scijava · hinerm · Jun 28, 2021 · Mar 14, 2021 · Mar 18, 2021 · Mar 18, 2021
diff --git a/ci-build.sh b/ci-build.sh
@@ -0,0 +1,210 @@
+#!/bin/bash
+
+#
+# ci-build.sh - A script to build and/or release SciJava-based projects
+#                          automatically using a continuous integration
+#                          service.
+#
+# Required environment variables:
+#   BUILD_OS             - the operating system running the current build (e.g. macOS)
+#   BUILD_REPOSITORY     - the repository slug (org/repo) running the current build
+
+dir="$(dirname "$0")"
+
+success=0
+checkSuccess() {
+	# Log non-zero exit code.
+	test $1 -eq 0 || echo "==> FAILED: EXIT CODE $1" 1>&2
+
+	# Record the first non-zero exit code.
+	test $success -eq 0 && success=$1
+}
+
+# Build Maven projects.
+if [ -f pom.xml ]; then
+	echo ::group::"= Maven build ="
+	echo
+	echo "== Configuring Maven =="
+
+	# NB: Suppress "Downloading/Downloaded" messages.
+	# See: https://stackoverflow.com/a/35653426/1207769
+	export MAVEN_OPTS="$MAVEN_OPTS -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn"
+
+	# Populate the settings.xml configuration.
+	mkdir -p "$HOME/.m2"
+	settingsFile="$HOME/.m2/settings.xml"
+	customSettings=.ci/settings.xml
+	if [ -f "$customSettings" ]; then
+		cp "$customSettings" "$settingsFile"
+	else
+		cat >"$settingsFile" <<EOL
+<settings>
+	<servers>
+		<server>
+			<id>scijava.releases</id>
+			<username>$MAVEN_USER</username>
+			<password>$MAVEN_PASS</password>
+		</server>
+		<server>
+			<id>scijava.snapshots</id>
+			<username>$MAVEN_USER</username>
+			<password>$MAVEN_PASS</password>
+		</server>
+		<server>
+			<id>sonatype-nexus-releases</id>
+			<username>scijava-ci</username>
+			<password>$OSSRH_PASS</password>
+		</server>
+	</servers>
+EOL
+		cat >>"$settingsFile" <<EOL
+	<profiles>
+		<profile>
+			<id>gpg</id>
+			<activation>
+				<file>
+					<exists>$HOME/.gnupg</exists>
+				</file>
+			</activation>
+			<properties>
+				<gpg.keyname>$GPG_KEY_NAME</gpg.keyname>
+				<gpg.passphrase>$GPG_PASSPHRASE</gpg.passphrase>
+			</properties>
+		</profile>
+	</profiles>
+</settings>
+EOL
+	fi
+
+	# Determine whether deploying will be possible.
+	deployOK=
+	ciURL=$(mvn -q -Denforcer.skip=true -Dexec.executable=echo -Dexec.args='${project.ciManagement.url}' --non-recursive validate exec:exec 2>&1)
+
+	if [ $? -ne 0 ]; then
+		echo "No deploy -- could not extract ciManagement URL"
+		echo "Output of failed attempt follows:"
+		echo "$ciURL"
+	else
+		ciRepo=${ciURL##*/}
+		ciPrefix=${ciURL%/*}
+		ciOrg=${ciPrefix##*/}
+		if [ ! "$SIGNING_ASC" ] || [ ! "$GPG_KEY_NAME" ] || [ ! "$GPG_PASSPHRASE" ] || [ ! "$MAVEN_PASS" ] || [ ! "$OSSRH_PASS" ]; then
+			echo "No deploy -- secure environment variables not available"
+		elif [ "$BUILD_REPOSITORY" != "$ciOrg/$ciRepo" ]; then
+			echo "No deploy -- repository fork: $BUILD_REPOSITORY != $ciOrg/$ciRepo"
+		else
+			echo "All checks passed for artifact deployment"
+			deployOK=1
+		fi
+	fi
+
+	# Install GPG on OSX/macOS
+	if [ $BUILD_OS = 'macOS' ]; then
+		HOMEBREW_NO_AUTO_UPDATE=1 brew install gnupg2
+	fi
+
+	# Import the GPG signing key.
+	keyFile=.ci/signingkey.asc
+	if [ "$deployOK" ]; then
+		echo "== Importing GPG keypair =="
+		mkdir -p .ci
+		echo "$SIGNING_ASC" > "$keyFile"
+		ls -la "$keyFile"
+		gpg --batch --fast-import "$keyFile"
+		checkSuccess $?
+	fi
+
+	# Run the build.
+	BUILD_ARGS='-B -Djdk.tls.client.protocols="TLSv1,TLSv1.1,TLSv1.2"'
+	if [ "$deployOK" ]; then
+		echo
+		echo "== Building and deploying master SNAPSHOT =="
+		mvn -Pdeploy-to-scijava $BUILD_ARGS deploy
+		checkSuccess $?
+	elif [ "$deployOK" -a -f release.properties ]; then
+		echo
+		echo "== Cutting and deploying release version =="
+		mvn -B $BUILD_ARGS release:perform
+		checkSuccess $?
+		echo "== Invalidating SciJava Maven repository cache =="
+		curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/master/maven-helper.sh &&
+			gav=$(sh maven-helper.sh gav-from-pom pom.xml) &&
+			ga=${gav%:*} &&
+			echo "--> Artifact to invalidate = $ga" &&
+			echo "machine maven.scijava.org" >"$HOME/.netrc" &&
+			echo "        login $MAVEN_USER" >>"$HOME/.netrc" &&
+			echo "        password $MAVEN_PASS" >>"$HOME/.netrc" &&
+			sh maven-helper.sh invalidate-cache "$ga"
+		checkSuccess $?
+	else
+		echo
+		echo "== Building the artifact locally only =="
+		mvn $BUILD_ARGS install javadoc:javadoc
+		checkSuccess $?
+	fi
+	echo ::endgroup::
+fi
+
+# Configure conda environment, if one is needed.
+if [ -f environment.yml ]; then
+	echo ::group::"= Conda setup ="
+
+	condaDir=$HOME/miniconda
+	condaSh=$condaDir/etc/profile.d/conda.sh
+	if [ ! -f "$condaSh" ]; then
+		echo
+		echo "== Installing conda =="
+		python_version=${python -V}
+		python_version=${python_version:7:3} # get python version in the format like '2.7'
+		if [ "${python_version}" = "2.7" ]; then
+			wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
+		else
+			wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+		fi
+		rm -rf "$condaDir"
+		bash miniconda.sh -b -p "$condaDir"
+		checkSuccess $?
+	fi
+
+	echo
+	echo "== Updating conda =="
+	. "$condaSh" &&
+		conda config --set always_yes yes --set changeps1 no &&
+		conda update -q conda &&
+		conda info -a
+	checkSuccess $?
+
+	echo
+	echo "== Configuring environment =="
+	condaEnv=ci-scijava
+	test -d "$condaDir/envs/$condaEnv" && condaAction=update || condaAction=create
+	conda env "$condaAction" -n "$condaEnv" -f environment.yml &&
+		conda activate "$condaEnv"
+	checkSuccess $?
+
+	echo ::endgroup::
+fi
+
+# Execute Jupyter notebooks.
+if which jupyter >/dev/null 2>/dev/null; then
+	echo ::group::"= Jupyter notebooks ="
+	# NB: This part is fiddly. We want to loop over files even with spaces,
+	# so we use the "find ... -print0 | while read $'\0' ..." idiom.
+	# However, that runs the piped expression in a subshell, which means
+	# that any updates to the success variable will not persist outside
+	# the loop. So we suppress all stdout inside the loop, echoing only
+	# the final value of success upon completion, and then capture the
+	# echoed value back into the parent shell's success variable.
+	success=$(find . -name '*.ipynb' -print0 | {
+		while read -d $'\0' nbf; do
+			echo 1>&2
+			echo "== $nbf ==" 1>&2
+			jupyter nbconvert --execute --stdout "$nbf" >/dev/null
+			checkSuccess $?
+		done
+		echo $success
+	})
+	echo ::endgroup::
+fi
+
+exit $success
diff --git a/github-action-ci.sh b/github-action-ci.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#
+# github-action-ci.sh - A script to set up ci-related environment variables from GitHub Actions
+#
+
+echo "BUILD_REPOSITORY=${GITHUB_REPOSITORY}"
+echo "BUILD_OS=${RUNNER_OS}" 
+
+echo "BUILD_REPOSITORY=${GITHUB_REPOSITORY}" >> $GITHUB_ENV
+echo "BUILD_OS=${RUNNER_OS}" >> $GITHUB_ENV