NEWS.md

In acidgenomics/WormBase: WormBase Annotation Data

WormBase 0.5.0 (2023-09-28)

Major changes:

• Now enforcing strict camel case for function names. Renamed geneIDs to geneIds and geneOtherIDs to geneOtherIds.
• description: Reworked internal sanitization of the input data file.
• Removed stringi dependency in favor of using our string splitting functions in AcidBase instead.

Minor changes:

• Reworked internal string splitting to use base R approach via AcidBase instead of relying on compiled C code in stringi package.
• Reworked internal code to not use pasteURL for incomplete URLs.
• Updated unit tests for invalid REST API URLs.
• Classing internally on DFrame instead of DataFrame virtual class.

WormBase 0.4.2 (2023-08-11)

Minor changes:

• Needed to add a URLencode step to URL parsing of our {{release}} placeholder. Our change to pasteURL in AcidBase broke this approach.
• Enabled testthat unit tests to run in parallel.

WormBase 0.4.1 (2023-07-06)

Major changes:

• Migrated internal REST API code from httr to httr2.

Minor changes:

• Updated Acid Genomics dependencies.
• Preparing release for bioconda.

WormBase 0.4.0 (2022-06-08)

Major changes:

• Now requiring R 4.2 / Bioconductor 3.15.
• Split out basejump imports into component packages.
• Reworked internal code to use stringi instead of stringr.
• rnaiPhenotypes: Addressed FTP server reorganization of rna_phenotypes_quick.wb files, which was previously located in ontologies directory, but was moved to annotations directory starting with WS280.

Minor changes:

• Updated lintr checks and testthat unit tests.

WormBase 0.3.0 (2021-02-18)

Major changes:

• Package now uses BiocFileCache (via pipette) internally to cache files from WormBase FTP server.
• Sped up internal code significantly, making use of CharacterList, which helps avoid the need for BiocParallel bplapply calls.
• Reworked NAMESPACE and dependencies to extend on top of basejump v0.14 release series.
• Renamed version argument to release, for better consistency with naming conventions used in basejump packages, such as AcidGenomes.

WormBase 0.2.12 (2020-07-23)

Minor changes:

• Maintenance release, updating R dependency to 4.0.

WormBase 0.2.11 (2020-01-26)

Major changes:

• Renamed package from "wormbase" to "WormBase".

Minor changes:

• Updated basejump dependencies.
• Now using cli package to display messages.

WormBase 0.2.10 (2020-01-03)

Minor changes:

• Working example and unit test updates for description function, now that the corresponding file on the WormBase FTP server is no longer malformed. This has been fixed as of WS274.
• Updated REST API queries to use "https://wormbase.org/rest". Previously, this called "http://api.wormbase.org/rest", which no longer works.

WormBase 0.2.9 (2019-08-29)

Major changes:

• Functions now return DataFrame instead of tbl_df.
• Updated R dependency to 3.6.
• Reworked internal code to use base R / Bioconductor methods, instead of tidyverse / dplyr approach.

Minor changes:

• Improved documentation and updated basejump dependency versions.

WormBase 0.2.8 (2019-07-24)

• Updated basejump dependency versions.

WormBase 0.2.7 (2019-03-26)

• Added support for WS269 release. Functions that parse files from the WormBase FTP server had to be modified to ensure only annotations matching N2 gene identifiers (e.g. WBGene) are returned.
• Removed dir argument for all functions that parse files from WormBase FTP server. Files now always download to tempdir instead.
• Improved internal tidyeval code where applicable, notably inside mutate calls using sym and := rlang functions.

WormBase 0.2.6 (2019-03-23)

• Migrated code to Acid Genomics.

WormBase 0.2.5 (2019-03-19)

• Reworked progress bar handling via pbapply::pblapply. This is now disabled for all functions by default, but can be enabled with progress = TRUE. pbapply package is now declared in "Enhances:" rather than "Imports:".
• Switched all internal assert checks to goalie package from assertive.

WormBase 0.2.4 (2018-11-21)

• Maintenance release updating the package to require R 3.5.
• Improved documentation for functions and rebuild pkgdown website.
• Added progress = TRUE option for functions that can take a long time to parse data. Previously, this was always enabled but now can be disabled using this progress = FALSE. Note that invisible(capture.output(x)) also works to suppress progress bars.

WormBase 0.2.3 (2018-07-21)

• Fixed geneID() function to work with latest WormBase release that now returns an extra biotype column.
• Removed internal parallel mclapply() calls in favor of pblapply() for better compatibility across platforms.

WormBase 0.2.2 (2018-04-23)

• Broke out assertive imports into separate packages: assertive.properties, assertive.strings, assertive.types.
• Removed todo comment in description.R file.

WormBase 0.2.1 (2018-04-18)

• Renamed gene column to geneID where applicable.
• Removed fs package dependency.
• Added progress bars for functions that take a long time to load.

WormBase 0.2.0 (2018-03-04)

• Renamed package to wormbase from worminfo.
• Simplified core functionality to simply pull genome annotations from the WormBase website into R.
• Previous functionality querying the ENSEMBL, PANTHER, and EggNOG databases will be split out into organism-agnostic packages.
• RNAi clone support is being migrated to the rnaiscreen package.

WormBase 0.1.0 (2018-02-14)

(worminfo): Pre-release using internal build annotations from WormBase, ENSEMBL, PANTHER, and EggNOG databases. RNAi clone support for ORFeome (WORFDB), Ahringer, and Ruvkun Lab cherrypick libraries.

WormBase 0.0.99 (2017-12-06)

(worminfo): Initial pre-release version.

acidgenomics/WormBase documentation built on Oct. 2, 2023, 11:44 a.m.