upgrade

.github/workflows/build.yml

@@ -0,0 +1,46 @@
+name: build
+
+on:
+  push:
+    branches: "*"
+  pull_request:
+    branches: "*"
+
+jobs:
+  build-n-test-n-coverage:
+    name: Build, test and code coverage
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9"]
+    env:
+      OS: ubuntu-latest
+      PYTHON: "3.9"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade setuptools          
+          pip install -e .[base,test]
+          pip install tox-gh-actions
+          pip install papermill testbook
+          pip install ipykernel;python -m ipykernel install --user --name beditor
+      - name: Run the tests
+        run: tox
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false

.github/workflows/release.yml

@@ -0,0 +1,36 @@
+name: release
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+#       Uncomment for your project
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -0,0 +1,75 @@
+*.pyc
+*.ipynb_checkpoints
+
+build
+#docs
+#docs/*.rst
+#docs/*.py
+#docs/_build
+#docs/generated
+#docs/_static
+#docs/_templates
+#docs/Makefile
+
+ms_datasets/*
+update_forks
+beditor/bin/*
+beditor/beditor_dependencies/*
+beditor.egg-info/*
+dist/*
+
+test/test_beditor/*
+test/.log*
+test_dataset/*
+
+# logs 
+.log*
+
+paper/latex.template
+paper/.Rhistory
+pub
+beditor/lib/global_vars_crispror.py
+beditor/lib/tmp/
+beditor/data/data_feats_aas.txt
+beditor/_bin/
+beditor/lib/_pub/
+beditor/deps/
+docs/_build/*
+.Rhistory
+docs/README.pdf
+docs/api.rst
+docs/make.bat
+beditor/deps.zip
+examples/inputs/*.pickle
+examples/inputs/*.db
+examples/inputs/dna.fa.gz.*
+examples/outputs*
+examples/inputs/*.tsv
+examples/docs/
+examples/dataset_
+examples/dataset_*
+examples/inputs/*/
+examples/inputs_*
+inputs/ann.gtf.*
+examples/inputs/ann.gtf.*
+examples/inputs/dna.fa.**
+examples/inputs/dna.fa.*
+examples/*_outputs/
+celerybeat
+django*
+welcome.md
+*celerybeat*
+examples/demo*
+_del*
+celery.sqlite
+examples/test_*
+test_*.ipynb*.beditor_gui_sessions/
+*-Copy1.ipynb
+examples/24*
+examples/*.log
+examples/test/
+untitled.txt
+examples/.beditor_gui_sessions/
+_*
+docs/_static
+docs

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "bwa"]
+	path = beditor/bwa
+	url = https://github.com/lh3/bwa.git
+[submodule "beditor/bwa"]
+	path = beditor/bwa
+	url = https://github.com/lh3/bwa.git

CITATION.cff

@@ -0,0 +1,15 @@
+cff-version: 1.2.0
+title: 'beditor: A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated
+  Base Editing'
+message: If you use this software, please cite it using the metadata from this file.
+type: software
+authors:
+- given-names: Rohan
+  family-names: Dandage
+  orcid: https://orcid.org/0000-0002-6421-2067
+identifiers:
+- type: doi
+  value: 10.1534/genetics.119.302089
+repository-code: https://github.com/rraadd88/beditor
+version: v2.0.0
+date-released: '2024-01-31'