adding fixes (#1516)

* adding fixes

* happy

* happy

* fix local files

* fix spacing

* i hate space

* spacing pt3 the space wars

* further down the bunny trail

.automation/upload-docker.sh

@@ -17,16 +17,16 @@
 ###########
 # Globals #
 ###########
-GITHUB_WORKSPACE="${GITHUB_WORKSPACE}"   # GitHub Workspace
-GITHUB_REPOSITORY="${GITHUB_REPOSITORY}" # GitHub Org/Repo passed from system
-DOCKER_USERNAME="${DOCKER_USERNAME}"     # Username to login to DockerHub
-DOCKER_PASSWORD="${DOCKER_PASSWORD}"     # Password to login to DockerHub
-GCR_USERNAME="${GCR_USERNAME}"           # Username to login to GitHub package registry
-GCR_TOKEN="${GCR_TOKEN}"                 # Password to login to GitHub package registry
-REGISTRY="${REGISTRY}"                   # What registry to upload | <GCR> or <Docker>
-IMAGE_REPO="${IMAGE_REPO}"               # Image repo to upload the image
-IMAGE_VERSION="${IMAGE_VERSION}"         # Version to tag the image
-DOCKERFILE_PATH="${DOCKERFILE_PATH}"     # Path to the Dockerfile to be uploaded
+# GITHUB_WORKSPACE="${GITHUB_WORKSPACE}"   # GitHub Workspace
+# GITHUB_REPOSITORY="${GITHUB_REPOSITORY}" # GitHub Org/Repo passed from system
+# DOCKER_USERNAME="${DOCKER_USERNAME}"     # Username to login to DockerHub
+# DOCKER_PASSWORD="${DOCKER_PASSWORD}"     # Password to login to DockerHub
+# GCR_USERNAME="${GCR_USERNAME}"           # Username to login to GitHub package registry
+# GCR_TOKEN="${GCR_TOKEN}"                 # Password to login to GitHub package registry
+# REGISTRY="${REGISTRY}"                   # What registry to upload | <GCR> or <Docker>
+# IMAGE_REPO="${IMAGE_REPO}"               # Image repo to upload the image
+# IMAGE_VERSION="${IMAGE_VERSION}"         # Version to tag the image
+# DOCKERFILE_PATH="${DOCKERFILE_PATH}"     # Path to the Dockerfile to be uploaded
 MAJOR_TAG=''         # Major tag version if we need to update it
 UPDATE_MAJOR_TAG=0   # Flag to deploy the major tag version as well
 GCR_URL='ghcr.io'    # URL to Github Container Registry

.automation/validate-docker-labels.sh

@@ -7,9 +7,9 @@
 ###########
 # Globals #
 ###########
-GITHUB_WORKSPACE="${GITHUB_WORKSPACE}"                                               # GitHub Workspace
-GITHUB_SHA="${GITHUB_SHA}"                                                           # Sha used to create this branch
-BUILD_DATE="${BUILD_DATE}"                                                           # Date the container was built
+# GITHUB_WORKSPACE="${GITHUB_WORKSPACE}" # GitHub Workspace
+# GITHUB_SHA="${GITHUB_SHA}"   # Sha used to create this branch
+# BUILD_DATE="${BUILD_DATE}"   # Date the container was built
 BUILD_REVISION="${GITHUB_SHA}"                                                       # GitHub Sha
 BUILD_VERSION="${GITHUB_SHA}"                                                        # Version of the container
 ORG_REPO="github/super-linter"                                                       # Org/repo

.github/workflows/deploy-DEV.yml

@@ -103,9 +103,10 @@ jobs:
           VALIDATE_ALL_CODEBASE: false
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      ###########################################################################################
-      # Fix file and dir ownership. Workaround for https://github.com/actions/runner/issues/434 #
-      ###########################################################################################
+      ###############################################################
+      # Fix file and dir ownership.                                 #
+      # Workaround for https://github.com/actions/runner/issues/434 #
+      ###############################################################
       - name: Fix file and directory ownership
         shell: bash
         run: |
@@ -124,6 +125,9 @@ jobs:
       ##########################
       - name: Upload the code coverage report
         uses: codacy/codacy-coverage-reporter-action@1.0.1
+        # Dependabot does not have priv to see the secret, so will
+        # fail opn bump jobs...
+        continue-on-error: true
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: test/reports/cobertura/runTests.sh/cobertura.xml

.github/workflows/deploy-PROD.yml

@@ -17,6 +17,7 @@ on:
   push:
     branches:
       - 'master'
+      - 'main'
 
 ###############
 # Set the Job #

.github/workflows/draft-release.yml

@@ -1,15 +1,24 @@
-# We have this file on hold as its an Action that would trigger another action, and not currently supported.
-# This then causes the deployRelease action to never fun, which is far more important than auto drafting
-# Until we have a better solution, this needs to remain on hold
-
+---
+###########################################
+###########################################
+## Draft releases on Push to master/main ##
+###########################################
+###########################################
 name: Release Drafter
 
+###########################
+# Start on push to master #
+###########################
 on:
   push:
     # branches to consider in the event; optional, defaults to all
     branches:
       - master
+      - main
 
+#################
+# Start the job #
+#################
 jobs:
   update_release_draft:
     runs-on: ubuntu-latest

Dockerfile

@@ -18,9 +18,9 @@ FROM wata727/tflint:0.28.0 as tflint
 FROM mvdan/shfmt:v3.2.4 as shfmt
 FROM accurics/terrascan:1.5.1 as terrascan
 FROM hadolint/hadolint:latest-alpine as dockerfile-lint
-FROM ghcr.io/assignuser/lintr-lib:0.2.0 as lintr-lib
 FROM ghcr.io/assignuser/chktex-alpine:0.1.1 as chktex
 FROM garethr/kubeval:0.15.0 as kubeval
+FROM ghcr.io/assignuser/lintr-lib:0.2.0 as lintr-lib
 
 ##################
 # Get base image #
@@ -211,11 +211,6 @@ COPY --from=editorconfig-checker /usr/bin/ec /usr/bin/editorconfig-checker
 ###############################
 COPY --from=dockerfile-lint /bin/hadolint /usr/bin/hadolint
 
-#################
-# Install lintr #
-#################
-COPY --from=lintr-lib /usr/lib/R/library/ /home/r-library/
-
 ##################
 # Install chktex #
 ##################
@@ -231,6 +226,11 @@ COPY --from=kubeval /kubeval /usr/bin/
 #################
 COPY --from=shfmt /bin/shfmt /usr/bin/
 
+#################
+# Install Litnr #
+#################
+COPY --from=lintr-lib /usr/lib/R/library/ /home/r-library
+
 ##################
 # Install ktlint #
 ##################
@@ -376,7 +376,7 @@ COPY --from=base_image /usr/include/ /usr/include/
 COPY --from=base_image /lib/ /lib/
 COPY --from=base_image /bin/ /bin/
 COPY --from=base_image /node_modules/ /node_modules/
-COPY --from=base_image /home/r-library/ /home/r-library/
+COPY --from=base_image /home/r-library /home/r-library
 
 ########################################
 # Add node packages to path and dotnet #

lib/functions/log.sh

@@ -20,7 +20,8 @@ declare -Agr F=(
   [W]=$(echo -e "\e[0;37m")
   [Y]=$(echo -e "\e[0;33m")
 )
-readonly NC=$(echo -e "\e[0m")
+NC=$(echo -e "\e[0m")
+readonly NC
 
 export B
 export F

lib/linter.sh

@@ -10,7 +10,7 @@
 # Debug Vars                                                     #
 # Define these early, so we can use debug logging ASAP if needed #
 ##################################################################
-RUN_LOCAL="${RUN_LOCAL}"                              # Boolean to see if we are running locally
+# RUN_LOCAL="${RUN_LOCAL}"                            # Boolean to see if we are running locally
 ACTIONS_RUNNER_DEBUG="${ACTIONS_RUNNER_DEBUG:-false}" # Boolean to see even more info (debug)
 
 ##################################################################
@@ -151,7 +151,7 @@ SNAKEMAKE_SNAKEFMT_FILE_NAME="${SNAKEMAKE_SNAKEFMT_CONFIG_FILE:-.snakefmt.toml}"
 # shellcheck disable=SC2034  # Variable is referenced indirectly
 SUPPRESS_POSSUM="${SUPPRESS_POSSUM:-false}"
 # shellcheck disable=SC2034  # Variable is referenced indirectly
-SSL_CERT_SECRET="${SSL_CERT_SECRET}"
+# SSL_CERT_SECRET="${SSL_CERT_SECRET}"
 # shellcheck disable=SC2034  # Variable is referenced indirectly
 SQL_FILE_NAME="${SQL_CONFIG_FILE:-.sql-config.json}"
 # shellcheck disable=SC2034  # Variable is referenced indirectly
@@ -270,20 +270,20 @@ LINTED_LANGUAGES_ARRAY=() # Will be filled at run time with all languages that w
 ###################
 # GitHub ENV Vars #
 ###################
-ANSIBLE_DIRECTORY="${ANSIBLE_DIRECTORY}"         # Ansible Directory
-DEFAULT_BRANCH="${DEFAULT_BRANCH:-master}"       # Default Git Branch to use (master by default)
-DISABLE_ERRORS="${DISABLE_ERRORS}"               # Boolean to enable warning-only output without throwing errors
-FILTER_REGEX_INCLUDE="${FILTER_REGEX_INCLUDE}"   # RegExp defining which files will be processed by linters (all by default)
-FILTER_REGEX_EXCLUDE="${FILTER_REGEX_EXCLUDE}"   # RegExp defining which files will be excluded from linting (none by default)
-GITHUB_EVENT_PATH="${GITHUB_EVENT_PATH}"         # Github Event Path
-GITHUB_REPOSITORY="${GITHUB_REPOSITORY}"         # GitHub Org/Repo passed from system
-GITHUB_RUN_ID="${GITHUB_RUN_ID}"                 # GitHub RUn ID to point to logs
-GITHUB_SHA="${GITHUB_SHA}"                       # GitHub sha from the commit
-GITHUB_TOKEN="${GITHUB_TOKEN}"                   # GitHub Token passed from environment
-GITHUB_WORKSPACE="${GITHUB_WORKSPACE}"           # Github Workspace
+# ANSIBLE_DIRECTORY="${ANSIBLE_DIRECTORY}"         # Ansible Directory
 MULTI_STATUS="${MULTI_STATUS:-true}"       # Multiple status are created for each check ran
-TEST_CASE_RUN="${TEST_CASE_RUN}"                 # Boolean to validate only test cases
-VALIDATE_ALL_CODEBASE="${VALIDATE_ALL_CODEBASE}" # Boolean to validate all files
+DEFAULT_BRANCH="${DEFAULT_BRANCH:-master}" # Default Git Branch to use (master by default)
+# DISABLE_ERRORS="${DISABLE_ERRORS}"               # Boolean to enable warning-only output without throwing errors
+# FILTER_REGEX_INCLUDE="${FILTER_REGEX_INCLUDE}"   # RegExp defining which files will be processed by linters (all by default)
+# FILTER_REGEX_EXCLUDE="${FILTER_REGEX_EXCLUDE}"   # RegExp defining which files will be excluded from linting (none by default)
+# GITHUB_EVENT_PATH="${GITHUB_EVENT_PATH}"         # Github Event Path
+# GITHUB_REPOSITORY="${GITHUB_REPOSITORY}"         # GitHub Org/Repo passed from system
+# GITHUB_RUN_ID="${GITHUB_RUN_ID}"                 # GitHub RUn ID to point to logs
+# GITHUB_SHA="${GITHUB_SHA}"                       # GitHub sha from the commit
+# GITHUB_TOKEN="${GITHUB_TOKEN}"                   # GitHub Token passed from environment
+# GITHUB_WORKSPACE="${GITHUB_WORKSPACE}"           # Github Workspace
+# TEST_CASE_RUN="${TEST_CASE_RUN}"                 # Boolean to validate only test cases
+# VALIDATE_ALL_CODEBASE="${VALIDATE_ALL_CODEBASE}" # Boolean to validate all files
 
 IGNORE_GITIGNORED_FILES="${IGNORE_GITIGNORED_FILES:-false}"
 
@@ -310,7 +310,7 @@ export TEST_CASE_FOLDER             # Workaround SC2034
 ##############
 # Format     #
 ##############
-OUTPUT_FORMAT="${OUTPUT_FORMAT}"                      # Output format to be generated. Default none
+# OUTPUT_FORMAT="${OUTPUT_FORMAT}"                    # Output format to be generated. Default none
 OUTPUT_FOLDER="${OUTPUT_FOLDER:-super-linter.report}" # Folder where the reports are generated. Default super-linter.report
 OUTPUT_DETAILS="${OUTPUT_DETAILS:-simpler}"           # What level of details. (simpler or detailed). Default simpler