Update to support python3.11

.github/workflows/main-publish.yml

@@ -18,19 +18,21 @@ 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/checkout@v3
       - uses: actions/setup-python@v2
         with:
-           python-version: 3.8
+          python-version: 3.11
+      - name: Install Python dependencies for publish
+        run: python -m pip install dcicutils==8.0.0
       - name: Publish
         env:
           PYPI_USER: ${{ secrets.PYPI_USER }}
           PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
-          pip install poetry
-          poetry publish --no-interaction --build --username=$PYPI_USER --password=$PYPI_PASSWORD
+          make configure
+          make publish-for-ga

.github/workflows/main.yml

@@ -18,27 +18,28 @@ 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
     strategy:
       matrix:
-        python_version: [3.7, 3.8, 3.9]
+        python_version: ['3.8', '3.9', '3.10', '3.11']
 
     # 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/checkout@v3
       - uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python_version }}
 
       - name: Install Deps
         run: |
-          pip install poetry coveralls codacy-coverage
+          make build
+          pip install coveralls codacy-coverage
 
       - name: QA
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          poetry install
+          make configure
           poetry run coverage run --source=wranglertools -m pytest -vv tests -m 'not ftp'
           poetry run coveralls --service=github

Makefile

@@ -4,7 +4,7 @@ clear-poetry-cache:  # clear poetry/pypi cache. for user to do explicitly, never
 	poetry cache clear pypi --all
 
 configure:  # does any pre-requisite installs
-	pip install poetry==1.3.2
+	pip install poetry==1.4.2
 
 lint:
 	flake8 wranglertools

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "Submit4DN"
-version = "3.4.2"
+version = "4.0.0"
 description = "Utility package for submitting data to the 4DN Data Portal"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -12,11 +12,11 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.7.0,<3.10"
+python = ">=3.8.0,<3.12"
 python-magic = ">=0.4.12,<1"
 attrs = "^22.2"
 openpyxl = "^3.1.2"
-dcicutils = "^7.9.0"
+dcicutils = "^8.0.0"
 # awscli is not directly imported but is required for aws cp operation
 awscli = "^1.27"
 

tests/test_import_data.py

@@ -131,13 +131,13 @@ def test_reader_with_sheetname(vendor_raw_xls_fields, workbooks):
 
 @pytest.mark.file_operation
 def test_reader_wrong_sheetname(capsys):
-    msg = "string indices must be integers\nEnzyme\nERROR: Can not find the collection sheet in excel file (openpyxl error)\n"
+    msg_end = "Enzyme\nERROR: Can not find the collection sheet in excel file (openpyxl error)\n"
     sheet = 'Vendor'
     sheetkey = "{}.xlsx".format(sheet)
     readxls = imp.reader(sheetkey, 'Enzyme')
     assert readxls is None
     out = capsys.readouterr()[0]
-    assert out == msg
+    assert out.endswith(msg_end)
 
 
 def test_cell_value(workbooks):

wranglertools/import_data.py

@@ -1436,6 +1436,7 @@ def user_workflow_reader(workbook, sheet, connection):
 def get_upload_creds(file_id, connection, extfilecreds=False):  # pragma: no cover
     creds2return = 'upload_credentials'
     url = f"{file_id}/upload/"
+    import pdb; pdb.set_trace()
     if extfilecreds:
         creds2return = 'extra_files_creds'
         req = ff_utils.authorized_request(f"{connection.key.get('server')}/{url}", auth=ff_utils.get_authentication_with_server(connection.key)).json()