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macrostrat

A geological data platform for exploration, integration, and analysis

https://github.com/uw-macrostrat/macrostrat

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A geological data platform for exploration, integration, and analysis

Basic Info
  • Host: GitHub
  • Owner: UW-Macrostrat
  • License: apache-2.0
  • Language: PLpgSQL
  • Default Branch: main
  • Size: 26.5 MB
Statistics
  • Stars: 5
  • Watchers: 7
  • Forks: 1
  • Open Issues: 87
  • Releases: 0
Created over 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

Macrostrat

A geological data platform for exploration, integration, and analysis (v2).

This repository represents the core of the Macrostrat system, containing its database schema and control scripts to maintain it. As such, it provides a "build recipe" for the open-source core of Macrostrat, which in v2 will be provided publicly as a runnable platform for curating geologic maps and other datasets.

The core component packaged here is a Python application designed to control various aspects of Macrostrat's system and supporting processes (e.g., map caching and harmonization).

Key components in this repository

Management utilities

Services

  • API v3: An API for managing Macrostrat elements, and authentication
  • Macrostrat task runner: coming soon

Other Macrostrat services (e.g., read-only APIs) are housed in other repositories.

Installation

  • Running make will install the Python dependencies and build the application.
  • make test will run the test suite.
  • make install will install the application into the local root.

Setting the MACROSTRAT_PYROOT environment variable allows a different root Python version to be installed. This can be used to add new plugins or application dependencies.

Usage

Once a Macrostrat configuration file is defined, the Macrostrat command-line app presents a broad list of management functionality for Macrostrat's system. Subsystems (in progress) define functionality for specific aspects of the system.

This CLI is rapidly evolving so expect breakage!

Most functionality requires docker, and either docker compose or kubectl (for Kubernetes) to run.

``` Usage: macrostrat [OPTIONS] COMMAND [ARGS]...

Macrostrat control interface Active environment: local

╭─ Options ──────────────────────────────────────────────────────────────────────────────────╮ │ --verbose [env var: MACROSTRATLOCALVERBOSE] │ │ --help Show this message and exit. │ ╰────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─ Commands ─────────────────────────────────────────────────────────────────────────────────╮ │ secrets Get a secret from the Kubernetes cluster │ │ shell Start an IPython shell │ │ env Set the active environment │ │ install Install Macrostrat subsystems into the Python root. │ │ run Run a command in the Macrostrat command-line context │ │ db Manage the Macrostrat database │ │ config Manage configuration │ │ v1 Macrostrat CLI v1 commands │ ╰────────────────────────────────────────────────────────────────────────────────────────────╯ ╭─ Subsystems ───────────────────────────────────────────────────────────────────────────────╮ │ raster Raster data integration │ │ maps Map integration system (partial overlap with v1 commands) │ │ tileserver Control Macrostrat's tileserver │ │ paleogeography Manage paleogeography data │ │ self Manage the Macrostrat CLI itself │ ╰────────────────────────────────────────────────────────────────────────────────────────────╯ ```

Documentation

Documentation is a work in progress. We have starting points for:

Other documentation of general interest can be found in the docs/ directory.

Owner

  • Name: Macrostrat
  • Login: UW-Macrostrat
  • Kind: organization
  • Location: Madison, WI

Supported by the US National Science Foundation, DARPA, and UW-Madison Dept. Geoscience

GitHub Events

Total
  • Issues event: 49
  • Watch event: 2
  • Delete event: 74
  • Issue comment event: 64
  • Push event: 283
  • Pull request review event: 35
  • Pull request review comment event: 46
  • Pull request event: 82
  • Create event: 75
Last Year
  • Issues event: 49
  • Watch event: 2
  • Delete event: 74
  • Issue comment event: 64
  • Push event: 283
  • Pull request review event: 35
  • Pull request review comment event: 46
  • Pull request event: 82
  • Create event: 75

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 80
  • Total pull requests: 81
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 13 days
  • Total issue authors: 9
  • Total pull request authors: 6
  • Average comments per issue: 0.41
  • Average comments per pull request: 0.56
  • Merged pull requests: 64
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 36
  • Pull requests: 51
  • Average time to close issues: 14 days
  • Average time to close pull requests: 6 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 0.22
  • Average comments per pull request: 0.55
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • davenquinn (60)
  • amyfromandi (6)
  • davidsklar99 (4)
  • mwestphall (3)
  • brianaydemir (2)
  • RichardScottOZ (2)
  • cambro (1)
  • abodeuis (1)
  • CannonLock (1)
Pull Request Authors
  • davenquinn (46)
  • amyfromandi (12)
  • davidsklar99 (11)
  • brianaydemir (5)
  • CannonLock (4)
  • mwestphall (3)
Top Labels
Issue Labels
map-ingestion (3) enhancement (2) ingestion (2) api (1) command-line (1) bug (1) documentation (1)
Pull Request Labels
command-line (2) ingestion (1) map-ingestion (1) documentation (1) authentication (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 219 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: rmacrostrat

Fetch Geologic Data from the 'Macrostrat' Platform

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 219 Last month
Rankings
Dependent packages count: 28.5%
Dependent repos count: 35.1%
Average: 50.1%
Downloads: 86.8%
Maintainers (1)
LewisA.Jones@outlook.com
Last synced: 10 months ago

Dependencies

macrostrat-cli/Dockerfile docker
  • python 3.10 build
v2-transition/backup-system/Dockerfile docker
  • alpine 3.15 build
v2-transition/server-configs/dev-server/gateway/Dockerfile docker
  • jonasal/nginx-certbot 3 build
v2-transition/server-configs/dev-server/varnish/Dockerfile docker
  • varnish 7.1 build
map-integration/v1/package.json npm
  • async ^2.5.0
  • google-translate-api ^2.3.0
  • inquirer ^1.1.2
  • mkdirp ^0.5.1
  • pg ^6.0.2
  • yamljs ^0.2.8
map-integration/v1/tile-tester/package.json npm
  • @turf/random ^4.2.0
  • @turf/sample ^4.2.0
  • @turf/within ^4.2.0
  • express ^4.14.0
  • mapnik ^3.5.14
  • tilestrata ^2.0.2
  • tilestrata-etag ^0.1.1
  • tilestrata-mapnik ^0.4.1
  • tilestrata-vtile ^0.5.3
map-integration/v1/tiles/package.json npm
  • async ^1.4.2
  • carto ^0.15.2
  • fs-extra ^0.26.6
  • geojson-bounds ^1.0.0
  • inquirer ^0.12.0
  • mapnik ^3.5.0
  • minimist ^1.2.0
  • mkdirp ^0.5.1
  • pg ^4.4.2
  • portscanner ^1.0.0
  • progress ^1.1.8
  • redis ^2.5.3
  • request ^2.69.0
  • tile-cover ^3.0.1
  • tilestrata ^2.0.1
  • tilestrata-mapnik ^0.4.1
  • tilestrata-vtile ^0.5.3
macrostrat-cli/poetry.lock pypi
  • appnope 0.1.3
  • asttokens 2.2.1
  • attrs 23.1.0
  • backcall 0.2.0
  • certifi 2023.7.22
  • charset-normalizer 3.2.0
  • click 8.1.7
  • click-plugins 1.1.1
  • cligj 0.7.2
  • colorama 0.4.6
  • colorlog 6.7.0
  • colormath 3.0.0
  • decorator 5.1.1
  • dynaconf 3.2.2
  • exceptiongroup 1.1.3
  • executing 1.2.0
  • fiona 1.9.4.post1
  • geoalchemy2 0.9.4
  • geojson 2.5.0
  • geopandas 0.12.2
  • greenlet 2.0.2
  • idna 3.4
  • ipython 8.15.0
  • jedi 0.19.0
  • macrostrat-app-frame 1.1.0
  • macrostrat-database 2.1.3
  • macrostrat-utils 1.1.0
  • markdown-it-py 3.0.0
  • matplotlib-inline 0.1.6
  • mdurl 0.1.2
  • networkx 3.1
  • numpy 1.25.2
  • packaging 23.1
  • pandas 2.1.0
  • parso 0.8.3
  • pexpect 4.8.0
  • pickleshare 0.7.5
  • portforward 0.6.0
  • prompt-toolkit 3.0.39
  • psycopg2-binary 2.9.7
  • ptyprocess 0.7.0
  • pure-eval 0.2.2
  • pydantic 1.10.12
  • pygeos 0.14
  • pygments 2.16.1
  • pymysql 1.1.0
  • pyproj 3.6.0
  • python-dateutil 2.8.2
  • python-dotenv 1.0.0
  • pytz 2023.3
  • pyyaml 6.0.1
  • requests 2.31.0
  • rich 13.5.2
  • scipy 1.9.3
  • shapely 2.0.1
  • six 1.16.0
  • spectra 0.0.11
  • sqlalchemy 1.4.49
  • sqlalchemy-utils 0.37.9
  • sqlparse 0.4.4
  • stack-data 0.6.2
  • tiletanic 1.1.0
  • tqdm 4.66.1
  • traitlets 5.9.0
  • typer 0.9.0
  • typing-extensions 4.7.1
  • tzdata 2023.3
  • urllib3 2.0.4
  • wcwidth 0.2.6
macrostrat-cli/pyproject.toml pypi
  • Fiona ^1.8.22
  • PyMySQL ^1.0.2
  • PyYAML ^6.0
  • SQLAlchemy ^1.4.42
  • dynaconf ^3.1.12
  • geopandas ^0.12.0
  • ipython ^8.5.0
  • macrostrat.app-frame ^1.1.0
  • macrostrat.database ^2.0.0
  • numpy ^1.23.4
  • portforward ^0.6.0
  • psycopg2-binary ^2.9.4
  • pygeos ^0.14
  • pyproj ^3.4.0
  • python ^3.10
  • python-dotenv ^1.0.0
  • requests ^2.28.1
  • rich ^13
  • scipy ^1.9.3
  • shapely ^2.0.1
  • spectra ^0.0.11
  • tiletanic ^1.1.0
  • tqdm ^4.65.0
  • typer ^0.9.0
macrostrat-cli/setup.py pypi
  • fiona *
  • numpy *
  • psycopg2 *
  • pymysql *
  • pyproj *
  • pyyaml *
  • requests *
  • scipy *
  • shapely *
  • spectra *
  • sqlalchemy *
  • tiletanic *
  • tqdm *
map-integration/poetry.lock pypi
  • appnope 0.1.3
  • asttokens 2.2.1
  • attrs 22.2.0
  • backcall 0.2.0
  • black 22.12.0
  • certifi 2022.12.7
  • click 8.1.3
  • click-plugins 1.1.1
  • cligj 0.7.2
  • colorama 0.4.6
  • colorlog 6.7.0
  • decorator 5.1.1
  • executing 1.2.0
  • fiona 1.9.1
  • geoalchemy2 0.9.4
  • geopandas 0.12.2
  • greenlet 2.0.2
  • ipython 8.10.0
  • jedi 0.18.2
  • macrostrat-database 2.1.3
  • macrostrat-utils 1.1.0
  • markdown-it-py 3.0.0
  • matplotlib-inline 0.1.6
  • mdurl 0.1.2
  • munch 2.5.0
  • mypy-extensions 1.0.0
  • numpy 1.24.2
  • packaging 23.0
  • pandas 1.5.3
  • parso 0.8.3
  • pathspec 0.11.0
  • pexpect 4.8.0
  • pickleshare 0.7.5
  • platformdirs 3.0.0
  • prompt-toolkit 3.0.38
  • psycopg2-binary 2.9.5
  • ptyprocess 0.7.0
  • pure-eval 0.2.2
  • pydantic 1.10.5
  • pygeos 0.14
  • pygments 2.14.0
  • pyproj 3.4.1
  • python-dateutil 2.8.2
  • python-dotenv 1.0.0
  • pytz 2022.7.1
  • pyyaml 6.0
  • rich 13.6.0
  • scipy 1.9.3
  • setuptools 67.4.0
  • shapely 2.0.1
  • six 1.16.0
  • sqlalchemy 1.4.46
  • sqlalchemy-utils 0.37.9
  • sqlparse 0.4.3
  • stack-data 0.6.2
  • tomli 2.0.1
  • traitlets 5.9.0
  • typer 0.9.0
  • typing-extensions 4.5.0
  • wcwidth 0.2.6
map-integration/pyproject.toml pypi
  • SQLAlchemy ^1.4.42
  • geopandas ^0.12.0
  • ipython ^8.5.0
  • macrostrat.database ^2.0.0
  • numpy ^1.23.4
  • psycopg2-binary ^2.9.4
  • pygeos ^0.14
  • pyproj ^3.4.0
  • python ^3.10
  • python-dotenv ^1
  • pyyaml ^6.0
  • rich ^13
  • scipy ^1.9.3
  • shapely ^2.0.1
  • typer ^0.9.0
py-root/poetry.lock pypi
  • 124 dependencies
py-root/pyproject.toml pypi
  • macrostrat.package_tools * develop
  • corelle.engine *
  • macrostrat.app_frame *
  • macrostrat.cli *
  • macrostrat.map_integration *
  • macrostrat.tileserver *
  • python ^3.11
v2-transition/poetry.lock pypi
  • 106 dependencies
v2-transition/pyproject.toml pypi
  • ansible ^8.0.0
  • digitalcrust.weaver *
  • macrostrat.cli *
  • macrostrat.map_integration *
  • macrostrat.tileserver *
  • python ^3.10