Chore/migrate to GitHub actions

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+# push will run on every pushed commit to any branch (so this will rerun the tests
+# once a branch gets merged to main in addition to any new commits on any branch)
+on: push
+
+name: CI
+
+concurrency:
+  group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
+  cancel-in-progress: true
+
+jobs:
+  Security:
+    name: Security Pipeline
+    uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
+    with:
+      python-poetry: 'true'
+    secrets: inherit
+  UnitTest:
+    name: Python Unit Test with Postgres
+    uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
+    with:
+      python-version: '3.9'
+      use-cache: true
+
+  # this creates linter settings and uploads to an artifact so the configs can be pulled and used across jobs
+  LintConfig:
+    name: Get Lint Config
+    uses: uc-cdis/.github/.github/workflows/lint-create-config.yaml@master
+    with:
+      python-module-name: "cdislogging"
+
+  #  # (optional) modify the linter configurations from above. You could omit this if you didn't need to do this
+  #  CustomizeLintConfig:
+  #    runs-on: ubuntu-latest
+  #    name: Customize Lint Config
+  #    needs: [LintConfig]
+  #    steps:
+  #      - uses: actions/download-artifact@v3
+  #        with:
+  #          # this is uploaded by the lint-create-config.yaml workflow
+  #          name: linters-config
+  #          path: .github/linters
+  #
+  #      # modify default isort to specify the module name for proper formatting
+  #      - run: echo "known_first_party=gen3userdatalibrary" >> .github/linters/.isort.cfg
+  #
+  #      # now we need to re-upload the artifacts with the changes
+  #      - uses: actions/upload-artifact@v3
+  #        with:
+  #          name: linters-config
+  #          path: |
+  #            .github/linters/
+  #          if-no-files-found: error
+# TODO: Uncomment after repo is public
+
+
+  RequiredLint:
+    name: Run Required Linters
+    needs: [ LintConfig ]
+    uses: uc-cdis/.github/.github/workflows/required_lint_check.yaml@master
+    with:
+      python-version: '3.9'
+      use-cache: true
+  InformationalLint:
+   name: Run Informational Linters
+   needs: [ LintConfig ] #TODO Add UnitTest
+   if: github.ref != 'refs/heads/main'
+   uses: uc-cdis/.github/.github/workflows/optional_lint_check.yaml@master
+   with:
+     python-version: '3.9'
+     use-cache: true

.github/workflows/pypi.yml

@@ -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 }}

.github/workflows/wool.yaml

@@ -0,0 +1,15 @@
+on:
+    pull_request
+
+name: Wool
+
+jobs:
+  runWool:
+    name: Run black
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+
+    - uses: uc-cdis/wool@master
+    env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: git@github.com:Yelp/detect-secrets
-    rev: v0.13.1
+    rev: v1.4.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
@@ -13,6 +13,6 @@ repos:
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --branch, main, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 23.3.0
     hooks:
     -   id: black

.secrets.baseline

@@ -1,19 +1,18 @@
 {
-  "exclude": {
-    "files": ".lock",
-    "lines": null
-  },
-  "generated_at": "2020-10-26T20:51:00Z",
+  "version": "1.4.0",
   "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
     {
       "name": "AWSKeyDetector"
     },
     {
-      "name": "ArtifactoryDetector"
+      "name": "AzureStorageKeyDetector"
     },
     {
-      "base64_limit": 4.5,
-      "name": "Base64HighEntropyString"
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
     },
     {
       "name": "BasicAuthDetector"
@@ -22,8 +21,14 @@
       "name": "CloudantDetector"
     },
     {
-      "hex_limit": 3,
-      "name": "HexHighEntropyString"
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3.0
     },
     {
       "name": "IbmCloudIamDetector"
@@ -35,41 +40,99 @@
       "name": "JwtTokenDetector"
     },
     {
-      "keyword_exclude": null,
-      "name": "KeywordDetector"
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
     },
     {
       "name": "MailchimpDetector"
     },
+    {
+      "name": "NpmDetector"
+    },
     {
       "name": "PrivateKeyDetector"
     },
+    {
+      "name": "SendGridDetector"
+    },
     {
       "name": "SlackDetector"
     },
     {
       "name": "SoftlayerDetector"
     },
+    {
+      "name": "SquareOAuthDetector"
+    },
     {
       "name": "StripeDetector"
     },
     {
       "name": "TwilioKeyDetector"
     }
   ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
   "results": {
+    ".github/workflows/ci.yml": [
+      {
+        "type": "Secret Keyword",
+        "filename": ".github/workflows/ci.yml",
+        "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0",
+        "is_verified": false,
+        "line_number": 17
+      }
+    ],
     ".travis.yml": [
       {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
         "hashed_secret": "5e82431714e70b91ba45fb02ac5b0f71d2e287a0",
         "is_verified": false,
-        "line_number": 27,
-        "type": "Base64 High Entropy String"
+        "line_number": 26
+      },
+      {
+        "type": "Base64 High Entropy String",
+        "filename": ".travis.yml",
+        "hashed_secret": "ea0ba5e253d998709fb91d850c1fc1c4674642d0",
+        "is_verified": false,
+        "line_number": 30
       }
     ]
   },
-  "version": "0.13.1",
-  "word_list": {
-    "file": null,
-    "hash": null
-  }
+  "generated_at": "2025-02-14T20:30:33Z"
 }