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Merged
george42-ctds merged 12 commits into from
Oct 2, 2024
Merged

Chore/update gen3datamodel #31

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69d4c20
(PPS-710): migrate to poetry, use new branches of gen3datamodel
george42-ctds Aug 2, 2024
24edd05
(PPS-710): add github actions
george42-ctds Aug 2, 2024
459f658
(PPS-710): remove travis file
george42-ctds Aug 2, 2024
436b433
(PPS-710): update Dockerfile to python=3.9 and use poetry
george42-ctds Aug 3, 2024
a02c8fe
(PPS-710): fix typo in Dockerfile
george42-ctds Aug 3, 2024
3f008ab
(PPS-710): add 'poetry show' to Dockerfile and remove python installs
george42-ctds Aug 3, 2024
8cacd42
(PPS-710): set USE_QUAY_ONLY for debugging
george42-ctds Aug 3, 2024
400a2e9
(PPS-710): update black
george42-ctds Aug 26, 2024
da6a6b9
(PPS-710): add utility scripts to pyproject.toml scripts
george42-ctds Aug 26, 2024
8059729
(PPS-710): add conditional to GRANT
george42-ctds Sep 11, 2024
2319a97
Update .secrets.baseline
george42-ctds Oct 1, 2024
f391968
(PPS-710): revert USE_QUAY_ONLY
george42-ctds Oct 1, 2024
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16 changes: 16 additions & 0 deletions .github/workflows/ci.yaml
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@@ -0,0 +1,16 @@
name: CI

on: [push]

jobs:
Security:
name: Security Pipeline
uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
with:
python-poetry: 'false'
secrets: inherit # pragma: allowlist secret
UnitTest:
name: Python Unit Test
uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
with:
python-version: '3.9'
13 changes: 13 additions & 0 deletions .github/workflows/image_build_push.yaml
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@@ -0,0 +1,13 @@
name: Build Image and Push

on: push

jobs:
ci:
name: Build Image and Push
uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
secrets:
ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}
16 changes: 16 additions & 0 deletions .github/workflows/pypi.yaml
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@@ -0,0 +1,16 @@
name: PyPI
on:
push:
tags:
- '*'
jobs:
PyPIPoetryPublish:
name: PyPI Poetry Publish
uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master
with:
PYTHON_VERSION: '3.9'
# This will attempt push to test PyPI first and only push to prod if it works
DO_TEST_PUBLISH_FIRST: true
secrets:
PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }}
PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -11,6 +11,6 @@ repos:
- id: no-commit-to-branch
args: [--branch, develop, --branch, master, --pattern, release/.*]
- repo: https://github.com/psf/black
rev: 19.10b0
rev: 22.3.0
hooks:
- id: black
21 changes: 5 additions & 16 deletions .secrets.baseline
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@@ -1,10 +1,9 @@
{
"custom_plugin_paths": [],
"exclude": {
"files": null,
"lines": null
},
"generated_at": "2020-07-24T04:12:49Z",
"generated_at": "2024-10-01T20:14:55Z",
"plugins_used": [
{
"name": "AWSKeyDetector"
Expand Down Expand Up @@ -59,26 +58,16 @@
}
],
"results": {
".travis.yml": [
"poetry.lock": [
{
"hashed_secret": "f1393dd73285bb82299e9fcb766e6492add3b90c",
"is_secret": false,
"hashed_secret": "cd225e5bd7bd52a6573408826b520b643f2bd3e2",
"is_verified": false,
"line_number": 26,
"type": "Base64 High Entropy String"
}
],
"Pipfile.lock": [
{
"hashed_secret": "77ce225436e7b798cc312adf2c7eb3b73f3f1ccf",
"is_secret": false,
"is_verified": false,
"line_number": 4,
"line_number": 840,
"type": "Hex High Entropy String"
}
]
},
"version": "0.14.1",
"version": "0.13.1",
"word_list": {
"file": null,
"hash": null
Expand Down
33 changes: 0 additions & 33 deletions .travis.yml
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18 changes: 6 additions & 12 deletions Dockerfile
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@@ -1,9 +1,7 @@
# To run: docker run -v /path/to/wsgi.py:/var/www/datamodelutils/wsgi.py --name=datamodelutils -p 81:80 datamodelutils
# To check running container: docker exec -it datamodelutils /bin/bash

FROM ubuntu:16.04

ENV DEBIAN_FRONTEND=noninteractive
FROM quay.io/cdis/python:python3.9-buster-2.0.0

RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential \
Expand All @@ -17,18 +15,14 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
libssl-dev \
libxml2-dev \
libxslt1-dev \
python3.6 \
python-dev \
python-pip \
python-setuptools \
sudo \
vim \
&& pip install pip==9.0.3 \
&& pip install --upgrade setuptools
vim

COPY . /datamodelutils
WORKDIR /datamodelutils
RUN pwd

RUN pip install -r requirements.txt
RUN pip install .
RUN pip install --upgrade pip && pip3 install poetry
RUN poetry config virtualenvs.create false
RUN poetry install -vv
RUN poetry show
14 changes: 0 additions & 14 deletions Pipfile
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