Merge pull request #27 from arogozhnikov/dev

Update github workflows and move to pyproject.toml

.github/workflows/publish.yml

@@ -1,4 +1,4 @@
-name: publish
+name: Deploy to pypi
 
 on:
     release:
@@ -9,20 +9,19 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Checkout sources
-              uses: actions/checkout@v2
+              uses: actions/checkout@v4
 
             - name: Set up Python
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.8"
 
             - name: Install dependencies
               run: |
-                  pip install .
-
-            - name: Publish to PyPi
+                  pip install . && pip install hatch
+            - name: Publish einops to PyPi
               env:
-                  TWINE_USERNAME: "__token__"
-                  TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+                  HATCH_INDEX_USER: "__token__"
+                  HATCH_INDEX_AUTH: ${{ secrets.PYPI_TOKEN }}
               run: |
-                  source deploy_to_pypi.sh
+                  hatch run pypi:deploy

.github/workflows/run_test.yml

@@ -5,13 +5,12 @@ on: push
 jobs:
   run-my-tests:
     name: Run tests
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: '3.10'
     - name: Install package and dependencies
       run: |
         python -m pip install pytest

demuxalot/cellranger_specific.py

@@ -1,6 +1,6 @@
 """
 This file defines callbacks that are optimized for cellranger
-and can overcome some of issues in cellranger output.
+and can overcome some of the issues in cellranger output.
 
 If some other aligner is used, you can use simpler callbacks (e.g. using only mapq).
 """

examples/1-plain_demultiplexing.py

@@ -1,6 +1,5 @@
 """
-Simple demultiplexing
-with known genotypes.
+Simple demultiplexing with known genotypes.
 """
 from demuxalot import Demultiplexer, BarcodeHandler, ProbabilisticGenotypes, count_snps
 

pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = ["hatchling>=1.21.0"]
+build-backend = "hatchling.build"
+
+[project]
+name = "demuxalot"
+
+description = "Scalable and reliable demulitplexing for single-cell RNA sequencing."
+readme = "README.md"
+requires-python = ">=3.8"
+
+keywords = [
+    "genotype learning",
+    "single cell RNA sequencing",
+    "demultiplexing",
+    "bayesian modelling",
+]
+
+license = { text = "MIT" }
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+]
+
+dependencies = [
+    "pysam", # reads BAM files (alignment)
+    "scipy",
+    "numpy",
+    "joblib", # multiprocessing in separate processes
+    "pandas",
+    "pyarrow", # required to read and write parquet files
+]
+dynamic = ["version"]
+authors = [{ name = "Alex Rogozhnikov, System1 Biosciences" }]
+
+[project.urls]
+Homepage = "https://github.com/arogozhnikov/demuxalot"
+
+[tool.setuptools]
+packages = ["demuxalot"]
+
+[tool.hatch.version]
+path = "demuxalot/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+    "/.github",
+    "/.idea",
+    "/.pytest_cache",
+    "/build",
+    "/dist",
+    "/tests",
+    "/examples",
+]
+
+[tool.hatch.build.targets.wheel]
+# should use packages from main section
+
+
+[tool.hatch.envs.pypi.scripts]
+# hatch run pypi:deploy_test
+deploy_test = "hatch build --clean && hatch publish -r test"
+deploy = "hatch build --clean && hatch publish"
+
+
+[tool.hatch.envs.testing.scripts]
+# hatch run testing:test
+test = "pytest tests"
+
+
+[tool.ruff]
+line-length = 120