Move fourfront from pytest 2.9 to 3.10 (ALT)#1437

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netsettler wants to merge 70 commits into

kmp_pytest_3.10-alt

Commits on Feb 16, 2021

Experiment with updated settings.
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Commits on Feb 17, 2021

Add a few other files that don't need to go into git.
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Updates to psql-start and kibana-start migrated from cgap.
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Port various utilities from cgap's src/encoded/util.py just to have utilities level. (Many are unused but may back other code we want to port.) Rename src/encoded/utils.py to src/encoded/util.py so…
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Use new kibana-start and psql-start scripts to support psql-test and kibana-start-test and use poetry 1.1.4 in Makefile.
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Add extra newline to 13_run_npm.config for parity with cgap-portal diff.
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Confirm rename.
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Port cgap handling of tilde in setup_eb.py into fourfront.
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Port some light refactoring and a bug fix (missing module prefix zipfile.ZipFile) from cgap-portal version of scr/encoded/xlreader.py
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Add test cases for setup_eb.fix_requirement to test_setup_eb.py
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Rearrange imports and light PEP8 in src/encoded/root.py
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Suppress some noisy deprecation warnings in src/encoded/types/page.py beause they'd be complicated to fix right now.
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Port the post_only= argument to load_all and load_all_gen in src/encoded/loadxl.py.
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Use .hash instead of .encrypt in src/encoded/types/access_key.py and src/encoded/tests/test_access_key.py
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Add a pytest_configure in conftest.py that sets tempfile.tempdir to '/tmp'.
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Also .hash instead of .encrypt in src/encoded/tests/test_edw_hash.py
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Bump versions of awscli, boto3, botocore, netaddr, boto3-stubs.
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Bump patch version.
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Make jwt algorithms explicit in src/encoded/authentication.py. Also don't special-case GET and HEAD methods.
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PyCharm PEP8 hint in src/encoded/dev_servers.py
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Use new ACCESSION_PREFIX variable to minimize number of places code diverges. Add a TEST_PREFIX variable for symmetry. Compute the letter pairs needed for accession ids by looking at the schema files.
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In conftest.py, change htmltestapp and anonhtmltestapp to pass HTTP_ACCEPT, which is more like what browsers would do and is needed for some ported changes from cgap-portal. Light PEP8. Remove pyte…
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Use dcicutils.misc_utils.TestApp in src/commands/add_date_created.py, import_data.py
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Remove an internal import in src/encoded/commands/spreadsheet_to_json.py
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Unmark biosample_relation as a fixture. It is not a fixture.
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Port recent tweens work related to mime type selection in src/encoded/renderers.py. Some PEP8.
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Port test_renderers.py from cgap-portal.
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PEP8
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Use dcicutils.misc_utils.TestApp in src/encoded/commands/load_access_keys.py
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Add a use of set(...) in purge_item_type.py to remove duplicates. Change the way commits work to be more incremental.
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Backport a TODO comment about {'use_ssl': True} in src/encoded/commands/configure_kibana_index.py
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Merge branch 'master' into kmp_pytest_3.10
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Rename test_utils.py to test_util.py
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Delete test_utils.py because it was renamed to test_util.py
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Update lock file.
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Commits on Feb 18, 2021

A few more bits of leveling with cgap in test_indexing.py.
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Commits on Feb 22, 2021

Commits on Feb 26, 2021

Uncomment an important import.
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