From 335c1e9454f0fbfea43a0f9e00663698ed5b921d Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 12:09:14 -0800 Subject: [PATCH 1/8] updated docs --- binder/postBuild | 3 +++ .../R_integration_guide/DESeq2_GeneSets.ipynb | 13 +++++++--- .../R_integration_guide/EdgeR_GeneSets.ipynb | 25 ++++++++++++++----- .../R_GEM_normalizations.ipynb | 25 ++++++++++++++----- 4 files changed, 51 insertions(+), 15 deletions(-) create mode 100644 binder/postBuild diff --git a/binder/postBuild b/binder/postBuild new file mode 100644 index 0000000..a200839 --- /dev/null +++ b/binder/postBuild @@ -0,0 +1,3 @@ +#!/bin/bash +GSFORGE_DEMO_DATA="${HOME}/GSForge_demo_data" +osf -p rbhfz clone "$GSFORGE_DEMO_DATA" diff --git a/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb b/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb index 077ef43..3280822 100644 --- a/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb +++ b/examples/user_guide/R_integration_guide/DESeq2_GeneSets.ipynb @@ -4,8 +4,6 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# DESeq2 Integration\n", - "\n", "*This notebook covers how to run and load a basic `DESeq2` DEG result as a `GSForge.GeneSet`.*\n", "\n", "---" @@ -393,8 +391,17 @@ "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.3" + }, + "pycharm": { + "stem_cell": { + "cell_type": "raw", + "source": [], + "metadata": { + "collapsed": false + } + } } }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb b/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb index 409f046..08710e0 100644 --- a/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb +++ b/examples/user_guide/R_integration_guide/EdgeR_GeneSets.ipynb @@ -1,11 +1,15 @@ { "cells": [ { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] + "cell_type": "markdown", + "metadata": { + "pycharm": { + "name": "#%% md\n" + } + }, + "source": [ + "Coming soon..." + ] } ], "metadata": { @@ -25,8 +29,17 @@ "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.3" + }, + "pycharm": { + "stem_cell": { + "cell_type": "raw", + "source": [], + "metadata": { + "collapsed": false + } + } } }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb b/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb index 409f046..42ef6aa 100644 --- a/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb +++ b/examples/user_guide/R_integration_guide/R_GEM_normalizations.ipynb @@ -1,11 +1,15 @@ { "cells": [ { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] + "cell_type": "markdown", + "metadata": { + "pycharm": { + "name": "#%% md\n" + } + }, + "source": [ + "Coming soon...\n" + ] } ], "metadata": { @@ -25,8 +29,17 @@ "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.3" + }, + "pycharm": { + "stem_cell": { + "cell_type": "raw", + "source": [], + "metadata": { + "collapsed": false + } + } } }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file From 59b617c7c366af0bde4de592a9cc37f63dcaf78f Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 12:14:51 -0800 Subject: [PATCH 2/8] binder and doc updates --- binder/postBuild | 1 + doc/user_guide/index.rst | 3 --- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/binder/postBuild b/binder/postBuild index a200839..345cd15 100644 --- a/binder/postBuild +++ b/binder/postBuild @@ -1,3 +1,4 @@ #!/bin/bash GSFORGE_DEMO_DATA="${HOME}/GSForge_demo_data" +pip install osfclient osf -p rbhfz clone "$GSFORGE_DEMO_DATA" diff --git a/doc/user_guide/index.rst b/doc/user_guide/index.rst index 5bc653d..449e7a8 100644 --- a/doc/user_guide/index.rst +++ b/doc/user_guide/index.rst @@ -2,9 +2,6 @@ User Guide ********** -*Under Construction...* - - Getting Started --------------- From 011ef76e61bdb940247e5b6d7d7511184f1e61bf Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 13:29:17 -0800 Subject: [PATCH 3/8] binder battles --- binder/setup.py | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 binder/setup.py diff --git a/binder/setup.py b/binder/setup.py new file mode 100644 index 0000000..c1434be --- /dev/null +++ b/binder/setup.py @@ -0,0 +1,40 @@ +from setuptools import setup, find_packages + +setup( + name='GSForge', + version='0.2', + packages=find_packages(), + url='https://systemsgenetics.github.io/GSForge/', + license='LICENSE.txt', + author='Tyler Biggs', + author_email='tyler.biggs@wsu.edu', + description='Feature (gene) selection package for gene expression data.', + install_requires="""\ +Boruta +bokeh +click +datashader +h5py +holoviews +jupyter +matplotlib +methodtools +netcdf4 +numpy +pandas +panel +param +scikit-learn +scipy +seaborn +statsmodels +tqdm +umap_learn +xarray""".split(), + # + # ['boruta', 'umap_learn', 'h5py', 'netcdf4', + # 'xarray', 'pandas', 'numpy', 'lightgbm', + # 'param', 'scipy', 'scikit-learn', 'click', + # 'methodtools', 'datashader', 'seaborn'], +) + From 95e670784924e4b814dd6c2dd695c7a6d48c7f19 Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 13:40:55 -0800 Subject: [PATCH 4/8] more binder reqs... --- binder/setup.py | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/binder/setup.py b/binder/setup.py index c1434be..a76398c 100644 --- a/binder/setup.py +++ b/binder/setup.py @@ -1,15 +1,6 @@ from setuptools import setup, find_packages -setup( - name='GSForge', - version='0.2', - packages=find_packages(), - url='https://systemsgenetics.github.io/GSForge/', - license='LICENSE.txt', - author='Tyler Biggs', - author_email='tyler.biggs@wsu.edu', - description='Feature (gene) selection package for gene expression data.', - install_requires="""\ +requirements = """\ Boruta bokeh click @@ -30,11 +21,18 @@ statsmodels tqdm umap_learn -xarray""".split(), - # - # ['boruta', 'umap_learn', 'h5py', 'netcdf4', - # 'xarray', 'pandas', 'numpy', 'lightgbm', - # 'param', 'scipy', 'scikit-learn', 'click', - # 'methodtools', 'datashader', 'seaborn'], +xarray""".split() + +setup( + name='GSForge', + version='0.2', + packages=find_packages(), + url='https://systemsgenetics.github.io/GSForge/', + license='LICENSE.txt', + author='Tyler Biggs', + author_email='tyler.biggs@wsu.edu', + description='Feature (gene) selection package for gene expression data.', + python_requires='>3.6', + install_requires=requirements, ) From 805edab0ba794dee6a61e9f74517a8f6e27f25f5 Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 13:41:38 -0800 Subject: [PATCH 5/8] more binder reqs --- binder/environment.yml | 28 ++++++++++++++++++++++++++++ binder/setup.py | 38 -------------------------------------- setup.py | 30 ++++++++++++++---------------- 3 files changed, 42 insertions(+), 54 deletions(-) create mode 100644 binder/environment.yml delete mode 100644 binder/setup.py diff --git a/binder/environment.yml b/binder/environment.yml new file mode 100644 index 0000000..fb3178f --- /dev/null +++ b/binder/environment.yml @@ -0,0 +1,28 @@ +name: GSForge +channels: + - conda-forge +dependencies: + - python=3.7 + - boruta_py + - bokeh + - click + - datashader + - h5py + - holoviews + - jupyter + - matplotlib + - netcdf4 + - numpy + - pandas + - panel + - param + - scikit-learn + - scipy + - seaborn + - statsmodels + - tqdm + - umap-learn + - pip + - pip: + - methodtools + - git+https://github.com/SystemsGenetics/GSForge diff --git a/binder/setup.py b/binder/setup.py deleted file mode 100644 index a76398c..0000000 --- a/binder/setup.py +++ /dev/null @@ -1,38 +0,0 @@ -from setuptools import setup, find_packages - -requirements = """\ -Boruta -bokeh -click -datashader -h5py -holoviews -jupyter -matplotlib -methodtools -netcdf4 -numpy -pandas -panel -param -scikit-learn -scipy -seaborn -statsmodels -tqdm -umap_learn -xarray""".split() - -setup( - name='GSForge', - version='0.2', - packages=find_packages(), - url='https://systemsgenetics.github.io/GSForge/', - license='LICENSE.txt', - author='Tyler Biggs', - author_email='tyler.biggs@wsu.edu', - description='Feature (gene) selection package for gene expression data.', - python_requires='>3.6', - install_requires=requirements, -) - diff --git a/setup.py b/setup.py index c1434be..a76398c 100644 --- a/setup.py +++ b/setup.py @@ -1,15 +1,6 @@ from setuptools import setup, find_packages -setup( - name='GSForge', - version='0.2', - packages=find_packages(), - url='https://systemsgenetics.github.io/GSForge/', - license='LICENSE.txt', - author='Tyler Biggs', - author_email='tyler.biggs@wsu.edu', - description='Feature (gene) selection package for gene expression data.', - install_requires="""\ +requirements = """\ Boruta bokeh click @@ -30,11 +21,18 @@ statsmodels tqdm umap_learn -xarray""".split(), - # - # ['boruta', 'umap_learn', 'h5py', 'netcdf4', - # 'xarray', 'pandas', 'numpy', 'lightgbm', - # 'param', 'scipy', 'scikit-learn', 'click', - # 'methodtools', 'datashader', 'seaborn'], +xarray""".split() + +setup( + name='GSForge', + version='0.2', + packages=find_packages(), + url='https://systemsgenetics.github.io/GSForge/', + license='LICENSE.txt', + author='Tyler Biggs', + author_email='tyler.biggs@wsu.edu', + description='Feature (gene) selection package for gene expression data.', + python_requires='>3.6', + install_requires=requirements, ) From f961dfdd5a3abc569348055c988a3f67e13050fd Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 13:43:20 -0800 Subject: [PATCH 6/8] binder go --- setup.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/setup.py b/setup.py index a76398c..dc00439 100644 --- a/setup.py +++ b/setup.py @@ -32,7 +32,6 @@ author='Tyler Biggs', author_email='tyler.biggs@wsu.edu', description='Feature (gene) selection package for gene expression data.', - python_requires='>3.6', + python_requires='>3.7', install_requires=requirements, ) - From f4e17f0c6b48a3459de557318e65b672c5b31254 Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 14:21:53 -0800 Subject: [PATCH 7/8] notebook for binder --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index fbc9617..7d741b2 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,6 @@ [![Build Status](https://travis-ci.com/SystemsGenetics/GSForge.svg?branch=master)](https://travis-ci.com/SystemsGenetics/GSForge) +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/SystemsGenetics/GSForge/master?filepath=examples%2FWelcome.ipynb) + # GSForge From 872bb0f9b6733fcbe78420b8e9b534575cc3c5f0 Mon Sep 17 00:00:00 2001 From: Tyler Date: Tue, 7 Jan 2020 14:22:59 -0800 Subject: [PATCH 8/8] updated readme --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 7d741b2..d892df7 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ [![Build Status](https://travis-ci.com/SystemsGenetics/GSForge.svg?branch=master)](https://travis-ci.com/SystemsGenetics/GSForge) -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/SystemsGenetics/GSForge/master?filepath=examples%2FWelcome.ipynb) - +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/SystemsGenetics/GSForge/master?filepath=examples%2Fuser_guide.ipynb) # GSForge