Break up actions

.github/workflows/python-app.yml → .github/workflows/python-build.yml

@@ -1,36 +1,45 @@
+
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: diploshic
+name: Build
 
-on:
- push:
- branches: [ master ]
- pull_request:
- branches: [ master ]
+on: push
 
 jobs:
- build:
-
+ Build_Package:
  runs-on: ubuntu-latest
-
+ strategy:
+ fail-fast: false
+ matrix:
+ python-version: ["3.8", "3.9", "3.10", "3.11"]
  steps:
- - uses: actions/checkout@v2
- - name: Set up Python 3.10
- uses: actions/setup-python@v2
+ - uses: actions/checkout@v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v3
  with:
- python-version: "3.10"
- - name: Install dependencies
+ python-version: ${{ matrix.python-version }}
+ - name: Setup conda
+ uses: s-weigand/setup-conda@v1
+ with:
+ activate-conda: true
+ update-conda: true
+ python-version: ${{ matrix.python-version }}
+ conda-channels: conda-forge
+ - name: Install dependencies 
  run: |
+ conda install pip setuptools
  python -m pip install --upgrade pip
  pip install flake8 pytest
- if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
  - name: Lint with flake8
  run: |
  # stop the build if there are Python syntax errors or undefined names
  flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
  # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
  flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- - name: Test with pytest
+ - name: Install diploSHIC
+ run: |
+ pip install .
+ - name: List installed
  run: |
- pytest
+ conda list 

.github/workflows/python-publish.yml

@@ -6,12 +6,18 @@
 # separate terms of service, privacy policy, and support
 # documentation.
 
-name: Upload Python Package
+name: Publish
 
-on: [push, pull_request]
+on:
+ push:
+ branches:
+ - main
+ - master
+ tags:
+ - v*
 
 jobs:
- manylinux:
+ Build_Wheel:
  runs-on: ubuntu-latest
  steps:
  - name: Checkout

diploshic/fvTools.py

@@ -252,6 +252,7 @@ def readFa(faFileName, upper=False):
  fopen = open
  with fopen(faFileName, "rt") as faFile:
  reading = False
+ currChr = None
  for line in faFile:
  if line.startswith(">"):
  if reading:
@@ -493,6 +494,10 @@ def readMaskDataForTraining(
  readingMasks = False
  isAccessible, isAccessibleArm = [], []
  genoMaskInfo = []
+ currChr = None
+ genos = None
+ positions = None
+ positions2SnpIndices = None
  with fopen(maskFileName, "rt") as maskFile:
  for line in maskFile:
  if line.startswith(">"):
@@ -916,7 +921,7 @@ def calcAndAppendStatValDiplo(
  - statVals["pi"][instanceIndex][subWinIndex]
  )
  elif statName == "HapCount":
- statVals[statName][instanceIndex].append(len(hapsInSubWin.distinct()))
+ statVals[statName][instanceIndex].append(len(genosInSubWin.distinct()))
  elif statName == "nDiplos":
  diplotypeCounts = dps.getHaplotypeFreqSpec(genosNAlt)
  nDiplos = diplotypeCounts[genosNAlt.shape[1]]
@@ -1021,7 +1026,7 @@ def calcAndAppendStatValForScanDiplo(
  )
  elif statName == "HapCount":
  # AK: undefined variables
- statVals[statName].append(len(hapsInSubWin.distinct()))
+ statVals[statName].append(len(genosInSubWin.distinct()))
  elif statName == "nDiplos":
  diplotypeCounts = dps.getHaplotypeFreqSpec(genosNAlt)
  nDiplos = diplotypeCounts[genosNAlt.shape[1]]