FIX: Create separate conda and pip maturin builds

.github/workflows/pypi.yml

@@ -26,7 +26,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml --features cli 
+          args: --release --out dist --find-interpreter --manifest-path ./pip/Cargo.toml
           sccache: 'true'
           manylinux: auto
       - name: Upload wheels
@@ -53,7 +53,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml --features cli 
+          args: --release --out dist --find-interpreter --manifest-path ./pip/Cargo.toml
           sccache: 'true'
           manylinux: musllinux_1_2
       - name: Upload wheels
@@ -79,7 +79,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml --features cli 
+          args: --release --out dist --find-interpreter --manifest-path ./pip/Cargo.toml
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v4
@@ -105,7 +105,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter --manifest-path ./pykmertools/Cargo.toml --features cli 
+          args: --release --out dist --find-interpreter --manifest-path ./pip/Cargo.toml
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v4

Cargo.toml

@@ -6,5 +6,5 @@ package.description = "kmertools is a k-mer based feature extraction tool design
 package.readme = "README.md"
 package.license-file = "LICENSE"
 
-members = ["composition", "coverage", "kmertools", "kmer", "ktio", "counter", "misc", "pykmertools"]
+members = ["composition", "coverage", "kmertools", "kmer", "ktio", "counter", "misc", "pybindings", "pip", "conda"]
 resolver = "2"

conda/Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+name = "conda"
+version.workspace = true
+edition.workspace = true
+authors.workspace = true
+description.workspace = true
+readme.workspace = true
+license-file.workspace = true
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "pykmertools"
+crate-type = ["cdylib"]
+test = false
+
+[dependencies]
+pyo3 = { version = "0.22.0", "features" = ["abi3-py39"] }
+rayon = "1.10.0"
+clap = { version = "4.5.4" }
+pybindings = { path = "../pybindings" }

conda/pyproject.toml

@@ -0,0 +1,23 @@
+[build-system]
+requires = ["maturin>=1.7,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "pykmertools"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+dynamic = ["version", "description", "license", "readme"]
+keywords = ["genomics", "bioinformatics"]
+
+
+[project.urls]
+Documentation = "https://github.com/anuradhawick/kmertools/wiki"
+"Bug Tracker" = "https://github.com/anuradhawick/kmertools/issues"
+"Source Code" = "https://github.com/anuradhawick/kmertools/"
+
+[tool.maturin]
+features = ["pyo3/extension-module"]

conda/src/lib.rs

@@ -0,0 +1,23 @@
+use pybindings::{
+    cgr::CgrComputer, kmer::KmerGenerator, min::MinimiserGenerator, oligo::OligoComputer,
+};
+use pyo3::prelude::*;
+
+/// Pykmertools: kmertools python wrapper
+/// Modules:
+///     OligoComputer      - computing oligonucleotide frequency vectors
+///                          from DNA sequences
+///     CgrComputer        - computing chaos game representations
+///                           for DNA sequences
+///     KmerGenerator      - an iterator object to generate k-mers
+///                          as (forward, reverse) numeric kmer tuples
+///     MinimiserGenerator - an iterator object to iterate minimisers
+///                          as (kmer, start, end) numeric minimiser tuples
+#[pymodule]
+fn pykmertools(m: &Bound<'_, PyModule>) -> PyResult<()> {
+    m.add_class::<OligoComputer>()?;
+    m.add_class::<CgrComputer>()?;
+    m.add_class::<KmerGenerator>()?;
+    m.add_class::<MinimiserGenerator>()?;
+    Ok(())
+}

pip/.gitignore

@@ -0,0 +1,72 @@
+/target
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version

pykmertools/Cargo.toml → pip/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "pykmertools"
+name = "pip"
 version.workspace = true
 edition.workspace = true
 authors.workspace = true
@@ -17,9 +17,5 @@ test = false
 pyo3 = { version = "0.22.0", "features" = ["abi3-py39"] }
 rayon = "1.10.0"
 clap = { version = "4.5.4" }
-composition = { path = "../composition" }
-kmer = { path = "../kmer" }
+pybindings = { path = "../pybindings" }
 kmertools = { path = "../kmertools" }
-
-[features]
-cli = []

pykmertools/src/lib.rs → pip/src/lib.rs

@@ -1,18 +1,10 @@
-mod cgr;
-mod kmer;
-mod min;
-mod oligo;
-use cgr::CgrComputer;
-#[cfg(feature = "cli")]
 use clap::Parser;
-use kmer::KmerGenerator;
-#[cfg(feature = "cli")]
 use kmertools::args::{cli, Cli};
-use min::MinimiserGenerator;
-use oligo::OligoComputer;
+use pybindings::{
+    cgr::CgrComputer, kmer::KmerGenerator, min::MinimiserGenerator, oligo::OligoComputer,
+};
 use pyo3::prelude::*;
 
-#[cfg(feature = "cli")]
 #[pyfunction]
 // TODO: remove after https://github.com/PyO3/maturin/issues/368 is resolved
 fn run_cli(_py: Python) -> PyResult<()> {
@@ -38,7 +30,6 @@ fn pykmertools(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<CgrComputer>()?;
     m.add_class::<KmerGenerator>()?;
     m.add_class::<MinimiserGenerator>()?;
-    #[cfg(feature = "cli")]
     m.add_function(wrap_pyfunction!(run_cli, m)?)?;
     Ok(())
 }

pybindings/.gitignore

@@ -0,0 +1,72 @@
+/target
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version

pybindings/Cargo.toml

@@ -0,0 +1,20 @@
+[package]
+name = "pybindings"
+version.workspace = true
+edition.workspace = true
+authors.workspace = true
+description.workspace = true
+readme.workspace = true
+license-file.workspace = true
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "pybindings"
+test = false
+
+[dependencies]
+pyo3 = { version = "0.22.0", "features" = ["abi3-py39"] }
+rayon = "1.10.0"
+clap = { version = "4.5.4" }
+composition = { path = "../composition" }
+kmer = { path = "../kmer" }

pybindings/src/lib.rs

@@ -0,0 +1,4 @@
+pub mod cgr;
+pub mod kmer;
+pub mod min;
+pub mod oligo;