refactoring for packaging and tests (#1)

* refactoring for packaging and tests
* added CI for testing and packaging

.github/workflows/python-package.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --builtins=snakemake
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --builtins=snakemake
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

MANIFEST.in

@@ -0,0 +1,3 @@
+recursive-include denoise_fmri/resources *
+recursive-include denoise_fmri/config *
+recursive-include denoise_fmri/workflow *

README.md → README.rst

@@ -1,4 +1,5 @@
-# snakebids app for denoising fmriprep output
+denoise-fmri
+============
 
 Known issues:
  - pybids has an incompatibility with the latest fmriprep (20.2.0) dataset_description.json, need to replace this with the version in resources/dataset_description.json for now 

denoise_fmri/pipeline_description.json

@@ -0,0 +1,15 @@
+{
+    "Name": "denoise_fmri - BIDS app for denoising fmriprep outputs",
+    "BIDSVersion": "1.4.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "denoise_fmri",
+            "Version": "0.1.0",
+            "CodeURL": "http://github.com/akhanf/denoise-fmri",
+            "Author": "Ali Khan",
+            "AuthorEmail": "[email protected]"
+
+        }
+    ]
+}

run.py → denoise_fmri/run.py

@@ -3,8 +3,13 @@
 from snakebids.app import SnakeBidsApp
 
 
-def main():
+def get_parser():
+    """Exposes parser for sphinx doc generation, cwd is the docs dir"""
+    app = SnakeBidsApp('../denoise_fmri',skip_parse_args=True)
+    return app.parser
+
 
+def main():
     app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__)))
     app.run_snakemake()
 

docs/.gitignore

@@ -0,0 +1 @@
+_build

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+import sphinx_rtd_theme
+
+
+# -- Project information -----------------------------------------------------
+
+
+project = 'app_name'
+copyright = '2020, Authors here'
+author = 'Authors here'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx_rtd_theme",
+    "sphinxarg.ext",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+master_doc = 'index'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+
+

docs/getting_started/installation.rst

@@ -0,0 +1,56 @@
+Installation
+============
+
+Template snakebids BIDS App 
+
+
+Requirements
+------------
+
+Docker (Mac/Windows/Linux) or Singularity (Linux)
+
+Docker:
+^^^^^^^
+
+Pull the container:
+
+.. code-block::
+
+   docker pull khanlab/app_name:latest
+
+do a dry run, printing the command at each step:
+
+.. code-block::
+
+   docker run -it --rm -v PATH_TO_BIDS_DIR:/bids:ro -v PATH_TO_OUTPUT_DIR:/output khanlab/app_name:latest /bids /output participant -np 
+
+run it with maximum number of cores:
+
+.. code-block::
+
+   docker run -it --rm -v PATH_TO_BIDS_DIR:/bids:ro -v PATH_TO_OUTPUT_DIR:/output khanlab/app_name:latest /bids /output participant -p --cores all
+
+
+Singularity:
+^^^^^^^^^^^^
+
+Pull the container:
+
+.. code-block::
+
+   singularity pull khanlab_app_name_latest.sif docker://khanlab/app_name:latest
+
+do a dry run, printing the command at each step:
+
+.. code-block::
+
+   singularity run -e khanlab_app_name_latest.sif khanlab/app_name:latest PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant -np 
+
+run it with maximum number of cores:
+
+.. code-block::
+
+   singularity run -e khanlab_app_name_latest.sif khanlab/app_name:latest PATH_TO_BIDS_DIR PATH_TO_OUTPUT_DIR participant  -p --cores all
+
+
+

docs/index.rst

@@ -0,0 +1,32 @@
+.. hippunfold documentation master file, created by
+   sphinx-quickstart on Thu Jul 30 10:15:34 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. include:: ../README.rst
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+
+.. toctree::
+   :caption: Getting started
+   :name: getting_started
+   :hidden:
+   :maxdepth: 1
+
+   getting_started/installation
+
+.. toctree::
+  :caption: Usage 
+  :name: usage
+  :hidden:
+  :maxdepth: 1
+
+  usage/app_cli
+  usage/snakemake_cli
+
+
+
+

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx-argparse
+sphinx_rtd_theme
+snakebids==0.2.0

docs/usage/app_cli.rst

@@ -0,0 +1,9 @@
+Command line interface
+--------------------
+
+.. argparse::
+   :filename: ../app_name/run.py
+   :func: get_parser
+   :prog: hippunfold
+
+

docs/usage/snakemake_cli.rst

@@ -0,0 +1,9 @@
+Snakemake Command line interface
+________________________________
+
+.. argparse::
+   :module: snakemake
+   :func: get_argument_parser
+   :prog: snakemake
+
+

requirements.txt

@@ -0,0 +1,48 @@
+amply==0.1.4
+appdirs==1.4.4
+attrs==20.3.0
+bids-validator==1.5.8
+certifi==2020.12.5
+chardet==3.0.4
+click==7.1.2
+ConfigArgParse==1.2.3
+datrie==0.8.2
+docopt==0.6.2
+docutils==0.16
+gitdb==4.0.5
+GitPython==3.1.11
+idna==2.10
+ipython-genutils==0.2.0
+joblib==1.0.0
+jsonschema==3.2.0
+jupyter-core==4.7.0
+nbformat==5.0.8
+nibabel==3.2.1
+nilearn==0.7.0
+num2words==0.5.10
+numpy==1.19.4
+packaging==20.8
+pandas==1.1.5
+patsy==0.5.1
+psutil==5.7.3
+PuLP==2.3.1
+pybids==0.12.3
+pyparsing==2.4.7
+pyrsistent==0.17.3
+python-dateutil==2.8.1
+pytz==2020.4
+PyYAML==5.3.1
+ratelimiter==1.2.0.post0
+requests==2.25.0
+scikit-learn==0.23.2
+scipy==1.5.4
+six==1.15.0
+smmap==3.0.4
+snakebids==0.2.0
+snakemake==5.30.1
+SQLAlchemy==1.3.20
+threadpoolctl==2.1.0
+toposort==1.5
+traitlets==5.0.5
+urllib3==1.26.2
+wrapt==1.12.1