Merge pull request #48 from cmatKhan/develop

remove vector_crosser; improve logging; parallelize over clusters; CI

.flake8

@@ -0,0 +1,14 @@
+[flake8]
+ignore = E226,E302,E41
+max-line-length = 88
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    scripts/*,
+    docs/*,
+	.venv/*,
+	.pytest_cache/*,
+	.devcontainer/*,
+	.vscode/*,

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/isocomp.yaml → .github/workflows/python-package.yml

@@ -1,24 +1,19 @@
-name: Python package with Poetry and MkDocs Deploy
+name: Python package with Poetry
 
 on:
   push:
-    branches:
-      - main
-      - develop
+    branches: [ "main", "develop" ]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [ "main", "develop" ]
 
 jobs:
   build:
+
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11"]
-
-    runs-on: ${{ matrix.os }}
+        python-version: ["3.9"]
 
     steps:
     - uses: actions/checkout@v2
@@ -40,6 +35,7 @@ jobs:
       run: |
         poetry install
     - name: Lint with flake8 using Poetry
+      continue-on-error: true
       run: |
         # stop the build if there are Python syntax errors or undefined names
         poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
@@ -48,27 +44,3 @@ jobs:
     - name: Test with pytest using Poetry
       run: |
         poetry run python -m pytest
-
-  deploy:
-    needs: build
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
-
-    - name: Install MkDocs
-      run: pip install mkdocs
-
-    - name: Build MkDocs documentation
-      run: mkdocs build
-
-    - name: Deploy to GitHub Pages
-      run: |
-        git config user.name "GitHub Actions"
-        git config user.email "[email protected]"
-        mkdocs gh-deploy --force
-
-    - name: Clean up
-      run: |
-        rm -rf site

README.md

@@ -1,3 +1,5 @@
+[![Python package with Poetry](https://github.com/cmatKhan/isocomp/actions/workflows/python-package.yml/badge.svg)](https://github.com/cmatKhan/isocomp/actions/workflows/python-package.yml)
+
 # Isocomp: comparing high-quality IsoSeq3 isoforms between samples
 
 ![](images/logo.png)