optional dependencies (#281)

* xgboost optional

* pin conda/mamba in tests again

* travis, why no build?

.rtd-environment.yml

@@ -9,28 +9,28 @@ dependencies:
   - sphinx_bootstrap_theme
 
   # gimme packages (without the motif discovery tools)
-  - bioconda::biofluff >=3.0.4    # Necessary for coverage_table()
+  - biofluff >=3.0.4              # necessary for coverage_table()
   - configparser
-  - conda-forge::diskcache
-  - conda-forge::feather-format
-  - bioconda::genomepy >=0.13.0
-#  - ipywidgets                    # Necessary for progress bar in Jupyter notebook
-  - conda-forge::iteround
+  - diskcache
+  - feather-format
+  - genomepy >=0.13.0
+  - ipywidgets                    # optional: progress bar in Jupyter notebook
+  - iteround
   - jinja2
-  - bioconda::logomaker
+  - logomaker
   - loguru
   - matplotlib-base >=3.3         # https://matplotlib.org/stable/devel/min_dep_policy.html#list-of-dependency-versions
   - numpy >=1.18                  # https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table
-  - pandas >=1.3.0                # Necessary for ExtraStyler.render()
-  - bioconda::pybedtools >=0.9.0
-  - bioconda::pysam >=0.16
+  - pandas >=1.3.0                # version necessary for ExtraStyler.render()
+  - pybedtools >=0.9.0
+  - pysam >=0.16
   - python >=3.6
   - python-xxhash
-  - conda-forge::qnorm  >=0.8.1
+  - qnorm  >=0.8.1
   - scikit-learn >=0.23.2         # https://scikit-learn.org/stable/install.html#installing-the-latest-release
   - scipy >=1.5                   # https://docs.scipy.org/doc/scipy/dev/toolchain.html#numpy
   - seaborn >=0.10.1
   - statsmodels
   - tqdm >=4.46.1
   - xdg
-  - xgboost >=1.0.2
+  #  - xgboost >=1.0.2            # optional: xgboost regressor for MOAP (1 GB)

.travis.yml

@@ -14,16 +14,14 @@ env:
 
 before_install:
   # setup miniconda
-#  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-  - wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.11.0-Linux-x86_64.sh -O miniconda.sh
+  - 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
 
 install:
-#  - conda install conda-forge::mamba
-  - conda install -c conda-forge conda=4.11.0 mamba=0.20.0  # conda/mamba issue
+  - 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

CHANGELOG.md

@@ -7,6 +7,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Changed
 
+- made xgboost an optional dependency (to save space on bioconda)
 - an existing config will now update available tools when accessed (e4b3275)
 - applied the bioconda patch to compile_externals.py (11b0c2c)
 - `coverage_table` and `combine_peaks` have their positional arguments under positional arguments (20819ee)
@@ -15,10 +16,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 ### Fixed
 
 - biofluff dependency back in requirements
-- pinned conda and mamba versions in `.travis.yaml` 
+- pinned conda and mamba versions in `.travis.yaml`
   - temp fix until conda>=4.12 can install mamba properly
 - documentation is working again!
-- code in gimmemotifs.report now supports pandas >=1.30
+- gimmemotifs now supports pandas >=1.30
 
 ### Removed