Merge pull request #117 from 4dn-dcic/ajs_upd_dependencies

Ajs upd dependencies

Author: aschroed

.github/workflows/main-publish.yml

@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: 3.11
       - name: Install Python dependencies for publish
-        run: python -m pip install dcicutils==8.0.0
+        run: python -m pip install dcicutils==8.17.0
       - name: Publish
         env:
           PYPI_USER: ${{ secrets.PYPI_USER }}

.github/workflows/main.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11']
+        python_version: ['3.9', '3.10', '3.11', '3.12']
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

CHANGELOG.rst

@@ -6,6 +6,14 @@ dcicwrangling
 Change Log
 ------
 
+4.0.0
+=====
+
+* drop support for python 3.8
+* add python 3.12
+* update lock file 
+* update mail-publish.yml to use new dcicutils
+
 
 3.2.1
 =====

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicwrangling"
-version = "3.2.1"
+version = "4.0.0"
 description = "Scripts and Jupyter notebooks for 4DN wrangling"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -10,8 +10,8 @@ repository = "https://github.com/4dn-dcic/dcicwrangling"
 packages = [{ include="scripts", from="." }]
 
 [tool.poetry.dependencies]
-python = ">=3.8.0, <3.12"
-dcicutils = "^8.0.0"
+python = ">=3.9, <3.13"
+dcicutils = "^8.13.0"
 openpyxl = "^3.0.9"
 Biopython = "^1.80"
 GEOparse = "^2.0.1"

pyproject.toml

@@ -142,7 +142,6 @@ def main():
     args = get_args(sys.argv[1:])
     auth = scu.authenticate(key=args.key, keyfile=args.keyfile, env=args.env)
     dryrun = not args.dbupdate
-
     file_list = scu.get_item_ids_from_args(args.input, auth, args.search)
     wf_data = get_metadata(args.workflow, auth)
     for f in file_list:

scripts/generate_wfr_from_pf.py

@@ -266,15 +266,15 @@ def test_get_item_uuid_w_atid(mocker, auth):
     atid = '/labs/test-lab'
     mt = mocker.patch('functions.script_utils.get_metadata', return_value={'uuid': 'test_uuid'})
     result = scu.get_item_uuid(atid, auth)
-    assert mt.called_with(atid, auth)
+    mt.assert_called_with(atid, auth)
     assert result == 'test_uuid'
 
 
 def test_get_item_uuid_not_found(mocker, auth):
     atid = '/labs/non-lab'
     mt = mocker.patch('functions.script_utils.get_metadata', return_value={'status': 'error'})
     result = scu.get_item_uuid(atid, auth)
-    assert mt.called_with(atid, auth)
+    mt.assert_called_with(atid, auth)
     assert result is None