dbverse
**Note: work in progress **
diff --git a/overview/index.html b/overview/index.html index e7ecef2..ebc2284 100644 --- a/overview/index.html +++ b/overview/index.html @@ -259,97 +259,96 @@dbverse","text":"**Note: work in progress **
The dbverse is an ecosystem of open-source and composable database libraries for larger-than-memory scientific data analysis. The dbverse provides object relational mappings for common scientific data objects, including sparse and dense matrices, spatial geometries, and others, and is powered by DuckDB.
The goal of dbverse is to enable larger-than-memory scientific data analysis across programming languages with databases. Please visit the packages page for details about each dbverse package. On release, the dbverse is compatible with R with support for other languages planned in the future.
We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
"},{"location":"conduct/#our-standards","title":"Our Standards","text":"Examples of behavior that contributes to a positive environment for our community include:
Examples of unacceptable behavior include:
Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
"},{"location":"conduct/#scope","title":"Scope","text":"This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official email address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
"},{"location":"conduct/#enforcement","title":"Enforcement","text":"Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at ecr7407@gmail.com. All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the reporter of any incident.
"},{"location":"conduct/#enforcement-guidelines","title":"Enforcement Guidelines","text":"Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
"},{"location":"conduct/#1-correction","title":"1. Correction","text":"Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
"},{"location":"conduct/#2-warning","title":"2. Warning","text":"Community Impact: A violation through a single incident or series of actions.
Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
"},{"location":"conduct/#3-temporary-ban","title":"3. Temporary Ban","text":"Community Impact: A serious violation of community standards, including sustained inappropriate behavior.
Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
"},{"location":"conduct/#4-permanent-ban","title":"4. Permanent Ban","text":"Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
Consequence: A permanent ban from any sort of public interaction within the community.
"},{"location":"conduct/#attribution","title":"Attribution","text":"This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
Community Impact Guidelines were inspired by Mozilla's code of conduct enforcement ladder.
For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.
"},{"location":"contribute/","title":"Contribute","text":"TODO
"},{"location":"overview/","title":"dbverse","text":"Note: {dbverse} is in early development. Changes to the below are likely to occur.
classDiagram\ndirection LR\n\nnamespace Data {\n\n class tabular{\n .mtx\n .csv\n .parquet\n dgCMatrix\n data.frames\n }\n\n class geometries{\n .shp\n .geojson\n sf::sf\n terra::spatVector\n }\n\n}\n\nnamespace dbverse {\n\n class dbMatrix_lib{\n\n }\n\n class dbSpatial_lib{\n\n }\n\n class dbData_lib{\n\n }\n\n}\n\nnamespace dbData_lib {\n class dbData {\n <<base virtual class>>\n + value: duckdb_table\n + name: character string\n + init: boolean\n - DBI::*()\n }\n\n}\n\nnamespace dbSpatial_lib {\n\n class dbSpatial{\n - ST_*(geom) [DuckDB_spatial]\n }\n\n class dbSpatialPoints{\n - ST_*(geom_point) \n }\n\n class dbSpatialPolygons{\n - ST_*(geom_polygon)\n }\n}\n\nnamespace dbMatrix_lib {\n class dbMatrix {\n + dim_names: [enum,enum]\n + dims: [int, int]\n + class: \"sparse\" | \"dense\"\n - dbMatrix::*()\n - dbMatrixStats::*()\n }\n\n class dbSparseMatrix{\n\n }\n\n class dbDenseMatrix{\n\n }\n}\n\n\ntabular <..> dbData_lib : read/write\ngeometries <..> dbData_lib : read/write\n\ndbData_lib --> dbMatrix_lib\ndbData_lib --> dbSpatial_lib\n\ndbSpatial --> dbSpatialPoints\ndbSpatial --> dbSpatialPolygons\n\ndbMatrix --> dbDenseMatrix\ndbMatrix --> dbSparseMatrix\ndbverse currently consists of four core libraries that contain classes, generics, and methods for representing and analyzing scientific data objects in a DuckDB database.
{dbMatrix} - A library for sparse/dense matrix operations in a database.{dbSpatial} - A library for spatial operations in a database.{dbData} - A library with specifications for base class of dbverse. In progress.{dbSequence} - A library for genomic sequence operations in a database. In progress.R Packages that use dbverse. Want to be added to this list? Please submit an issue or pull request on our Github.
dbverse","text":"**Note: work in progress **
The dbverse is an ecosystem of open-source and composable database libraries for larger-than-memory scientific data analysis. The dbverse provides object relational mappings for common scientific data objects, including sparse and dense matrices, spatial geometries, and others, and is powered by DuckDB.
The goal of dbverse is to enable larger-than-memory scientific data analysis across programming languages with databases. Please visit the packages page for details about each dbverse package. On release, the dbverse is compatible with R with support for other languages planned in the future.
We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
"},{"location":"conduct/#our-standards","title":"Our Standards","text":"Examples of behavior that contributes to a positive environment for our community include:
Examples of unacceptable behavior include:
Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
"},{"location":"conduct/#scope","title":"Scope","text":"This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official email address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
"},{"location":"conduct/#enforcement","title":"Enforcement","text":"Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at ecr7407@gmail.com. All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the reporter of any incident.
"},{"location":"conduct/#enforcement-guidelines","title":"Enforcement Guidelines","text":"Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
"},{"location":"conduct/#1-correction","title":"1. Correction","text":"Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
"},{"location":"conduct/#2-warning","title":"2. Warning","text":"Community Impact: A violation through a single incident or series of actions.
Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
"},{"location":"conduct/#3-temporary-ban","title":"3. Temporary Ban","text":"Community Impact: A serious violation of community standards, including sustained inappropriate behavior.
Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
"},{"location":"conduct/#4-permanent-ban","title":"4. Permanent Ban","text":"Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
Consequence: A permanent ban from any sort of public interaction within the community.
"},{"location":"conduct/#attribution","title":"Attribution","text":"This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.
Community Impact Guidelines were inspired by Mozilla's code of conduct enforcement ladder.
For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.
"},{"location":"contribute/","title":"Contribute","text":"TODO
"},{"location":"overview/","title":"dbverse","text":"Note: {dbverse} is in early development. Changes to the below are likely to occur.
classDiagram\ndirection LR\n\nnamespace Input_Data {\n class numerical{\n .mtx\n .csv\n .parquet\n dgcMatrix\n matrix\n data.frame\n data.table\n }\n\n class geometries{\n 50+ spatial file formats\n sf::sf\n terra::spatVector\n }\n\n class sequences{\n 10+ genomic file formats\n }\n}\n\nnamespace computer {\n class database\n}\n\nnamespace dbverse {\n class dbMatrix_lib{\n class dbMatrix\n }\n\n class dbSpatial_lib{\n class dbSpatial\n }\n\n class dbSequence_lib{\n class dbSequence\n }\n\n class dbData_lib{\n class dbData\n }\n}\n\nnamespace dbMatrix_lib {\n class dbMatrix {\n + dbData: dbData\n + dim_names: [enum,enum]\n + dims: [int, int]\n + class: \"dbSparseMatrix\" | \"dbDenseMatrix\"\n - Arith\n - Ops\n - matrix summary functions()\n }\n}\n\nnamespace dbSpatial_lib {\n class dbSpatial{\n + dbData: dbData\n - ST_*(geom) [DuckDB Spatial Extension]\n }\n}\n\nnamespace dbSequence_lib {\n class dbSequence{\n + dbData: dbData\n }\n}\n\nnamespace dbData_lib {\n class dbData {\n <<base virtual class>>\n + value: Input_Data\n + name: table_name\n + init: boolean\n + conn: DuckDB connection\n - DBI::()\n - dplyr::()\n }\n}\n\nnumerical <..> dbMatrix_lib : read/write\ngeometries <..> dbSpatial_lib : read/write\nsequences <..> dbSequence_lib : read/write\n\ndbMatrix_lib --> dbData_lib\ndbSpatial_lib --> dbData_lib\ndbSequence_lib --> dbData_lib\n\ndbData_lib <..> database : connect/disconnect/cache\ndbverse currently consists of four core libraries that contain classes, generics, and methods for representing and analyzing scientific data objects in a DuckDB database.
{dbMatrix} - A library for sparse/dense matrix operations in a database.{dbSpatial} - A library for spatial operations in a database.{dbData} - A library with specifications for base class of dbverse. In progress.{dbSequence} - A library for genomic sequence operations in a database. In progress.R Packages that use dbverse. Want to be added to this list? Please submit an issue or pull request on our Github.