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the-mayer committed Oct 22, 2024
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2 changes: 2 additions & 0 deletions .github/.gitignore
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*.html

/.quarto/
83 changes: 64 additions & 19 deletions .github/CONTRIBUTING.md
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Expand Up @@ -5,42 +5,87 @@ For a detailed discussion on contributing to this and other tidyverse packages,

## Fixing typos

You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.
You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.
You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.

## Bigger changes

If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
If you’ve found a bug, please file an issue that illustrates the bug with a minimal
If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
If you’ve found a bug, please file an issue that illustrates the bug with a minimal
[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.

### Pull request process

* Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("JRaviLab/MolEvolvR", fork = TRUE)`.
- Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis`.

* Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`.
If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing.
* Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
- Install and load the `usethis` package with:

* Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
The title of your PR should briefly describe the change.
The body of your PR should contain `Fixes #issue-number`.
```
install.packages("usethis")
* For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
library("usethis")
```

- Clone and fork the MolEvolvR package using:
```
usethis::create_from_github("JRaviLab/MolEvolvR", fork = TRUE)
```
- Install BiocManager from Bioconductor:

```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.19")
```

- Install other development dependencies and then ensure that the package passes R CMD check using `devtools`:

```
install.packages("devtools")
library("devtools")
devtools::install_dev_deps()
devtools::check()
```

_If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing._

- Create a Git branch for your pull request (PR). We recommend using:

```
usethis::pr_init("brief-description-of-change")
```

- Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
The title of your PR should briefly describe the change.
The body of your PR should contain `Fixes #issue-number`.

<!-- * For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>. -->

<!-- No NEWS.md file exists at the moment. Suggest restoring this line when the file exists to avoid a y confusion.-->

### Code style

* New code should follow the tidyverse [style guide](https://style.tidyverse.org).
You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.

* Lint Your Code: Ensure your code adheres to our style guidelines by using [lintr](https://lintr.r-lib.org/): `lintr::lint("path/to/your/file.R")`
- New code should follow the tidyverse [style guide](https://style.tidyverse.org).
You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
- Lint Your Code: Ensure your code adheres to our style guidelines by using [lintr](https://lintr.r-lib.org/):

```
install.packages("lintr")
library("lintr")
lintr::lint("path/to/your/file.R")
```

* We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
- We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.

* We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
Contributions with test cases included are easier to accept.
- We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
Contributions with test cases included are easier to accept.

## Code of Conduct

Expand Down
55 changes: 27 additions & 28 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -4,64 +4,60 @@ export(BinaryDomainNetwork)
export(GCA2Lineage)
export(GenContextNetwork)
export(IPG2Lineage)
export(RepresentativeAccNums)
export(acc2FA)
export(acc2Lineage)
export(acc2fa)
export(addLeaves2Alignment)
export(addLineage)
export(addName)
export(addTaxID)
export(add_leaves)
export(add_name)
export(advanced_opts2est_walltime)
export(alignFasta)
export(assign_job_queue)
export(assignJobQueue)
export(calculateEstimatedWallTimeFromOpts)
export(calculateProcessRuntime)
export(cleanClusters)
export(cleanDomainArchitecture)
export(cleanGeneDescription)
export(cleanGenomicContext)
export(cleanLineage)
export(cleanSpecies)
export(combine_files)
export(combine_full)
export(combine_ipr)
export(combineFiles)
export(combineFullAnalysis)
export(combineIPR)
export(condenseRepeatedDomains)
export(convert2TitleCase)
export(convertAlignment2FA)
export(convertAlignment2Trees)
export(convertFA2Tree)
export(convert_aln2fa)
export(countByColumn)
export(createFA2Tree)
export(createJobResultsURL)
export(createJobStatusEmailMessage)
export(createLineageLookup)
export(createRepresentativeAccNum)
export(createWordCloud2Element)
export(createWordCloudElement)
export(create_lineage_lookup)
export(domain_network)
export(downloadAssemblySummary)
export(efetchIPG)
export(extractAccNum)
export(filterByDomains)
export(filterByFrequency)
export(findParalogs)
export(find_top_acc)
export(formatJobArgumentsHTML)
export(gc_undirected_network)
export(generateAllAlignments2FA)
export(generate_all_aln2fa)
export(generate_msa)
export(get_accnums_from_fasta_file)
export(get_proc_medians)
export(get_proc_weights)
export(ipr2viz)
export(ipr2viz_web)
export(make_opts2procs)
export(getAccNumFromFA)
export(getProcessRuntimeWeights)
export(getTopAccByLinDomArch)
export(mapAcc2Name)
export(map_acc2name)
export(map_advanced_opts2procs)
export(mapAdvOption2Process)
export(mapOption2Process)
export(msa_pdf)
export(plotEstimatedWallTimes)
export(plotIPR2Viz)
export(plotIPR2VizWeb)
export(plotLineageDA)
export(plotLineageDomainRepeats)
export(plotLineageHeatmap)
Expand All @@ -72,7 +68,6 @@ export(plotStackedLineage)
export(plotSunburst)
export(plotTreemap)
export(plotUpSet)
export(plot_estimated_walltimes)
export(prepareColumnParams)
export(prepareSingleColumnParams)
export(proteinAcc2TaxID)
Expand All @@ -83,28 +78,27 @@ export(removeTails)
export(renameFA)
export(rename_fasta)
export(replaceQuestionMarks)
export(reveql)
export(reverse_operon)
export(reverseOperonSeq)
export(runDeltaBlast)
export(runRPSBlast)
export(selectLongestDuplicate)
export(sendJobStatusEmail)
export(shortenLineage)
export(sinkReset)
export(straightenOperonSeq)
export(summarizeByLineage)
export(summarizeDomArch)
export(summarizeDomArch_ByLineage)
export(summarizeGenContext)
export(summarizeGenContext_ByDomArchLineage)
export(summarizeGenContext_ByLineage)
export(theme_genes2)
export(to_titlecase)
export(themeGenes2)
export(totalGenContextOrDomArchCounts)
export(validateCountDF)
export(wordcloud3)
export(write.MsaAAMultipleAlignment)
export(write_proc_medians_table)
export(write_proc_medians_yml)
export(writeMSA_AA2FA)
export(writeProcessRuntime2TSV)
export(writeProcessRuntime2YML)
importFrom(Biostrings,AAStringSet)
importFrom(Biostrings,readAAStringSet)
importFrom(Biostrings,toString)
Expand All @@ -117,6 +111,7 @@ importFrom(assertthat,assert_that)
importFrom(assertthat,has_name)
importFrom(base64enc,base64encode)
importFrom(biomartr,getKingdomAssemblySummary)
importFrom(d3r,d3_nest)
importFrom(data.table,as.data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
Expand Down Expand Up @@ -181,6 +176,7 @@ importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_grey)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,adjustcolor)
Expand Down Expand Up @@ -237,13 +233,15 @@ importFrom(readr,write_file)
importFrom(readr,write_lines)
importFrom(readr,write_tsv)
importFrom(rentrez,entrez_fetch)
importFrom(rlang,.data)
importFrom(rlang,as_string)
importFrom(rlang,sym)
importFrom(sendmailR,mime_part)
importFrom(sendmailR,sendmail)
importFrom(seqinr,dist.alignment)
importFrom(seqinr,read.alignment)
importFrom(shiny,showNotification)
importFrom(stats,as.formula)
importFrom(stats,complete.cases)
importFrom(stats,logLik)
importFrom(stats,na.omit)
Expand All @@ -264,6 +262,7 @@ importFrom(stringr,str_sub)
importFrom(stringr,str_trim)
importFrom(stringr,word)
importFrom(sunburstR,sunburst)
importFrom(sunburstR,sund2b)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,drop_na)
Expand Down
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