Merge pull request #3 from akhanf/dev-0.2.0

updates for 0.2.0

requirements.txt

@@ -0,0 +1,43 @@
+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
+jsonschema==3.2.0
+jupyter-core==4.7.0
+nbformat==5.0.8
+nibabel==3.2.1
+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
+scipy==1.5.4
+six==1.15.0
+smmap==3.0.4
+snakemake==5.30.1
+SQLAlchemy==1.3.20
+toposort==1.5
+traitlets==5.0.5
+urllib3==1.26.2
+wrapt==1.12.1

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="snakebids", 
-    version="0.1.5",
+    version="0.2.0",
     author="Ali Khan",
     author_email="[email protected]",
     description="BIDS integration into snakemake workflows",

snakebids/app.py

@@ -57,7 +57,7 @@ def run(command, env={}):
 
 class SnakeBidsApp:
 
-    def __init__(self, snakemake_dir):
+    def __init__(self, snakemake_dir, skip_parse_args=False):
 
         #input argument is the dir where snakemake would be run
         # we use this to locate the config file, and snakefile adding them to generated_config
@@ -95,27 +95,32 @@ def __init__(self, snakemake_dir):
 
 
 
-
-        self.parse_args()
+        self.__load_config()
 
         #add path to snakefile to the config -- so workflows can grab files relative to the snakefile folder  
         self.config['snakemake_dir'] = snakemake_dir
 
-        self.write_updated_config()
+        self.parser = self.__create_parser()
 
+        if not skip_parse_args:
+            self.__parse_args()
 
 
-
 
-    def parse_args(self):
-
-        #replace with proper name of pipeline here
-        parser = argparse.ArgumentParser(description='snakebids-app')
+    def __load_config(self):
 
         #load up workflow config file
         with open(self.snakebids_config, 'r') as infile:
             self.config = yaml.load(infile, Loader=yaml.FullLoader)
 
+
+
+
+    def __create_parser(self):      
+
+        #replace with proper name of pipeline here
+        parser = argparse.ArgumentParser(description='snakebids-app')
+
         #update the parser with config options
         for name, parse_args in self.config['parse_args'].items():
             parser.add_argument(name, **parse_args)
@@ -133,14 +138,17 @@ def parse_args(self):
                                 help=f'Filters (PyBIDS) for {input_type}, where {arginstance} is '
                                        f'key=value pair(s) (default: {arglist_default_string})')
 
+        return parser
+
+
+    def __parse_args(self):
+
 
-        all_args = parser.parse_known_args()
+        all_args = self.parser.parse_known_args()
 
         args = all_args[0]
         snakemake_args = all_args[1]
 
-
-
 
         #add arguments to config
         self.config.update(args.__dict__)
@@ -160,7 +168,8 @@ def parse_args(self):
         self.config['output_dir'] = os.path.realpath(self.config['output_dir'])
 
 
-    def write_updated_config(self):
+
+    def __write_updated_config(self):
         #create an updated snakebids config file
         self.updated_config = os.path.join(self.config['output_dir'],'config','snakebids.yml')
 
@@ -176,6 +185,9 @@ def write_updated_config(self):
     #workflow snakefile will read snakebids config, create inputs_config, read that in
     def run_snakemake(self):
 
+        #write updated config
+        self.__write_updated_config()
+
         # running the chosen participant level
 
         analysis_level = self.config['analysis_level']

snakebids/tests/test_bids.py

@@ -0,0 +1,6 @@
+from ..  import bids
+
+def test_bids_subj():
+    assert bids(root='bids',subject='001',suffix='T1w.nii.gz') == 'bids/sub-001/sub-001_T1w.nii.gz'
+
+

template_app/README.rst

@@ -0,0 +1,4 @@
+Template App
+============
+
+Description of app goes here

template_app/pipeline_description.json → template_app/app_name/pipeline_description.json

@@ -4,9 +4,12 @@
     "DatasetType": "derivative",
     "GeneratedBy": [
         {
-            "Name": "appname",
+            "Name": "app_name",
             "Version": "0.1.0",
-            "CodeURL": "http://github.com/org/name"
+            "CodeURL": "http://github.com/org/name",
+            "Author": "Author name here",
+            "AuthorEmail": "Author email"
+
         }
     ]
 }

template_app/run.py → template_app/app_name/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('../app_name',skip_parse_args=True)
+    return app.parser
+
 
+def main():
     app = SnakeBidsApp(os.path.abspath(os.path.dirname(__file__)))
     app.run_snakemake()
 

template_app/docs/.gitignore

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

template_app/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)

template_app/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']
+
+
+
+

template_app/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
+
+
+

template_app/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
+
+
+
+

template_app/docs/requirements.txt

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

template_app/docs/usage/app_cli.rst

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

template_app/docs/usage/snakemake_cli.rst

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