From 2d16fd158ecb8adde6f78626d1d63c76ed873086 Mon Sep 17 00:00:00 2001
From: Bruce Edelman <bruce.edelman@ligo.org>
Date: Wed, 15 Nov 2023 12:34:58 -0800
Subject: [PATCH 1/2] Break up actions into one that does linting and tests
 python build and other that builds and publishes the wheel

---
 .../workflows/{ => deprecated}/deploy.yaml    |  0
 .../{python-app.yml => python-build.yml}      | 43 +++++++++++--------
 .github/workflows/python-publish.yml          | 12 ++++--
 3 files changed, 35 insertions(+), 20 deletions(-)
 rename .github/workflows/{ => deprecated}/deploy.yaml (100%)
 rename .github/workflows/{python-app.yml => python-build.yml} (51%)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deprecated/deploy.yaml
similarity index 100%
rename from .github/workflows/deploy.yaml
rename to .github/workflows/deprecated/deploy.yaml
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-build.yml
similarity index 51%
rename from .github/workflows/python-app.yml
rename to .github/workflows/python-build.yml
index a9a4dcc..35e91fb 100644
--- a/.github/workflows/python-app.yml
+++ b/.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 
\ No newline at end of file
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 2f80821..3469abf 100644
--- a/.github/workflows/python-publish.yml
+++ b/.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

From 7018cf424ad6cdea7b9d98c2b8dee5bc89296e75 Mon Sep 17 00:00:00 2001
From: Bruce Edelman <bedelman@uoregon.edu>
Date: Wed, 15 Nov 2023 20:56:04 +0000
Subject: [PATCH 2/2] fix flake8 errors for undefined variables (it cant tell
 about going through loops or cases that end up defining variables before
 being called

---
 diploshic/fvTools.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/diploshic/fvTools.py b/diploshic/fvTools.py
index a2faa6f..63f184c 100644
--- a/diploshic/fvTools.py
+++ b/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]]