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Upgrade to Python 3.11 #754

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Oct 10, 2023
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ec081f6
j
dmichaels-harvard Sep 26, 2023
f215817
Comments in CHANGELOG.rst
dmichaels-harvard Sep 26, 2023
0f5dc2e
Changed import of Mapping from collections to collections.abc
dmichaels-harvard Sep 26, 2023
7dbf212
Typo!
dmichaels-harvard Sep 26, 2023
e5f396d
Update snovault version
dmichaels-harvard Sep 26, 2023
9f26298
update version
dmichaels-harvard Sep 26, 2023
27f5a78
TEMPORARILY putting access_key.py/json back to debug GA failure.
dmichaels-harvard Sep 26, 2023
74db13e
Update access_key.{json,py} back.
dmichaels-harvard Sep 27, 2023
a2ffd0f
debug
dmichaels-harvard Sep 27, 2023
22db0bc
Remove 3.11 from .github/workflows/main.yml for testing/debugging pur…
dmichaels-harvard Sep 27, 2023
4024635
Put 3.11 back into .github/workflows/main.yml but removed 3.8 so only…
dmichaels-harvard Sep 27, 2023
393bd25
Now put back both 3.8 and 3.11 in .github/workflows/main.yml
dmichaels-harvard Sep 27, 2023
3f2b191
Again remove 3.8 from .github/workflows/main.yml so again there is on…
dmichaels-harvard Sep 27, 2023
1458193
Added back both 3.8 and 3.11 in .github/workflows/main.yml and added …
dmichaels-harvard Sep 27, 2023
c1320f4
Backed out both 3.8 and 3.11 from .github/workflows/main.yml - just 3…
dmichaels-harvard Sep 27, 2023
0236869
update versions: dcicutils, dcicsnovault
dmichaels-harvard Sep 28, 2023
8d1e9e2
update snovault version
dmichaels-harvard Sep 28, 2023
35f6670
update versions: dcicsnovault
dmichaels-harvard Sep 28, 2023
123251a
Updated Dockerfile with python:3.11.5-slim-bullseye and install_nginx…
dmichaels-harvard Sep 28, 2023
973b70d
Minro update to main.yml for GA
dmichaels-harvard Sep 29, 2023
0467c8b
Removed Python 3.7 from list in pyproject.toml
dmichaels-harvard Sep 29, 2023
5931f51
Update dcicpyvcf to use latest version (3.0.0a4).
netsettler Oct 4, 2023
6c4cd78
Use dcicpyvcf ^3.0.0
netsettler Oct 5, 2023
3580110
Update snovault version
dmichaels-harvard Oct 5, 2023
0944ee6
Merge underlying branch upgrade-python-20230925 to take change in dci…
netsettler Oct 10, 2023
ccea5c0
Merge pull request #756 from dbmi-bgm/kmp_dcicpyvcf_v3
netsettler Oct 10, 2023
af58b4b
Update to 15.0.0; ready for merge to master.
dmichaels-harvard Oct 10, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ jobs:
matrix:
test_type: ['UNIT', 'INDEX', 'DOCKER']
# We are really not set up for these next two to be multiplicative, so be careful adding more.
python_version: ['3.8']
python_version: ['3.11']
node_version: ['18']

# Steps represent a sequence of tasks that will be executed as part of the job
Expand Down
13 changes: 13 additions & 0 deletions CHANGELOG.rst
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,19 @@ cgap-portal
Change Log
----------

15.0.0
======
* Upgrade to Python 3.11.
* Changed pyyaml version to ^6.0.1.
* Updated boto versions.
* Removed types/access_key.py and schemas/access_key.json as the ones in snovault are sufficient.
* Added generate-local-access-key script (from snovault) to pyproject.toml;
orignally created for smaht-portal since early in development no way to
create an access-key normally using the UI; but generall useful/convenient.
* Added generate-local-access-key script (defined in snovault).
* Added view-local-object script (defined in snovault).


14.3.1
======
`PR 753: Auth0 Symlink Bugfix <https://github.com/dbmi-bgm/cgap-portal/pull/753>`_
Expand Down
988 changes: 445 additions & 543 deletions poetry.lock

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26 changes: 15 additions & 11 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[tool.poetry]
# Note: Various modules refer to this system as "encoded", not "cgap-portal".
name = "encoded"
version = "14.3.1"
version = "14.3.1.1b2" # TODO: To become 15.0.0
description = "Computational Genome Analysis Platform"
authors = ["4DN-DCIC Team <[email protected]>"]
license = "MIT"
Expand Down Expand Up @@ -33,13 +33,16 @@ classifiers = [
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.7',
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This line (about 3.7) should be deleted.

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Oversight, thanks, deleted.

'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
]

[tool.poetry.dependencies]
python = ">=3.8.1,<3.10"
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Do we definitely mean 3.8.1 or did you just change the 7 to an 8? Is it not just >=3.8?

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I didn't change that from master, it used to be: python = ">=3.8.1,<3.10" ... not sure why it would be 3.8.1 ...

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I think I recall from a long time ago 3.8.1 has some specific issues with cgap-portal IRC hence the explicit exclusion

awscli = ">=1.27.79"
boto3 = "^1.26.133"
botocore = "^1.29.79"
python = ">=3.8.1,<3.12"
awscli = ">=1.29.54"
boto3 = "^1.28.54"
botocore = "^1.31.54"
certifi = ">=2021.5.30"
chardet = "3.0.4"
codeguru-profiler-agent = "^1.2.4"
Expand All @@ -49,8 +52,8 @@ codeguru-profiler-agent = "^1.2.4"
cryptography = "39.0.2"
colorama = "0.3.3"
dcicpyvcf = "1.0.0.1b0" # "^1.0.0"
dcicsnovault = "^10.0.2"
dcicutils = "^7.7.0"
dcicsnovault = "10.0.4.1b18"
dcicutils = "7.12.0.2b6"
elasticsearch = "7.13.4"
execnet = "1.4.1"
future = ">=0.18.2,<1"
Expand Down Expand Up @@ -88,7 +91,7 @@ python-dateutil = "^2.8.2"
# python-magic is presently pinned to 0.4.15 in lockstep with dcicsnovault's requirements. See explanation there.
python_magic = ">=0.4.24,<1"
pytz = ">=2021.3"
PyYAML = "5.3.1"
PyYAML = "^6.0.1"
rdflib = "^4.2.2"
rdflib-jsonld = ">=0.5.0,<1.0.0"
# repoze.debug is needed to use pyramid.pserve - Will Feb 17 2022
Expand Down Expand Up @@ -122,12 +125,11 @@ WSGIProxy2 = "0.4.2"
"zope.deprecation" = "^4.4.0"
"zope.interface" = ">=4.7.2,<6"
"zope.sqlalchemy" = "1.6"
pyyaml = "5.3.1"

[tool.poetry.dev-dependencies]
# PyCharm says boto3-stubs contains useful type hints
boto3-stubs = "^1.26.79"
botocore-stubs = "^1.29.79"
boto3-stubs = "^1.28.54"
botocore-stubs = "^1.31.54"
coverage = ">=6.2"
codacy-coverage = ">=1.3.11"
coveralls = ">=3.3.1"
Expand Down Expand Up @@ -179,6 +181,7 @@ dis2pheno = "encoded.commands.parse_hpoa:main"
es-index-data = "snovault.commands.es_index_data:main"
export-data = "encoded.commands.export_data:main"
extract-test-data = "encoded.commands.extract_test_data:main"
generate-local-access-key = "snovault.commands.generate_local_access_key:main"
import-data = "encoded.commands.import_data:main"
jsonld-rdf = "encoded.commands.jsonld_rdf:main"
load-access-keys = "encoded.commands.load_access_keys:main"
Expand All @@ -203,6 +206,7 @@ submission-test = "encoded.commands.submission_test:main"
# submit-metadata-bundle = "encoded.commands.submit_metadata_bundle:main"
update-inserts-from-server = "encoded.commands.update_inserts_from_server:main"
verify-item = "encoded.commands.verify_item:main"
view-local-object= "snovault.commands.view_local_object:main"
# cgap-specific commands
clear-variants-and-genes = "encoded.commands.clear_variants_and_genes:main"
gene-table-intake = "encoded.commands.gene_table_intake:main"
Expand Down
2 changes: 1 addition & 1 deletion src/encoded/ingestion/table_utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import io
import json
import logging
from collections import Mapping
from collections.abc import Mapping
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Bleah. Yeah, this is fine. But we see Python 3.11 makes an incompatible change. Sigh. (They might console themselves that they announced it earlier, but not as a 3.0 change. It only had compatibility support added in 3.4.) Once again we see semantic versioning apparently means nothing in Python. :(

from ..util import resolve_file_path

logger = logging.getLogger(__name__)
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69 changes: 0 additions & 69 deletions src/encoded/schemas/access_key.json

This file was deleted.

2 changes: 1 addition & 1 deletion src/encoded/tests/test_schemas.py
Original file line number Diff line number Diff line change
Expand Up @@ -249,7 +249,7 @@ def test_linkTo_saves_uuid(root, bgm_user, institution):


def test_mixinProperties():
schema = load_schema('encoded:schemas/access_key.json')
schema = load_schema('snovault:schemas/access_key.json')
assert schema['properties']['uuid']['type'] == 'string'


Expand Down
161 changes: 0 additions & 161 deletions src/encoded/types/access_key.py

This file was deleted.

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