diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 49e075edb..7d842e098 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.8, 3.9] + python-version: [3.9] steps: - uses: actions/checkout@v3 @@ -35,7 +35,7 @@ jobs: - name: 🔧 - Install Dependencies run: | - pip install install .[tests] + pip install .[tests] pip freeze - name: Check for unmigrated code changes diff --git a/emgapi/models.py b/emgapi/models.py index 31db68bb3..7490feb47 100644 --- a/emgapi/models.py +++ b/emgapi/models.py @@ -1698,10 +1698,11 @@ def available(self, request=None): - all | has access to public analyses - authenticated | has access to public and private analyses they own - Filtered out analyses for SUPPRESSED samples + Filtered out analyses for SUPPRESSED studies """ query_filters = { "all": [ + Q(study__is_suppressed=False), Q(study__is_private=False), Q(run__is_private=False) | Q(assembly__is_private=False), Q(is_suppressed=False), diff --git a/emgcli/settings.py b/emgcli/settings.py index c778d1f5a..7d936b765 100644 --- a/emgcli/settings.py +++ b/emgcli/settings.py @@ -128,12 +128,12 @@ }, }, 'loggers': { - 'emgena': { + 'emgena': { 'handlers': ['notify'], 'level': 'INFO', 'propagate': False }, - 'emgapianns.management.commands': { + 'emgapianns.management.commands': { 'handlers': ['default', 'console'], 'level': 'INFO', 'propagate': False @@ -339,8 +339,8 @@ def create_secret_key(var_dir): if 'ena' in DATABASES and 'ena_pro' not in DATABASES: DATABASES['ena_pro'] = DATABASES['ena'] -# this is required to use the djang-mysql QS Hints -# https://django-mysql.readthedocs.io/en/latest/queryset_extensions.html?highlight=DJANGO_MYSQL_REWRITE_QUERIES#query-hints +# this is required to use the djang-mysql QS Hints +# https://django-mysql.readthedocs.io/en/latest/queryset_extensions.html?highlight=DJANGO_MYSQL_REWRITE_QUERIES#query-hints DJANGO_MYSQL_REWRITE_QUERIES = True try: diff --git a/pyproject.toml b/pyproject.toml index cc8e6e465..6e0b7e08f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,12 +71,12 @@ tests = [ "pytest==6.2.5", "pytest-django==4.4.0", "pytest-xdist==2.3.0", - "model_bakery==1.3.2", + "model_bakery==1.17.0", "mock_services==0.3.1", "mongomock==3.23.0", "jsonapi-client==0.9.9", "pytest-cov==2.12.1", - "pandas==1.3.2", + "pandas==2.2.1", "responses==0.23.1", "Faker==19.6.2", ] diff --git a/tests/webuploader/test_study_summary_generator.py b/tests/webuploader/test_study_summary_generator.py index 6fa6ecfe2..cd507ef36 100644 --- a/tests/webuploader/test_study_summary_generator.py +++ b/tests/webuploader/test_study_summary_generator.py @@ -19,7 +19,7 @@ import pandas as pd import pytest from model_bakery import baker -from pandas.util.testing import assert_frame_equal +from pandas.testing import assert_frame_equal from emgapianns.management.lib import study_summary_generator # noqa: E402