From 350ccd1bdafb712a0daa3dd3f60716c29c41ba27 Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 09:58:19 +0100 Subject: [PATCH 1/7] Add status badge remove DOI badge --- README.Rmd | 2 +- README.md | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index 87727b71..78259940 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,12 +20,12 @@ knitr::opts_chunk$set( +[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem) [![R build status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions) [![Coverage](https://codecov.io/github/ropensci/webchem/coverage.svg?branch=master)](https://codecov.io/gh/ropensci/webchem/branch/master) [![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem) [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/webchem?color=blue)](https://cran.r-project.org/package=webchem) -[![DOI](https://zenodo.org/badge/17223/ropensci/webchem.svg)](https://zenodo.org/badge/latestdoi/17223/ropensci/webchem) diff --git a/README.md b/README.md index 8441d388..0eebd792 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ +[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem) [![R build status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions) @@ -12,7 +13,6 @@ status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](ht [![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem) [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/webchem?color=blue)](https://cran.r-project.org/package=webchem) -[![DOI](https://zenodo.org/badge/17223/ropensci/webchem.svg)](https://zenodo.org/badge/latestdoi/17223/ropensci/webchem) @@ -52,7 +52,7 @@ documentation (CIR)](http://cactus.nci.nih.gov/chemical/structure) - [Chemical Translation Service (CTS)](http://cts.fiehnlab.ucdavis.edu/) - - [ChemIDplus](http://chem.sis.nlm.nih.gov/chemidplus/) + - [ChemIDplus](https://chem.nlm.nih.gov/chemidplus/) - [ChemSpider](http://www.chemspider.com/) (requires an [API token](\(https://developer.rsc.org/\))) - [ETOX](http://webetox.uba.de/webETOX/index.do) From d78c789bf78d18f8f9c4771df9cd847f1dbd7207 Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 09:59:25 +0100 Subject: [PATCH 2/7] Remove reference to 2020 survey --- README.Rmd | 6 ------ README.md | 11 ----------- 2 files changed, 17 deletions(-) diff --git a/README.Rmd b/README.Rmd index 78259940..07040aa8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -35,12 +35,6 @@ This package interacts with a suite of web APIs to retrieve chemical information The functions in the package that hit a specific API have a prefix and suffix separated by an underscore (`prefix_suffix()`). They follow the format of `source_functionality`, with the exception of functions that retrieve database identifiers which follow the format of `get_identifier`. e.g.`cs_compinfo` uses ChemSpider to retrieve compound informations and `get_csid()` retrieves ChemSpider IDs. -## Fill out the survey! - -Do you use chemical information databases in your work? Help us help you by filling out our short survey at https://forms.gle/V7dfGGn73dkesn5L6. - -The `webchem` survey allows us to learn which databases you use and how you interact with chemical data. This is extremely valuable information for us and guides our development efforts. The survey takes about 5 minutes to fill out. - ## Chemical databases currently accessed by webchem At least some of the data in the following sources is accesible through `webchem` functions. To learn more about what is available, browse the documentation [here](https://docs.ropensci.org/webchem/reference/index.html). diff --git a/README.md b/README.md index 0eebd792..90f4e3d3 100644 --- a/README.md +++ b/README.md @@ -27,17 +27,6 @@ retrieve database identifiers which follow the format of `get_identifier`. e.g.`cs_compinfo` uses ChemSpider to retrieve compound informations and `get_csid()` retrieves ChemSpider IDs. -## Fill out the survey\! - -Do you use chemical information databases in your work? Help us help you -by filling out our short survey at -. - -The `webchem` survey allows us to learn which databases you use and how -you interact with chemical data. This is extremely valuable information -for us and guides our development efforts. The survey takes about 5 -minutes to fill out. - ## Chemical databases currently accessed by webchem At least some of the data in the following sources is accesible through From 1461a5af37696d75cf6deb142127de4f8d36574a Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 10:04:27 +0100 Subject: [PATCH 3/7] Remove reference to related projects --- README.Rmd | 7 ------- README.md | 12 ------------ 2 files changed, 19 deletions(-) diff --git a/README.Rmd b/README.Rmd index 07040aa8..82677204 100644 --- a/README.Rmd +++ b/README.Rmd @@ -92,13 +92,6 @@ If you use `webchem` in a publication, please cite our paper: ### Acknowledgements Without the fantastic web services `webchem` wouldn't be here. Therefore, kudos to the web service providers and developers! Please remember to acknowledge these data resources in your work using `webchem`. - -### Related Projects - -You can find some related packages in the [ChemPhys CRAN Task View](https://cran.r-project.org/web/views/ChemPhys.html) - -If you're more familiar with Python you should check out [Matt Swains](https://github.com/mcs07) repositories: [ChemSpiPy](https://github.com/mcs07/ChemSpiPy), [PubChemPy](https://github.com/mcs07/PubChemPy) and [CirPy](https://github.com/mcs07/CIRpy) provide similar functionality as `webchem`. - ### Want to contribute? Check out our [contribution guide here](https://github.com/ropensci/webchem/blob/master/CONTRIBUTING.md). diff --git a/README.md b/README.md index 90f4e3d3..b55f782b 100644 --- a/README.md +++ b/README.md @@ -111,18 +111,6 @@ Therefore, kudos to the web service providers and developers\! Please remember to acknowledge these data resources in your work using `webchem`. -### Related Projects - -You can find some related packages in the [ChemPhys CRAN Task -View](https://cran.r-project.org/web/views/ChemPhys.html) - -If you’re more familiar with Python you should check out [Matt -Swains](https://github.com/mcs07) repositories: -[ChemSpiPy](https://github.com/mcs07/ChemSpiPy), -[PubChemPy](https://github.com/mcs07/PubChemPy) and -[CirPy](https://github.com/mcs07/CIRpy) provide similar functionality as -`webchem`. - ### Want to contribute? Check out our [contribution guide From db7de821cc3fed29f159aa8201746abe0ee516a8 Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 10:07:07 +0100 Subject: [PATCH 4/7] Separate section for citation --- README.Rmd | 2 ++ README.md | 2 ++ 2 files changed, 4 insertions(+) diff --git a/README.Rmd b/README.Rmd index 82677204..31983df6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -84,6 +84,8 @@ Have you used `webchem` in your work? Please let us know by opening an issue or - Brokl M, Morales V, Bishop L, et al (2019) Comparison of Mainstream Smoke Composition from CR20 Resin Filter and Empty-Cavity Filter Cigarettes by Headspace SPME Coupled with GC×GC TOFMS and Chemometric Analysis. Beiträge zur Tabakforschung International/Contributions to Tobacco Research 28:231–249. https://doi.org/10.2478/cttr-2019-0004 - Münch D, Galizia CG (2016) DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses. Scientific Reports 6:21841. https://doi.org/10.1038/srep21841 +### Citation + If you use `webchem` in a publication, please cite our paper: - Szöcs E, Stirling T, Scott ER, et al (2020) webchem: An R Package to Retrieve Chemical Information from the Web. J Stat Soft 93:. https://doi.org/10.18637/jss.v093.i13 diff --git a/README.md b/README.md index b55f782b..5f23692e 100644 --- a/README.md +++ b/README.md @@ -98,6 +98,8 @@ issue or making a pull request to edit this section\! Drosophila melanogaster Odorant Responses. Scientific Reports 6:21841. +### Citation + If you use `webchem` in a publication, please cite our paper: - Szöcs E, Stirling T, Scott ER, et al (2020) webchem: An R Package to From a54347adad24eff750802f1eecc414c36fadd93f Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 10:09:40 +0100 Subject: [PATCH 5/7] Update Version and Date --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 08eab507..f39efef6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,8 +7,8 @@ Description: Chemical information from around the web. This package interacts Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem, SRS, Wikidata. Type: Package -Version: 1.1.0 -Date: 2020-10-01 +Version: 1.1.1 +Date: 2021-02-07 License: MIT + file LICENSE URL: https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem BugReports: https://github.com/ropensci/webchem/issues From 87ece5b24159c9e4e2ca63b1e1e6ab123f4d21b9 Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 10:10:55 +0100 Subject: [PATCH 6/7] Update structure for webchem 1.1.1 entries --- NEWS.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index b85f652a..949b9f52 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,12 @@ -# webchem 1.1.0.9001 +# webchem 1.1.1. + +## NEW FEATURES + +* Fetch LIPID MAPS and SwissLipids identifiers from Wikidata. ## BUG FIXES * Fix get_csid() so it doesn't break when a query is invalid. -* Typo fix in Wikidata.R -* Added support for fetching LIPID MAPS and SwissLipids identifiers from Wikidata. # webchem 1.1.0. From b0d1d44e19087874319d21343f885011a4d2698c Mon Sep 17 00:00:00 2001 From: stitam Date: Fri, 5 Feb 2021 10:11:25 +0100 Subject: [PATCH 7/7] Update codemeta.json --- codemeta.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/codemeta.json b/codemeta.json index 55668f6e..8059f618 100644 --- a/codemeta.json +++ b/codemeta.json @@ -15,7 +15,7 @@ ], "issueTracker": "https://github.com/ropensci/webchem/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.1.0", + "version": "1.1.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -399,5 +399,6 @@ } } } - ] + ], + "developmentStatus": "https://www.repostatus.org/#active" }