Merge pull request #288 from stan-dev/v1.0

Release version 1.0

Author: MansMeg

.github/workflows/posteriordb_content.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('DESCRIPTION') }}

LICENCE.md

@@ -0,0 +1,14 @@
+BSD 3-Clause License
+
+Copyright (c) 2011-2024, Stan Developers and their Assignees
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.Rmd

@@ -34,6 +34,11 @@ See [DATABASE_CONTENT.md](https://github.com/stan-dev/posteriordb/blob/master/do
 
 We are happy with any help in adding posteriors, data, and models to the database! See [CONTRIBUTING.md](https://github.com/stan-dev/posteriordb/blob/master/doc/CONTRIBUTING.md) for the details on how to contribute.
 
+## Licensing
+The posteriordb is licensed under the [new BSD
+license](https://github.com/stan-dev/posteriordb/LICENCE.md).
+
+Most model code are using the the same BSD-3 licence. Although, some models and some data might have other open licences such as MIT. Each model has a ```licence``` element in the info JSON files that specifies the actual licence of the model. Some data might also have licences, then that is specified in a similar way.
 
 ## Using `posteriordb`
 

README.md

@@ -7,19 +7,16 @@ Content](https://github.com/stan-dev/posteriordb/actions/workflows/posteriordb_c
 coverage](https://codecov.io/gh/stan-dev/posteriordb-r/branch/main/graph/badge.svg)](https://codecov.io/gh/stan-dev/posteriordb-r?branch=main)
 [![Python](https://github.com/stan-dev/posteriordb-python/actions/workflows/push.yml/badge.svg)](https://github.com/stan-dev/posteriordb-python/actions/workflows/push.yml)
 
-`posteriordb`: a database of Bayesian posterior inference
-=========================================================
+# `posteriordb`: a database of Bayesian posterior inference
 
-What is `posteriordb`?
-----------------------
+## What is `posteriordb`?
 
 `posteriordb` is a set of posteriors, i.e. Bayesian statistical models
 and data sets, reference implementations in probabilistic programming
 languages, and reference posterior inferences in the form of posterior
 samples.
 
-Why use `posteriordb`?
-----------------------
+## Why use `posteriordb`?
 
 `posteriordb` is designed to test inference algorithms across a wide
 range of models and data sets. Applications include testing for
@@ -36,34 +33,42 @@ definitions, well-curated data sets, and reference posteriors.
 Python.
 
 For more details regarding the use cases of `posteriordb`, see
-[doc/use\_cases.md](https://github.com/stan-dev/posteriordb/blob/master/doc/use_cases.md).
+[doc/use_cases.md](https://github.com/stan-dev/posteriordb/blob/master/doc/use_cases.md).
 
-Content
--------
+## Content
 
 See
-[DATABASE\_CONTENT.md](https://github.com/stan-dev/posteriordb/blob/master/doc/DATABASE_CONTENT.md)
+[DATABASE_CONTENT.md](https://github.com/stan-dev/posteriordb/blob/master/doc/DATABASE_CONTENT.md)
 for the details content of the posterior database.
 
-Contributing
-------------
+## Contributing
 
 We are happy with any help in adding posteriors, data, and models to the
 database! See
 [CONTRIBUTING.md](https://github.com/stan-dev/posteriordb/blob/master/doc/CONTRIBUTING.md)
 for the details on how to contribute.
 
-Using `posteriordb`
--------------------
+## Licensing
+
+The posteriordb is licensed under the [new BSD
+license](https://github.com/stan-dev/posteriordb/LICENCE.md).
+
+Most model code are using the the same BSD-3 licence. Although, some
+models and some data might have other open licences such as MIT. Each
+model has a `licence` element in the info JSON files that specifies the
+actual licence of the model. Some data might also have licences, then
+that is specified in a similar way.
+
+## Using `posteriordb`
 
 To simplify the use of `posteriordb`, there are convenience functions
-both in R and in Python. 
-- For R, see the [posteriordb-r](https://github.com/stan-dev/posteriordb-r) repository.
-- For Python, see the [posteriordb-python](https://github.com/stan-dev/posteriordb-python)
+both in Python and in R. To use R, see the
+[posteriordb-r](https://github.com/stan-dev/posteriordb-r) repository,
+and to use Python, see the
+[posteriordb-python](https://github.com/stan-dev/posteriordb-python)
 repository.
 
-Citing `posteriordb`
---------------------
+## Citing `posteriordb`
 
 Developing and maintaining open-source software is an important yet
 often underappreciated contribution to scientific progress. Thus, please
@@ -81,8 +86,7 @@ M., Brubaker M., Guo J., Li P., and Riddell A. (2017). Stan: A
 probabilistic programming language. Journal of Statistical Software.
 76(1). 10.18637/jss.v076.i01
 
-Design choices (so far)
------------------------
+## Design choices (so far)
 
 The main focus of the database is simplicity, both in understanding and
 in use.
@@ -108,8 +112,7 @@ database.
     included in the PPL syntax files as comments, not in the
     model.info.json files.
 
-Versioning of models
---------------------
+## Versioning of models
 
 We might update models included in posteriordb over time. However, the
 models will only have the same name in posteriordb if the log density is

croissant.json

@@ -0,0 +1,118 @@
+{
+  "@context": {
+    "@language": "en",
+    "@vocab": "https://schema.org/",
+    "citeAs": "cr:citeAs",
+    "column": "cr:column",
+    "conformsTo": "dct:conformsTo",
+    "cr": "http://mlcommons.org/croissant/",
+    "rai": "http://mlcommons.org/croissant/RAI/",
+    "data": {
+      "@id": "cr:data",
+      "@type": "@json"
+    },
+    "dataType": {
+      "@id": "cr:dataType",
+      "@type": "@vocab"
+    },
+    "dct": "http://purl.org/dc/terms/",
+    "examples": {
+      "@id": "cr:examples",
+      "@type": "@json"
+    },
+    "extract": "cr:extract",
+    "field": "cr:field",
+    "fileProperty": "cr:fileProperty",
+    "fileObject": "cr:fileObject",
+    "fileSet": "cr:fileSet",
+    "format": "cr:format",
+    "includes": "cr:includes",
+    "isLiveDataset": "cr:isLiveDataset",
+    "jsonPath": "cr:jsonPath",
+    "key": "cr:key",
+    "md5": "cr:md5",
+    "parentField": "cr:parentField",
+    "path": "cr:path",
+    "recordSet": "cr:recordSet",
+    "references": "cr:references",
+    "regex": "cr:regex",
+    "repeated": "cr:repeated",
+    "replace": "cr:replace",
+    "sc": "https://schema.org/",
+    "separator": "cr:separator",
+    "source": "cr:source",
+    "subField": "cr:subField",
+    "transform": "cr:transform"
+  },
+  "@type": "sc:Dataset",
+  "name": "posteriordb",
+  "description": " Probabilistic programming languages (PPL), such as Stan, Tensorflow Probability, PyMC, Pyro, and Turing.jl,are becoming increasingly popular for Bayesian probabilistic data analysis and predictive modelling.  These languages all rely on general inference algorithms such as Markov chain Monte Carlo sampling or black-box variational inference. We introduce posteriordb, a database of models, compatible data sets, and reference posteriors intended to make evaluatingand comparing models easier and more trustworthy. Posteriordb currently includes mixed effect regressions, time series, hierarchical Gaussian processes, hidden Markov models, mixture models, ordinary differential equation models, and more. ",
+  "conformsTo": "http://mlcommons.org/croissant/1.0",
+  "url": "https://https://github.com/stan-dev/posteriordb",
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "@id": "github-repository",
+      "name": "github-repository",
+      "description": "PosteriorDB's GitHub repository.",
+      "contentUrl": "https://https://github.com/stan-dev/posteriordb",
+      "encodingFormat": "git+https",
+      "sha256": "main"
+    },
+    {
+      "@type": "cr:FileSet",
+      "@id": "data-zip-files",
+      "name": "data-zip-files",
+      "description": "Datasets in json format stored in zip files.",
+      "containedIn": {
+        "@id": "github-repository"
+      },
+      "encodingFormat": "application/zip",
+      "includes": "posterior_database/data/data/*.zip"
+    },
+    {
+      "@type": "cr:FileSet",
+      "@id": "data-csv-files",
+      "name": "data-csv-files",
+      "description": "Datasets stored in csv format.",
+      "containedIn": {
+        "@id": "github-repository"
+      },
+      "encodingFormat": "application/zip",
+      "includes": "posterior_database/data/data-raw/*.csv"
+    },
+    {
+      "@type": "cr:FileSet",
+      "@id": "draws-zip-files",
+      "name": "draws-zip-files",
+      "description": "Posterior samples in json format stored in zip files.",
+      "containedIn": {
+        "@id": "github-repository"
+      },
+      "encodingFormat": "application/zip",
+      "includes": "posterior_database/reference_posteriors/draws/draws/*.zip"
+    },
+    {
+      "@type": "cr:FileSet",
+      "@id": "stan-model-files",
+      "name": "stan-model-files",
+      "description": "Posterior models in .stan format.",
+      "containedIn": {
+        "@id": "github-repository"
+      },
+      "encodingFormat": "application/stan",
+      "includes": "posterior_database/models/stan/*.stan"
+    },
+    {
+      "@type": "cr:FileSet",
+      "@id": "pymc3-model-files",
+      "name": "pymc3-model-files",
+      "description": "Posterior pymc3 models in .py format.",
+      "containedIn": {
+        "@id": "github-repository"
+      },
+      "encodingFormat": "application/py",
+      "includes": "posterior_database/models/pymc3/*.py"
+    }
+  ]
+}

doc/use_cases.md

@@ -3,7 +3,7 @@
 posteriordb has different uses. Below is list of example use cases and what features are important in each use case.
 
 
-## Unit testing
+## Testing
 
 Developers of different algorithms can use the posterior database to get data, models and reference posteriors to asses that the software is working as it should.
 

posterior_database/models/info/2pl_latent_reg_irt.info.json

@@ -3,7 +3,7 @@
   "keywords": "item response model",
   "title": "Two-parameter logistic item theory model with latent regression",
   "description": "The Rasch model (Rasch 1960) is an item response theory model for dichotomous items. The two-parameter logistic model (2PL) (Swaminathan and Gifford 1985) is an item response theory model that includes parameters for both the difficulty and discrimination of dichotomous items. The version presented includes a latent regression. However, the latent regression part of the model may be restricted to an intercept only, resulting in a regular 2PL.",
-  "urls": "https://github.com/danielcfurr/edstan",
+  "urls": ["https://github.com/danielcfurr/edstan", "https://mc-stan.org/users/documentation/case-studies/rasch_and_2pl.html"],
   "references": null,
   "added_by": "Keane Nguyen",
   "added_date": "2021-08-03",
@@ -12,5 +12,6 @@
       "model_code": "models/stan/2pl_latent_reg_irt.stan",
       "stan_version": ">=2.26.0"
     }
-  }
+  },
+  "licence": "BSD3"
 }

posterior_database/models/info/GLMM1_model.info.json

@@ -12,5 +12,6 @@
       "model_code": "models/stan/GLMM1_model.stan",
       "stan_version": ">=2.26.0"
     }
-  }
+  },
+  "licence": "BSD3"
 }

posterior_database/models/info/GLMM_Poisson_model.info.json

@@ -12,5 +12,6 @@
       "model_code": "models/stan/GLMM_Poisson_model.stan",
       "stan_version": ">=2.26.0"
     }
-  }
+  },
+  "licence": "BSD3"
 }

posterior_database/models/info/GLM_Binomial_model.info.json

@@ -12,5 +12,6 @@
       "model_code": "models/stan/GLM_Binomial_model.stan",
       "stan_version": ">=2.26.0"
     }
-  }
+  },
+  "licence": "BSD3"
 }