| refs/tags/v0.2.3 | v0.2.3 | 81394c0 | manubot version 0.2.3 release notes =================================== Manubot version 0.2.3 contains various enhancements. In addition, the source code location has moved from <https://github.com/greenelab/manubot> to <https://github.com/manubot/manubot> (see [GH94](https://github.com/manubot/manubot/issues/94)). New features ------------ Citations of shortDOIs are now supported (see [GH92](https://github.com/manubot/manubot/issues/92) and [GH93](https://github.com/manubot/manubot/pull/93)). [shortDOIs](http://shortdoi.org/), which start with `10/` rather than `10.`, can now be cited just like a DOI. For example, `@doi:10/gddkhn` is a supported citation. Manubot expands shortDOI citations to their regular DOIs, e.g. `@doi:10.1098/rsif.2017.0387`, such that `manubot process` will treat both the short and regular form as the same citation. Bug fixes --------- Queries to Manubot's translation-server now specify `single=1` to enforce returning a single record per persistent identifier (see [GH90](https://github.com/manubot/manubot/pull/90)). Previously, multiple results were [sometimes](https://github.com/zotero/translation-server/issues/65) returned, causing Manubot's JSON CSL retrieval to fail. Furthermore, Zotero child notes are now ignored, fixing another [failure mode](https://github.com/zotero/translation-server/issues/67) for CSL export of Zotero metadata. Null authors are now allowed in `metadata.yaml` and do not crash Manubot with a TypeError (see [GH91](https://github.com/manubot/manubot/pull/91)). The codebase has been updated to avoid deprecation warnings in Pandas v0.24 (see [GH95](https://github.com/manubot/manubot/pull/95)). | 12 February 2019, 03:09:58 UTC |
| refs/tags/v0.2.2 | v0.2.2 | dae5703 | manubot version 0.2.2 release notes =================================== Manubot version 0.2.2 contains citation and web request enhancements. New features ------------ This release adds citation support for two additional types of identifiers (`isbn` and `wikidata`). ISBNs are the primary persistent identifier for many books, so many books no longer need to be cited by URL (see [GH79](https://github.com/greenelab/manubot/pull/79) and [GH14](https://github.com/greenelab/manubot/issues/14)). However, ISBN metadata is sometimes missing or erroneous. Users may need to still need to set manual CSL JSON, but Manubot can at least produce a reasonable starting template. Try for example `manubot cite isbn:9780062316097`. [Wikidata](https://www.wikidata.org) is a free and open knowledge base that contains many records of scholarly works. Wikidata can store metadata on records that do not have their own persistent identifiers, and thus can help Manubot users assign a stable identifier to works that otherwise would not have one (see [GH67](https://github.com/greenelab/manubot/issues/67) and [GH86](https://github.com/greenelab/manubot/pull/86)). Try for example `manubot cite wikidata:Q50051684`. Manubot now uses Zotero's [translation-server](https://github.com/zotero/translation-server) infrastructure to provide metadata for wikidata, ISBN, and URL citations (see [GH70](https://github.com/greenelab/manubot/issues/70) and [GH84](https://github.com/greenelab/manubot/pull/84)). Manubot now hosts its own instance of translation-server at https://translate.manubot.org (see [GH82](https://github.com/greenelab/manubot/issues/82)). As such, Manubot users can benefit from Zotero's impressive collection of [translators](https://github.com/zotero/translators) for retrieving metadata from different webpages. Manubot's ISBN and URL citation metadata retrievers now first attempt to generate metadata using translation-server, and fallback to other methods if that fails. Bug fixes --------- NCBI E-Utility requests are now rate limited to 2 per second (see [GH83](https://github.com/greenelab/manubot/pull/83)). Previously, certain situations that caused rapid E-Utility requests would return status code 429 for "too many requests". Internal changes ---------------- Outgoing web requests made by Manubot now set the User-Agent header (see [GH83](https://github.com/greenelab/manubot/pull/83)). These headers provide high-level information of a user's system, as shown in the following examples: ``` manubot/0.2.2 (Linux; Python/3.6) <contact@manubot.org> manubot/0.2.2 (Windows; Python/3.7) <contact@manubot.org> ``` Setting the header will help upstream resources contact the Manubot developers should our requests be problematic or should downtime be anticipated. Furthermore, it will allow Manubot's translation-server to monitor Manubot usage, including which operating system, Python version, and package version are being used. Manubot's test suite has been reorganized such that testing modules correspond one-to-one with package modules (see [GH87](https://github.com/greenelab/manubot/pull/87)). | 17 December 2018, 21:55:46 UTC |
| refs/tags/v0.2.1 | v0.2.1 | afa55f8 | manubot version 0.2.1 release notes =================================== Manubot version 0.2.1 contains several improvements to the package's citation infrastructure. New features ------------ Support has been added for `raw` citations for references without supported persistent identifiers (see [GH62](https://github.com/greenelab/manubot/issues/62) and [GH74](https://github.com/greenelab/manubot/pull/74)). Raw citations require the user to manually specify the corresponding CSL JSON. Error messages for invalid citations have been improved (see [GH76](https://github.com/greenelab/manubot/pull/76) and [GH71](https://github.com/greenelab/manubot/issues/71)). More types of incorrect citations are now caught internally before any external APIs are queried to retrieve metadata. The `manubot cite` command has been updated to generate metadata for all valid citations, while logging error messages for invalid citations (see [GH77](https://github.com/greenelab/manubot/pull/77)). Previously, a single invalid citation would cause the program to exit before outputting references for valid citations. Bug fixes --------- Previously, metadata for `pmcid` citations was retrieved from the NCBI Citation Exporter. This service was [taken offline](https://twitter.com/dhimmel/status/1061787168820092929) without notice causing citation retrieval to fail. NCBI replaced the previous service with the [Literature Citation Exporter](https://api.ncbi.nlm.nih.gov/lit/ctxp). The `manubot.cite.pubmed.get_pmc_citeproc` function has been changed to use the new service (see [GH80](https://github.com/greenelab/manubot/pull/80)). Previously, CSL JSON Items were being generated with empty `date-parts` arrays, which would cause pandoc-citeproc to fail. Manubot's CSL JSON pruning infrastructure has been updated to delete empty `date-parts` arrays (see [GH66](https://github.com/greenelab/manubot/issues/66) and [GH65](https://github.com/greenelab/manubot/pull/65)). Entrez E-Utils returned integer-encoded months for certain `pmid` citations causing `citeproc_from_pubmed_article` to fail. Both integer and character month encodings are now supported (see [GH72](https://github.com/greenelab/manubot/pull/72)). | 15 November 2018, 18:59:42 UTC |
| refs/tags/v0.2.0 | v0.2.0 | 5e2eeeb | Manubot version 0.2.0 introduces subcommands to the command line interface. The previous command `manubot` to process manuscript content for Pandoc is now `manubot process`. New functionality has been added via the `manubot cite` subcommand to retrieve bibliographic metadata for citations (see [GH37](https://github.com/greenelab/manubot/issues/37)). The cite subcommand can either return CSL JSON (default) or formatted references (--render, requires Pandoc, see [GH48](https://github.com/greenelab/manubot/issues/48)). This release adds support for removing invalid fields from CSL JSON Data, which is enabled by default (see [GH47](https://github.com/greenelab/manubot/issues/47)). Previously, certain citeproc APIs returned CSL JSON with extra fields or fields with invalid values according to the CSL JSON Schema. Now CSL JSON is validated against the schema, with invalid fields removed. Now PMID & PMCID fields are automatically populated when generating CSL data for DOIs (see [GH45](https://github.com/greenelab/manubot/issues/45)). CSL for DOIs now uses shortDOIs in the URL field. As this package now supports more varied use cases and workflows, the code has been refactored to use lazy imports (see [GH56](https://github.com/greenelab/manubot/pull/56)). Most functions directly under `manubot.cite` and `manubot.process` have been moved to `util` submodules. `manubot.cite.citation_to_citeproc` and `manubot.cite.standardize_citation` remain for backward compatibility. | 07 October 2018, 12:11:45 UTC |
| refs/tags/v0.1.0 | v0.1.0 | d80b2c9 | Upgrade to v0.1.0 | 04 August 2018, 18:35:11 UTC |
