Reorganize project to allow building Python package from the main rep…

…ository

.gitignore

@@ -1,2 +1,143 @@
-/target
-/Cargo.lock
+
+# Created by https://www.gitignore.io/api/rust,python
+# Edit at https://www.gitignore.io/?templates=rust,python
+
+callgrind.out.*
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don’t work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### Rust ###
+# Generated by Cargo
+# will have compiled files and executables
+/target/
+.cargo
+Cargo.lock
+
+# These are backup files generated by rustfmt
+**/*.rs.bk
+
+# cargo vendor
+.cargo/config.toml
+crates/
+
+# End of https://www.gitignore.io/api/rust,python

MANIFEST.in

@@ -0,0 +1,14 @@
+include setup.*
+include COPYING
+include CHANGELOG.md
+include README.md
+include pyproject.toml
+
+exclude Cargo.toml
+exclude Cargo.lock
+
+recursive-include lightmotif      *.rs Cargo.toml README.md
+recursive-include lightmotif-py*  *.rs Cargo.toml README.md *.py 
+
+include .cargo/config.toml
+recursive-include crates *

lightmotif-py/Cargo.toml

@@ -13,7 +13,7 @@ build = "build.rs"
 
 [lib]
 crate-type = ["cdylib", "rlib"]
-path = "lightmotif/lib/lib.rs"
+path = "lightmotif/lib.rs"
 
 [build-dependencies.built]
 version = "0.6"

lightmotif-py/lightmotif/tests/test_dna.py

@@ -25,8 +25,8 @@
 class TestDNAMotif(unittest.TestCase):
 
     def test_calculate(self):
-        counts = lightmotif.create(["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"])
-        frequencies = counts.normalize(0.1)
+        motif = lightmotif.create(["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"])
+        frequencies = motif.counts.normalize(0.1)
         pssm = frequencies.log_odds()
 
         seq = lightmotif.EncodedSequence(SEQUENCE)

pyproject.toml

@@ -0,0 +1,4 @@
+[build-system]
+requires = ['setuptools', 'setuptools_rust']
+build-backend = "setuptools.build_meta"
+

lightmotif-py/setup.cfg → setup.cfg

@@ -8,7 +8,7 @@ author = Martin Larralde
 author_email = [email protected]
 home_page = https://github.com/althonos/lightmotif
 description = PyO3 bindings and Python interface to lightmotif, a library for platform-accelerated biological motif scanning using position weight matrices.
-long_description = file: README.md
+long_description = file: lightmotif-py/README.md
 long_description_content_type = text/markdown
 license = MIT
 platform = any
@@ -40,9 +40,13 @@ project_urls =
 
 [options]
 zip_safe = true
+package_dir =
+    lightmotif = lightmotif-py
+    lightmotif.lib = lightmotif-py
+    lightmotif.tests = lightmotif-py
 packages =
     lightmotif
-    lightmotif._lib
+    lightmotif.lib
     lightmotif.tests
 test_suite = lightmotif.tests
 python_requires = >=3.7
@@ -54,9 +58,10 @@ setup_requires =
 lightmotif =
     py.typed
     *.pyi
-lightmotif._lib =
+lightmotif.lib =
     *.rs
 lightmotif.tests =
+    *.rs
     requirements.txt
 
 [bdist_wheel]
@@ -94,4 +99,4 @@ warn_unused_ignores = true
 warn_return_any = true
 
 [mypy-lightmotif.tests.*]
-ignore_errors = True
+ignore_errors = True

lightmotif-py/setup.py → setup.py

@@ -86,19 +86,19 @@ def setup_temp_rustc_unix(self, toolchain, profile):
 
     def get_dylib_ext_path(self, ext, module_name):
         ext_path = _build_rust.get_dylib_ext_path(self, ext, module_name)
-        if self.inplace:
-            base = os.path.basename(ext_path)
-            folder = os.path.dirname(os.path.realpath(__file__))
-            prefix = os.path.sep.join(ext.name.split(".")[:-1])
-            ext_path = os.path.join(folder, prefix, base)
+        # if self.inplace:
+        #     base = os.path.basename(ext_path)
+        #     folder = os.path.dirname(os.path.realpath(__file__))
+        #     prefix = os.path.sep.join(ext.name.split(".")[:-1])
+        #     ext_path = os.path.join(folder, prefix, base)
         return ext_path
 
 
 # HACK: Use the `configparser` from Python to read the `Cargo.toml`
 #       manifest file (this... works) so that the package version
 #       can be extracted from there and synchronized everywhere.
 parser = configparser.ConfigParser()
-parser.read(os.path.join(os.path.dirname(__file__), "Cargo.toml"))
+parser.read(os.path.join(os.path.dirname(__file__), "lightmotif-py", "Cargo.toml"))
 version = parser.get("package", "version").strip('"')
 
 setuptools.setup(
@@ -107,7 +107,7 @@ def get_dylib_ext_path(self, ext, module_name):
     cmdclass=dict(sdist=sdist, build_rust=build_rust),
     rust_extensions=[rust.RustExtension(
         "lightmotif.lib",
-        path="Cargo.toml",
+        path=os.path.join("lightmotif-py", "Cargo.toml"),
         binding=rust.Binding.PyO3,
         strip=rust.Strip.Debug,
         features=["extension-module"],