Merge branch 'release/0.17.0'

.gitignore

@@ -21,7 +21,9 @@ website/**/*
 .eggs/
 .pytest_cache/
 .cache/
+.idea/
 **/.ipynb_checkpoints/
+.idea/
 .vscode
 .coverage*
 coverage.xml

.pre-commit-config.yaml

@@ -1,5 +1,9 @@
 repos:
  - repo: https://github.com/ambv/black
- rev: 20.8b1
+ rev: 21.5b1
  hooks:
  - id: black
+ - repo: https://gitlab.com/pycqa/flake8
+ rev: 3.9.2
+ hooks:
+ - id: flake8

.travis.yml

@@ -1,3 +1,9 @@
+# run travis on these branches (and all PRs)
+branches:
+ only:
+ - master
+ - develop
+
 matrix:
  allow_failures:
  - os: osx
@@ -32,10 +38,11 @@ install:
  - conda config --add channels defaults
  - conda config --add channels bioconda
  - conda config --add channels conda-forge
+ - conda install mamba -y
  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
- conda env create -q -f conda_env.dev.txt -n gimme;
+ mamba env create -q -f conda_env.dev.txt -n gimme;
  else
- conda env create -q -f conda_env.osx.txt -n gimme;
+ conda env create -q -f conda_env.osx.txt -n gimme; # somehow mamba timesout on osx
  fi
  - conda activate gimme
  - conda list
@@ -52,10 +59,8 @@ before_script:
  - ./cc-test-reporter before-build
 
 script:
- - black --check gimmemotifs/ setup.py scripts/
- - flake8 setup.py gimmemotifs/ scripts/
  - python -c 'from gimmemotifs.config import CACHE_DIR;print(CACHE_DIR)'
- - pytest -v --disable-pytest-warnings --cov=scripts --cov=gimmemotifs --cov-report=xml test/
+ - pytest -vv --disable-pytest-warnings --cov=scripts --cov=gimmemotifs --cov-report=xml test/
 
 after_script:
  # upload test coverage data to Code Climate

CHANGELOG.md

@@ -14,6 +14,53 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 ### Removed
 
 
+## [0.17.0] - 2021-12-22
+
+### Added
+
+* Added `--genomes_dir` argument to `gimme motif2factors`.
+* Added `--version` flag.
+* Function `sample()` for fast sequence sampling from a `Motif()` instance.
+* Added JASPAR 2022 motif databases.
+* Updated Homer motif database.
+* Operators:
+ * `+` - take the combination of two motifs (average), based on pfm, which means that motifs with higher counts will be weighed more heavily.
+ * `&` - take the combination of two motifs (average), based on the ppm, which means that both motifs will be weighed equally.
+ * `<<` - "shift" motif left (adding a non-informative position to the right side)
+ * `>>` - "shift" motif right (adding a non-informative position to the left side)
+ * `~` - reverse complement
+ * `*` - multiply the pfm by a value
+* Progress bar for scanning.
+* `list_installed_libraries()` to list available motif libraries.
+
+### Changed
+
+* `Motif()` class completely restructured:
+ * Split into multiple files with coherent function.
+ * Uses `numpy.array` internally.
+ * All functions that mention `pwm` renamed to `ppm` (position-probability matrix), as the definition of a PWM is usually a log-odds matrix, not a probability matrix.
+ * `to_pwm()` is deprecated, use `to_ppm()` instead.
+ * Changed functions `pwm_min_score()` and `pwm_max_score()` to properties `max_score` and `min_score`.
+ * All internal data is correctly updated when `Motif()` is changed, for instance by trimming (#218).
+
+
+### Fixed
+
+* `gimme motif2factors` can now unzip genome fastas.
+* `gimme motif2factors` will sanitize genome names.
+* Fixed bugs related to partial rerun of `gimme motif2factors`.
+* Fixed unhandled `OSError` during installation on Mac.
+* Fixed bug related to `RFE()` (#226).
+* Positional probability matrix now sum to 1 over all positions (#209).
+* Fixed issue with pandas >= 1.3.
+* Fixed issue with `non_reducing_slice` import from pandas.
+* Fix threshold calculation if more than 20,000 sequences are supplied.
+* Fix issue with config file getting corrupted.
+* Fix FPR threshold calculation.
+
+### Removed
+
+
 ## [0.16.1] - 2021-06-28
 
 Bugfix release.

conda_env.dev.txt

@@ -35,10 +35,11 @@ weeder
 xdg
 xgboost >=0.71
 xxmotif
+iteround
 
 # development-specific
-black
-flake8
+black=21.5b1 # same as in .pre-commit-config.yaml
+flake8=3.9.2 # same as in .pre-commit-config.yaml
 flake8-bugbear
 pre-commit
 pytest

conda_env.osx.txt

@@ -35,11 +35,13 @@ weeder
 xdg
 xgboost=0.72
 xxmotif
+iteround
 
 # development-specific
-black
-flake8
+black=21.5b1 # same as in .pre-commit-config.yaml
+flake8=3.9.2 # same as in .pre-commit-config.yaml
 flake8-bugbear
+pre-commit
 pytest
 pytest-cov
 twine

conda_env.test.txt

@@ -36,3 +36,4 @@ weeder
 xdg
 xgboost >=0.71
 xxmotif
+iteround

conda_env.txt

@@ -35,3 +35,4 @@ weeder
 xdg
 xgboost >=0.71
 xxmotif
+iteround