Merge branch 'develop'

Author: Maarten-vd-Sande

.gitignore

@@ -23,19 +23,22 @@ website/**/*
 .cache/
 .idea/
 **/.ipynb_checkpoints/
-.idea/
 .vscode
 .coverage*
 coverage.xml
 
 test/data/maelstrom/activity*
 test/data/maelstrom/final*
 test/data/maelstrom/*png
+test/data/maelstrom/*pfm
+test/data/maelstrom/*txt*
 test/data/maelstrom/motif.freq.txt
 test/data/maelstrom/gimme.vertebrate.v3.1.motif2factors.txt
 test/data/maelstrom/gimme.vertebrate.v3.1.pwm
 test/data/maelstrom/input.table.txt
-test/**/*fai
+test/**/*.fa.fai
+test/**/*.fa.sizes
+test/**/*.gaps.bed
 
 tmp/*
 

.pre-commit-config.yaml

@@ -1,9 +1,18 @@
 repos:
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    - id: isort
+
   - repo: https://github.com/ambv/black
-    rev: 21.5b1
+    rev: 22.3.0
     hooks:
     - id: black
+
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+    rev: 4.0.1
     hooks:
     - id: flake8
+      additional_dependencies: [
+          'flake8-bugbear==22.4.25',
+          ]

.rtd-environment.yml

@@ -1,37 +1,34 @@
-name: gimmemotifs
 channels:
-  - defaults
-  - bioconda
   - conda-forge
+  - bioconda
+  - defaults
 dependencies:
-  - biofluff
+  # docs specific packages
+  - sphinx_bootstrap_theme
+
+  # gimme packages (without the motif discovery tools)
   - configparser
-  - diskcache
-  - feather-format
-  - genomepy >=0.8.3
+  - conda-forge::diskcache
+  - conda-forge::feather-format
+  - bioconda::genomepy >=0.11.1
+  - ipywidgets  # Necessary for progress bar in Jupyter notebook
+  - conda-forge::iteround
   - jinja2
-  - logomaker
+  - bioconda::logomaker
+  - loguru
   - matplotlib-base >=3.1.2
-  - ncurses
-  - numpy
-  - pandas >=1.0.3
-  - pillow
-  - pip
+  - numpy >= 1.6.0
+  - pandas >=1.0.3, <=1.1.5  # 1.3.5/1.4.2 are bugged
   - pyarrow >=0.16.0
-  - pybedtools
-  - pybigwig
-  - python >=3
-  - pyyaml >=3.10
-  - qnorm
-  - represent
-  - scikit-learn >=0.18
-  - scipy >=1.3.0
-  - seaborn
+  - bioconda::pybedtools >=0.9.0
+  - bioconda::pysam >=0.16
+  - python >=3.8
+  - python-xxhash
+  - conda-forge::qnorm  >=0.8.1
+  - scikit-learn >=0.23.2
+  - scipy >=1.4.1
+  - seaborn >=0.10.1
   - statsmodels
-  - tqdm >=4.27.0
+  - tqdm >=4.46.1
   - xdg
-  - xgboost >=0.71
-  - sphinx_bootstrap_theme
-  - numpydoc
-  - pip:
-    - xxhash
+  - xgboost >=1.0.2

.travis.yml

@@ -4,64 +4,41 @@ branches:
   - master
   - develop
 
-matrix:
-  allow_failures:
-    - os: osx
-  include:
-    - os: osx
-      language: generic
-    - os: linux
-      language: python
-      python: "3.6"
+os: linux
+dist: focal
+language: minimal
 
 env:
   global:
     - CC_TEST_REPORTER_ID=3865090108d29191b1d34760d2ed5825d67b7566f0f87090e688b7513fdef063
 
 before_install:
   # setup miniconda
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
-    fi
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b -p $HOME/miniconda -f
-  - source "$HOME/miniconda/etc/profile.d/conda.sh"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda info -a
-  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then ulimit -S -n 4096; ulimit -a; fi
+  - export PATH=$HOME/miniconda/bin:$PATH;
+  - conda config --set always_yes True
 
 install:
-  - conda config --add channels defaults
-  - conda config --add channels bioconda
-  - conda config --add channels conda-forge
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-      conda install mamba -y;
-      mamba env create -q -f conda_env.dev.txt -n gimme;
-    else
-      conda env create -q -f conda_env.osx.txt -n gimme; 
-    fi
-  - conda activate gimme
-  - conda list
-  - python setup.py build && pip install -e .
+  - conda install conda-forge::mamba
+  - mamba env create -f requirements.yaml
+  - source activate gimme
+  - python setup.py build  # installs the motif discovery tools
+  - pip install -e .  # installs gimme (in editable mode)
 
 before_script:
   # install Code Climate test coverage reporter
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-        wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64;
-    else
-        wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-darwin-amd64;
-    fi
+  - wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64
   - chmod +x ./cc-test-reporter
   - ./cc-test-reporter before-build
 
 script:
+  # generate the config and print the cache location
   - python -c 'from gimmemotifs.config import CACHE_DIR;print(CACHE_DIR)'
-  - pytest -vv --disable-pytest-warnings --cov=scripts --cov=gimmemotifs --cov-report=xml test/
+  # run the tests
+  - pytest -vvv --disable-pytest-warnings --cov=scripts --cov=gimmemotifs --cov-report=xml test/
 
 after_script:
   # upload test coverage data to Code Climate
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT; fi
+  - ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT

CHANGELOG.md

@@ -7,12 +7,32 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- `requirements.yaml` contains all conda dependencies.
+  - packages available from one channel have been pinned (for solving speed)
+  - packages have minimum versions where known (for solving speed)
+
 ### Changed
 
+- alphabetized tools everywhere (how could you live like that!?)
+- updated `setup.py`
+- updated installation instructions
+
 ### Fixed
 
+- Yamda is now recognized in the config
+- most tools work with the editable installation again 
+- all tests work for unix
+  - there were still some flakey values, where randomness is involved.
+- background.py updated to work with the specified minimum `genomepy` version
+- all `sphinx-build docs build` warnings
+
 ### Removed
 
+- a bunch of redundant requirement files.
+- OSX tests. Possibly temporary.
+  - The tests haven't working for ages, so I have no idea where to begin.
+  - and Travis asks 5x credits for OSX machines...
+
 
 ## [0.17.0] - 2021-12-22
 

MANIFEST.in

@@ -1,24 +1,16 @@
-include README.md
-include INSTALL
-include COPYING
 include CHANGELOG.md
-include run_tests.py
+include CITATION.cff
+include COPYING
+include INSTALL
 include compile_externals.py
-recursive-include src *
-recursive-include test/data/ *
-include test/*.py
-include test/data/*/*
-include scripts/gimme
-include scripts/coverage_table
-include scripts/combine_peaks
+include README.md
 
+prune test/
 graft data/
-recursive-exclude data/examples/ *
-include data/examples/TAp73alpha.bed
-include data/examples/TAp73alpha.fa
-include data/examples/test.small.fa
-include data/examples/example.pfm
-include data/examples/Gm12878.CTCF.top500.w200.fa
-include data/examples/MA0099.3.jaspar
+graft src/
+graft scripts/
+exclude scripts/download_motif_databases.py
+exclude scripts/gimme_benchmark
+
 include versioneer.py
 include gimmemotifs/_version.py