CI: minor update for running actions from bfio and filepattern (#548)

* ci: changed actions to point to polusai repo

* docs: added marker for when to remove manual filter on broken tools

* fix: accepting ict.yaml and ict.yml instead of only one

.github/workflows/find-all-tools.yml

@@ -27,15 +27,17 @@ jobs:
         run: |
           # List of directories to ignore
           ignored_dirs="polus-python-template ftl-label .venv"
+
+          # TODO: Remove these after merging PR #547
           # List of tools that are broken for known reasons
-          broken_tools="binary-operations basic-flatfield-estimation microjson-to-ome cell-border-segmentation precompute-slide"
+          broken_tools="binary-operations basic-flatfield-estimation microjson-to-ome cell-border-segmentation precompute-slide vector-to-label"
 
           # Initialize variables
           ignored_dirs="$ignored_dirs $broken_tools"
           ignored_dirs=$(echo $ignored_dirs | xargs)
           tool_dirs=""
 
-          # Get all directories in the current directory
+          # Get all sub-directories in the current directory
           dirs=$(find $(pwd) -type d)
 
           # Get all directories that have a "pyproject.toml" file

.github/workflows/package-filter.yml

@@ -42,7 +42,7 @@ jobs:
         id: package-filter
         run: |
           PACKAGE_DIRS=""
-          COMPANION_FILES="VERSION .bumpversion.cfg ict.yml"
+          COMPANION_FILES="VERSION .bumpversion.cfg"
 
           # echo the base ref
           base_ref=${{ github.base_ref }}
@@ -93,6 +93,13 @@ jobs:
                 fi
               done
 
+              # Check if ict.yml or ict.yaml exists
+              if [ ! -f "${pkg_dir}/ict.yml" ] && [ ! -f "${pkg_dir}/ict.yaml" ]
+              then
+                found_all=false
+                echo "::warning::${pkg_dir} does not have an ict.yml or ict.yaml file"
+              fi
+
               # Check that the version is a dev version
               echo "Checking for dev version in $pkg_dir"
               if [[ $(cat $pkg_dir/VERSION) != *"dev"* ]]