diff --git a/.Rbuildignore b/.Rbuildignore index 2623983..0227be7 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,11 +1,8 @@ -Makefile README.Rmd ^cran-comments.md$ ^.*\.Rproj$ ^\.Rproj\.user$ ^README_DEV.md$ -cdk/ -cdk.zip revdep/ ^CRAN-SUBMISSION$ ^_pkgdown\.yml$ @@ -13,3 +10,5 @@ revdep/ ^pkgdown$ ^\.github$ ^cran-comments\.md$ +^Makefile$ +^build$ diff --git a/DESCRIPTION b/DESCRIPTION index 228eaa2..56607f0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rcdklibs -Version: 2.11 -Date: 2025-09-10 +Version: 2.13 +Date: 2026-10-19 Authors@R: c( person('Rajarshi', 'Guha', ,'rajarshi.guha@gmail.com', role=c('aut'), comment = c(ORCID = "0000-0001-7403-8819")), diff --git a/Makefile b/Makefile index 5b2f8ca..251c3dd 100644 --- a/Makefile +++ b/Makefile @@ -1,30 +1,18 @@ - -CDK_VERSION=2.11 -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-$(CDK_VERSION).zip - - -build: cdk.zip - unzip cdk.zip -d cdk - # 88 - 92 is cdk-pdb - # 148-157 is cdk-builder3d and builder3d-tools - # 248-252 is cdk-pdbcml - # 372-378 is cdk-iordf - sed -i .bak -e '88,92d;148,157d;248,252d;372,378d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml - cd cdk/cdk-cdk-$(CDK_VERSION)/bundle && mvn compile war:war -P jdk11-plus && cd ../../.. - - -prepare: build - # find cdk/ -name "*.jar" | parallel "cp {} inst/cont/{/}" - cp $(JAR_DIR)/*jar inst/cont/ - +CDK_VERSION=2.13 +BASE_URL=https://github.com/cdk/cdk/releases/download/cdk-$(CDK_VERSION) +JAR=cdk-$(CDK_VERSION).jar +SUMS=cdk-$(CDK_VERSION)-checksums-sha256.txt + +# Download the CDK release uberjar, verify it, and install it in inst/cont +prepare: + mkdir -p build + curl -fL -o build/$(JAR) $(BASE_URL)/$(JAR) + curl -fL -o build/$(SUMS) $(BASE_URL)/$(SUMS) + cd build && grep " $(JAR)$$" $(SUMS) | shasum -a 256 -c - + rm -f inst/cont/*.jar + cp build/$(JAR) inst/cont/ clean: - rm cdk.zip - rm -rf cdk/ - + rm -rf build all: clean prepare - diff --git a/NEWS.md b/NEWS.md index 70e6cdc..b0cedf3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# v2.13 + +- Update to CDK 2.13 libraries. +- Bundle the official CDK release uberjar (`cdk-2.13.jar`) instead of ~90 individual jars; the Makefile now just downloads and verifies it. + # v2.11 - Update to CDK 2.11 libraries. diff --git a/README.Rmd b/README.Rmd index 9d4f01c..c6ab8da 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,7 +25,7 @@ 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 [2.9 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9) +API. The libs provided in this release correspond to the [2.13 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.13) ``` @@ -62,4 +62,3 @@ And the development version from [GitHub](https://github.com/) with: # install.packages("devtools") devtools::install_github("https://github.com/CDK-R/rcdklibs") ``` - diff --git a/README.md b/README.md index 14e8ba0..6707dce 100644 --- a/README.md +++ b/README.md @@ -18,8 +18,8 @@ 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 [2.9 -Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9) +in this release correspond to the [2.13 +Release](https://github.com/cdk/cdk/releases/tag/cdk-2.13) # Example library(rcdklibs) diff --git a/README_DEV.md b/README_DEV.md index 3c30875..381207b 100644 --- a/README_DEV.md +++ b/README_DEV.md @@ -1,26 +1,13 @@ # Packaging CDK -The CDK2.0 release is 25MB. To try to reduce this size we built a version of the CDK libs that removes several sub-libraries. - -``` -git clone https://github.com/cdk/cdk.git - -cd cdk/bundle - -#checkout the tag of the released version -git checkout -b rcdk2 cdk2-2.0 - -vi pox.xml - -# remove the entries for: -# builder3d -# builder3d-tools -# cdk-pdb -# cdk-pdbcml - -mvn package -``` - -You can now use the target/cdk-2.0.jar for inclusion in rcdklibs +rcdklibs bundles the official CDK release uberjar (`cdk-.jar`, published +with each [CDK release](https://github.com/cdk/cdk/releases)) as the only jar in +`inst/cont/`. It already includes all CDK modules and their dependencies, so no +custom build is needed. +To update to a new CDK release: +1. Set `CDK_VERSION` in the `Makefile`. +2. Run `make all`. This downloads the uberjar, verifies its SHA-256 checksum and + replaces the contents of `inst/cont/`. +3. 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