b2w rewrite to Python

.github/workflows/tests.yaml

@@ -0,0 +1,12 @@
+on: [push]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    name: Tests
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Run test cases
+        id: hello
+        uses: ./

.gitignore

@@ -3,6 +3,7 @@
 
 # Autotools cruft (NEVER check this into VCS)
 Makefile
+!docs/Makefile
 Makefile.in
 .version
 aclocal.m4
@@ -21,16 +22,10 @@ missing
 py-compile
 ar-lib
 test-driver
-/shorah
 
 # generated tarball
 shorah*.tar.bz2
 
-# executables
-b2w
-diri_sampler
-fil
-
 # samtools lib
 libbam.a
 
@@ -42,11 +37,11 @@ __pycache__/
 # OS X temporary files that should never be committed
 .DS_Store
 *.swp
-*.lock
 profile
 
 # other intermediate stuff
 build
+_build
 .eggs
 src/ShoRAH.egg-info/
 

.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.10
+
+ENV POETRY_VERSION=1.1.12
+
+RUN apt-get update -y && \
+    apt-get install -y libhts-dev libboost-random-dev
+
+RUN pip install "poetry==$POETRY_VERSION"
+
+COPY . /usr/app/
+
+# GitHub Actions chimes in here and sets docker's WORKDIR=${GITHUB_WORKSPACE}
+# https://docs.github.com/en/actions/creating-actions/dockerfile-support-for-github-actions#workdir
+
+ENTRYPOINT ["./entrypoint.sh"]
+
+CMD cd ./tests && poetry run pytest

README.md

@@ -158,13 +158,19 @@ file in directory
 
 
 ## Coding style
-All changes to the C++ code in `src/cpp` should always be formatted according to the included `.clang-format` style by doing
+All changes to the C++ code in `lib` should always be formatted according to the included `.clang-format` style by doing
 
 	clang-format -style=file -i src/cpp/*.[ch]pp
 
 in the root of the repository.
 
-All changes to the python code in `src/shorah` should always be formatted conforming to the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style guide. To this end, we advise to use [autopep8](https://pypi.python.org/pypi/autopep8).
+All changes to the python code in `shorah` should always be formatted conforming to the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style guide. To this end, we advise to use [autopep8](https://pypi.python.org/pypi/autopep8).
+
+## Development/CI with Docker
+The following command will run the CI locally within Docker. 
+```bash
+docker run --rm -w="/usr/app" -it $(docker build -q .) bash
+```
 
 ## Contact
 

action.yaml

@@ -0,0 +1,7 @@
+name: 'Test container'
+outputs:
+  out: 
+    description: 'The output'
+runs:
+  using: 'docker'
+  image: 'Dockerfile'