Merge pull request #5 from CDK-R/202402-29

Update CDK Jars to 2.9

.Rbuildignore

@@ -8,3 +8,7 @@ cdk/
 cdk.zip
 revdep/
 ^CRAN-SUBMISSION$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -3,4 +3,5 @@
 .RData
 .Ruserdata
 cdk/
-revdep/
+revdep/
+docs

DESCRIPTION

@@ -1,9 +1,12 @@
 Package: rcdklibs
-Version: 2.8
-Date: 2022-09-20
-Authors@R: c(person('Rajarshi', 'Guha', role=c('aut'), email='[email protected]'),
-             person('Zachary', 'Charlop-Powers', role=c('cre'), email='[email protected]'),
-             person('CDK Project', '', role=c('ctb', 'cph'), comment='CDK Java library contained in multiple jar files'))
+Version: 2.9
+Date: 2024-03-02
+Authors@R: c(
+  person('Rajarshi', 'Guha', ,'[email protected]', role=c('aut'),
+    comment = c(ORCID = "0000-0001-7403-8819")),
+  person('Zachary', 'Charlop-Powers', ,'[email protected]',role=c('cre'), 
+      comment = c(ORCID = "0000-0001-8816-4680")),
+  person('CDK Project', '', role=c('ctb', 'cph'), comment='CDK Java library contained in multiple jar files'))
 Depends:
     R (>= 2.0.0),
     rJava
@@ -16,4 +19,5 @@ Description: An R interface to the Chemistry Development Kit, a Java library
     interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more
     idiomatic way. The CDK library itself is released as LGPL and the sources can be
     obtained from <https://github.com/cdk/cdk>.
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
+URL: https://cdk-r.github.io/rcdklibs/

Makefile

@@ -1,6 +1,6 @@
 
-CDK_VERSION=2.8
-JAR_DIR=cdk/cdk-cdk-$(CDK_VERSION)/bundle/target/cdk-bundle-2.8/WEB-INF/lib
+CDK_VERSION=2.9
+JAR_DIR=cdk/cdk-cdk-$(CDK_VERSION)/bundle/target/cdk-bundle-$(CDK_VERSION)/WEB-INF/lib
 
 cdk.zip:
 	wget -O cdk.zip https://github.com/cdk/cdk/archive/refs/tags/cdk-$(CDK_VERSION).zip
@@ -10,17 +10,13 @@ build: cdk.zip
 	unzip cdk.zip -d cdk
 	# 88 - 92 is cdk-pdb
 	# 148-157 is cdk-builder3d and builder3d-tools
-	# 238-242 is cdk-pdbcml
-	# 343-337 is cdk-iordf 
-	sed -i .bak -e '88,92d;148,157d;238,242d;343,347d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
+	# 248-252 is cdk-pdbcml
+	# 372-376 is cdk-iordf 
+	sed -i .bak -e '88,92d;148,157d;248,252d;372,376d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
 	cd cdk/cdk-cdk-$(CDK_VERSION)/bundle && mvn compile war:war -P jdk11-plus && cd ../../..
 
-# guava:
-# 	wget -O inst/cont/guava-31.1-jre.jar https://repo1.maven.org/maven2/com/google/guava/guava/31.1-jre/guava-31.1-jre.jar
-# 	wget -O inst/cont/failureaccess-1.0.1.jar https://repo1.maven.org/maven2/com/google/guava/failureaccess/1.0.1/failureaccess-1.0.1.jar
 
-
-prepare: build guava
+prepare: build
 	# find cdk/ -name "*.jar" | parallel "cp {}  inst/cont/{/}"	
 	cp $(JAR_DIR)/*jar inst/cont/
 

NEWS.md

@@ -1,3 +1,9 @@
+# v2.9
+
+- Update to CDK 2.9 libraries.
+- Removing a number of less-used jars prior to upload to CRAN. See the Makefile
+
+
 # v2.8
 
 - Update to CDK 2.8 libraries.

README.Rmd

@@ -26,7 +26,7 @@ The goal of rcdklibs is to provide the [CDK](https://github.com/cdk/cdk) jarfile
 and thereby facilitate chemoinformatic analysis within the R ecosystem. The 
 primary consumer of `rcdklibs` is the [rcdk](https://github.com/CDK-R/cdkr) package
 but all of CDK's functionality can be accessed by the standard [rJava]( https://CRAN.R-project.org/package=rJava)
-API. The libs provided in this release correspond to the [2.8 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.8)
+API. The libs provided in this release correspond to the [2.9 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9)
 
 
 ```

README.md

@@ -21,8 +21,8 @@ ecosystem. The primary consumer of `rcdklibs` is the
 [rcdk](https://github.com/CDK-R/cdkr) package but all of CDK’s
 functionality can be accessed by the standard
 [rJava](https://CRAN.R-project.org/package=rJava) API. The libs provided
-in this release correspond to the [2.8
-Release](https://github.com/cdk/cdk/releases/tag/cdk-2.8)
+in this release correspond to the [2.9
+Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9)
 
     # Example
     library(rcdklibs)

_pkgdown.yml

@@ -0,0 +1,8 @@
+url: https://cdk-r.github.io/rcdklibs/
+template:
+  bootstrap: 5
+  bslib:
+    primary: "#0054AD"
+    border-radius: 0.5rem
+    btn-border-radius: 0.25rem
+