36 prepare for cran release 110

.Rbuildignore

@@ -11,4 +11,5 @@
 ^\.github$
 ^vignettes/articles$
 ^CRAN-SUBMISSION$
-
+CONTRIBUTING.md
+^revdep$

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CONTRIBUTING.md

@@ -0,0 +1,40 @@
+---
+title: "Contributing"
+---
+
+
+Filing issues
+-------------
+
+Please read these points carefully and follow them while filing issues.
+
+- **One issue for one purpose**. Don't add more than one *bug*, *feature request*, or *documentation request* on to the same issue. Take the time to read through the current issues to ensure your issue is not already listed.
+- If you've found a *bug*, thank you for reporting! Please include a reproducible example of your bug in the issue. 
+- If you need *support* or have a general *question*, please consider asking the question on [StackOverflow](http://www.stackoverflow.com)
+- For the project contributors, please label new issues using the following rules:
+  - *bugs* should be labeled "bug"
+  - *feature requests* or *suggestions* should be labeled "enhancement"
+  - *questions* or *requests for support* should be labeled "question"
+
+Pull Requests
+-------------
+
+Please file an issue before creating PRs so that it can be discussed first *before* you invest time implementing it.
+
+1. Please create all pull requests (PR) against the `dev` branch.
+2. Create **one PR per feature/bug fix**. Each PR should be associated with an Issue.
+3. Create a branch for that feature/bug fix, named 'issue-N' where N is the Issue number, and use that as a base for your pull requests. Pull requests directly against your version of `dev` will not be accepted.
+4. Please squash temporary stage commits together before issuing a PR.
+5. All commit messages should have two components: (1) a header on the first line beginning with "issue-N:" and containing no more than 50 characters, and (2) a body with 1 empty line after the header then at least a sentence or two in the commit body detailing all changes and justifications. Lines in the commit body should be wrapped to no more than 72 characters per line, and can contain multiple paragraphs.<sup>[1](#myfootnote1)</sup>
+5. In your pull request's description, please state clearly as to what your PR does, i.e., what FR or bug your PR addresses, along with the issue number. For e.g, "Closes #13: Added CRAN version and monthly download bages."
+7. Please build and test the package using `R CMD check --as-cran` against your branch source package archive `.tar.gz` file. You may want to add `--no-manual`, `--no-build-vignettes` or `--ignore-vignettes` (R 3.3.0+) options to reduce dependencies required to perform check. PRs that fail `check` cannot be merged.
+8. The NEWS file also has to be updated while fixing or implementing an issue. It should mention the issue number and what the issue is being closed. Also add a "Thanks to @your_name for the PR".
+
+**References:** If you are not sure how to issue a PR, but would like to contribute, these links should help get you started:
+
+1. **[How to Github: Fork, Branch, Track, Squash and Pull request](https://gun.io/blog/how-to-github-fork-branch-and-pull-request/)**.
+2. **[Squashing Github pull requests into a single commit](http://eli.thegreenplace.net/2014/02/19/squashing-github-pull-requests-into-a-single-commit)**.
+
+*This guide was modified from the contributing guide for the [data.table](https://github.com/Rdatatable/data.table) repository*
+
+<a name="myfootnote1">1</a>: To make it easier to count the characters per line you can edit your $HOME/.vimrc ($HOME/_vimrc on Windows) to include ":set ruler" which will display the line and position numbers in the bottom right corner of the terminal when editing the commit messages.

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ctxR
 Title: Utilities for Interacting with the 'CTX' APIs
-Version: 1.0.0.9000
+Version: 1.1.0
 Authors@R: c(
             person("Paul", "Kruse", email = "[email protected]", 
               role = c("aut", "cre"), 
@@ -19,11 +19,11 @@ Authors@R: c(
     	        )
 Description: Access chemical, hazard, bioactivity, and exposure data from the 
    Computational Toxicology and Exposure ('CTX') APIs 
-   <https://api-ccte.epa.gov/docs/>. 'ctxR' was developed to streamline the 
-   process of accessing the information available through the 'CTX' APIs 
-   without requiring prior knowledge of how to use APIs. Most data is also 
-   available on the CompTox Chemical Dashboard ('CCD') 
-   <https://comptox.epa.gov/dashboard/> and other resources found at the 
+   <https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>. 
+   'ctxR' was developed to streamline the process of accessing the information 
+   available through the 'CTX' APIs without requiring prior knowledge of how to 
+   use APIs. Most data is also available on the CompTox Chemical Dashboard 
+   ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the 
    EPA Computational Toxicology and Exposure Online Resources 
    <https://www.epa.gov/comptox-tools>. 
 License: GPL (>= 3)

NEWS.md

@@ -1,26 +1,48 @@
-# ctxR (development version)
+# ctxR 1.1.0
 
 
 ## Minor improvements and fixes
 
+* Fixed broken link to `CONTRIBUTING.md` in README (@c1au6i0, #37)
+
+* Updated `get_chemical_synonym()`, `get_chemical_synonym_batch()` to handle returned data more efficiently (#30).
+
+* Updated documentation of internal helper functions `create_data.table_chemical_details()`, `prepare_word()` (#24).
+
+* Fixed `get_bioactivity_details()` to handle case when `mc6Param` field of returned data is NULL (#18).
+
+* Fixed `get_bioactivity_details()` to handle `m4id` parameter values that do not exist (#16).
+
 * Adjusted `chemical_contains()`, `chemical_equal()`, and 
 `chemical_starts_with()` to handle http 400 errors and returned information from
 those requests. Adjusted the `chemical_contains_batch()`, 
-`chemical_equals_batch()`, and `chemical_starts_with_batch()` to return named
-lists of valid and invalid search results, with invalid results containing 
-information from 400 errors (@kisaacs1, #11).
+`chemical_equals_batch()`, and `chemical_starts_with_batch()` to return named lists of valid and invalid search results, with invalid results containing information from 400 errors (@kisaacs1, #12).
+
+* Added examples in `Chemical.Rmd` vignette for  `get_chemical_details_batch()` (#8).
 
 ## New features
 
-* Added `check_existence_by_dtxsid()`, `check_existence_by_dtxsid_batch()` 
-functions. Updated the `Chemical.Rmd` vignette to include examples of how to use
-these functions (#27).
+* Added warning for missing `API_key` parameter and missing stored API key to all functions that wrap API endpoints (#35).
+
+* Added error handling for invalid API key inputs to all functions that wrap an API endpoint (#33).
+
+* Added functions `get_all_list_types()`, `get_chemicals_in_list_start()`, `get_chemicals_in_list_start_batch()` `get_chemicals_in_list_exact()`, `get_chemicals_in_list_exact_batch()`, `get_chemicals_in_lists_contain()`, `get_chemicals_in_lists_contain_batch`(). Added `gsid` parameter to `get_chemical_image()`. Updated `Chemical.rmd` vignette to include examples for new chemical functions and new features (#30).
+
+* Added `check_existence_by_dtxsid()`, `check_existence_by_dtxsid_batch()` functions. Updated the `Chemical.Rmd` vignette to include examples of how to use these functions and `ctxR` hex logo location (#28).
+
+* Added parameter `limit` and default value 200 to `generate_ranges()` function and fixed. Fixed request limit in `chemical_equal_batch()` function (@seanthimons, #26).
+
+* Added pkgdown website for development version of package (#22).
+
+* Added monthly download and CRAN version badges to `README.md` and `README.Rmd` files (#14).
 
 * Added `get_httk_data()`, `get_httk_data_batch()`, 
 `get_general_exposure_prediction()`, `get_general_exposure_prediction_batch()`,
 `get_demographic_exposure_prediction()`, 
 `get_demographic_exposure_prediction_batch()` functions. Updated the 
-`Exposure.Rmd` vignette to include examples of how to use these functions (#6).
+`Exposure.Rmd` vignette to include examples of how to use these functions (#10).
+
+* Added pkgdown site for CRAN version of `ctxR` (#20).
 
 
 # ctxR 1.0.0

README.Rmd

@@ -28,11 +28,11 @@ Package website: [release](https://usepa.github.io/ctxR/) | [dev](https://usepa.
 
 ## Welcome to the GitHub repository for the ctxR package
 
-<a href="https://cran.r-project.org/web/packages/ctxR/index.html"><img src="vignettes/Pictures/ctxR_hex.png" width="200" align="right" /></a>
+<a href="https://CRAN.R-project.org/package=ctxR"><img src="vignettes/Pictures/ctxR_hex.png" width="200" align="right" /></a>
 
 ctxR was developed to streamline the process of accessing the information available through the [Computational Toxicology and Exposure (CTX) APIs](https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis) without requiring prior knowledge of how to use APIs. Chemical, hazard, bioactivity, and exposure data in available from the CTX APIs. Most data is also available on the [CompTox Chemical Dashboard (CCD)](https://comptox.epa.gov/dashboard/) or within other [Computational Toxicology and Exposure Online Resources](https://www.epa.gov/comptox-tools).
 
-If you are interested in contributing or want to report a bug, please submit a issue or start a discussion. See [CONTRIBUTING](CONTRIBUTING.md) for more information.
+If you are interested in contributing or want to report a bug, please submit a issue or start a discussion. See [CONTRIBUTING](https://github.com/USEPA/ctxR/blob/dev/CONTRIBUTING.md) for more information.
 
 To install the current development version, run the following command: 
 

README.md

@@ -18,7 +18,7 @@ Downloads](https://cranlogs.r-pkg.org/badges/last-month/ctxR?color=7BAFD4)](http
 
 ## Welcome to the GitHub repository for the ctxR package
 
-<a href="https://cran.r-project.org/web/packages/ctxR/index.html"><img src="vignettes/Pictures/ctxR_hex.png" width="200" align="right" /></a>
+<a href="https://CRAN.R-project.org/package=ctxR"><img src="vignettes/Pictures/ctxR_hex.png" width="200" align="right" /></a>
 
 ctxR was developed to streamline the process of accessing the
 information available through the [Computational Toxicology and Exposure
@@ -32,8 +32,7 @@ is also available on the [CompTox Chemical Dashboard
 Resources](https://www.epa.gov/comptox-tools).
 
 If you are interested in contributing or want to report a bug, please
-submit a issue or start a discussion. See
-[CONTRIBUTING](CONTRIBUTING.md) for more information.
+submit a issue or start a discussion.
 
 To install the current development version, run the following command:
 

cran-comments.md

@@ -1,50 +1,34 @@
 ## Test environments
 
+* macOS 13.3.1, Apple clang version 14.0.0 (clang-1400.0.29.202), GNU Fortran (GCC) 12.2.0, macOS Ventura 13.3.1
+* R Under development (unstable) (2024-11-26 r87383 ucrt), Windows Server 2022 x64 (build 20348)
 * local Windows 10 install, R 4.4.0
-* R Under development (unstable) (2024-06-27 r86847 ucrt), 
-Windows Server 2022 x64 (build 20348)
-
-
-* Rhub/actions Windows Server 2022 x64 (build 20348)
-* Rhub/actions Ubuntu 22.04.4 LTS, clang-asan, R-devel (2024-06-27 r86847)
-* Rhub/actions macos-13 on GitHub, Apple clang version 14.0.0 
-(clang-1400.0.29.202), GNU Fortran (GCC) 12.2.0, macOS  Venture 13.6.7
+* Rhub/actions Ubuntu 22.04.5 LTS, clang-asan, R-devel (2024-11-26 r87383)
 
 ## rhub CMD check results
 
 Status: OK
 
-* elapsed time (Windows Server 2022 x64) : 1:50
-* elapsed time (Ubuntu 22.04.4 LTS) : 0:56
-* elapsed time (macos-13 on GitHub) : 1:50
+* elapsed time (Ubuntu 22.04.4 LTS) : 1:38
+
+## mac release check results
+
+0 errors | 0 warnings | 0 notes
 
 
 ## win devel check results
-1 NOTE - CRAN incoming feasibility
-Indicated possibly misspelled words in DESCRIPTION (APIs, CompTox, bioactivity). 
-These are all correctly spelled.
+
+* 1 NOTE - CRAN incoming feasibility.
+  Indicated possible invalid URL. This URL works correctly and is stored in data retrieved from an API request, so we cannot alter it.
 
 
 ## local R CMD check results
 
-* checking CRAN incoming feasibility ... NOTE
-  Maintainer: 'Paul Kruse <[email protected]>'
-
-  New submission
-
-
-0 errors | 0 warnings | 1 note
-
-* This is a new release. It is a renamed version of the ccdR 1.0.0 package. 
-There are a few reasons for renaming this package. ccdR was developed when the
-APIs it wraps were primarily pulling data from the CompTox Chemicals Dashboard 
-(CCD) and named to reflect that. More data is now available from the APIs than 
-is represented by the CCD. The APIs have been renamed to be the 
-Computational Toxicology and Exposure (CTX) APIs, which is a stable name that 
-more appropriately represents the data domain and area of research the tools 
-and resources related to the data represent. ctxR is much more representative 
-than ccdR of the current APIs and data. Additionally, the US EPA is 
-coordinating several API clients written in different languages to use the 
-consistent package name ctx_, where '_' is used to represent the language in 
-which a client is developed (e.g. ctxR for R, ctxPy for Python). Renaming ccdR 
-to ctxR reflects this harmonization of CTX API clients across languages.
+0 errors | 0 warnings | 0 notes
+
+## revdepcheck results
+
+We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages

revdep/.gitignore

@@ -0,0 +1,7 @@
+checks
+library
+checks.noindex
+library.noindex
+cloud.noindex
+data.sqlite
+*.html

revdep/README.md

@@ -0,0 +1,35 @@
+# Platform
+
+|field    |value                                    |
+|:--------|:----------------------------------------|
+|version  |R version 4.4.0 (2024-04-24 ucrt)        |
+|os       |Windows 11 x64 (build 22621)             |
+|system   |x86_64, mingw32                          |
+|ui       |RStudio                                  |
+|language |(EN)                                     |
+|collate  |English_United States.utf8               |
+|ctype    |English_United States.utf8               |
+|tz       |America/New_York                         |
+|date     |2024-11-27                               |
+|rstudio  |2024.04.0+735 Chocolate Cosmos (desktop) |
+|pandoc   |NA                                       |
+
+# Dependencies
+
+|package    |old   |new        |Δ  |
+|:----------|:-----|:----------|:--|
+|ctxR       |1.0.0 |1.0.0.9000 |*  |
+|askpass    |NA    |1.2.1      |*  |
+|cli        |NA    |3.6.3      |*  |
+|cpp11      |NA    |0.5.0      |*  |
+|curl       |NA    |6.0.1      |*  |
+|data.table |NA    |1.16.2     |*  |
+|glue       |NA    |1.8.0      |*  |
+|jsonlite   |NA    |1.8.9      |*  |
+|openssl    |NA    |2.2.2      |*  |
+|Rcpp       |NA    |1.0.13-1   |*  |
+|sys        |NA    |3.4.3      |*  |
+|withr      |NA    |3.0.2      |*  |
+
+# Revdeps
+

revdep/cran.md

@@ -0,0 +1,7 @@
+## revdepcheck results
+
+We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages
+

revdep/failures.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

revdep/problems.md

@@ -0,0 +1 @@
+*Wow, no problems at all. :)*

vignettes/Bioactivity.Rmd

@@ -54,7 +54,7 @@ registerS3method(
 
 ```
 
-<a href="https://cran.r-project.org/web/packages/ctxR/index.html"><img src="Pictures/ctxR_hex.png" width="200" align="right" style="float: right; margin-left: 10px; margin-bottom: 20px;"/></a>
+<a href="https://CRAN.R-project.org/package=ctxR"><img src="Pictures/ctxR_hex.png" width="200" align="right" style="float: right; margin-left: 10px; margin-bottom: 20px;"/></a>
 
 # Introduction