Merge branch 'release/0.18.2'

Author: siebrenf

.codeclimate.yml

@@ -21,23 +21,19 @@ checks:
 
 exclude_patterns:
   - ".*"
+  - "*.cfg"
   - "*.md"
+  - "*.txt"
   - "*.yml"
   - "*.yaml"
-  - "*.cff"
-  - "*.txt"
-  - "*.cfg"
-  - "*.py"
+  - "custom_build.py"
   - "COPYING"
-  - "INSTALL"
-  - "MANIFEST.in"
   - "**/__*"
   - "**/*.c"
   - "**/*.ccp"
   - "binder/*"
   - "data/*"
   - "docs/*"
+  - "scripts/*"
   - "src/*"
   - "test/*"
-  - "script/download_motif_databases.py"
-  - "gimmemotifs/_version.py"

.gitattributes

@@ -1,32 +1,23 @@
-**/*.swp
-*egg-info/
-gimmemotifs/*.pyc
-gimmemotifs/*.so
-test/*.pyc
-build/*
-doc/*
-!doc/*.tex
-!doc/*.pdf
-!doc/*.txt
-!doc/*.md
-docs/_build/*
-data/examples/*
-!data/examples/*.bed
-!data/examples/*.fa
-!data/examples/example.pfm
-!data/examples/*jaspar
-*.pyc
-dist/*
-website/**/*
-.eggs/
-.pytest_cache/
-.cache/
+# caching
 .idea/
-**/.ipynb_checkpoints/
-.vscode
-.coverage*
-coverage.xml
+__pycache__/
+.ipynb_checkpoints/
+.vscode/
+*.pyc
 
+# development
+build/
+dist/
+docs/_build/
+gimmemotifs/*.so
+gimmemotifs/included_tools/
+gimmemotifs.egg-info/
+src/
+test_py/
+venv/
+
+# tests
+.pytest_cache/
 test/data/maelstrom/activity*
 test/data/maelstrom/final*
 test/data/maelstrom/*png
@@ -39,10 +30,5 @@ test/data/maelstrom/input.table.txt
 test/**/*.fa.fai
 test/**/*.fa.sizes
 test/**/*.gaps.bed
-
-tmp/*
-
-src/meme_4.6.0
-src/meme_4.6.0/src/dir.h
-src/BioProspector/BioProspector
-src/MDmodule/MDmodule
+.coverage*
+coverage.xml

.gitignore

@@ -12,8 +12,7 @@ dependencies:
   - configparser
   - diskcache
   - feather-format
-  - genomepy >=0.14.0
-  # - ipywidgets                    # optional: progress bar in Jupyter notebook
+  - genomepy >=0.16.3             # has no dependency on pkg_resources
   - iteround
   - jinja2
   - logomaker
@@ -23,7 +22,7 @@ dependencies:
   - pandas >=1.3, <3
   - pybedtools >=0.9.0
   - pysam >=0.16
-  - python >=3.7, <3.12           # Motifsampler & setuptools break from py3.12
+  - python >=3.9, <3.12           # Motifsampler & setuptools break from py3.12
   - python-xxhash
   - qnorm  >=0.8.1
   - scikit-learn >=0.23.2         # https://scikit-learn.org/stable/install.html#installing-the-latest-release
@@ -32,4 +31,3 @@ dependencies:
   - statsmodels
   - tqdm >=4.46.1
   - xdg
-  #  - xgboost >=1.0.2            # optional: xgboost regressor for MOAP (1 GB)

.pre-commit-config.yaml

@@ -13,19 +13,17 @@ env:
     - CC_TEST_REPORTER_ID=3865090108d29191b1d34760d2ed5825d67b7566f0f87090e688b7513fdef063
 
 before_install:
-  # setup miniconda
-  - wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b -p $HOME/miniconda -f
-  - export PATH=$HOME/miniconda/bin:$PATH;
-  - conda config --set always_yes True
+  # setup miniforge
+  - wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+  - bash Miniforge3.sh -b -p "${HOME}/conda" > /dev/null
+  - source "${HOME}/conda/etc/profile.d/conda.sh"
+  - source "${HOME}/conda/etc/profile.d/mamba.sh"
+  - mamba activate
 
 install:
-  - conda install -c conda-forge "conda>=4.12.0" "mamba>=0.27"
-  - mamba env create -f requirements.yaml
-  - source activate gimme
-  - python setup.py build  # installs the motif discovery tools
-  - pip install -e . --no-deps --ignore-installed  # installs gimme (in editable mode)
+  - mamba env create -n gimme -f requirements.yaml
+  - mamba activate gimme
+  - pip install --no-deps --no-cache-dir --use-pep517 -v -e .
 
 before_script:
   # install Code Climate test coverage reporter

.rtd-environment.yml

@@ -5,6 +5,31 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## Unreleased
 
+
+
+## [0.18.2] - 2026-04-03
+
+### Changed
+
+- packaging & deployment now uses `pyproject.toml` and wheel
+- motif tools installed more robustly 
+- update minimum python version to 3.9
+- updated the install instructions in the README and documentation
+- refactored command line interface
+  - all CLI functions are located in gimmemotifs/cli.py
+  - all functions now provide help when actions are unspecified
+- refactored test/test_09_cli.py to work with new CLI
+
+### Fixed
+
+- the roc report will now display a message when 0 motifs are enriched (if motifs were subset or not)
+
+### Removed
+
+- versioneer
+
+
+
 ## [0.18.1] - 2025-10-02
 
 ### Changed
@@ -21,6 +46,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - updated C code, fixes compiler warnings & error (thanks cameronraysmith!)
 - updated versioneer, able to update configparser now! resolves #315
 
+
+
 ## [0.18.0] - 2023-01-11
 
 ### Added
@@ -67,6 +94,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 - removed old python2 code (scanning with MOODS & import shenanigans)
 
+
+
 ## [0.17.2] - 2022-10-12
 
 ### Changed
@@ -90,6 +119,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - pyarrow dependency
 
 
+
 ## [0.17.1] - 2022-06-02
 
 ### Added
@@ -124,6 +154,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
   - and Travis asks 5x credits for OSX machines...
 
 
+
 ## [0.17.0] - 2021-12-22
 
 ### Added
@@ -168,7 +199,6 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 * Fix issue with config file getting corrupted.
 * Fix FPR threshold calculation.
 
-### Removed
 
 
 ## [0.16.1] - 2021-06-28
@@ -185,6 +215,8 @@ Bugfix release.
 * Fixed "Motif does not occur in motif database when running maelstrom" (#192).
 * Fixed bugs related to runs where no (significant) motifs is found.
 
+
+
 ## [0.16.0] - 2021-05-28
 
 Many bugfixes, thanks to @kirbyziegler, @irzhegalova, @wangmhan, @ClarissaFeuersteinAkgoz and @fgualdr for reporting and proposing solutions!
@@ -215,6 +247,8 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
 * Fix issue with running `gimme motifs` with the HOMER database (#135)
 * Fix issue with the `--size` parameter in `gimme motifs`, which now works as expected (#128)
 
+
+
 ## [0.15.3] - 2021-02-01
 
 ### Fixed
@@ -228,6 +262,7 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
   cache.
 
 
+
 ## [0.15.2] - 2020-11-26
 
 ### Changed
@@ -239,6 +274,8 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
 - Fix issue with -s parameter of `gimme motifs` (#146)
 - Fix issues (hopefully) with scanning large input files.
 
+
+
 ## [0.15.1] - 2020-10-07
 
 ### Added
@@ -250,6 +287,8 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
 - Support for pandas>=1.1
 - `coverage_table` doesn't add a newline at the end of the file.
 
+
+
 ## [0.15.0] - 2020-09-29
 
 ### Added
@@ -277,6 +316,8 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
 - `gimme motifs` doesn't crash when no motifs are found.
 - Fixed error with Ensembl chromosome names in `combine_peaks`.
 
+
+
 ## [0.14.4] - 2020-04-02
 
 ### Fixed
@@ -285,12 +326,16 @@ Thanks to @Maarten-vd-Sande for the speed improvements.
 - Fixed `combine_peaks` with Ensembl chromosome names (thanks @JGAsmits). 
 - Fixed bug with pandas>=1.0.
 
+
+
 ## [0.14.3] - 2020-02-19
 
 ### Fixed
 
 - Fixed 'AttributeError: can't delete attribute' in `gimme maelstrom` and `gimme motifs` (#108, #109).
 
+
+
 ## [0.14.2] - 2020-01-31
 
 Bugfix release
@@ -314,6 +359,7 @@ Bugfix release
 - Updated `tqdm` requirement (#98).
 
 
+
 ## [0.14.1] - 2019-12-19
 
 Bugfix release
@@ -323,6 +369,8 @@ Bugfix release
 - Fix function for locating a pwm/pfm motif database.
 - Added configparser dependency
 
+
+
 ## [0.14.0] - 2019-12-05
 
 ### Added
@@ -356,6 +404,8 @@ Bugfix release
 
 - Deprecated modules and scripts.
 
+
+
 ## [0.13.1] - 2018-12-04
 
 ### Added
@@ -376,6 +426,8 @@ Bugfix release
 - Changed "user" background to "custom" background.
 - Updated Posmo to run with a wider variety of settings.
 
+
+
 ## [0.13.0] - 2018-11-19
 
 ### Added
@@ -411,6 +463,8 @@ Bugfix release
 - Fixed `scale` for newer `pandas`/`sklearn` combo
 - FIxed bug related to backgroundgradient with new pandas
 
+
+
 ## [0.12.0] - 2018-07-10
 
 **Please note:** the way GimmeMotifs uses genome FASTA files has changed in a
@@ -449,3 +503,15 @@ manage your genomes.
 - Fixed issue with nested multiprocessing pools.
 - Fix numpy version because of DeprecationWarning in sklearn.
 - Updated xgboost dependency, where the API had changed.
+
+
+
+[Unreleased]: https://github.com/vanheeringen-lab/gimmemotifs/compare/master...develop
+[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
+[0.17.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.16.0...0.17.0
+[0.16.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.15.0...0.16.0
+[0.15.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.14.0...0.15.0
+[0.14.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.13.0...0.14.0
+[0.13.0]: https://github.com/vanheeringen-lab/gimmemotifs/compare/0.12.0...0.13.0