Add Makefile targets for udpates

Makefile

@@ -49,15 +49,16 @@ help:
 	@echo "VariantKey Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make c            : Build and test the C version"
-	@echo "    make go           : Build and test the GO version"
-	@echo "    make javascript   : Build and test the Javascript version"
-	@echo "    make python       : Build and test the Python version"
-	@echo "    make python-class : Build and test the Python wrapper class"
-	@echo "    make r            : Build and test the R version"
-	@echo "    make clean        : Remove any build artifact"
-	@echo "    make dbuild       : Build everything inside a Docker container"
-	@echo "    make tag          : Tag the Git repository"
+	@echo "  make c            : Build and test the C version"
+	@echo "  make go           : Build and test the GO version"
+	@echo "  make javascript   : Build and test the Javascript version"
+	@echo "  make python       : Build and test the Python version"
+	@echo "  make python-class : Build and test the Python wrapper class"
+	@echo "  make r            : Build and test the R version"
+	@echo "  make clean        : Remove any build artifact"
+	@echo "  make dbuild       : Build everything inside a Docker container"
+	@echo "  make tag          : Tag the Git repository"
+	@echo "  make versionup    : Increase the patch number in the VERSION file"
 	@echo ""
 
 all: c go javascript python python-class r
@@ -147,3 +148,9 @@ pubdocs:
 tag:
 	git tag -a "v$(VERSION)" -m "Version $(VERSION)" && \
 	git push origin --tags
+
+# Increase the patch number in the VERSION file
+.PHONY: versionup
+versionup:
+	echo ${VERSION} | gawk -F. '{printf("%d.%d.%d",$$1,$$2,(($$3+1)));}' > VERSION
+	$(MAKE) version

VERSION

@@ -1 +1 @@
-5.6.18
+5.6.19

c/Makefile

@@ -58,18 +58,18 @@ help:
 	@echo "$(PROJECT) Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make qa        : Run all the tests and static analysis reports"
-	@echo "    make test      : Run the unit tests"
-	@echo "    make tidy      : Check the code using clang-tidy"
-	@echo "    make build     : Build the library"
-	@echo "    make version   : Set version from VERSION file"
-	@echo "    make doc       : Generate source code documentation"
-	@echo "    make format    : Format the source code"
-	@echo "    make clean     : Remove any build artifact"
-	@echo "    make install   : Install the library"
-	@echo "    make uninstall : Uninstall the library"
-	@echo "    make rpm       : Build an RPM package"
-	@echo "    make deb       : Build a DEB package"
+	@echo "  make qa        : Run all the tests and static analysis reports"
+	@echo "  make test      : Run the unit tests"
+	@echo "  make tidy      : Check the code using clang-tidy"
+	@echo "  make build     : Build the library"
+	@echo "  make version   : Set version from VERSION file"
+	@echo "  make doc       : Generate source code documentation"
+	@echo "  make format    : Format the source code"
+	@echo "  make clean     : Remove any build artifact"
+	@echo "  make install   : Install the library"
+	@echo "  make uninstall : Uninstall the library"
+	@echo "  make rpm       : Build an RPM package"
+	@echo "  make deb       : Build a DEB package"
 	@echo ""
 
 all: clean version format test tidy build rpm deb package_vk doc

c/doc/Doxyfile

@@ -32,7 +32,7 @@ PROJECT_NAME           = "VariantKey"
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-PROJECT_NUMBER = 5.6.18
+PROJECT_NUMBER = 5.6.19
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer

go/Makefile

@@ -72,14 +72,18 @@ help:
 	@echo "GOPATH=$(GOPATH)"
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make clean    : Remove any build artifact"
-	@echo "    make coverage : Generate the coverage report"
-	@echo "    make deps     : Get dependencies"
-	@echo "    make format   : Format the source code"
-	@echo "    make linter   : Check code against multiple linters"
-	@echo "    make mod      : Download dependencies"
-	@echo "    make qa       : Run all tests and static analysis tools"
-	@echo "    make test     : Run unit tests"
+	@echo "  make clean      : Remove any build artifact"
+	@echo "  make coverage   : Generate the coverage report"
+	@echo "  make deps       : Get dependencies"
+	@echo "  make format     : Format the source code"
+	@echo "  make linter     : Check code against multiple linters"
+	@echo "  make mod        : Download dependencies"
+	@echo "  make qa         : Run all tests and static analysis tools"
+	@echo "  make test       : Run unit tests"
+	@echo "  make updateall  : Update everything"
+	@echo "  make updatego   : Update Go version"
+	@echo "  make updatelint : Update golangci-lint version"
+	@echo "  make updatemod  : Update dependencies"
 	@echo ""
 	@echo "Use DEVMODE=LOCAL for human friendly output."
 	@echo ""
@@ -159,3 +163,26 @@ test: ensuretarget
 	-coverprofile=target/report/coverage.out \
 	-v $(SRCDIR) $(TESTEXTRACMD)
 	@echo -e "\n\n>>> END: Unit Tests <<<\n\n"
+
+# Update everything
+.PHONY: updateall
+updateall: updatego updatelint updatemod
+
+# Update go version
+.PHONY: updatego
+updatego:
+	$(eval LAST_GO_TOOLCHAIN=$(shell curl -s https://go.dev/dl/ | grep -oP 'go[0-9]+\.[0-9]+\.[0-9]+\.linux-amd64\.tar\.gz' | head -n 1 | grep -oP 'go[0-9]+\.[0-9]+\.[0-9]+'))
+	$(eval LAST_GO_VERSION=$(shell echo ${LAST_GO_TOOLCHAIN} | grep -oP '[0-9]+\.[0-9]+'))
+	sed -i "s|^go [0-9]*\.[0-9]*$$|go ${LAST_GO_VERSION}|g" ../go.mod
+	sed -i "s|^toolchain go[0-9]*\.[0-9]*\.[0-9]*$$|toolchain ${LAST_GO_TOOLCHAIN}|g" ../go.mod
+
+# Update linter version
+.PHONY: updatelint
+updatelint:
+	$(eval LAST_GOLANGCILINT_VERSION=$(shell curl -sL https://github.com/golangci/golangci-lint/releases/latest | grep -oP '<title>Release \Kv[0-9]+\.[0-9]+\.[0-9]+'))
+	sed -i "s|^GOLANGCILINTVERSION=v[0-9]*\.[0-9]*\.[0-9]*$$|GOLANGCILINTVERSION=${LAST_GOLANGCILINT_VERSION}|g" Makefile
+
+# Update dependencies
+.PHONY: updatemod
+updatemod:
+	$(GO) get -t -u ./... && go mod tidy -compat=$(shell grep -oP 'go \K[0-9]+\.[0-9]+' ../go.mod)

javascript/Makefile

@@ -14,10 +14,10 @@ help:
 	@echo "Requires: node-js and uglify-js."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make test    : Run the unit tests against source code"
-	@echo "    make build   : Build and test a minified version of the library"
-	@echo "    make format  : Format the source code"
-	@echo "    make clean   : Remove any build artifact"
+	@echo "  make test   : Run the unit tests against source code"
+	@echo "  make build  : Build and test a minified version of the library"
+	@echo "  make format : Format the source code"
+	@echo "  make clean  : Remove any build artifact"
 	@echo ""
 
 all: clean format test build

python-class/Makefile

@@ -31,13 +31,13 @@ help:
 	@echo "${PROJECT} Python Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make build   : Build the library"
-	@echo "    make clean   : Remove any build artifact"
-	@echo "    make docs    : Generate documentation"
-	@echo "    make format  : Format the source code"
-	@echo "    make test    : Test the library"
-	@echo "    make venv    : Create a virtual environment"
-	@echo "    make version : Set the version from VERSION file"
+	@echo "  make build   : Build the library"
+	@echo "  make clean   : Remove any build artifact"
+	@echo "  make docs    : Generate documentation"
+	@echo "  make format  : Format the source code"
+	@echo "  make test    : Test the library"
+	@echo "  make venv    : Create a virtual environment"
+	@echo "  make version : Set the version from VERSION file"
 	@echo ""
 
 all: clean venv build test

python-class/setup.py

@@ -38,7 +38,7 @@ def run(self):
 
 setup(
     name="pyvariantkey",
-    version="5.6.18.0",
+    version="5.6.19.0",
     keywords=("variantkey variant key genetic genomics"),
     description="VariantKey Python wrapper class",
     long_description=read("../README.md"),
@@ -56,7 +56,7 @@ def run(self):
     ],
     install_requires=[
         "numpy>=1.24.2,<2",
-        "variantkey>=5.6.18.0",
+        "variantkey>=5.6.19.0",
     ],
     extras_require={
         "test": [

python/Makefile

@@ -31,13 +31,13 @@ help:
 	@echo "${PROJECT} Python Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make build   : Build the library"
-	@echo "    make clean   : Remove any build artifact"
-	@echo "    make docs    : Generate documentation"
-	@echo "    make format  : Format the source code"
-	@echo "    make test    : Test the library"
-	@echo "    make venv    : Create a virtual environment"
-	@echo "    make version : Set the version from VERSION file"
+	@echo "  make build   : Build the library"
+	@echo "  make clean   : Remove any build artifact"
+	@echo "  make docs    : Generate documentation"
+	@echo "  make format  : Format the source code"
+	@echo "  make test    : Test the library"
+	@echo "  make venv    : Create a virtual environment"
+	@echo "  make version : Set the version from VERSION file"
 	@echo ""
 
 all: clean venv build test

python/setup.py

@@ -30,7 +30,7 @@ def run(self):
 
 setup(
     name="variantkey",
-    version="5.6.18.0",
+    version="5.6.19.0",
     keywords=("variantkey variant key genetic genomics"),
     description="VariantKey Bindings for Python",
     long_description=read("../README.md"),

r/Makefile

@@ -43,11 +43,11 @@ help:
 	@echo "VariantKey R Makefile."
 	@echo "The following commands are available:"
 	@echo ""
-	@echo "    make build   : Build the library"
-	@echo "    make test    : Test the library"
-	@echo "    make format  : Format the source code"
-	@echo "    make clean   : Remove any build artifact"
-	@echo "    make devdoc  : Generate documentation"
+	@echo "  make build  : Build the library"
+	@echo "  make test   : Test the library"
+	@echo "  make format : Format the source code"
+	@echo "  make clean  : Remove any build artifact"
+	@echo "  make devdoc : Generate documentation"
 	@echo ""
 
 all: clean format build test

r/variantkey/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: variantkey
 Title: Genetic VariantKey
-Version: 5.6.18.0
+Version: 5.6.19.0
 Authors@R: person("Nicola", "Asuni", email = "[email protected]", role = c("aut", "cre"))
 Description: Tools to generate and process a 64 bit Unsigned Integer Keys for Human Genetic Variants.
     The VariantKey is sortable for chromosome and position,