commonmeta-ruby 3.2.3 → 3.2.5
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- checksums.yaml +4 -4
- data/Gemfile.lock +7 -6
- data/lib/commonmeta/author_utils.rb +11 -0
- data/lib/commonmeta/cli.rb +5 -1
- data/lib/commonmeta/readers/json_feed_reader.rb +9 -5
- data/lib/commonmeta/utils.rb +4 -2
- data/lib/commonmeta/version.rb +1 -1
- data/spec/author_utils_spec.rb +9 -8
- data/spec/cli_spec.rb +1 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/blog_post.yml +14 -14
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/all_posts.yml +3602 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed/behind_the_science.yml +1176 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_doi.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_without_doi.yml +196 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/jekyll_post.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post.yml +7 -7
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/json_feed_url/all_posts.yml +221 -0
- data/spec/readers/json_feed_reader_spec.rb +35 -10
- data/spec/utils_spec.rb +5 -0
- data/spec/writers/citation_writer_spec.rb +1 -1
- metadata +6 -15
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/blogger_post.yml +0 -141
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/ghost_post_with_doi.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/jekyll_post.yml +0 -134
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_metadata/wordpress_post.yml +0 -210
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/blogger_post.yml +0 -94
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/ghost_post.yml +0 -117
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/ghost_post_with_doi.yml +0 -117
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/jekyll_post.yml +0 -170
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_item_metadata/wordpress_post.yml +0 -163
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/blogger_post.yml +0 -141
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/ghost_post_with_doi.yml +0 -164
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/jekyll_post.yml +0 -134
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/wordpress_post.yml +0 -210
data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/blogger_post.yml
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string: '{"id":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","short_id":"1jgo59el","url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","title":"Ten
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years and a million links","summary":"As trailed on a Twitter thread last
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week I’ve been working on a manuscript describing the efforts to map taxonomic
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names to their original descriptions in the taxonomic literature. Putting
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together a...","date_published":"2023-05-31T17:26:00Z","date_modified":null,"authors":[{"url":null,"name":"Roderic
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Page"}],"image":null,"content_html":"<p>As trailed on a Twitter thread last
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week I’ve been working on a manuscript describing the efforts to map taxonomic
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names to their original descriptions in the taxonomic literature.</p>\n<blockquote
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class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Putting together a manuscript
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on linking taxonomic names to the primary literature, basically “um, what,
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exactly, have you been doing all these years?”. TL;DR Across fungi, plants,
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and animals approx 1.3 million names have been linked to a persistent identifier
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for a publication.</p>— Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
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25, 2023</a></blockquote> \n<p>The preprint is on bioRxiv <a href=\"https://doi.org/10.1101/2023.05.29.542697\">doi:10.1101/2023.05.29.542697</a></p>\n<blockquote>\n<p>A
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major gap in the biodiversity knowledge graph is a connection between taxonomic
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names and the taxonomic literature. While both names and publications often
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have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
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or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
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DOIs for publications. This article describes efforts to make those connections
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across three large taxonomic databases: Index Fungorum, International Plant
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Names Index (IPNI), and the Index of Organism Names (ION). Over a million
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names have been matched to DOIs or other persistent identifiers for taxonomic
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publications. This represents approximately 36% of names for which publication
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data is available. The mappings between LSIDs and publication PIDs are made
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available through ChecklistBank. Applications of this mapping are discussed,
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including a web app to locate the citation of a taxonomic name, and a knowledge
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graph that uses data on researcher’s ORCID ids to connect taxonomic names
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and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
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the work has been linking taxa to names, which still has huge gaps. There
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are also interesting differences in coverage between plants, animals, and
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fungi (see preprint for details).</p>\n\n<div class=\"separator\" style=\"clear:
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both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"
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class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"
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class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"
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style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
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is also a simple app to demonstrate these links, see <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
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with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","blog_id":"tyfqw20","blog":{"id":"tyfqw20","title":"iPhylo","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default?alt=rss","home_page_url":"https://iphylo.blogspot.com/","license":"https://creativecommons.org/licenses/by/4.0/legalcode","category":"Natural
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Sciences"}}'
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data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_post_metadata/ghost_post_with_doi.yml
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it compose?","summary":"One question I have increasingly asked myself in the
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past few years. Meaning Can I run this open source software using Docker containers
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and a Docker Compose file?As the Docker project turned ten this...","date_published":"2023-05-16T11:36:56Z","date_modified":"2023-05-16T11:36:56Z","authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
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Fenner"}],"image":"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib=rb-4.0.3&q=80&w=2000","content_html":"
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<p><img src=\"https://images.unsplash.com/photo-1523351964962-1ee5847816c3?crop=entropy&cs=tinysrgb&fit=max&fm=jpg&ixid=M3wxMTc3M3wwfDF8c2VhcmNofDUzfHxjb250YWluZXJ8ZW58MHx8fHwxNjg0MjMyMTQ0fDA&ixlib=rb-4.0.3&q=80&w=2000\"></p><p>One
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question I have increasingly asked myself in the past few years. Meaning </p><blockquote>Can
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I run this open source software using Docker containers and a Docker Compose
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file?</blockquote><p>As the Docker project <a href=\"https://snyk.io/blog/the-docker-project-turns-10/\">turned
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ten this spring</a>, it has become standard practice to distribute open source
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software via Docker images and to provide a <a href=\"https://docs.docker.com/compose/\">Docker
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Compose</a> file to run the software together with other dependencies. The
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<a href=\"https://github.com/docker/awesome-compose\">Awesome Compose</a>
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project has collected many examples, and all you need is a <code>docker-compose.yml</code>file
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and a recent installation of Docker, e.g. <a href=\"https://www.docker.com/products/docker-desktop/\">Docker
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Desktop</a>. Be aware that Docker Compose has evolved over the years. It started
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out as a dedicated Python application but was later integrated into the Docker
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application (written in Go) as Compose V2.</p><p>Docker and Docker Compose
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allow you to run pretty complex applications without first addressing a long
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list of requirements (which might conflict with other software you have installed),
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or needing a long and complex build step where many things can go wrong. For
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example a self-hosted instance of Supabase (a hosted Postgres database with
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additional features) that I installed last week following <a href=\"https://supabase.com/docs/guides/self-hosting/docker\">these
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instructions</a>.</p><p>An important open source project that I am involved
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in is <a href=\"https://inveniordm.docs.cern.ch/\">InvenioRDM</a>, the turn-key
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research data management repository. InvenioRDM started in 2019, with a first
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production-suitable version in August 2021, and the <a href=\"https://inveniosoftware.org/products/rdm/#status\">next
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major goal </a>is to have the large and popular <a href=\"https://zenodo.org/\">Zenodo</a>
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repository running on top of InvenioRDM. Zenodo <a href=\"https://blog.zenodo.org/2023/05/08/2023-05-08-10years/\">turned
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ten last week</a>, a few weeks after Docker. Interestingly, my personal tenth
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anniversary was last year in May as I became a full-time software developer
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and left academic medicine as a medical doctor treating cancer patients in
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<a href=\"https://doi.org/10.53731/r294649-6f79289-8cw2j\">May 2012</a>.</p><p>Unfortunately,
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InvenioRDM \"doesn''t compose\" yet. It is very close, but there are no ready-made
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Docker images to download, and the <a href=\"https://inveniordm.docs.cern.ch/install/\">installation
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there is no official solution from the InvenioRDM project yet. For this reason,
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repository on Github. It contains a Docker Compose file that uses pre-built
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on your local computer should give you a running InvenioRDM within 15 minutes:</p><figure
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class=\"kg-card kg-image-card\"><img src=\"https://blog.front-matter.io/content/images/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png\"
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class=\"kg-image\" alt loading=\"lazy\" width=\"2000\" height=\"1210\" srcset=\"https://blog.front-matter.io/content/images/size/w600/2023/05/Bildschirmfoto-2023-05-11-um-10.37.55.png
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2193w\" sizes=\"(min-width: 720px) 720px\"></figure><p>I started this recently
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and obviously want to move forward in two directions:</p><ul><li>fine-tune
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project, extending the <a href=\"https://github.com/inveniosoftware/docker-invenio\">docker-invenio</a>
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projects using the Invenio software.</li></ul><p>But of course, Docker Compose
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For production environments, most people shy away from using Docker Compose.
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The reasons for that and the alternatives will be the topic of a future blog
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post (spoiler: there is exciting news).</p><p>Docker Compose also needs more
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work to be set up correctly for development environments. It is a common practice
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and a workflow I used while working at DataCite (where we launched Docker-based
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infrastructure in 2016), but for now, the easiest way to set up InvenioRDM
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development environments is using the <a href=\"https://inveniordm.docs.cern.ch/install/\">invenio-cli
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tool with a local development environment</a>.</p><p>Please reach out to me
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with feedback on running Docker Compose for InvenioRDM (use the <a href=\"https://github.com/front-matter/docker-invenio-rdm/discussions\">discussions</a>
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feature in the GitHub repo), or if you have questions about running InvenioRDM
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in production.</p> ","tags":["News"],"language":"en","blog_id":"f0m0e38","blog":{"id":"f0m0e38","title":"Front
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additions, principally new item types, fields, and terms. We’re seeking public
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comment on the planned released from now until <strong>July 26, 2020, 12pm
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EDT</strong>.</p>\n\n<p>A non-technical summary of the release can be found
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in a <a href=\"https://docs.google.com/document/d/1wY1cOOamDYYh8VNW7h_uleqieBDGOa_LYsRiVdQy1RI/edit#heading=h.wsywjzy5t4j6\">google
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doc here</a>. For more technical details, you can follow the development on
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the <a href=\"https://github.com/orgs/citation-style-language/projects/3\">github
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project board</a>. We welcome feedback directly on the google doc, in specific
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github issues, or on our <a href=\"https://discourse.citationstyles.org/\">forums</a>.</p>\n\n<p>Tremendous
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thanks to Bruce D’Arcus, Denis Maier, and Brenton Wiernik, who did the bulk
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of the work of organizing proposals accumulated over the last 8 years and
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preparing the release.</p>\n\n<h2 id=\"previewing-csl-11\">Previewing CSL
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significant extensions of CSL functionality. While we’ll have a separate public
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comment period for this release, we’re happy for input on the ongoing discussions
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implementing CSL styles, both in a citeproc and in user-facing applications
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such as reference managers or citation formatters.</p>\n\n<p>This release
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will primarily add the following new features:</p>\n<ul>\n <li>Full support
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for narrative citation styles (“Like Doe (2018)”).</li>\n <li>Ability to
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specify more complex conditional logic.</li>\n <li>Ability to independently
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format subtitles and main titles.</li>\n <li>A new “related” attribute to
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express related reviewed and original items (still in discussion).</li>\n <li>Improvements
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to the CSL input format(s):\n <ul>\n <li>Adopting the new EDTF ISO
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standard, which offers full support for date ranges, seasons, uncertain and
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approximate qualifiers, and decades and centuries.</li>\n <li>A new “custom”
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property to add extension metadata.</li>\n <li>New related modelling
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to match the new style attribute (as above, still in discussion).</li>\n <li>An
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official YAML representation, which can be validated with the same JSON schemas.</li>\n </ul>\n </li>\n</ul>","tags":[],"language":"en","blog_id":"prmb582","blog":{"id":"prmb582","title":"Citation
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