Ac removered

.github/workflows/cgatapps_python.yml

@@ -47,3 +47,4 @@ jobs:
           pip install nose
           nosetests -v tests/test_style.py
           nosetests -v tests/test_scripts.py
+          nosetests -v tests/test_import.py

.github/workflows/release.yaml

@@ -0,0 +1,73 @@
+name: Publish cgat-apps wheels to PyPI and TestPyPI
+
+on:
+  push:
+    branches:
+      - v[0-9]+.[0-9]+.x
+    tags:
+      - v*
+  release:
+    types:
+      - published
+
+jobs:
+
+  build_sdist:
+
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os: [ubuntu, macos]
+        python-version: [3.10]
+
+    steps:
+      - name: Checkout cgat-apps
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install prerequisite Python libraries
+        run:  |
+          python -m pip install --upgrade pip
+          pip install wheel
+
+      - name: Create source distribution
+        run:  python setup.py sdist bdist_wheel
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+      - uses: actions/upload-artifact@v2          
+        with:
+          path: dist/*.whl
+
+  upload_pypi:
+
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Get Artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish distribution to Test PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'published'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+

cgat/AGP.py

@@ -9,7 +9,22 @@
 
 """
 
+import functools
 
+
+def deprecated_class(cls):
+    orig_init = cls.__init__
+
+    @functools.wraps(orig_init)
+    def new_init(self, *args, **kwargs):
+        warnings.warn(f"{cls.__name__} is deprecated and will be removed in the next release.", DeprecationWarning)
+        orig_init(self, *args, **kwargs)
+
+    cls.__init__ = new_init
+    return cls
+
+
+@deprecated_class
 class ObjectPosition(object):
 
     def map(self, start, end):
@@ -19,6 +34,7 @@ def map(self, start, end):
             return end + self.start, start + self.start
 
 
+@deprecated_class
 class AGP(object):
     """Parser for AGP formatted files."""