mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-15 16:18:22 +01:00
cleaning up r-build
This commit is contained in:
Charlton, Scott R
parent
de3cd91cff
commit
547c6ed33d
18
.github/workflows/cmake.yml
vendored
18
.github/workflows/cmake.yml
vendored
@ -122,21 +122,13 @@ jobs:
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shell: Rscript {0}
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- name: versioning
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run: ./jenkins-R-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
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run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
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# - name: versioning
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# run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
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- name: build
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run: cd R && make build
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# - name: R
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# run: |
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# cd R
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# mkdir -p phreeqc/man
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# mkdir -p phreeqc/src/phreeqcpp
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# mkdir -p phreeqc/R
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# mkdir -p phreeqc/data
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# echo "# Generated by roxygen2: do not edit by hand" > phreeqc/NAMESPACE
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# DATE=$(date -d ${{ needs.init.outputs.DATE }} "+%Y-%m-%d")
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# make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=$DATE build
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- name: check
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run: cd R && make check
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- uses: actions/upload-artifact@v2
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with:
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82
R/Makefile
82
R/Makefile
@ -1,19 +1,36 @@
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# phreeqc TOPDIR
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# ├── data DATADIR
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# ├── inst INST
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# ├── man MAN
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# ├── R
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# └── src IDEST
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# └── phreeqcpp DEST
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#
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CP=cp -f
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TOPDIR=phreeqc
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IDEST=phreeqc/src
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DEST=phreeqc/src/phreeqcpp
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TOPDIR ?= phreeqc
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IDEST=$(TOPDIR)/src
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DEST=$(TOPDIR)/src/phreeqcpp
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ISRC=../src
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SRC=../src/phreeqcpp
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INST=phreeqc/inst
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INST=$(TOPDIR)/inst
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DBDIR=../database
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DATADIR=phreeqc/data
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DATADIR=$(TOPDIR)/data
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EXDIR=../phreeqc3-examples
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MAN=phreeqc/man
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MAN=$(TOPDIR)/man
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R=$(TOPDIR)/R
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SVN_URL := http://internalbrr.cr.usgs.gov/svn_GW
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RELEASE ?= $(shell svn info $(SVN_URL) | egrep "Revision:" | cut -b 10- | ( read one two ; echo $$one ) )
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_TOPDIR := $(shell mkdir -p $(TOPDIR))
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_IDEST := $(shell mkdir -p $(IDEST))
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_DEST := $(shell mkdir -p $(DEST))
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_INST := $(shell mkdir -p $(INST))
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_DATADIR := $(shell mkdir -p $(DATADIR))
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_MAN := $(shell mkdir -p $(MAN))
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_R := $(shell mkdir -p $(R))
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RELEASE ?= $(shell curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3 -)
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RELEASE_DATE ?= $(shell date "+%Y-%m-%d")
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VERSION ?= 1.0
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VERSION ?= $(shell curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | /bin/sh)
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DBS = \
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Amm.ascii \
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@ -281,11 +298,12 @@ $(DATADIR)/examples.rda : $(EXS) build-examples.R
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R --no-save --no-restore CMD BATCH build-examples.R
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rm -f .RData
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roxygenize $(MAN)/phreeqc-package.Rd : phreeqc/R/phreeqc.R
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rm -f $(RDFILES)
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rm -f .RData
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R --no-save --no-restore CMD BATCH roxygenize.R
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touch $(MAN)/phreeqc-package.Rd
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# roxygenize $(MAN)/phreeqc-package.Rd : $(R)/phreeqc.R
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# rm -f $(RDFILES)
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# rm -f .RData
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# # R --no-save --no-restore CMD BATCH roxygenize.R
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# # touch $(MAN)/phreeqc-package.Rd
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# Rscript -e 'devtools::document(pkg = "phreeqc")'
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##$(PSRC): $(DEST)
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@ -809,8 +827,18 @@ $(INST)/ex2 : ../phreeqc3-examples/ex2
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########################################
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roxygenize $(MAN)/phreeqc-package.Rd : $(R)/phreeqc.R
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rm -f $(RDFILES)
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rm -f .RData
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# R --no-save --no-restore CMD BATCH roxygenize.R
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# touch $(MAN)/phreeqc-package.Rd
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Rscript -e 'devtools::document(pkg = "phreeqc")'
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check : all
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Rscript -e "devtools::check('phreeqc')"
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Rscript -e "devtools::check(pkg = 'phreeqc')"
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# check_built :
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# Rscript -e "devtools::check_built()"
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valgrind : install
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R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
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@ -818,12 +846,14 @@ valgrind : install
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install : all
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R CMD INSTALL --build phreeqc
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$(TOPDIR)/R/phreeqc.R : phreeqc.R.in export_sed
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phreeqc/R/phreeqc.R : export_sed
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$(TOPDIR)/DESCRIPTION : DESCRIPTION.in export_sed
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phreeqc/DESCRIPTION : export_sed
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$(TOPDIR)/inst/CITATION : CITATION.in export_sed
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export_sed :
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.PHONY: export_sed
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export_sed : check-vars
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sed \
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-e 's/@VERSION@/$(VERSION)/g' \
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< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
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@ -831,6 +861,9 @@ export_sed :
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-e 's/@VERSION@/$(VERSION)/g' \
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-e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
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< phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
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echo "# Generated by roxygen2: do not edit by hand" > $(TOPDIR)/NAMESPACE
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$(CP) CITATION $(TOPDIR)/inst/CITATION
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$(CP) LICENSE.note $(TOPDIR)/LICENSE.note
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build : all
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R CMD build --resave-data phreeqc
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@ -847,10 +880,19 @@ $(IDEST)/R.cpp : R.cpp
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< $< > $@
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$(IDEST):
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mkdir $(IDEST)
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mkdir -p $(IDEST)
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$(DEST):
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mkdir $(DEST)
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mkdir -p $(DEST)
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clean :
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rm -f $(PSRC) $(XSRC) $(DEST)/*.o $(IDEST)/*.o $(DEST)/*.so
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.PHONY: check-vars
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check-vars:
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ifndef VERSION
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$(error VERSION is undefined)
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endif
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ifndef RELEASE_DATE
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$(error RELEASE_DATE is undefined)
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endif
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@ -4,28 +4,28 @@
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# set DATE
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#
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if [ -z "$DATE" ]; then
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DATE=$(date "+%x")
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DATE=$(date "+%x")
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fi
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DATE=$(date -d $DATE "+%Y-%m-%d")
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DATE=$(date -d $DATE --rfc-3339=date)
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#
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# set VER
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#
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if [ -z "$VER" ]; then
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###wget https://cran.r-project.org/package=phreeqc -O index.xhtml 2> /dev/null
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###VER=`xmlstarlet sel -t -m "/_:html/_:body/_:table[1]/_:tr[1]/_:td[2]" -v . -n index.xhtml 2> /dev/null`
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VER=$(curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/phreeqc-version.txt)
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ver_major=$(echo "$VER" | cut -d '.' -f 1)
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ver_minor=$(echo "$VER" | cut -d '.' -f 2)
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ver_patch=$(echo "$VER" | cut -d '.' -f 3)
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ver_patch=$((ver_patch+1))
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###wget https://cran.r-project.org/package=phreeqc -O index.xhtml 2> /dev/null
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###VER=`xmlstarlet sel -t -m "/_:html/_:body/_:table[1]/_:tr[1]/_:td[2]" -v . -n index.xhtml 2> /dev/null`
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VER=$(curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/phreeqc-version.txt)
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ver_major=$(echo "$VER" | cut -d '.' -f 1)
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ver_minor=$(echo "$VER" | cut -d '.' -f 2)
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ver_patch=$(echo "$VER" | cut -d '.' -f 3)
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ver_patch=$((ver_patch+1))
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else
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ver_major=$(echo "$VER" | cut -d '.' -f 1)
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ver_minor=$(echo "$VER" | cut -d '.' -f 2)
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ver_patch=$(echo "$VER" | cut -d '.' -f 3)
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ver_major=$(echo "$VER" | cut -d '.' -f 1)
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ver_minor=$(echo "$VER" | cut -d '.' -f 2)
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ver_patch=$(echo "$VER" | cut -d '.' -f 3)
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fi
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if [ -z "$ver_major" ] || [ -z "$ver_minor" ] || [ -z "$ver_patch" ]; then
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exit 1
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exit 1
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fi
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VER="${ver_major}.${ver_minor}.${ver_patch}"
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export VER
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@ -36,16 +36,11 @@ export VER
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curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/ver.py -o ver.py
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HEAD=$(python3 ver.py)
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if [ -z "$REL" ]; then
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REL="$HEAD"
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REL="$HEAD"
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fi
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# sed files
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/bin/sh jenkins-dist.sh -v ${VER} -r ${REL} -d ${DATE} -pr ${TAG}
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cd R
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mkdir -p phreeqc/man
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mkdir -p phreeqc/src/phreeqcpp
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mkdir -p phreeqc/R
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mkdir -p phreeqc/data
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echo "# Generated by roxygen2: do not edit by hand" > phreeqc/NAMESPACE
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# make VERSION=${VER} RELEASE_DATE=${DATE} build
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make VERSION=${VER} RELEASE_DATE=${DATE} build
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make VERSION=${VER} RELEASE_DATE=${DATE} check
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