Merge pull request #120 from brineylab/development

Development

.github/workflows/python-publish.yml

@@ -7,25 +7,58 @@ on:
   release:
     types: [created]
 
-jobs:
-  deploy:
 
+jobs:
+  pypi-publish:
+    name: upload release to PyPI
     runs-on: ubuntu-latest
-
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    # environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      # retrieve your distributions here
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+
+      - name: Build
+        run: |
+          python setup.py sdist bdist_wheel
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+
+# jobs:
+#   deploy:
+
+#     runs-on: ubuntu-latest
+
+#     steps:
+#     - uses: actions/checkout@v2
+#     - name: Set up Python
+#       uses: actions/setup-python@v2
+#       with:
+#         python-version: '3.x'
+#     - name: Install dependencies
+#       run: |
+#         python -m pip install --upgrade pip
+#         pip install setuptools wheel twine
+#     - name: Build and publish
+#       env:
+#         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+#         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+#       run: |
+#         python setup.py sdist bdist_wheel
+#         twine upload dist/*

abstar/__init__.py

@@ -1,9 +1,10 @@
 import warnings
+
 from Bio import BiopythonWarning
 
 warnings.simplefilter("ignore", BiopythonWarning)
+warnings.simplefilter(action="ignore", category=FutureWarning)
 
-from .core.abstar import run, run_standalone, main, create_parser, validate_args
-from .utils.preprocess import fastqc, adapter_trim, quality_trim
-
+from .core.abstar import create_parser, main, run, run_standalone, validate_args
+from .utils.preprocess import adapter_trim, fastqc, quality_trim
 from .version import __version__