.dockerignore
.gitignore
CHANGELOG.md
CITATION.cff
Dockerfile
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
.docs/Makefile
.docs/apidoc.sh
.docs/changelog.md
.docs/conf.py
.docs/index.rst
.docs/assets/logo-transparent.png
.docs/assets/logo.png
.docs/source/modules.rst
.docs/source/rse.app.rst
.docs/source/rse.app.views.rst
.docs/source/rse.client.rst
.docs/source/rse.logger.rst
.docs/source/rse.main.config.rst
.docs/source/rse.main.database.rst
.docs/source/rse.main.parsers.rst
.docs/source/rse.main.rst
.docs/source/rse.rst
.docs/source/rse.utils.rst
.github/FUNDING.yml
.github/ISSUE_TEMPLATE.md
.github/workflows/deploy.yml
.github/workflows/main.yml
docs/Gemfile
docs/_config.yml
docs/_data/links.yml
docs/_docs/_defaults.md
docs/_docs/contributing/code.md
docs/_docs/contributing/docs.md
docs/_docs/contributing/index.md
docs/_docs/getting-started/annotation.md
docs/_docs/getting-started/api.md
docs/_docs/getting-started/commands.md
docs/_docs/getting-started/configure.md
docs/_docs/getting-started/containers.md
docs/_docs/getting-started/dashboard.md
docs/_docs/getting-started/environment.md
docs/_docs/getting-started/index.md
docs/_docs/getting-started/parsers.md
docs/_docs/getting-started/scrapers.md
docs/_docs/getting-started/img/annotate/annotate-button.png
docs/_docs/getting-started/img/annotate/annotate-repo.png
docs/_docs/getting-started/img/annotate/annotate-taxonomy.png
docs/_docs/getting-started/img/annotate/annotate.png
docs/_docs/getting-started/img/api/criteria.png
docs/_docs/getting-started/img/api/dashboard.png
docs/_docs/getting-started/img/api/parser.png
docs/_docs/getting-started/img/api/repo.png
docs/_docs/getting-started/img/api/repos.png
docs/_docs/getting-started/img/api/root.png
docs/_docs/getting-started/img/api/taxonomy.png
docs/_docs/getting-started/img/dashboard/github.png
docs/_docs/getting-started/img/dashboard/gitlab.png
docs/_docs/getting-started/img/dashboard/prototype.png
docs/_docs/getting-started/img/dashboard/status.png
docs/_docs/getting-started/img/dashboard/topics.png
docs/_docs/install/index.md
docs/_docs/tutorials/annotation.md
docs/_docs/tutorials/index.md
docs/_docs/tutorials/python.md
docs/_includes/head.html
docs/_includes/navigation.html
docs/_layouts/default.html
docs/_posts/_defaults.md
docs/api/changelog.html
docs/api/genindex.html
docs/api/index.html
docs/api/objects.inv
docs/api/py-modindex.html
docs/api/search.html
docs/api/searchindex.js
docs/api/_sources/changelog.md.txt
docs/api/_sources/index.rst.txt
docs/api/_sources/source/modules.rst.txt
docs/api/_sources/source/rse.app.rst.txt
docs/api/_sources/source/rse.app.views.rst.txt
docs/api/_sources/source/rse.client.rst.txt
docs/api/_sources/source/rse.logger.rst.txt
docs/api/_sources/source/rse.main.config.rst.txt
docs/api/_sources/source/rse.main.database.rst.txt
docs/api/_sources/source/rse.main.parsers.rst.txt
docs/api/_sources/source/rse.main.rst.txt
docs/api/_sources/source/rse.rst.txt
docs/api/_sources/source/rse.utils.rst.txt
docs/api/assets/basic.css
docs/api/assets/doctools.js
docs/api/assets/documentation_options.js
docs/api/assets/file.png
docs/api/assets/jquery-3.5.1.js
docs/api/assets/jquery.js
docs/api/assets/language_data.js
docs/api/assets/logo-transparent.png
docs/api/assets/logo.png
docs/api/assets/minus.png
docs/api/assets/plus.png
docs/api/assets/pygments.css
docs/api/assets/searchtools.js
docs/api/assets/underscore-1.12.0.js
docs/api/assets/underscore.js
docs/api/assets/css/badge_only.css
docs/api/assets/css/theme.css
docs/api/assets/css/fonts/Roboto-Slab-Bold.woff
docs/api/assets/css/fonts/Roboto-Slab-Bold.woff2
docs/api/assets/css/fonts/Roboto-Slab-Regular.woff
docs/api/assets/css/fonts/Roboto-Slab-Regular.woff2
docs/api/assets/css/fonts/fontawesome-webfont.eot
docs/api/assets/css/fonts/fontawesome-webfont.svg
docs/api/assets/css/fonts/fontawesome-webfont.ttf
docs/api/assets/css/fonts/fontawesome-webfont.woff
docs/api/assets/css/fonts/fontawesome-webfont.woff2
docs/api/assets/css/fonts/lato-bold-italic.woff
docs/api/assets/css/fonts/lato-bold-italic.woff2
docs/api/assets/css/fonts/lato-bold.woff
docs/api/assets/css/fonts/lato-bold.woff2
docs/api/assets/css/fonts/lato-normal-italic.woff
docs/api/assets/css/fonts/lato-normal-italic.woff2
docs/api/assets/css/fonts/lato-normal.woff
docs/api/assets/css/fonts/lato-normal.woff2
docs/api/assets/js/badge_only.js
docs/api/assets/js/html5shiv-printshiv.min.js
docs/api/assets/js/html5shiv.min.js
docs/api/assets/js/theme.js
docs/api/modules/index.html
docs/api/modules/rse/client.html
docs/api/modules/rse/defaults.html
docs/api/modules/rse/exceptions.html
docs/api/modules/rse/main.html
docs/api/modules/rse/client/add.html
docs/api/modules/rse/client/clear.html
docs/api/modules/rse/client/config.html
docs/api/modules/rse/client/exists.html
docs/api/modules/rse/client/export.html
docs/api/modules/rse/client/generate.html
docs/api/modules/rse/client/get.html
docs/api/modules/rse/client/init.html
docs/api/modules/rse/client/listing.html
docs/api/modules/rse/client/search.html
docs/api/modules/rse/client/shell.html
docs/api/modules/rse/client/start.html
docs/api/modules/rse/client/update.html
docs/api/modules/rse/logger/message.html
docs/api/modules/rse/main/config.html
docs/api/modules/rse/main/criteria.html
docs/api/modules/rse/main/database.html
docs/api/modules/rse/main/parsers.html
docs/api/modules/rse/main/taxonomy.html
docs/api/modules/rse/main/database/base.html
docs/api/modules/rse/main/database/filesystem.html
docs/api/modules/rse/main/database/models.html
docs/api/modules/rse/main/database/relational.html
docs/api/modules/rse/main/database/sqlite.html
docs/api/modules/rse/main/parsers/base.html
docs/api/modules/rse/main/parsers/github.html
docs/api/modules/rse/utils/command.html
docs/api/modules/rse/utils/file.html
docs/api/modules/rse/utils/prompt.html
docs/api/source/modules.html
docs/api/source/rse.app.html
docs/api/source/rse.app.views.html
docs/api/source/rse.client.html
docs/api/source/rse.html
docs/api/source/rse.logger.html
docs/api/source/rse.main.config.html
docs/api/source/rse.main.database.html
docs/api/source/rse.main.html
docs/api/source/rse.main.parsers.html
docs/api/source/rse.utils.html
docs/assets/css/rse.css
docs/assets/fonts/helveticaneueout-webfont.woff
docs/assets/fonts/helveticaneueout-webfont.woff2
docs/assets/img/favicon.ico
docs/assets/img/logo-transparent.png
docs/assets/img/logo.png
docs/assets/img/logo_small.gif
docs/assets/js/lunr.min.js
docs/assets/js/search.js
docs/pages/404.md
docs/pages/changelog.html
docs/pages/index.md
docs/pages/robots.txt
docs/pages/search.html
rse/__init__.py
rse/defaults.py
rse/exceptions.py
rse/version.py
rse.egg-info/PKG-INFO
rse.egg-info/SOURCES.txt
rse.egg-info/dependency_links.txt
rse.egg-info/entry_points.txt
rse.egg-info/not-zip-safe
rse.egg-info/requires.txt
rse.egg-info/top_level.txt
rse/app/__init__.py
rse/app/api.py
rse/app/config.py
rse/app/export.py
rse/app/server.py
rse/app/static/css/style.css
rse/app/static/css/topics.css
rse/app/templates/base.html
rse/app/templates/search.html
rse/app/templates/annotate/criteria-static.html
rse/app/templates/annotate/criteria.html
rse/app/templates/annotate/repos.html
rse/app/templates/annotate/taxonomy-static.html
rse/app/templates/annotate/taxonomy.html
rse/app/templates/home/filesystem-index.html
rse/app/templates/home/index.html
rse/app/templates/main/criteria.html
rse/app/templates/main/taxonomy.html
rse/app/templates/parsers/github.html
rse/app/templates/parsers/gitlab.html
rse/app/templates/tables/criteria-answer-table.html
rse/app/templates/tables/criteria-table.html
rse/app/templates/tables/taxonomy-table.html
rse/app/templates/topics/base.html
rse/app/templates/topics/index.html
rse/app/views/__init__.py
rse/app/views/main.py
rse/app/views/repositories.py
rse/client/__init__.py
rse/client/add.py
rse/client/annotate.py
rse/client/clear.py
rse/client/config.py
rse/client/exists.py
rse/client/export.py
rse/client/generate.py
rse/client/get.py
rse/client/init.py
rse/client/label.py
rse/client/listing.py
rse/client/metrics.py
rse/client/scrape.py
rse/client/search.py
rse/client/shell.py
rse/client/start.py
rse/client/topics.py
rse/client/update.py
rse/logger/__init__.py
rse/logger/message.py
rse/main/__init__.py
rse/main/criteria.py
rse/main/taxonomy.py
rse/main/config/__init__.py
rse/main/config/config.ini
rse/main/database/__init__.py
rse/main/database/base.py
rse/main/database/filesystem.py
rse/main/database/models.py
rse/main/database/relational.py
rse/main/database/sqlite.py
rse/main/parsers/__init__.py
rse/main/parsers/base.py
rse/main/parsers/github.py
rse/main/parsers/gitlab.py
rse/main/parsers/zenodo.py
rse/main/scrapers/__init__.py
rse/main/scrapers/base.py
rse/main/scrapers/biotools.py
rse/main/scrapers/hal.py
rse/main/scrapers/joss.py
rse/main/scrapers/rsnl.py
rse/utils/__init__.py
rse/utils/colors.py
rse/utils/command.py
rse/utils/file.py
rse/utils/prompt.py
rse/utils/urls.py
tests/__init__.py
tests/criteria-issue.txt
tests/helpers.sh
tests/taxonomy-issue.txt
tests/test_client.sh
tests/test_database.py
tests/test_parser_github.py
tests/test_parser_gitlab.py
tests/test_parser_zenodo.py