Pseudobulk now does not need to resort fragment files.

Author: SeppeDeWinter

pycistopic-lib/Cargo.lock

@@ -0,0 +1,20 @@
+[package]
+name = "pycistopic-lib"
+version = "0.1.0"
+edition = "2021"
+
+[lib]
+# The name of the native library. This is the name which will be used in Python to import the
+# library (i.e. `import string_sum`). If you change this, you must also change the name of the
+# `#[pymodule]` in `src/lib.rs`.
+name = "pycistopic_lib"
+# "cdylib" is necessary to produce a shared library for Python to import from.
+#
+# Downstream Rust code (including code in `bin/`, `examples/`, and `tests/`) will not be able
+# to `use string_sum;` unless the "rlib" or "lib" crate type is also included, e.g.:
+# crate-type = ["cdylib", "rlib"]
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = { version = "0.23.5", features = ["extension-module"] }
+flate2 = {version = "1.1.0",features = ["zlib-ng"], default-features = false}

pycistopic-lib/Cargo.toml

@@ -0,0 +1,58 @@
+use pyo3::exceptions::{PyIOError, PyValueError};
+use std::fmt;
+use pyo3::PyErr;
+
+#[derive(Debug)]
+pub struct InvalidFragmentFileError {
+    pub filename: String,
+}
+
+impl InvalidFragmentFileError {
+    pub fn new(filename: &str) -> InvalidFragmentFileError {
+        InvalidFragmentFileError{
+            filename: filename.to_string()
+        }
+    }
+}
+
+impl std::error::Error for InvalidFragmentFileError{}
+
+impl fmt::Display for InvalidFragmentFileError {
+    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+        write!(f, "{}: Invalid fragment file.", self.filename)
+    }
+}
+
+impl From<InvalidFragmentFileError> for PyErr {
+    fn from(err: InvalidFragmentFileError) -> PyErr {
+        PyIOError::new_err(err.to_string())
+    }
+}
+
+#[derive(Debug)]
+pub struct ValueError {
+    pub message: String,
+}
+
+impl ValueError {
+    pub fn new(message: String) -> ValueError {
+        ValueError {
+           message
+        }
+    }
+}
+
+impl std::error::Error for ValueError{}
+
+impl fmt::Display for ValueError {
+    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+        write!(f, "{}", self.message)
+    }
+}
+
+impl From<ValueError> for PyErr {
+    fn from(err: ValueError) -> PyErr {
+        PyValueError::new_err(err.to_string())
+    }
+}
+

pycistopic-lib/src/custom_errors.rs

@@ -0,0 +1,14 @@
+mod pseudobulk;
+mod custom_errors;
+
+use pyo3::prelude::*;
+
+
+/// A Python module implemented in Rust. The name of this function must match
+/// the `lib.name` setting in the `Cargo.toml`, else Python will not be able to
+/// import the module.
+#[pymodule]
+fn pycistopic_lib(m: &Bound<'_, PyModule>) -> PyResult<()> {
+    m.add_function(wrap_pyfunction!(pseudobulk::split_fragment_files_by_cell_type, m)?)?;
+    Ok(())
+}