update scripts

scripts/clean.sh

@@ -1,13 +1,22 @@
 #!/bin/bash
 set -euxo pipefail
 
-# isort suspended till the CI-vs-local issue is resolved
-# isort cities/ tests/
+# isort suspended as conflicting with black
+# nbqa isort docs/guides/
+
+
+# this sometimes conflicts with black but does some
+# preliminary import sorting
+# and is then overriden by black
+isort cities/ tests/
+
+black ./cities/ ./tests/ ./docs/guides/
+
+black docs/guides/
 
-black cities/ tests/
 autoflake --remove-all-unused-imports --in-place --recursive ./cities ./tests
 
-nbqa autoflake --remove-all-unused-imports --recursive --in-place docs/guides/ 
-# nbqa isort docs/guides/
-nbqa black docs/guides/
+nbqa autoflake --nbqa-shell --remove-all-unused-imports --recursive --in-place docs/guides/ 
+
+#nbqa black docs/guides/
 

scripts/lint.sh

@@ -3,10 +3,10 @@ set -euxo pipefail
 
 mypy --ignore-missing-imports cities/
 #isort --check --diff cities/ tests/
-black --check cities/ tests/
+black --check cities/ tests/ docs/guides/
 flake8 cities/ tests/ --ignore=E203,W503 --max-line-length=127
 
 
-nbqa autoflake -v --recursive --check docs/guides/
+nbqa autoflake --nbqa-shell -v --recursive --check docs/guides/
 #nbqa isort --check  docs/guides/
-nbqa black --check docs/guides/
+

scripts/test_notebooks.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
 
-INCLUDED_NOTEBOOKS="docs/guides/ docs/testing_notebooks/"
+INCLUDED_NOTEBOOKS="docs/guides/ " # docs/testing_notebooks/"  will revert when the pyro-ppl 1.9 bug is fixed
 
 CI=1 pytest -v --nbval-lax --dist loadscope -n auto $INCLUDED_NOTEBOOKS