First pass at eliminating secrets

.github/workflows/ci.yaml

@@ -6,6 +6,10 @@ on:
   pull_request:
     branches: ["*"]
 
+permissions:
+  contents: read
+  id-token: write
+
 jobs:
   determine_version:
     runs-on: ubuntu-latest
@@ -58,14 +62,14 @@ jobs:
       # Run spec tests without coverage for non Python 3.9
       - name: Run spec_test
         env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}
         continue-on-error: true
         run: |  
            python -m unittest discover spec_tests
 
       # Run unittest without coverage
       - name: Test with unittest
         env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}
         run: |
           python -m unittest discover tests

.github/workflows/ci_cov.yaml

@@ -6,26 +6,13 @@ on:
   pull_request:
     branches: ["*"]
 
-jobs:
+permissions:
+  contents: read
+  id-token: write
 
-  check-secret:
-    runs-on: ubuntu-latest
-    outputs:
-      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
-    steps:
-      - name: Check for Secret availability
-        id: check-for-secrets
-        # perform secret check & put boolean result as an output
-        shell: bash
-        run: |
-          if [ "${{ secrets.QLTY_COVERAGE_TOKEN }}" != '' ]; then
-            echo "defined=true" >> $GITHUB_OUTPUT;
-          else
-            echo "defined=false" >> $GITHUB_OUTPUT;
-          fi
+jobs:
 
   build:
-    needs: check-secret
     strategy:
       matrix:
         platform: [ubuntu-latest]
@@ -57,24 +44,22 @@ jobs:
       # Run unittest with coverage
       - name: Test with unittest and coverage
         env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}
         continue-on-error: true
         run: |  
           coverage run -m unittest discover tests
 
       # Run spec tests with coverage
       - name: Run spec_test coverage
         env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}
         run: |  
           coverage run --append -m unittest discover spec_tests
           coverage xml
           ls -la
 
       # Upload coverage to qlty
       - name: Upload coverage to qlty
-        if: needs.check-secret.outputs.secrets-exist == 'true'
         uses: qltysh/qlty-action/coverage@v2
         with:
-          token: ${{ secrets.QLTY_COVERAGE_TOKEN }}
           files: coverage.xml

hed/models/base_input.py

@@ -3,10 +3,10 @@
 """
 import os
 from typing import Union
-
 import openpyxl
 import pandas as pd
-
+from hed.models.column_metadata import ColumnMetadata
+from hed.models.definition_dict import DefinitionDict
 from hed.models.column_mapper import ColumnMapper
 from hed.errors.exceptions import HedFileError, HedExceptions
 
@@ -269,11 +269,11 @@ def columns(self) -> list[str]:
             columns = list(self._dataframe.columns)
         return columns
 
-    def column_metadata(self) -> dict[int, 'ColumnMeta']:
+    def column_metadata(self) -> dict[int, 'ColumnMetadata']:
         """ Return the metadata for each column.
 
         Returns:
-            dict[int, 'ColumnMeta']: Number/ColumnMeta pairs.
+            dict[int, ColumnMetadata]: Number/ColumnMetadata pairs.
         """
         if self._mapper:
             return self._mapper._final_column_map

hed/models/column_mapper.py

@@ -206,16 +206,13 @@ def set_tag_columns(self, tag_columns=None, optional_tag_columns=None, finalize_
         if finalize_mapping:
             self._finalize_mapping()
 
-    def set_column_map(self, new_column_map=None) -> list[dict]:
+    def set_column_map(self, new_column_map=None):
         """ Set the column number to name mapping.
 
         Parameters:
             new_column_map (list or dict):  Either an ordered list of the column names or column_number:column name.
                 dictionary. In both cases, column numbers start at 0.
 
-        Returns:
-            list[dict]: List of issues. Each issue is a dictionary.
-
         """
         if new_column_map is None:
             new_column_map = {}

hed/schema/schema_io/schema_util.py

@@ -23,7 +23,10 @@ def get_api_key():
     try:
         return os.environ["HED_GITHUB_TOKEN"]
     except KeyError:
-        return github_api_access_token
+        try:
+            return os.environ["GITHUB_TOKEN"]
+        except KeyError:
+            return github_api_access_token
 
 
 def make_url_request(resource_url, try_authenticate=True):