update with FluSight hubverse template

elray1 · Sep 11, 2023 · e3dcdbd · e3dcdbd
1 parent 89740bc
commit e3dcdbd
Show file tree

Hide file tree

Showing 9 changed files with 467 additions and 123 deletions.
diff --git a/LICENSE b/LICENSE
@@ -1,121 +1,21 @@
-Creative Commons Legal Code
-
-CC0 1.0 Universal
-
-    CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
-    LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
-    ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS
-    INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES
-    REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
-    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
-    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
-    HEREUNDER.
-
-Statement of Purpose
-
-The laws of most jurisdictions throughout the world automatically confer
-exclusive Copyright and Related Rights (defined below) upon the creator
-and subsequent owner(s) (each and all, an "owner") of an original work of
-authorship and/or a database (each, a "Work").
-
-Certain owners wish to permanently relinquish those rights to a Work for
-the purpose of contributing to a commons of creative, cultural and
-scientific works ("Commons") that the public can reliably and without fear
-of later claims of infringement build upon, modify, incorporate in other
-works, reuse and redistribute as freely as possible in any form whatsoever
-and for any purposes, including without limitation commercial purposes.
-These owners may contribute to the Commons to promote the ideal of a free
-culture and the further production of creative, cultural and scientific
-works, or to gain reputation or greater distribution for their Work in
-part through the use and efforts of others.
-
-For these and/or other purposes and motivations, and without any
-expectation of additional consideration or compensation, the person
-associating CC0 with a Work (the "Affirmer"), to the extent that he or she
-is an owner of Copyright and Related Rights in the Work, voluntarily
-elects to apply CC0 to the Work and publicly distribute the Work under its
-terms, with knowledge of his or her Copyright and Related Rights in the
-Work and the meaning and intended legal effect of CC0 on those rights.
-
-1. Copyright and Related Rights. A Work made available under CC0 may be
-protected by copyright and related or neighboring rights ("Copyright and
-Related Rights"). Copyright and Related Rights include, but are not
-limited to, the following:
-
-  i. the right to reproduce, adapt, distribute, perform, display,
-     communicate, and translate a Work;
- ii. moral rights retained by the original author(s) and/or performer(s);
-iii. publicity and privacy rights pertaining to a person's image or
-     likeness depicted in a Work;
- iv. rights protecting against unfair competition in regards to a Work,
-     subject to the limitations in paragraph 4(a), below;
-  v. rights protecting the extraction, dissemination, use and reuse of data
-     in a Work;
- vi. database rights (such as those arising under Directive 96/9/EC of the
-     European Parliament and of the Council of 11 March 1996 on the legal
-     protection of databases, and under any national implementation
-     thereof, including any amended or successor version of such
-     directive); and
-vii. other similar, equivalent or corresponding rights throughout the
-     world based on applicable law or treaty, and any national
-     implementations thereof.
-
-2. Waiver. To the greatest extent permitted by, but not in contravention
-of, applicable law, Affirmer hereby overtly, fully, permanently,
-irrevocably and unconditionally waives, abandons, and surrenders all of
-Affirmer's Copyright and Related Rights and associated claims and causes
-of action, whether now known or unknown (including existing as well as
-future claims and causes of action), in the Work (i) in all territories
-worldwide, (ii) for the maximum duration provided by applicable law or
-treaty (including future time extensions), (iii) in any current or future
-medium and for any number of copies, and (iv) for any purpose whatsoever,
-including without limitation commercial, advertising or promotional
-purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each
-member of the public at large and to the detriment of Affirmer's heirs and
-successors, fully intending that such Waiver shall not be subject to
-revocation, rescission, cancellation, termination, or any other legal or
-equitable action to disrupt the quiet enjoyment of the Work by the public
-as contemplated by Affirmer's express Statement of Purpose.
-
-3. Public License Fallback. Should any part of the Waiver for any reason
-be judged legally invalid or ineffective under applicable law, then the
-Waiver shall be preserved to the maximum extent permitted taking into
-account Affirmer's express Statement of Purpose. In addition, to the
-extent the Waiver is so judged Affirmer hereby grants to each affected
-person a royalty-free, non transferable, non sublicensable, non exclusive,
-irrevocable and unconditional license to exercise Affirmer's Copyright and
-Related Rights in the Work (i) in all territories worldwide, (ii) for the
-maximum duration provided by applicable law or treaty (including future
-time extensions), (iii) in any current or future medium and for any number
-of copies, and (iv) for any purpose whatsoever, including without
-limitation commercial, advertising or promotional purposes (the
-"License"). The License shall be deemed effective as of the date CC0 was
-applied by Affirmer to the Work. Should any part of the License for any
-reason be judged legally invalid or ineffective under applicable law, such
-partial invalidity or ineffectiveness shall not invalidate the remainder
-of the License, and in such case Affirmer hereby affirms that he or she
-will not (i) exercise any of his or her remaining Copyright and Related
-Rights in the Work or (ii) assert any associated claims and causes of
-action with respect to the Work, in either case contrary to Affirmer's
-express Statement of Purpose.
-
-4. Limitations and Disclaimers.
-
- a. No trademark or patent rights held by Affirmer are waived, abandoned,
-    surrendered, licensed or otherwise affected by this document.
- b. Affirmer offers the Work as-is and makes no representations or
-    warranties of any kind concerning the Work, express, implied,
-    statutory or otherwise, including without limitation warranties of
-    title, merchantability, fitness for a particular purpose, non
-    infringement, or the absence of latent or other defects, accuracy, or
-    the present or absence of errors, whether or not discoverable, all to
-    the greatest extent permissible under applicable law.
- c. Affirmer disclaims responsibility for clearing rights of other persons
-    that may apply to the Work or any use thereof, including without
-    limitation any person's Copyright and Related Rights in the Work.
-    Further, Affirmer disclaims responsibility for obtaining any necessary
-    consents, permissions or other rights required for any use of the
-    Work.
- d. Affirmer understands and acknowledges that Creative Commons is not a
-    party to this document and has no duty or obligation with respect to
-    this CC0 or use of the Work.
+MIT License
+
+Copyright (c) 2022 Consortium of Infectious Disease Modeling Hubs
+
+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/README.md b/README.md
@@ -1,3 +1,3 @@
-# FluSight-forecast-hub
+# FluSight 2023-2024
 
-## Updates to follow for 2023-2024 season
+This repository is designed to collect forecast data for the 2023-2024 FluSight collaborative exercise run by the US CDC. This project collects forecasts for weekly new hospitalizations due to confirmed influenza.
diff --git a/hub-config b/hub-config
diff --git a/hub-config/README.md b/hub-config/README.md
@@ -0,0 +1,3 @@
+# Hub metadata
+
+This folder should contain configuration files for the Hub, following the recommended [Hub metadata guidelines in our documentation](https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html).
diff --git a/hub-config/admin.json b/hub-config/admin.json
@@ -0,0 +1,13 @@
+{
+    "schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v1.0.0/admin-schema.json",
+    "name": "US CDC FluSight",
+    "maintainer": "US CDC",
+    "contact": {
+        "name": "Rebecca Borchering",
+        "email": "[email protected]"
+    },
+    "repository_host": "GitHub",
+    "repository_url": "https://github.com/Infectious-Disease-Modeling-Hubs/FluSight-hubverse",
+    "file_format": ["csv"],
+    "timezone": "US/Eastern"
+}
diff --git a/hub-config/model-metadata-schema.json b/hub-config/model-metadata-schema.json
@@ -0,0 +1,143 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "title": "Schema for Modeling Hub model metadata",
+    "description": "This is the schema for model metadata files, please refer to https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe/wiki/Metadata for more information.",
+    "type": "object",
+    "properties": {
+        "schema_version": {
+            "type": "string",
+            "format": "uri"
+        },
+        "team_name": {
+            "description": "The name of the team submitting the model",
+            "type": "string"
+        },
+        "team_abbr": {
+            "description": "Abbreviated name of the team submitting the model",
+            "type": "string",
+            "pattern": "^[a-zA-Z0-9_+]+$",
+            "maxLength": 16
+        },
+        "model_name": {
+            "description": "The name of the model",
+            "type": "string"
+        },
+        "model_abbr": {
+            "description": "Abbreviated name of the model",
+            "type": "string",
+            "pattern": "^[a-zA-Z0-9_+]+$",
+            "maxLength": 16
+        },
+        "model_version": {
+            "description": "Identifier of the version of the model",
+            "type": "string"
+        },
+        "model_contributors": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "name": {
+                        "type": "string"
+                    },
+                    "affiliation": {
+                        "type": "string"
+                    },
+                    "orcid": {
+                        "type": "string",
+                        "pattern": "^\\d{4}\\-\\d{4}\\-\\d{4}\\-[\\dX]{4}$"
+                    },
+                    "email": {
+                        "type": "string",
+                        "format": "email"
+                    },
+                    "twitter": {
+                        "type": "string"
+                    },
+                    "additionalProperties": false
+                }
+            }
+        },
+        "website_url": {
+            "description": "Public facing website for the model",
+            "type": "string",
+            "format": "uri"
+        },
+        "repo_url": {
+            "description": "Repository containing code for the model",
+            "type": "string",
+            "format": "uri"
+        },
+        "license": {
+            "description": "License for use of model output data",
+            "type": "string",
+            "enum": [
+                "CC0-1.0",
+                "CC-BY-4.0",
+                "CC-BY_SA-4.0",
+                "PPDL",
+                "ODC-by",
+                "ODbL",
+                "OGL-3.0"
+            ]
+        },
+        "include_viz": {
+            "description": "Indicator for whether the model should be included in the Hub’s visualization",
+            "type": "boolean"
+        },
+        "include_ensemble": {
+            "description": "Indicator for whether the model should be included in the Hub’s ensemble",
+            "type": "boolean"
+        },
+        "include_eval": {
+            "description": "Indicator for whether the model should be scored for inclusion in the Hub’s evaluations",
+            "type": "boolean"
+        },
+        "citation": {
+            "description": "One or more citations for this model",
+            "type": "string",
+            "examples": "Gibson GC , Reich NG , Sheldon D. Real-time mechanistic bayesian forecasts of Covid-19 mortality. medRxiv. 2020. https://doi.org/10.1101/2020.12.22.20248736"
+        },
+        "team_funding": {
+            "description": "Any information about funding source for the team or members of the team.",
+            "type": "string",
+            "examples": "National Institutes of General Medical Sciences (R01GM123456). The content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS."
+        },
+        "model_details": {
+            "description": "Structured information about the model",
+            "type": "object",
+            "properties": {
+                "data_inputs": {
+                    "description": "List or description of data inputs used by the model",
+                    "type": "string"
+                },
+                "methods": {
+                    "description": "A brief (200 char.) description of the methods used by this model",
+                    "type": "string",
+                    "maxLength": 200
+                },
+                "methods_long": {
+                    "description": "A full description of the methods used by this model.",
+                    "type": "string"
+                }
+            },
+            "additionalProperties": false,
+            "required": ["data_inputs", "methods"]
+        },
+        "ensemble_of_hub_models": {
+            "description": "Indicator for whether this model is an ensemble of other Hub models",
+            "type": "boolean"
+        }
+    },
+    "additionalProperties": true,
+    "required": [
+        "schema_version",
+        "team_name",
+        "team_abbr",
+        "model_name",
+        "model_abbr",
+        "model_contributors",
+        "license",
+        "model_details"
+    ]
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Hub metadata

		This folder should contain configuration files for the Hub, following the recommended [Hub metadata guidelines in our documentation](https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html).