docs: update the README file

Signed-off-by: Ali Sajid Imami <[email protected]>
CogDisResLab · Dec 21, 2024 · ca7d4fd · ca7d4fd
1 parent 250c9ae
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Showing 7 changed files with 139 additions and 17 deletions.
diff --git a/.gitignore b/.gitignore
@@ -331,3 +331,6 @@ inst/doc
 # Ignore overrides
 
 !inst/extdata/*
+
+# Ignore env files
+*.env*
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: pathwayFindR
+Package: pathwayfindR
 Title: Done enrichR enrichment analysis from R
 Version: 0.0.0.9000
 Authors@R: c(
@@ -30,9 +30,16 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Suggests:
+    codemetar,
+    devtools,
+    lintr,
     spelling,
-    testthat (>= 3.0.0)
+    styler,
+    testthat (>= 3.0.0),
+    webmockr
+    vcr
 Config/testthat/edition: 3
 Language: en-US
 Imports:
-    lifecycle
+    httr2,
+    lifecycle,
diff --git a/README.Rmd b/README.Rmd
@@ -2,8 +2,6 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
     collapse = TRUE,
@@ -13,19 +11,30 @@ knitr::opts_chunk$set(
 )
 ```
 
-# pathwayFindR
+# pathwayfindR
 
 <!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Continuous Integration / R Workflows](https://github.com/CogDisResLab/pathwayFindR/actions/workflows/rworkflows.yml/badge.svg)](https://github.com/CogDisResLab/pathwayFindR/actions/workflows/rworkflows.yml)
+[![latest-version](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fcogdisreslab.r-universe.dev%2Fapi%2Fpackages%2FpathwayFindR&query=%24.Version&style=flat&label=latest-release&color=orange)](https://github.com/CogDisResLab/pathwayFindR/releases/latest)
+[![license](https://img.shields.io/github/license/CogDisResLab/pathwayFindR)](https://github.com/CogDisResLab/pathwayFindR/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/338354715.svg)](https://zenodo.org/badge/latestdoi/338354715)
+[![Codecov test coverage](https://codecov.io/gh/CogDisResLab/pathwayFindR/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/CogDisResLab/pathwayFindR?branch=devel)
 <!-- badges: end -->
 
 The goal of pathwayFindR is to ...
 
 ## Installation
 
-You can install the development version of pathwayFindR like so:
+You can install the released version of pathwayFindR from [r-universe](https://cogdisreslab.r-universe.dev/pathwayFindR) with:
 
-``` r
-# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
+```{r, eval = FALSE}
+install.packages("pathwayfindR",
+    repos = c(
+        "https://cogdisreslab.r-universe.dev",
+        "https://cran.r-project.org"
+    )
+)
 ```
 
 ## Example

diff --git a/README.md b/README.md
@@ -2,23 +2,33 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
 
 
-
-# pathwayFindR
+# pathwayfindR
 
 <!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Continuous Integration / R Workflows](https://github.com/CogDisResLab/pathwayFindR/actions/workflows/rworkflows.yml/badge.svg)](https://github.com/CogDisResLab/pathwayFindR/actions/workflows/rworkflows.yml)
+[![latest-version](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fcogdisreslab.r-universe.dev%2Fapi%2Fpackages%2FpathwayFindR&query=%24.Version&style=flat&label=latest-release&color=orange)](https://github.com/CogDisResLab/pathwayFindR/releases/latest)
+[![license](https://img.shields.io/github/license/CogDisResLab/pathwayFindR)](https://github.com/CogDisResLab/pathwayFindR/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/338354715.svg)](https://zenodo.org/badge/latestdoi/338354715)
+[![Codecov test coverage](https://codecov.io/gh/CogDisResLab/pathwayFindR/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/CogDisResLab/pathwayFindR?branch=devel)
 <!-- badges: end -->
 
 The goal of pathwayFindR is to ...
 
 ## Installation
 
-You can install the development version of pathwayFindR like so:
+You can install the released version of pathwayFindR from [r-universe](https://cogdisreslab.r-universe.dev/pathwayFindR) with:
+
 
 ``` r
-# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
+install.packages("pathwayfindR",
+    repos = c(
+        "https://cogdisreslab.r-universe.dev",
+        "https://cran.r-project.org"
+    )
+)
 ```
 
 ## Example

diff --git a/codemeta.json b/codemeta.json
@@ -1,9 +1,9 @@
 {
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
-  "identifier": "pathwayFindR",
+  "identifier": "pathwayfindR",
   "description": "This package implements access to the enrichR web tool developed by the Ma'yan Laboratory. This package allows you to input one or more genesets (along with background genesets if applicable) and access the results from a specified set of libraries.",
-  "name": "pathwayFindR: Done enrichR enrichment analysis from R",
+  "name": "pathwayfindR: Done enrichR enrichment analysis from R",
   "license": "https://spdx.org/licenses/MIT",
   "version": "0.0.0.9000",
   "programmingLanguage": {
@@ -45,6 +45,42 @@
     }
   ],
   "softwareSuggestions": [
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "codemetar",
+      "name": "codemetar",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=codemetar"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "devtools",
+      "name": "devtools",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=devtools"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "lintr",
+      "name": "lintr",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=lintr"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "spelling",
@@ -57,6 +93,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=spelling"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "styler",
+      "name": "styler",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=styler"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "testthat",
@@ -69,10 +117,27 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=testthat"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "webmockr\n    vcr",
+      "name": "webmockr\n    vcr"
     }
   ],
   "softwareRequirements": {
     "1": {
+      "@type": "SoftwareApplication",
+      "identifier": "httr2",
+      "name": "httr2",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=httr2"
+    },
+    "2": {
       "@type": "SoftwareApplication",
       "identifier": "lifecycle",
       "name": "lifecycle",
@@ -86,5 +151,9 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "168352.177KB"
+  "fileSize": "168353.591KB",
+  "codeRepository": "https://github.com/CogDisResLab/pathwayFindR",
+  "readme": "https://github.com/CogDisResLab/pathwayFindR/blob/main/README.md",
+  "contIntegration": ["https://github.com/CogDisResLab/pathwayFindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/pathwayFindR?branch=devel"],
+  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
 }
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -5,46 +5,64 @@ billyryan
 bioconductor
 changelog
 clipPath
+Codecov
+codecov
 codemeta
+codemetar
+codeRepository
+CogDisResLab
 commitizen
 ComputerLanguage
 Config
+contIntegration
 cran
 cre
 cz
 DejaVu
+developmentStatus
+devtools
 doi
+drugfindR
 ec
 enrichR
+env
 familyName
 fe
 fff
 fileSize
 genesets
 geometricPrecision
+gh
 github
 givenName
 gmail
 gpg
 http
+httr
 Imami
 img
+io
 johnm
 lifecycle
 linearGradient
 LinkingTo
+lintr
 Ma'yan
 md
 MERCHANTABILITY
 NONINFRINGEMENT
 ORCID
 orcid
 pathwayFindR
+pathwayfindR
 programmingLanguage
+readme
+README
 rect
 Roxygen
 RoxygenNote
 runtimePlatform
+rworkflows
 rx
 Sajid
 sameAs
@@ -53,15 +71,19 @@ softwareRequirements
 SoftwareSourceCode
 softwareSuggestions
 spdx
+styler
 sublicense
 svg
 SystemRequirements
 testthat
 textLength
+vcr
 vcs
 Verdana
 vergis
 Vergis
+webmockr
 www
 xlink
 xmlns
+yml
diff --git a/mise.toml b/mise.toml
@@ -0,0 +1,2 @@
+[env]
+'_'.file = ".env"