⬆️ Maintenance/week 12 test, tooling, libs/packages (#2916)

* upgrade pytest

* upgrade coverage

* upgrade pytest-asyncio

* disabling flaky test

* upgrade charset-normalizer

* upgrade service-integration datamodel-code-generator

* bumped openapi-schema-validator in service-integration

* upgraded service-library

* upgraded dask-task-models-library

* upgraded models-library

* upgraded postgres-database

* pinning openapi-spec-validator

* updated service-integration

* upgraded service-library

* upgraded settings-library

* upgraded simcore-sdk

* update failing test docs

* tooling repo wide

* more tooling

* idna constraint removed

* unpinning tomli

* more upgrades

* wrappe command nicely

* pylint fixes

* fix after upgrade

* removed unused comment

* removed comments and reverted skips

* fixed repor generation wording

* fix failing test

Co-authored-by: Andrei Neagu <neagu@itis.swiss>

api/tests/requirements.txt

@@ -19,9 +19,9 @@ attrs==21.4.0
     #   jsonschema
     #   openapi-core
     #   pytest
-charset-normalizer==2.0.11
+charset-normalizer==2.0.12
     # via aiohttp
-coverage[toml]==6.3.1
+coverage[toml]==6.3.2
     # via
     #   -r requirements.in
     #   pytest-cov
@@ -33,7 +33,7 @@ frozenlist==1.3.0
     #   aiosignal
 idna==3.3
     # via yarl
-importlib-resources==5.4.0 ; python_version < "3.9"
+importlib-resources==5.6.0 ; python_version < "3.9"
     # via
     #   -c ../../requirements/constraints.txt
     #   jsonschema
@@ -75,7 +75,7 @@ pyparsing==3.0.7
     # via packaging
 pyrsistent==0.18.1
     # via jsonschema
-pytest==7.0.0
+pytest==7.1.1
     # via
     #   -r requirements.in
     #   pytest-aiohttp
@@ -85,7 +85,7 @@ pytest==7.0.0
     #   pytest-sugar
 pytest-aiohttp==1.0.4
     # via -r requirements.in
-pytest-asyncio==0.18.0
+pytest-asyncio==0.18.3
     # via pytest-aiohttp
 pytest-cov==3.0.0
     # via -r requirements.in
@@ -103,9 +103,8 @@ six==1.16.0
     #   openapi-core
 termcolor==1.1.0
     # via pytest-sugar
-tomli==1.2.3
+tomli==2.0.1
     # via
-    #   -c ../../requirements/constraints.txt
     #   coverage
     #   pytest
 werkzeug==2.0.3

packages/dask-task-models-library/requirements/_base.in

@@ -8,8 +8,3 @@ dask[distributed]
 pydantic[email]
 # for the Annotated type
 typing_extensions; python_version < '3.9'
-
-#There are incompatible versions in the resolved dependencies:
-#  idna==3.1 (from -c requirements/_base.txt (line 13))
-#  idna<3,>=2.5 (from requests==2.25.1->coveralls==3.0.1->-r requirements/_test.in (line 24))
-idna<3,>=2.5

packages/dask-task-models-library/requirements/_base.txt

@@ -4,39 +4,36 @@
 #
 #    pip-compile --output-file=requirements/_base.txt --strip-extras requirements/_base.in
 #
-click==8.0.3
+click==8.0.4
     # via distributed
 cloudpickle==2.0.0
     # via
     #   dask
     #   distributed
-dask==2022.01.1
+dask==2022.03.0
     # via
     #   -r requirements/_base.in
     #   distributed
-distributed==2022.01.1
+distributed==2022.03.0
     # via dask
-dnspython==2.2.0
+dnspython==2.2.1
     # via email-validator
 email-validator==1.1.3
     # via pydantic
-fsspec==2022.1.0
+fsspec==2022.2.0
     # via dask
 heapdict==1.0.1
     # via zict
-idna==2.10
-    # via
-    #   -r requirements/../../../packages/models-library/requirements/_base.in
-    #   -r requirements/_base.in
-    #   email-validator
-jinja2==3.0.3
+idna==3.3
+    # via email-validator
+jinja2==3.1.1
     # via
     #   -c requirements/../../../packages/models-library/requirements/../../../requirements/constraints.txt
     #   -c requirements/../../../requirements/constraints.txt
     #   distributed
 locket==0.2.1
     # via partd
-markupsafe==2.0.1
+markupsafe==2.1.1
     # via jinja2
 msgpack==1.0.3
     # via distributed
@@ -73,12 +70,9 @@ toolz==0.11.2
     #   partd
 tornado==6.1
     # via distributed
-typing-extensions==4.0.1 ; python_version < "3.9"
+typing-extensions==4.1.1 ; python_version < "3.9"
     # via
     #   -r requirements/_base.in
     #   pydantic
-zict==2.0.0
+zict==2.1.0
     # via distributed
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools

packages/dask-task-models-library/requirements/_test.txt

@@ -10,7 +10,7 @@ aiohttp==3.8.1
     #   pytest-aiohttp
 aiosignal==1.2.0
     # via aiohttp
-astroid==2.9.3
+astroid==2.11.2
     # via pylint
 async-timeout==4.0.2
     # via aiohttp
@@ -20,28 +20,30 @@ attrs==21.4.0
     #   pytest
 certifi==2021.10.8
     # via requests
-charset-normalizer==2.0.11
+charset-normalizer==2.0.12
     # via
     #   aiohttp
     #   requests
-coverage==6.3.1
+coverage==6.3.2
     # via
     #   -r requirements/_test.in
     #   coveralls
     #   pytest-cov
 coveralls==3.3.1
     # via -r requirements/_test.in
+dill==0.3.4
+    # via pylint
 docopt==0.6.2
     # via coveralls
-faker==12.1.0
+faker==13.3.3
     # via -r requirements/_test.in
 frozenlist==1.3.0
     # via
     #   aiohttp
     #   aiosignal
 icdiff==2.0.4
     # via pytest-icdiff
-idna==2.10
+idna==3.3
     # via
     #   -c requirements/_base.txt
     #   requests
@@ -52,7 +54,7 @@ isort==5.10.1
     # via pylint
 lazy-object-proxy==1.7.1
     # via astroid
-mccabe==0.6.1
+mccabe==0.7.0
     # via pylint
 multidict==6.0.2
     # via
@@ -66,21 +68,21 @@ packaging==21.3
     #   pytest-sugar
 pint==0.18
     # via -r requirements/_test.in
-platformdirs==2.5.0
+platformdirs==2.5.1
     # via pylint
 pluggy==1.0.0
     # via pytest
 pprintpp==0.4.0
     # via pytest-icdiff
 py==1.11.0
     # via pytest
-pylint==2.12.2
+pylint==2.13.2
     # via -r requirements/_test.in
 pyparsing==3.0.7
     # via
     #   -c requirements/_base.txt
     #   packaging
-pytest==7.0.0
+pytest==7.1.1
     # via
     #   -r requirements/_test.in
     #   pytest-aiohttp
@@ -92,7 +94,7 @@ pytest==7.0.0
     #   pytest-sugar
 pytest-aiohttp==1.0.4
     # via -r requirements/_test.in
-pytest-asyncio==0.18.0
+pytest-asyncio==0.18.3
     # via pytest-aiohttp
 pytest-cov==3.0.0
     # via -r requirements/_test.in
@@ -102,7 +104,7 @@ pytest-instafail==0.4.2
     # via -r requirements/_test.in
 pytest-mock==3.7.0
     # via -r requirements/_test.in
-pytest-runner==5.3.1
+pytest-runner==6.0.0
     # via -r requirements/_test.in
 pytest-sugar==0.9.4
     # via -r requirements/_test.in
@@ -119,23 +121,21 @@ six==1.16.0
     # via python-dateutil
 termcolor==1.1.0
     # via pytest-sugar
-toml==0.10.2
-    # via pylint
-tomli==1.2.3
+tomli==2.0.1
     # via
-    #   -c requirements/../../../requirements/constraints.txt
     #   coverage
+    #   pylint
     #   pytest
-typing-extensions==4.0.1 ; python_version < "3.9"
+typing-extensions==4.1.1 ; python_version < "3.9"
     # via
     #   -c requirements/_base.txt
     #   astroid
     #   pylint
-urllib3==1.26.8
+urllib3==1.26.9
     # via
     #   -c requirements/../../../requirements/constraints.txt
     #   requests
-wrapt==1.13.3
+wrapt==1.14.0
     # via astroid
 yarl==1.7.2
     # via aiohttp

packages/dask-task-models-library/requirements/_tools.txt

@@ -10,16 +10,16 @@ bump2version==1.0.1
     # via -r requirements/../../../requirements/devenv.txt
 cfgv==3.3.1
     # via pre-commit
-click==8.0.3
+click==8.0.4
     # via
     #   -c requirements/_base.txt
     #   black
     #   pip-tools
 distlib==0.3.4
     # via virtualenv
-filelock==3.4.2
+filelock==3.6.0
     # via virtualenv
-identify==2.4.9
+identify==2.4.12
     # via pre-commit
 isort==5.10.1
     # via
@@ -35,7 +35,7 @@ pep517==0.12.0
     # via pip-tools
 pip-tools==6.5.1
     # via -r requirements/../../../requirements/devenv.txt
-platformdirs==2.5.0
+platformdirs==2.5.1
     # via
     #   -c requirements/_test.txt
     #   black
@@ -53,21 +53,18 @@ six==1.16.0
     #   -c requirements/_test.txt
     #   virtualenv
 toml==0.10.2
+    # via pre-commit
+tomli==2.0.1
     # via
     #   -c requirements/_test.txt
-    #   pre-commit
-tomli==1.2.3
-    # via
-    #   -c requirements/../../../requirements/constraints.txt
-    #   -c requirements/_test.txt
     #   black
     #   pep517
-typing-extensions==4.0.1 ; python_version < "3.9"
+typing-extensions==4.1.1 ; python_version < "3.9"
     # via
     #   -c requirements/_base.txt
     #   -c requirements/_test.txt
     #   black
-virtualenv==20.13.1
+virtualenv==20.14.0
     # via pre-commit
 wheel==0.37.1
     # via pip-tools

packages/models-library/requirements/_base.in

@@ -4,8 +4,3 @@
 --constraint ../../../requirements/constraints.txt
 
 pydantic[email]
-
-#There are incompatible versions in the resolved dependencies:
-#  idna==3.1 (from -c requirements/_base.txt (line 13))
-#  idna<3,>=2.5 (from requests==2.25.1->coveralls==3.0.1->-r requirements/_test.in (line 24))
-idna<3,>=2.5

packages/models-library/requirements/_base.txt

@@ -4,17 +4,15 @@
 #
 #    pip-compile --output-file=requirements/_base.txt --strip-extras requirements/_base.in
 #
-dnspython==2.2.0
+dnspython==2.2.1
     # via email-validator
 email-validator==1.1.3
     # via pydantic
-idna==2.10
-    # via
-    #   -r requirements/_base.in
-    #   email-validator
+idna==3.3
+    # via email-validator
 pydantic==1.9.0
     # via
     #   -c requirements/../../../requirements/constraints.txt
     #   -r requirements/_base.in
-typing-extensions==4.0.1
+typing-extensions==4.1.1
     # via pydantic