Update Dependabot for python virtual envs

* Simplify virtualenv installation to use multiple requirements files in
  a single directory. This eliminates the packages.txt file and provides
  an easier path to adding new tools in the future. It also allows us to
  simplify the dependenabot configuration as all requirements files are
  in a single directory.
* Update dependabot.yml to point to the new Python dependencies folder.

.github/dependabot.yml

@@ -33,7 +33,7 @@ updates:
 
   # Maintain dependencies for python with pip
   - package-ecosystem: "pip"
-    directory: "/dependencies"
+    directory: "/dependencies/python/"
     schedule:
       interval: "weekly"
     open-pull-requests-limit: 10

dependencies/python/build-venvs.sh

@@ -21,15 +21,12 @@ pip install virtualenv
 #########################################################
 # Itterate through requirments.txt to install bainaries #
 #########################################################
-while read -r LINE; do
+for DEP_FILE in *.txt; do
   # split the package name from its version
-  PACKAGE_NAME=$(cut -d'=' -f1 <<<"${LINE}")
+  PACKAGE_NAME=${DEP_FILE%.txt}
-  if [[ "${PACKAGE_NAME}" == *"["* ]]; then
-    PACKAGE_NAME=$(cut -d'[' -f1 <<<"${PACKAGE_NAME}")
-  fi
   echo "-------------------------------------------"
   mkdir -p "/venvs/${PACKAGE_NAME}"
-  cp "${PACKAGE_NAME}/requirements.txt" "/venvs/${PACKAGE_NAME}/requirements.txt"
+  cp "${DEP_FILE}" "/venvs/${PACKAGE_NAME}/requirements.txt"
   echo "Generating virtualenv for: [${PACKAGE_NAME}]"
   pushd "/venvs/${PACKAGE_NAME}"
   virtualenv .
@@ -40,4 +37,4 @@ while read -r LINE; do
   deactivate
   # pop the stack
   popd
-done <packages.txt
+done

dependencies/python/packages.txt

@@ -1,13 +0,0 @@
-ansible-lint[core]
-black
-cfn-lint
-cpplint
-flake8
-isort
-mypy
-pylint
-snakefmt
-snakemake
-sqlfluff
-yamllint
-yq