updated to make ci pass

src/simreaduntil/simulator/readpool.py

@@ -52,7 +52,7 @@ class ReadPool:
     Do not forget to call finish() when done.
     
     Args:
-        reads_per_channel: whether reads are channel-specific
+        reads_per_channel: whether reads are channel-specific or any read can be assigned to any channel
     """
     def __init__(self, reads_per_channel):
         self.lock = threading.Lock()
@@ -86,18 +86,19 @@ def _get_new_read(self, channel=None) -> Tuple[str, Any]:
         """
         raise NotImplementedError()
 
-    """
-    Stop the read pool
-    
-    For example, if it is threaded, stop the thread
-    """
     def finish(self):
+        """
+        Stop the read pool
+        
+        For example, if it is threaded, stop the thread
+        """
         pass
 
     def __enter__(self):
         return self
     def __exit__(self, exc_type, exc_value, traceback):
         self.finish()
+
 class ReadPoolFromIterable(ReadPool):
     """
     Read pool that requests reads from generator
@@ -166,11 +167,14 @@ def read_gen():
         self.shuffled = shuffle_rand_state is not None
         self.reads_file_or_dir = reads_file_or_dir
 
-    """
-    Check if the read pool can open the file/directory
-    """
     @staticmethod
     def can_handle(file: Path) -> bool:
+        """
+        Check if the read pool can open the file/directory
+        
+        Args:
+            file: file or directory
+        """
         file = Path(file)
         return (
             (file.is_dir() and any(file.glob("**/*.fasta"))) or
@@ -180,12 +184,13 @@ def can_handle(file: Path) -> bool:
     def __repr__(self):
         return f"ReadPool(file = {self.reads_file_or_dir}, shuffled = {self.shuffled})"
 
-"""
-Threaded ReadPool that wraps another ReadPool and reads from it in another thread using a queue
-
-Note: Using a rng with ThreadedPoolWrapper is not thread-safe if rng is accessed from multiple threads
-"""
 class ThreadedReadPoolWrapper(ReadPool):
+    """
+    Threaded ReadPool that wraps another ReadPool and reads from it in another thread using a queue
+
+    Note: Using a rng with ThreadedPoolWrapper is not thread-safe if rng is accessed from multiple threads
+    """
+
     def __init__(self, read_pool: ReadPool, queue_size: int):
         super().__init__(reads_per_channel=read_pool.reads_per_channel)
         self._read_pool = read_pool
@@ -195,13 +200,17 @@ def __init__(self, read_pool: ReadPool, queue_size: int):
         self._reader_thread.start()
         self.definitely_empty = False
 
-    """
-    Check if the read pool can open the file/directory
-    """
     def can_handle(self, *args, **kwargs) -> bool:
+        """
+        Check if the read pool can open the file/directory
+        
+        Params:
+            args, kwargs: passed to wrapped read pool
+        """
         return self._read_pool.can_handle(*args, **kwargs)
 
     def _fill_queue(self):
+        """Keep the queue filled"""
         try:
             while True:
                 read = self._read_pool.get_new_read()

src/simreaduntil/usecase_helpers/simulator_with_readfish.py

@@ -87,7 +87,7 @@ def get_sim_params(sim_params_file, n_channels) -> SimParams:
         if n_channels != sim_params.n_channels:
             logger.warning(f"Using sim_params.n_channels={sim_params.n_channels} instead of {n_channels} because it was saved in the sim_params_file")
 
-    assert sorted(list(sim_params.gap_samplers.keys())) == {f"ch{i+1}" for i in range(n_channels)} # assumed by downstream plotting scripts
+    assert sorted(list(sim_params.gap_samplers.keys())) == sorted([f"ch{i+1}" for i in range(n_channels)]) # assumed by downstream plotting scripts
 
     return sim_params
 

src/simreaduntil/usecase_helpers/utils.py

@@ -8,7 +8,7 @@
 import os
 from pathlib import Path
 from textwrap import dedent
-from typing import List, Optional
+from typing import List, Optional, Tuple
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -74,7 +74,7 @@ def random_nanosim_reads_gen(random_state=np.random.default_rng(2), length_range
 
 # to load the FASTA file when the function is called rather than when the first read is requested (which may delay the simulation if an index has to be built first)
 @force_eval_generator_function
-def perfect_reads_gen(fasta_filename: Path, read_lens_range: tuple[int], random_state=np.random.default_rng(1), nanosim_read_id=True):
+def perfect_reads_gen(fasta_filename: Path, read_lens_range: Tuple[int], random_state=np.random.default_rng(1), nanosim_read_id=True):
     """
     Generate perfect reads that align to the reference genome
     

usecases/compute_absolute_enrichment.ipynb

@@ -400,14 +400,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 21,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(1.41, 1.4929629629629628, 1.4478169014084508)"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "# yield-corrected\n",
-    "1.49 * 1.23/1.24,\\\n",
-    "2.2 * 1.44/1.89, \\\n",
-    "3.04 * 1.7/2.84"
+    "# # yield-corrected\n",
+    "# 1.49 * 1.23/1.24,\\\n",
+    "# 2.2 * 1.44/1.89, \\\n",
+    "# 3.04 * 1.7/2.84\n",
+    "1.41 * 1.24/1.24,\\\n",
+    "2.03 * 1.39/1.89, \\\n",
+    "2.67 * 1.54/2.84"
    ]
   },
   {