Merge branch 'release/0.18.3'

Author: siebrenf

.rtd-environment.yml

@@ -12,7 +12,7 @@ dependencies:
   - configparser
   - diskcache
   - feather-format
-  - genomepy >=0.16.3             # has no dependency on pkg_resources
+  - genomepy >=0.16.4             # has no dependency on pkg_resources
   - iteround
   - jinja2
   - logomaker

CHANGELOG.md

@@ -3,10 +3,36 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
+
+
 ## Unreleased
 
 
 
+## [0.18.3] - 2026-06-09
+
+### Added
+
+- `gimme motifs` & `gimme maelstrom` now accept argument `--noprogress` to silence tqdm progress bars
+
+### Changed
+
+- minor Scanner.set_threshold optimization
+
+### Fixed
+
+- Scanner.scan now returns sequence.ids along with results.
+  - if sequences cannot be parsed, both ids and results are omitted.
+
+### Removed
+
+- deprecated functions `pwm_scan` and `pwm_scan_all`
+- warning blacklists
+- unused functions `_moap_with_bg()` and `_moap_with_table()`
+- outdated copyright comments (copyright claims still found in docs and COPYING file)
+
+
+
 ## [0.18.2] - 2026-04-03
 
 ### Changed
@@ -507,6 +533,7 @@ manage your genomes.
 
 
 [Unreleased]: https://github.com/vanheeringen-lab/gimmemotifs/compare/master...develop
+[0.18.3]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.18.2...0.18.3
 [0.18.2]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.18.1...0.18.2
 [0.18.1]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.18.0...0.18.1
 [0.18.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.17.0...0.18.0

docs/release_checklist.md

@@ -5,10 +5,12 @@ This is mainly for personal use at the moment.
 ## 0. (Re)install gimmemotifs
 
 ```shell
-mamba activate base
-mamba env create --force -n gimme -f requirements.yaml
-mamba activate gimme
+conda activate base
+conda env remove -n gimme -yq
+mamba env create -n gimme -f requirements.yaml
+conda activate gimme
 pip install --no-deps --no-cache-dir --use-pep517 -v -e .
+
 ```
 
 ## 1. Make sure all tests pass.
@@ -17,6 +19,7 @@ pip install --no-deps --no-cache-dir --use-pep517 -v -e .
 rm ~/.config/gimmemotifs/gimmemotifs.cfg
 gimme -h
 pytest -vvv --disable-pytest-warnings
+
 ```
 
 ## 2. Create release candidate with `git flow`:
@@ -26,6 +29,7 @@ new_version=0.0.0
 echo ${new_version}
 
 git flow release start ${new_version}
+
 ```
 
 ## 3. Make sure `__about__.py`, `pyproject.toml`, `CHANGELOG.md` are up-to-date.
@@ -39,9 +43,11 @@ git flow release start ${new_version}
 ## 4. Test install using pip in fresh conda environment
 
 ```shell
+rm -rf dist
 pip wheel -w dist --no-deps --no-cache-dir --use-pep517 -v .
+conda env remove -n test -yq
 mamba env create --force -n test -f requirements.yaml
-mamba activate test
+conda activate test
 pip install --no-deps --no-cache-dir --use-pep517 -v dist/gimmemotifs*.whl
 
 rm ~/.config/gimmemotifs/gimmemotifs.cfg
@@ -54,20 +60,21 @@ pytest -vvv --disable-pytest-warnings
 
 For more info, see https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
 
-```
+```shell
 # Create the source distribution
-$ python3 -m pip install --upgrade build
-$ python3 -m build
+python3 -m pip install --upgrade build
+python3 -m build
 
 # Test the source distribution
-$ pip install --no-deps --no-cache-dir --use-pep517 -v dist/gimmemotifs*.tar.gz
-$ rm ~/.config/gimmemotifs/gimmemotifs.cfg
-$ gimme -h
-$ pytest -vvv --disable-pytest-warnings
+pip install --no-deps --no-cache-dir --use-pep517 -v dist/gimmemotifs*.tar.gz
+rm ~/.config/gimmemotifs/gimmemotifs.cfg
+gimme -h
+pytest -vvv --disable-pytest-warnings
 
 # Upload to pypi testing server
-$ python3 -m pip install --upgrade twine
-$ python3 -m twine upload --repository testpypi dist/*
+python3 -m pip install --upgrade twine
+python3 -m twine upload --repository testpypi dist/*
+
 ```
 
 ## 6. Finish release

gimmemotifs/__about__.py

@@ -1 +1 @@
-__version__ = "0.18.2"
+__version__ = "0.18.3"

gimmemotifs/__init__.py

@@ -1,38 +1,38 @@
 import atexit as _atexit
 import logging as _logging
-import warnings as _warnings
 from os import getpid as _getpid
 from shutil import rmtree as _rmtree
 from tempfile import mkdtemp as _mkdtemp
-from warnings import warn as _warn
 
-from .__about__ import __version__
-
-
-def _filtered_warn(*args, **kwargs):
-    """warnings.filterwarnings does not work."""
-    blacklist = [
-        # maelstrom sklearn SVM
-        "Liblinear failed to converge, increase the number of iterations.",
-        # report.py (pandas internal DeprecationWarning)
-        "The get_cmap function will be deprecated in a future version. "
-        "Use ``matplotlib.colormaps[name]`` or "
-        "``matplotlib.colormaps.get_cmap(obj)`` instead.",
-        # report.py pandas FutureWarning, alternative works differently
-        "this method is deprecated in favour of `Styler.to_html()`",
-        # scanner/base.py set_threshold
-        "DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, "
-        "which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. "
-        "To get a de-fragmented frame, use `newframe = frame.copy()`",
-    ]
-    message = str(args[0])
-    if message in blacklist:
-        pass
-    else:
-        _warn(*args, **kwargs)
+from loguru import logger as _loguru_logger
 
+from .__about__ import __version__
 
-_warnings.warn = _filtered_warn
+# import warnings as _warnings
+# def _filtered_warn(*args, **kwargs):
+#     """warnings.filterwarnings does not work."""
+#     blacklist = [
+#         # maelstrom sklearn SVM
+#         "Liblinear failed to converge, increase the number of iterations.",
+#         # report.py (pandas internal DeprecationWarning)
+#         "The get_cmap function will be deprecated in a future version. "
+#         "Use ``matplotlib.colormaps[name]`` or "
+#         "``matplotlib.colormaps.get_cmap(obj)`` instead.",
+#         # report.py pandas FutureWarning, alternative works differently
+#         "this method is deprecated in favour of `Styler.to_html()`",
+#         # scanner/base.py set_threshold
+#         "DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, "
+#         "which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. "
+#         "To get a de-fragmented frame, use `newframe = frame.copy()`",
+#     ]
+#     message = str(args[0])
+#     if message in blacklist:
+#         pass
+#     else:
+#         _warnings.warn(*args, **kwargs)
+#
+#
+# _warnings.warn = _filtered_warn
 
 
 def mytmpdir():
@@ -44,24 +44,26 @@ def mytmpdir():
 
 # setup logger
 logger = _logging.getLogger("gimme")
-if logger.hasHandlers():
-    logger.handlers.clear()
-
+logger.handlers.clear()
 logger.setLevel(_logging.DEBUG)
+logger.propagate = False
 
-# nice format
-screen_formatter = _logging.Formatter(
+_screen_formatter = _logging.Formatter(
     "%(asctime)s - %(levelname)s - %(message)s", "%H:%M:%S"
 )
+_sh = _logging.StreamHandler()
+_sh.setLevel(_logging.INFO)
+_sh.setFormatter(_screen_formatter)
+logger.addHandler(_sh)
+
+# bridge Loguru
+class _PropagateHandler(_logging.Handler):
+    def emit(self, record):
+        _logging.getLogger("gimme").handle(record)
 
-# log to screen
-sh = _logging.StreamHandler()
-sh.setLevel(_logging.INFO)
-sh.setFormatter(screen_formatter)
-logger.addHandler(sh)
-del screen_formatter
-del sh
 
+_loguru_logger.remove()
+_loguru_logger.add(_PropagateHandler(), format="{message}")
 
 # import submodules to enable module autocomplete in editor
 

gimmemotifs/background.py

@@ -1,9 +1,3 @@
-# Copyright (c) 2009-2019 Simon van Heeringen <simon.vanheeringen@gmail.com>
-#
-# This module is free software. You can redistribute it and/or modify it under
-# the terms of the MIT License, see the file COPYING included with this
-# distribution.
-
 """
 Classes to generate background files in FASTA format. Two different methods are
 included: MarkovFasta, which generates a background according to a 1st order

gimmemotifs/c_metrics.c

@@ -1,12 +1,5 @@
 /*
- * Copyright (c) 2009-2019 Simon van Heeringen <simon.vanheeringen@gmail.com>
- * 
- * This module is free software. You can redistribute it and/or modify it under 
- * the terms of the MIT License, see the file COPYING included with this 
- * distribution.
- *
  * This module contains all the code to compare motifs
- *
  */
 
 #include <Python.h>

gimmemotifs/cli.py

@@ -1,16 +1,14 @@
 #!/usr/bin/env python
-# Copyright (c) 2013-2019 Simon van Heeringen <simon.vanheeringen@gmail.com>
-#
-# This module is free software. You can redistribute it and/or modify it under
-# the terms of the MIT License, see the file COPYING included with this
-# distribution.
 import argparse
 import os
 import sys
+import warnings
 from io import StringIO
 
 from gimmemotifs.__about__ import __version__
 
+warnings.filterwarnings("ignore")
+
 
 def gimme():
     description = f"GimmeMotifs v{__version__}"
@@ -186,6 +184,13 @@ def gimme():
         default=params["size"],
         type=int,
     )
+    p.add_argument(
+        "--noprogress",
+        dest="noprogress",
+        help="Disable tqdm progress bars",
+        default=False,
+        action="store_true",
+    )
 
     p.set_defaults(func=commands.motifs)
 
@@ -410,6 +415,13 @@ def gimme():
         action="store_true",
         default=False,
     )
+    p.add_argument(
+        "--noprogress",
+        dest="noprogress",
+        help="Disable tqdm progress bars",
+        default=False,
+        action="store_true",
+    )
 
     p.set_defaults(func=commands.maelstrom)
 

gimmemotifs/commands/background.py

@@ -1,8 +1,3 @@
-# Copyright (c) 2009-2019 Simon van Heeringen <simon.vanheeringen@gmail.com>
-#
-# This module is free software. You can redistribute it and/or modify it under
-# the terms of the MIT License, see the file COPYING included with this
-# distribution.
 from gimmemotifs.background import create_background_file
 
 

gimmemotifs/commands/cluster.py

@@ -1,9 +1,4 @@
 #!/usr/bin/env python
-# Copyright (c) 2009-2019 Simon van Heeringen <s.vanheeringen@science.ru.nl>
-#
-# This module is free software. You can redistribute it and/or modify it under
-# the terms of the MIT License, see the file COPYING included with this
-# distribution.
 import logging
 import os