Merge pull request #311 from 4dn-dcic/python-3.12

Updating to Python 3.12

.github/workflows/main-publish.yml

@@ -18,15 +18,15 @@ jobs:
   # This workflow contains a single job called "build"
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install Python dependencies for publish
         run: pip install requests toml
       - name: Publish

.github/workflows/main.yml

@@ -23,7 +23,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python_version: [3.8, 3.9, 3.11]
+        python_version: [3.9, 3.11, 3.12]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

CHANGELOG.rst

@@ -6,6 +6,15 @@ dcicutils
 Change Log
 ----------
 
+8.13.0
+======
+* Updates related to Python 3.12.
+  - Had to update flake8 (from 5.0.4) to 7.1.0.
+  - Had to update lower bound of Python version (from 3.8.0) to 3.8.1.
+  - Had to update pyramid (from 1.10.4) to 2.0.2 (imp import not found).
+  - Had to update elasticsearch (from 7.13.4) to 7.17.9 (for snovault).
+
+
 8.12.0
 ======
 * Changes related to pyinstaller experimentation for smaht-submitr.

dcicutils/scripts/publish_to_pypi.py

@@ -203,7 +203,7 @@ def verify_untracked_files() -> bool:
     untracked_files = get_untracked_files()
     if untracked_files:
         PRINT(f"You are about to PUBLISH the following ({len(untracked_files)})"
-              f" UNTRACKED file{'' if len(untracked_files) == 1 else 's' } -> SECURITY risk:")
+              f" UNTRACKED file{'' if len(untracked_files) == 1 else 's'} -> SECURITY risk:")
         for untracked_file in untracked_files:
             PRINT(f"-- {untracked_file}")
         PRINT("DO NOT continue UNLESS you KNOW what you are doing!")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.12.0"
+version = "8.13.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -32,14 +32,15 @@ classifiers = [
     'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
-    'Programming Language :: Python :: 3.11'
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12'
 ]
 
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.13"
-boto3 = "^1.34.93"
-botocore = "^1.34.93"
+python = ">=3.8.1,<3.13"
+boto3 = "^1.34.136"
+botocore = "^1.34.136"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
@@ -49,35 +50,38 @@ chardet = "^5.2.0"
 docker = "^4.4.4"
 gitpython = "^3.1.2"
 jsonc-parser = "^1.1.5"
-jsonschema = "^4.19.0"
+jsonschema = "^4.22.0"
 openpyxl = "^3.1.2"
 opensearch-py = "^2.0.1"
 pyOpenSSL = "^23.1.1"
 PyJWT = "^2.6.0"
-pyramid = "1.10.4"
+#pyramid = "^2.0.2"
+pyramid = "1.10.8"
 pytz = ">=2020.4"
 redis = "^4.5.1"
 pyperclip = "^1.8.2"
 PyYAML = "^6.0.1"
+# N.B. 2024-06-30: Updating (via poetry update) from requests 2.31.0 (2023-05-22)
+# to 2.32.3 (2024-05-29) causes utils GA/CI to fail (on test_ecr_utils_workflow) for some reason.
 requests = "^2.21.0"
 rfc3986 = "^1.4.0"
 shortuuid = "^1.0.13"
 structlog = "^19.2.0"
 toml = ">=0.10.1,<1"
 tqdm = "^4.66.2"
 typing-extensions = ">=3.8"  # Fourfront uses 3.8
-urllib3 = "^1.26.6"
+urllib3 = "^1.26.19"
 webtest = "^2.0.34"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.34.93"
-botocore-stubs = "^1.34.93"
-coverage = ">=7.2.3"
+boto3-stubs = "^1.34.136"
+botocore-stubs = "^1.34.136"
+coverage = "^7.5.4"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023
 # coveralls = ">=3.3.1"
-flake8 = ">=3.9.2"
+flake8 = "^7.1.0"
 flaky = ">=3.7.0"
 pip-licenses = "^4.3.3"
 pytest = "^7.4.2"