Merge branch 'prep_0.1.21' into 'master'

prepare 0.1.21

See merge request minknow/pod5-file-format!245

CHANGELOG.md

@@ -7,11 +7,11 @@ All notable changes, updates, and fixes to pod5 will be documented here
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [0.1.21] 2023-04-27
 
 ### Fixed
 
-- Repacker reads_completed value while copying a selection of reads.
+- Repacker `reads_completed` value while copying a selection of reads.
 - Fixed crash when trying to load files with a bad footer.
 
 ## [0.1.20] 2023-04-20

python/pod5/pyproject.toml

@@ -30,7 +30,7 @@ classifiers=[
 dependencies = [
     "iso8601",
     "jsonschema",
-    "lib_pod5 ~= 0.1.20dev0",
+    "lib_pod5 ~= 0.1.21dev0",
     "more_itertools",
     "numpy >= 1.20.0",
     "pyarrow ~= 11.0.0",

python/pod5/src/pod5/repack.py

@@ -8,7 +8,8 @@
 import lib_pod5 as p5b
 
 import pod5 as p5
-from tqdm import tqdm
+from pod5.tools.utils import PBAR_DEFAULTS
+from tqdm.auto import tqdm
 
 # The default interval in seconds to check for completion
 DEFAULT_INTERVAL = 0.5
@@ -161,10 +162,10 @@ def wait(
         disable_pbar = not bool(int(os.environ.get("POD5_PBAR", 1))) or not show_pbar
         pbar = tqdm(
             total=self.reads_requested,
-            ascii=True,
             disable=disable_pbar,
             leave=leave_pbar,
             unit="Reads",
+            **PBAR_DEFAULTS,
         )
 
         last_time, last_bytes, last_reads = time.time(), 0, 0
@@ -187,7 +188,6 @@ def wait(
             pbar.total = self.reads_requested
             pbar.update(self.reads_completed - last_reads)
             last_reads = self.reads_completed
-            # tqdm.write(f"{self.reads_completed} , {self.reads_requested}")
 
         if finish:
             self.finish()

python/pod5/src/pod5/tools/pod5_convert_from_fast5.py

@@ -26,7 +26,7 @@
 import pod5 as p5
 from pod5.signal_tools import DEFAULT_SIGNAL_CHUNK_SIZE, vbz_compress_signal_chunked
 from pod5.tools.parsers import pod5_convert_from_fast5_argparser, run_tool
-from pod5.tools.utils import is_pod5_debug, iterate_inputs
+from pod5.tools.utils import PBAR_DEFAULTS, is_pod5_debug, iterate_inputs
 
 READ_CHUNK_SIZE = 400
 TIMEOUT_SECONDS = 600
@@ -371,12 +371,11 @@ def __init__(self, paths: List[Path]):
         disable_pbar = not bool(int(os.environ.get("POD5_PBAR", 1)))
         self.pbar = tqdm(
             total=self.total_reads,
-            ascii=True,
             disable=disable_pbar,
             desc=f"Converting {len(self.path_reads)} Fast5s",
             unit="Reads",
             leave=True,
-            dynamic_ncols=True,
+            **PBAR_DEFAULTS,
         )
 
     @property

python/pod5/src/pod5/tools/pod5_merge.py

@@ -10,6 +10,7 @@
 import pod5 as p5
 import pod5.repack as p5_repack
 from pod5.tools.parsers import prepare_pod5_merge_argparser, run_tool
+from pod5.tools.utils import PBAR_DEFAULTS
 from tqdm import tqdm
 
 # Default number of files to merge at a time
@@ -75,9 +76,9 @@ def merge_pod5(
         disable_pbar = not bool(int(os.environ.get("POD5_PBAR", 1)))
         pbar = tqdm(
             total=len(inputs),
-            ascii=True,
             disable=disable_pbar or len(chunks) == 1,
             unit="Files",
+            **PBAR_DEFAULTS,
         )
 
         for chunk in chunks:

python/pod5/src/pod5/tools/pod5_repack.py

@@ -6,7 +6,8 @@
 import sys
 import typing
 from pathlib import Path
-from tqdm import tqdm
+from pod5.tools.utils import PBAR_DEFAULTS
+from tqdm.auto import tqdm
 
 import pod5 as p5
 import pod5.repack
@@ -51,7 +52,9 @@ def repack_pod5(
     futures = {}
     with ProcessPoolExecutor(max_workers=threads) as executor:
 
-        pbar = tqdm(total=len(inputs), ascii=True, disable=disable_pbar, unit="Files")
+        pbar = tqdm(
+            total=len(inputs), disable=disable_pbar, unit="Files", **PBAR_DEFAULTS
+        )
 
         for src in inputs:
             dest = output / src.name

python/pod5/src/pod5/tools/pod5_subset.py

@@ -12,7 +12,8 @@
 
 import jsonschema
 import pandas as pd
-from tqdm import tqdm
+from pod5.tools.utils import PBAR_DEFAULTS
+from tqdm.auto import tqdm
 
 import pod5 as p5
 import pod5.repack as p5_repack
@@ -353,9 +354,9 @@ def subset_pod5s_with_mapping(
     with ProcessPoolExecutor(max_workers=n_workers) as executor:
         pbar = tqdm(
             total=len(transfers),
-            ascii=True,
             disable=(disable_pbar or single_transfer),
             unit="Files",
+            **PBAR_DEFAULTS,
         )
 
         # Launch the subsetting jobs

python/pod5/src/pod5/tools/utils.py

@@ -7,6 +7,9 @@
 from pathlib import Path
 
 
+PBAR_DEFAULTS = dict(ascii=True, smoothing=0.0, dynamic_ncols=True)
+
+
 def iterate_inputs(
     input_items: typing.Iterable[Path], recursive: bool, file_pattern: str
 ) -> typing.Generator[Path, None, None]: