-CONDUCT.rst => CODE-OF-CONDUCT.md | 49 ++++++++++------------- 1 file changed, 21 insertions(+), 28 deletions(-) rename CODE-OF-CONDUCT.rst => CODE-OF-CONDUCT.md (70%) diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.md similarity index 70% rename from CODE-OF-CONDUCT.rst rename to CODE-OF-CONDUCT.md index 90a7c19..14aae39 100644 --- a/CODE-OF-CONDUCT.rst +++ b/CODE-OF-CONDUCT.md @@ -1,8 +1,6 @@ -Contributor Covenant Code of Conduct -==================================== +# Contributor Covenant Code of Conduct -Our Pledge ----------- +## Our Pledge In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and @@ -11,31 +9,29 @@ size, disability, ethnicity, sex characteristics, gender identity and expression level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. -Our Standards -------------- +## Our Standards Examples of behavior that contributes to creating a positive environment include: -* Using welcoming and inclusive language -* Being respectful of differing viewpoints and experiences -* Gracefully accepting constructive criticism -* Focusing on what is best for the community -* Showing empathy towards other community members +- Using welcoming and inclusive language +- Being respectful of differing viewpoints and experiences +- Gracefully accepting constructive criticism +- Focusing on what is best for the community +- Showing empathy towards other community members Examples of unacceptable behavior by participants include: -* The use of sexualized language or imagery and unwelcome sexual attention or +- The use of sexualized language or imagery and unwelcome sexual attention or advances -* Trolling, insulting/derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or electronic +- Trolling, insulting/derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or electronic address, without explicit permission -* Other conduct which could reasonably be considered inappropriate in a +- Other conduct which could reasonably be considered inappropriate in a professional setting -Our Responsibilities --------------------- +## Our Responsibilities Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in @@ -47,8 +43,7 @@ that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Scope ------ +## Scope This Code of Conduct applies within all project spaces, and it also applies when an individual is representing the project or its community in public spaces. @@ -57,11 +52,10 @@ project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. -Enforcement ------------ +## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported by contacting the project team at csdms@colorado.edu. All +reported by contacting the project team at . All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. @@ -71,13 +65,12 @@ Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. -Attribution ------------ +## Attribution This Code of Conduct is adapted from the -`Contributor Covenant `_, version 1.4, +[Contributor Covenant](https://www.contributor-covenant.org), version 1.4, available at -``_. +[https://www.contributor-covenant.org/version/1/4/code-of-conduct.html](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html). For answers to common questions about this code of conduct, see -``_. +[https://www.contributor-covenant.org/faq](https://www.contributor-covenant.org/faq). From b2128e484870b66d9e277e441c5a67a6e73db343 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 11:19:30 +0000 Subject: [PATCH 04/10] convert license to myst --- LICENSE | 21 --------------------- LICENSE.md | 20 ++++++++++++++++++++ 2 files changed, 20 insertions(+), 21 deletions(-) delete mode 100644 LICENSE create mode 100644 LICENSE.md diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 0f18cdf..0000000 --- a/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -The MIT License (MIT) - -Copyright (c) 2014 Community Surface Dynamics Modeling System - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..abba72f --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,20 @@ +# The MIT License (MIT) + +Copyright (c) `2014` `Community Surface Dynamics Modeling System` + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. From 14808b0193efa5700fc39dd4a4a0ac8ead505237 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 11:19:46 +0000 Subject: [PATCH 05/10] convert readme to myst --- README.rst | 149 ----------------------------------------------------- 1 file changed, 149 deletions(-) delete mode 100644 README.rst diff --git a/README.rst b/README.rst deleted file mode 100644 index 09f24b8..0000000 --- a/README.rst +++ /dev/null @@ -1,149 +0,0 @@ -.. role:: raw-html-m2r(raw) - :format: html - - -.. raw:: html - -

- - - -

- -.. raw:: html - -

The Basic Model Interface

- - - -.. raw:: html - -

- - - DOI - - JOSS article - - Documentation Status - - License: MIT - -

- -

- - The Basic Model Interface (BMI) is a standardized set of functions - that allows coupling of models to models and models to data. - -

- -The *Basic Model Interface* (BMI), -developed by the `Community Surface Dynamics Modeling System`_ (CSDMS), -is a standardized set of control and query functions that, -when added to a software element such as a model or a dataset, -makes that software easier to couple with other software that also exposes a BMI. - -A BMI makes a model self-describing and fully controllable -by a modeling framework or application. -By design, the BMI functions are straightforward to implement in -any language, using basic data types from standard language libraries. -Also by design, the BMI functions are noninvasive. -This means that a model's BMI does not make calls to other -components or tools and is not modified to use any -framework-specific data structures. A BMI, therefore, introduces no -dependencies into a model, so the model can still be used -in a stand-alone manner. - -The BMI is expressed -in the `Scientific Interface Definition Language`_ (SIDL). -From `bmi.sidl <./bmi.sidl>`_, -CSDMS has derived BMI specifications -for five languages--C, C++, Fortran, Java, -and Python. -For each language, -links to the specification and an example implementation -are listed in the table below. - -.. table:: BMI languages - :align: center - :widths: 10, 10, 15 - - ======== ============== ====================== - Language Specification Example implementation - ======== ============== ====================== - C `bmi-c`_ `bmi-example-c`_ - C++ `bmi-cxx`_ `bmi-example-cxx`_ - Fortran `bmi-fortran`_ `bmi-example-fortran`_ - Java `bmi-java`_ `bmi-example-java`_ - Python `bmi-python`_ `bmi-example-python`_ - ======== ============== ====================== - -Detailed instructions for building the specifications and examples -are given at each link above. -Alternatively, the specifications can be installed through conda -(C, C++, Fortran, Python) or Maven (Java). -See the links above for details. - -While CSDMS currently supports the languages listed above, -a BMI specification can be written for any language. -BMI is a community-driven standard; -`contributions `_ -that follow the `contributor code of conduct <./CODE-OF-CONDUCT.rst>`_ -are welcomed, -and are `acknowledged <./AUTHORS.rst>`_. - -The table below lists community-contributed -language specifications and examples -for two languages, Javascript and Julia. - -.. table:: Community-contributed BMI languages - :align: center - :widths: 10, 10, 15 - - ========== ============= ====================== - Language Specification Example implementation - ========== ============= ====================== - Javascript `bmi-js`_ `bmi-example-js`_ - Julia `bmi-julia`_ `bmi-example-julia`_ - ========== ============= ====================== - -The default branch of this repository -reflects the current state of development for the BMI. -When implementing a BMI, -please use the `latest release`_ listed in the right sidebar; -currently this is `Basic Model Interface 2.0`_. -For more information on implementing a BMI, -see the `documentation`_. - -BMI is open source software released under the `MIT License <./LICENSE>`_. -BMI is an element of the `CSDMS Workbench`_, -an integrated system of software tools, technologies, and standards -for building and coupling models. - -*The Community Surface Dynamics Modeling System -is supported by the National Science Foundation.* - - -.. Links - -.. _Community Surface Dynamics Modeling System: https://csdms.colorado.edu -.. _Scientific Interface Definition Language: https://doi.org/10.1177/1094342011414036 -.. _bmi-c: https://github.com/csdms/bmi-c -.. _bmi-cxx: https://github.com/csdms/bmi-cxx -.. _bmi-fortran: https://github.com/csdms/bmi-fortran -.. _bmi-java: https://github.com/csdms/bmi-java -.. _bmi-python: https://github.com/csdms/bmi-python -.. _bmi-js: https://github.com/uihilab/bmi-js -.. _bmi-julia: https://github.com/Deltares/BasicModelInterface.jl -.. _bmi-example-c: https://github.com/csdms/bmi-example-c -.. _bmi-example-cxx: https://github.com/csdms/bmi-example-cxx -.. _bmi-example-fortran: https://github.com/csdms/bmi-example-fortran -.. _bmi-example-java: https://github.com/csdms/bmi-example-java -.. _bmi-example-python: https://github.com/csdms/bmi-example-python -.. _bmi-example-js: https://github.com/uihilab/bmi-example-js -.. _bmi-example-julia: https://github.com/csdms/bmi-example-julia -.. _latest release: https://github.com/csdms/bmi/releases -.. _Basic Model Interface 2.0: https://github.com/csdms/bmi/releases/tag/v2.0 -.. _documentation: https://bmi.readthedocs.io -.. _CSDMS Workbench: https://csdms.colorado.edu/wiki/Workbench From b8ee87cb5f020155eef6c7a1573a0f9fe8e32787 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 12:53:38 +0000 Subject: [PATCH 06/10] fix include path to citation --- docs/source/citation.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/source/citation.md b/docs/source/citation.md index fedf91b..7bfb2f2 100644 --- a/docs/source/citation.md +++ b/docs/source/citation.md @@ -1,3 +1,2 @@ -```{eval-rst} -.. include:: ../../CITATION.rst -``` +:::{include} ../../CITATION.md +::: From 696924d0599f2308ea94b252c995851d10d64a3e Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 12:53:50 +0000 Subject: [PATCH 07/10] fix include path to conduct --- docs/source/conduct.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/source/conduct.md b/docs/source/conduct.md index 4c81971..782cf0f 100644 --- a/docs/source/conduct.md +++ b/docs/source/conduct.md @@ -1,3 +1,2 @@ -```{eval-rst} -.. include:: ../../CODE-OF-CONDUCT.rst -``` +:::{include} ../../CODE-OF-CONDUCT.md +::: From 730edb5ba924b5792d9b8756e013fe1ae4ab7531 Mon Sep 17 00:00:00 2001 From: mcflugen Date: Wed, 6 Nov 2024 12:54:21 +0000 Subject: [PATCH 08/10] fix include path to credits --- docs/source/credits.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/source/credits.md b/docs/source/credits.md index 677dfca..56bfe51 100644 --- a/docs/source/credits.md +++ b/docs/source/credits.md @@ -1,3 +1,2 @@ -```{eval-rst} -.. include:: ../../AUTHORS.rst -``` +:::{include} ../../AUTHORS.md +::: From c4afbd997c131675765248d20c4c96194f5d47fa Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 8 Nov 2024 16:13:27 -0700 Subject: [PATCH 09/10] add license to the docs --- docs/source/license.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 docs/source/license.md diff --git a/docs/source/license.md b/docs/source/license.md new file mode 100644 index 0000000..2fdacf1 --- /dev/null +++ b/docs/source/license.md @@ -0,0 +1,2 @@ +:::{include} ../../LICENSE.md +::: From 8adabc989e40d6e396480834a3df209bb3e6762e Mon Sep 17 00:00:00 2001 From: mcflugen Date: Fri, 8 Nov 2024 16:13:40 -0700 Subject: [PATCH 10/10] link to license in the about section --- docs/source/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/index.md b/docs/source/index.md index 6cdf91e..3ddfb27 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -131,6 +131,7 @@ credits Governance council partners +License ``` ```{toctree}