Merge pull request #12 from dbmi-bgm/python-3.12

Python 3.12

.github/workflows/main-publish.yml

@@ -0,0 +1,38 @@
+# PyPi publish for granite-suite
+
+name: PUBLISH
+
+# Controls when the action will run.
+on:
+
+  # Publish on all tags
+  push:
+    tags:
+    - '*'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    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/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install Python dependencies for publish
+        run: pip install requests toml
+      - name: Publish
+        env:
+          PYPI_USER: ${{ secrets.PYPI_USER }}
+          PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: | 
+          make configure
+          make publish-for-ga

.github/workflows/main.yml

@@ -20,10 +20,10 @@ jobs:
     name: Test granite with Python ${{ matrix.python_version }}
 
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python_version: [3.6, 3.7, 3.8, 3.9]
+        python_version: [3.9, 3.11, 3.12]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

CHANGELOG.rst

@@ -0,0 +1,24 @@
+=============
+granite-suite
+=============
+
+----------
+Change Log
+----------
+
+0.3.0
+=====
+* Added this CHANGELOG.rst.
+* Updated to support Python 3.12.
+  - updated bitarray: ">=1.2.0" -> "^2.9.2"
+  - updated h5py: ">=2.10.0" -> "^3.11.0"
+  - updated matplotlib: "==3.3.4" -> "^3.9.0"
+  - udpated numpy: ">=1.18.0" -> "^1.26.4"
+  - updated pysam ">=0.15.0" -> "^0.22.1"
+  - updated pytabix: ">=0.0.2" -> "^0.1"
+* Supported Python versions now are: 3.9, 3.10, 3.11, 3.12
+* Note specifically that Python 3.8 is no longer supported (end of life: October 2024).
+
+0.2.0
+=====
+* Original.

Makefile

@@ -24,3 +24,11 @@ info:
 	   $(info - Use 'make update' to update dependencies and the lock file.)
 	   $(info - Use 'make build' to install entry point commands.)
 	   $(info - Use 'make test' to run tests.)
+
+publish:
+	pip install dcicutils
+	poetry run publish-to-pypi
+
+publish-for-ga:
+	pip install dcicutils
+	python -m dcicutils.scripts.publish_to_pypi --noconfirm