Update GitHub actions (#461)

* Ranaming `master` branch to `main`.

* Update GitHub Actions to latest versions

Upgraded various GitHub Actions in ci.yml, docker.yml, and swagger.yml to their latest major versions for improved security and maintenance. Also updated environment variable naming and DockerHub description action usage in docker.yml for consistency and compatibility.

* fix resolvers

small tweak to dockerfile to remove warning

* second reference to as in dockerfile

* another location where typesafe has wrong url

* Remove iRods integration: delete iRods storage service, plugin, config, and docs. Update changelog. Users must use another storage backend (filesystem, MongoDB GridFS, or AWS S3).

* remove typesafe references from jar file

* Fix upload artifact

* more version bumps

* fix python version

---------

Co-authored-by: Luigi Marini <[email protected]>

Author: robkooper

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ on:
 
   push:
     branches:
-      - master
+      - main
       - develop
 
   pull_request:
@@ -30,7 +30,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: github branch
         run: |
           if [ "${{ github.event.release.target_commitish }}" != "" ]; then
@@ -39,7 +39,7 @@ jobs:
             BRANCH=${GITHUB_REF##*/}
           fi
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
-          if [ "$BRANCH" == "master" ]; then
+          if [ "$BRANCH" == "main" ]; then
             echo "CLOWDER_VERSION=$(awk '/version = / { print $4 }' project/Build.scala | sed 's/"//g')" >> $GITHUB_ENV
           elif [ "$BRANCH" == "develop" ]; then
             echo "CLOWDER_VERSION=develop" >> $GITHUB_ENV
@@ -51,12 +51,12 @@ jobs:
           distribution: 'zulu'
           java-version: 8
       - name: Cache SBT ivy cache
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ~/.ivy2/cache
           key: ${{ runner.os }}-sbt-ivy-cache-${{ hashFiles('project/Build.scala') }}
       - name: Cache SBT
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ~/.sbt
           key: ${{ runner.os }}-sbt-${{ hashFiles('project/Build.scala') }}
@@ -85,7 +85,7 @@ jobs:
         ports:
           - 27017:27017
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: github branch
         run: |
           if [ "${{ github.event.release.target_commitish }}" != "" ]; then
@@ -94,7 +94,7 @@ jobs:
             BRANCH=${GITHUB_REF##*/}
           fi
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
-          if [ "$BRANCH" == "master" ]; then
+          if [ "$BRANCH" == "main" ]; then
             echo "CLOWDER_VERSION=$(awk '/version = / { print $4 }' project/Build.scala | sed 's/"//g')" >> $GITHUB_ENV
           elif [ "$BRANCH" == "develop" ]; then
             echo "CLOWDER_VERSION=develop" >> $GITHUB_ENV
@@ -130,7 +130,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: build
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: github branch
         run: |
           if [ "${{ github.event.release.target_commitish }}" != "" ]; then
@@ -139,7 +139,7 @@ jobs:
             BRANCH=${GITHUB_REF##*/}
           fi
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
-          if [ "$BRANCH" == "master" ]; then
+          if [ "$BRANCH" == "main" ]; then
             echo "CLOWDER_VERSION=$(awk '/version = / { print $4 }' project/Build.scala | sed 's/"//g')" >> $GITHUB_ENV
           elif [ "$BRANCH" == "develop" ]; then
             echo "CLOWDER_VERSION=develop" >> $GITHUB_ENV
@@ -177,13 +177,13 @@ jobs:
           done
           rm ${ZIPFILE}
           zip -r ${ZIPFILE} ${DIR}
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: clowder.zip
           path: target/universal/clowder-*.zip
       - name: Upload files to a GitHub release
         if: github.event_name == 'release' && github.event.action == 'created'
-        uses: svenstaro/upload-release-action@1.1.0
+        uses: svenstaro/upload-release-action@v2
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ github.ref }}
@@ -207,7 +207,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: build
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: github branch
         run: |
           if [ "${{ github.event.release.target_commitish }}" != "" ]; then
@@ -216,7 +216,7 @@ jobs:
             BRANCH=${GITHUB_REF##*/}
           fi
           echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
-          if [ "$BRANCH" == "master" ]; then
+          if [ "$BRANCH" == "main" ]; then
             echo "CLOWDER_VERSION=$(awk '/version = / { print $4 }' project/Build.scala | sed 's/"//g')" >> $GITHUB_ENV
           elif [ "$BRANCH" == "develop" ]; then
             echo "CLOWDER_VERSION=develop" >> $GITHUB_ENV
@@ -237,18 +237,18 @@ jobs:
         with:
           path: ~/.sbt
           key: ${{ runner.os }}-sbt-${{ hashFiles('project/Build.scala') }}
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.11
       - name: sbt doc
         run: ./sbt doc
         env:
           BRANCH: ${{ env.GITHUB_BRANCH }}
           VERSION: ${{ env.CLOWDER_VERSION }}
           BUILDNUMBER: ${{ github.run_number }}
           GITSHA1: ${{ github.sha  }}
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: ScalaDoc
           path: target/scala-*/api/
@@ -266,7 +266,7 @@ jobs:
           cd doc/src/sphinx/
           python -m pip install -r requirements.txt
           make html epub
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: HTML Documentation
           path: doc/src/sphinx/_build/html
@@ -279,13 +279,13 @@ jobs:
           key: ${{ secrets.SCP_KEY }}
           files: "doc/src/sphinx/_build/html/*"
           target: "CATS/${{ env.CLOWDER_VERSION }}/documentation/sphinx"
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: EPUB Documentation
           path: doc/src/sphinx/_build/epub/Clowder.epub
       - name: Upload files to a GitHub release
         if: github.event_name == 'release' && github.event.action == 'created'
-        uses: svenstaro/upload-release-action@1.1.0
+        uses: svenstaro/upload-release-action@v2
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
           tag: ${{ github.ref }}

.github/workflows/docker.yml

@@ -5,7 +5,7 @@ name: Docker
 # and would not set the right version flags.
 
 # This will run when:
-# - when new code is pushed to master/develop to push the tags
+# - when new code is pushed to main/develop to push the tags
 #   latest and develop
 # - when a pull request is created and updated  to make sure the
 #   Dockerfile is still valid.
@@ -16,14 +16,14 @@ name: Docker
 on:
   push:
     branches:
-      - master
+      - main
       - develop
 
   pull_request:
 
-# Certain actions will only run when this is the master repo.
+# Certain actions will only run when this is the main repo.
 env:
-  MASTER_REPO: clowder-framework/clowder
+  MAIN_REPO: clowder-framework/clowder
   DOCKERHUB_ORG: clowder
 
 jobs:
@@ -64,7 +64,7 @@ jobs:
             PLATFORM: "linux/amd64"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # calculate some variables that are used later
       - name: variable setup
@@ -77,7 +77,7 @@ jobs:
             BRANCH=${GITHUB_REF##*/}
           fi
 
-          if [ "$BRANCH" == "master" ]; then
+          if [ "$BRANCH" == "main" ]; then
             version="$(awk '/version = / { print $4 }' project/Build.scala | sed 's/"//g')"
             tags="latest"
             oldversion=""
@@ -115,11 +115,11 @@ jobs:
 
       # setup docker build
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Inspect Builder
         run: |
@@ -132,13 +132,13 @@ jobs:
       # login to registries
       - name: Login to DockerHub
         if: env.dockerhub != ''
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -147,7 +147,7 @@ jobs:
       # build the clowder docker images
       - name: Build and push ${{ matrix.IMAGE }}-build
         if: matrix.IMAGE == 'clowder'
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6
         with:
           push: true
           context: ${{ matrix.FOLDER }}
@@ -164,7 +164,7 @@ jobs:
 
       - name: Build and push ${{ matrix.IMAGE }}-runtime
         if: matrix.IMAGE == 'clowder'
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6
         with:
           push: true
           context: ${{ matrix.FOLDER }}
@@ -182,7 +182,7 @@ jobs:
       # build the other docker images
       - name: Build and push ${{ matrix.IMAGE }}
         if: matrix.IMAGE != 'clowder'
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v6
         with:
           push: true
           context: ${{ matrix.FOLDER }}
@@ -198,10 +198,10 @@ jobs:
 
       # update README at DockerHub
       - name: Docker Hub Description
-        if: env.dockerhub != '' && matrix.README != '' && github.event_name == 'push' && github.repository == env.MASTER_REPO && env.BRANCH == 'master'
-        uses: peter-evans/dockerhub-description@v2
-        env:
-          DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
-          DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
-          DOCKERHUB_REPOSITORY: ${{ env.DOCKERHUB_ORG }}/${{ matrix.IMAGE }}
-          README_FILEPATH: ${{ matrix.README }}
+        if: env.dockerhub != '' && matrix.README != '' && github.event_name == 'push' && github.repository == env.MAIN_REPO && env.BRANCH == 'main'
+        uses: peter-evans/dockerhub-description@v4
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          repository: ${{ env.DOCKERHUB_ORG }}/${{ matrix.IMAGE }}
+          readme-filepath	: ${{ matrix.README }}

.github/workflows/swagger.yml

@@ -1,14 +1,14 @@
 name: swagger
 
 # This will run when:
-# - when new code is pushed to master/develop to make sure the
+# - when new code is pushed to main/develop to make sure the
 #   code does compile.
 # - when a pull request is created and updated to make sure the
 #   code does compile.
 on:
   push:
     branches:
-      - master
+      - main
       - develop
 
   pull_request:
@@ -20,7 +20,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: openapi-lint 
         uses: mbowman100/swagger-validator-action@master

CHANGELOG.md

@@ -5,6 +5,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+
+### Fixed
+- Removed refrences to repo.typesafe.com from sbt-launch.jar and build.scala
+
+### Removed
+- Removed iRods integration and dependencies. The iRods file storage service and plugin have been completely removed from the codebase. Users who were using iRods for file storage will need to configure an alternative storage backend (filesystem, MongoDB GridFS, or AWS S3).
+
 ## 1.22.1 - 2023-11-10
 
 ### Fixed

CONTRIBUTING.md

@@ -5,7 +5,7 @@ below. By participating in this project, you agree to abide by the [code of cond
 Before your code can be accepted, you will have to sign a [CLA](https://clowderframework.org/pdf/Clowder-CLA.pdf)
 and mail it to [email protected].
 
-Most of the core development happens on [NCSA Bitbucket][bitbucket]. The `master` and `develop` branches are pushed to 
+Most of the core development happens on [NCSA Bitbucket][bitbucket]. The `` and `develop` branches are pushed to 
 [GitHub][github] nightly.
 
 We encourage contributors to create an account on [NCSA Bitbucket][bitbucket] and make pull requests there. We also accept 

Dockerfile

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 # BUILD CLOWDER DIST
 # ----------------------------------------------------------------------
-FROM openjdk:8-jdk-bullseye as clowder-build
+FROM openjdk:8-jdk-bullseye AS clowder-build
 
 ARG BRANCH="unknown"
 ARG VERSION="unknown"
@@ -40,7 +40,7 @@ RUN rm -rf target/universal/clowder-*.zip clowder clowder-* \
 # ----------------------------------------------------------------------
 # BUILD CLOWDER
 # ----------------------------------------------------------------------
-FROM openjdk:8-jre-bullseye as clowder-runtime
+FROM openjdk:8-jre-bullseye AS clowder-runtime
 
 # environemnt variables
 ARG BRANCH="unknown"

INSTALL.md

@@ -85,7 +85,7 @@ Next we install the script that will install or update clowder.
 cat > /home/browndog/update-clowder.sh << EOF
 #!/bin/bash
 
-# CATS-WWW (master) is the main branch for this server
+# CATS-WWW () is the main branch for this server
 # CATS-WWW1 (develop) if you want the latest version
 clowder_BRANCH=${clowder_BRANCH:-"CATS-WWW1"}