Update to biopython 1.87 (#587)

* update to biopython 1.87

* update pydivsufsort, trying to avoid louisabraham/pydivsufsort#53

* update deps

* test cache-clear in ci

Author: manulera

.github/workflows/publish-docs.yml

@@ -36,7 +36,7 @@ jobs:
         run: poetry config --list
 
       - name: 🔩 Install with Poetry
-        run: poetry install --all-extras --with docs
+        run: poetry cache clear --all && poetry install --all-extras --with docs
 
       - name: Build documentation
         run: |

.github/workflows/pydna_test_and_coverage_workflow.yml

@@ -77,7 +77,7 @@ jobs:
         if: matrix.fresh-install == 'true'
 
       - name: 🔩 Install with Poetry
-        run: poetry install --all-extras
+        run: poetry cache clear --all && poetry install --all-extras
 
       - name: 🔎 poetry run python run_test.py
         # Don't run tests if we're just checking hooks