Merge pull request #4 from domonik/new-dev

New dev

.github/test-package.yml

@@ -0,0 +1,42 @@
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-package:
+    runs-on: "ubuntu-22.04"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.10", "3.11", "3.12" ]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: create environment with mamba
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge,defaults,bioconda
+          auto-activate-base: false
+          activate-environment: RNAdistEnv
+          environment-file: environment.yml
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package
+        run: |
+          conda activate RNAdistEnv
+          pip install ./ --no-deps --no-build-isolation
+          pip install pytest
+
+      - name: test package
+        run: |
+          pytest --pyargs RNAdist

MANIFEST.in

@@ -2,7 +2,7 @@ include versioneer.py
 include RNAdist/_version.py
 include RNAdist/dp/_dp_calculations.pyx
 include *.pyx
-include RNAdist/sampling/cpp/*.h
+global-include cpp/*.h
 global-include tests/*.py
 global-include tests/test_data/*
 prune */__pycache__/

RNAdist/cpp/RNAHelpers.cpp

@@ -0,0 +1,14 @@
+//
+// Created by rabsch on 18.11.24.
+//
+
+#include "RNAHelpers.h"
+
+
+
+vrna_fold_compound_t *swigFcToFc(PyObject *swig_fold_compound) {
+    SwigPyObject *swf = (SwigPyObject*) swig_fold_compound;
+    vrna_fold_compound_t *fc = (vrna_fold_compound_t*) swf->ptr;
+    return fc;
+}
+

RNAdist/cpp/RNAHelpers.h

@@ -0,0 +1,33 @@
+//
+// Created by rabsch on 18.11.24.
+//
+
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+#define PYBIND11_DETAILED_ERROR_MESSAGES
+
+#ifndef RNADIST_RNAHELPERS_H
+#define RNADIST_RNAHELPERS_H
+#endif //RNADIST_RNAHELPERS_H
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/stl.h>
+
+extern "C"
+{
+#include "ViennaRNA/fold_compound.h"
+}
+
+
+
+typedef struct {
+    PyObject_HEAD
+    void *ptr;
+    void *ty;
+    int own;
+    PyObject *next;
+    PyObject *dict;
+} SwigPyObject;
+
+vrna_fold_compound_t *swigFcToFc(PyObject *swig_fold_compound);
+