Maintenance: upgrades requirements of packages and web-server (#1696)

* Adds info con constraint for isort

* Block upgrade of package and test reqs

* Upgrades deprecated positional argument

Fixes pytest.PytestDeprecationWarning: Passing arguments to pytest.fixture() as positional arguments is deprecated - pass them as a keyword argument instead

* Upgrade to latest pip 20.2.2

* No need for code coverage while testing api specs

* upgrades webserver

* Adds ERD for all pg models

* Adds check to avoid wrong py version

* Fixes reqs after master merge

* Fixes undefined variables

Raised UnboundLocalError: local variable 'log_type' referenced before assignment

api/tests/conftest.py

@@ -64,7 +64,7 @@ def api_specs_info(api_specs_dir):
     return info
 
 
-@pytest.fixture("session")
+@pytest.fixture(scope="session")
 def all_api_specs_tails(api_specs_dir):
     """ Returns openapi/jsonschema spec files path relative to specs_dir
 

api/tests/requirements.txt

@@ -8,37 +8,38 @@ aiohttp==3.6.2            # via -r requirements.in, pytest-aiohttp
 async-timeout==3.0.1      # via aiohttp
 attrs==19.3.0             # via aiohttp, jsonschema, openapi-core, pytest
 chardet==3.0.4            # via aiohttp
-coverage==5.2             # via -r requirements.in, pytest-cov
+coverage==5.2.1           # via -r requirements.in, pytest-cov
 idna-ssl==1.1.0           # via aiohttp
 idna==2.10                # via idna-ssl, yarl
 importlib-metadata==1.7.0  # via jsonschema, pluggy, pytest
-isodate==0.6.0            # via openapi-schema-validator
+iniconfig==1.0.1          # via pytest
+isodate==0.6.0            # via openapi-core, openapi-schema-validator
 jsonschema==3.2.0         # via openapi-schema-validator, openapi-spec-validator
-lazy-object-proxy==1.5.0  # via openapi-core
+lazy-object-proxy==1.5.1  # via openapi-core
 more-itertools==8.4.0     # via openapi-core, pytest
 multidict==4.7.6          # via aiohttp, yarl
-openapi-core==0.13.3      # via -r requirements.in
+openapi-core==0.13.4      # via -r requirements.in
 openapi-schema-validator==0.1.1  # via openapi-core
-openapi-spec-validator==0.2.8  # via openapi-core
+openapi-spec-validator==0.2.9  # via openapi-core
 packaging==20.4           # via pytest, pytest-sugar
-parse==1.15.0             # via openapi-core
+parse==1.16.0             # via openapi-core
 pluggy==0.13.1            # via pytest
 py==1.9.0                 # via pytest
 pyparsing==2.4.7          # via packaging
 pyrsistent==0.16.0        # via jsonschema
 pytest-aiohttp==0.3.0     # via -r requirements.in
-pytest-cov==2.10.0        # via -r requirements.in
+pytest-cov==2.10.1        # via -r requirements.in
 pytest-instafail==0.4.2   # via -r requirements.in
 pytest-sugar==0.9.4       # via -r requirements.in
-pytest==5.4.3             # via -r requirements.in, pytest-aiohttp, pytest-cov, pytest-instafail, pytest-sugar
+pytest==6.0.1             # via -r requirements.in, pytest-aiohttp, pytest-cov, pytest-instafail, pytest-sugar
 pyyaml==5.3.1             # via openapi-spec-validator
 six==1.15.0               # via isodate, jsonschema, openapi-core, openapi-schema-validator, openapi-spec-validator, packaging
 strict-rfc3339==0.7       # via openapi-schema-validator
 termcolor==1.1.0          # via pytest-sugar
-typing-extensions==3.7.4.2  # via aiohttp
-wcwidth==0.2.5            # via pytest
+toml==0.10.1              # via pytest
+typing-extensions==3.7.4.2  # via aiohttp, yarl
 werkzeug==1.0.1           # via openapi-core
-yarl==1.4.2               # via aiohttp
+yarl==1.5.1               # via aiohttp
 zipp==3.1.0               # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:

api/tests/test_individual_openapi_schemas.py

@@ -94,7 +94,7 @@ def change_references_to_schemas(filepath: Path, specs: dict):
                     specs[key] = file_ref + "#" + section_ref
 
 
-@pytest.fixture("session")
+@pytest.fixture(scope="session")
 def converted_specs_testdir(api_specs_dir, all_api_specs_tails, tmpdir_factory):
     """
         - All api_specs files are copied into tmpdir

ci/github/unit-testing/api.bash

@@ -10,8 +10,7 @@ install() {
 }
 
 test() {
-  pytest --cov=api --durations=10 --cov-append \
-          --color=yes --cov-report=term-missing --cov-report=xml --cov-config=.coveragerc \
+  pytest --durations=10 \
           -v -m "not travis" api/tests
 }
 

ci/helpers/ensure_python_pip.bash

@@ -9,7 +9,7 @@ set -euo pipefail
 IFS=$'\n\t'
 
 # Pin pip version to a compatible release https://www.python.org/dev/peps/pep-0440/#compatible-release
-PIP_VERSION=20.1.1
+PIP_VERSION=20.2.2
 
 echo "INFO:" "$(python --version)" "@" "$(command -v python)"
 

ci/travis/unit-testing/api.bash

@@ -32,8 +32,7 @@ before_script() {
 script() {
     if bash ci/travis/helpers/test-for-changes.bash "${FOLDER_CHECKS[@]}";
     then
-        pytest --cov=api --durations=10 --cov-append \
-          --color=yes --cov-report=term-missing --cov-report=xml --cov-config=.coveragerc \
+        pytest --durations=10 \
           -v -m "not travis" api/tests
     else
         echo "No changes detected. Skipping unit-testing of apihub."

packages/postgres-database/doc/database-models.md

@@ -8,3 +8,23 @@
 
 - Isolate package with all table schemas per database and service
 - Models shall not be implemented inheriting from Base. Use instead [explicit table definitions](https://docs.sqlalchemy.org/en/latest/orm/mapping_styles.html#classical-mappings)
+
+## Entity Relationship Diagram (ERD)
+
+Current models in ``simcore-postgres-database``:
+
+![scripts/create_erd.py-output](img/postgres-database-models.svg)
+
+To produce the diagram above
+
+```bash
+make devenv
+source .venv/bin/activate
+
+cd packages/postgres-database
+make install-dev
+
+cd scripts
+pip install eralchemy
+python create_erd.py
+```