diff --git a/nfdocs-parser.py b/nfdocs-parser.py index 1cd586b..4f864f8 100755 --- a/nfdocs-parser.py +++ b/nfdocs-parser.py @@ -1,10 +1,12 @@ #!/usr/bin/env python -import sys import yaml from docutils import nodes from docutils.parsers.rst import Directive +from docutils.parsers.rst import directives class NFDocs(Directive): + # Class default overrides + required_arguments = 1 # Declare the docstring starting characters DOC_STARTER = "/// " @@ -37,7 +39,7 @@ class NFDocs(Directive): tuple_item += nodes.paragraph(text="Tuple:") tuple_list = nodes.bullet_list() for io in params["tuple"]: - tuple_list += params_to_list(io) + tuple_list += self.params_to_list(io) tuple_item += tuple_list return tuple_item else: @@ -48,75 +50,76 @@ class NFDocs(Directive): io_item += nodes.paragraph(text=params["description"]) return io_item - # Take path as single argument for now - nextflow_path = sys.argv[1] - with open(nextflow_path) as nextflow_file: + def run(self): + # Take path as single argument for now + nextflow_path = self.arguments[0] + with open(nextflow_path) as nextflow_file: - # Split by lines - nextflow_lines = nextflow_file.readlines() + # Split by lines + nextflow_lines = nextflow_file.readlines() - # Declare some variables to keep track of where the docstrings begin and end - doc_start = 0 - doc_end = 0 + # Declare some variables to keep track of where the docstrings begin and end + doc_start = 0 + doc_end = 0 - # Declare dictionaries to keep track of the docstrings - docstring_positions = [] + # Declare dictionaries to keep track of the docstrings + docstring_positions = [] - # Calculate the start and end positions of each docstring - for i, line in enumerate(nextflow_lines): - # Check if this is a docstring - if line.startswith(DOC_STARTER): - # It is: check the next and previous lines to see if this is part of a block - line_previous = nextflow_lines[i-1] - line_next = nextflow_lines[i+1] - if not line_previous.startswith(DOC_STARTER): - doc_start = i - if not line_next.startswith(DOC_STARTER): - doc_end = i + # Calculate the start and end positions of each docstring + for i, line in enumerate(nextflow_lines): + # Check if this is a docstring + if line.startswith(self.DOC_STARTER): + # It is: check the next and previous lines to see if this is part of a block + line_previous = nextflow_lines[i-1] + line_next = nextflow_lines[i+1] + if not line_previous.startswith(self.DOC_STARTER): + doc_start = i + if not line_next.startswith(self.DOC_STARTER): + doc_end = i - # Check if we've reached the end of a docstring block - if doc_end == i: - # Add this docstring position to the array - docstring_positions.append(range(doc_start, doc_end+1)) + # Check if we've reached the end of a docstring block + if doc_end == i: + # Add this docstring position to the array + docstring_positions.append(range(doc_start, doc_end+1)) - # Create dictionaries for each of the block types - docstrings = { - "process": {}, - "workflow": {}, - "function": {} - } + # Create dictionaries for each of the block types + docstrings = { + "process": {}, + "workflow": {}, + "function": {} + } - # Parse out the docstrings and put them in the appropriate dictionary - for pos in docstring_positions: - proc_name, proc_type = definition_type(nextflow_lines[pos[-1]+1]) - doc_yaml = "" - for i in pos: - doc_yaml = doc_yaml + nextflow_lines[i].replace(DOC_STARTER, "") - docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml) + # Parse out the docstrings and put them in the appropriate dictionary + for pos in docstring_positions: + proc_name, proc_type = self.definition_type(nextflow_lines[pos[-1]+1]) + doc_yaml = "" + for i in pos: + doc_yaml = doc_yaml + nextflow_lines[i].replace(self.DOC_STARTER, "") + docstrings[proc_type][proc_name] = yaml.safe_load(doc_yaml) - # Create any array to return from the plugin - return_nodes = [] + # Create any array to return from the plugin + return_nodes = [] - # Try to convert each definition to a node - for block_type, block_docs in docstrings.items(): - block_section = nodes.section() - block_section += nodes.title(text=block_type) - for proc_name, proc_docs in block_docs.items(): - proc_section = nodes.section() - proc_section += nodes.title(text=proc_name) - proc_section += nodes.paragraph(text=proc_docs["summary"]) - io_methods = ["input", "output"] - for met in io_methods: - if met in proc_docs.keys(): - io_section = nodes.section() - io_section += nodes.title(text=met) - io_list = nodes.bullet_list() - for io in proc_docs[met]: - io_list += params_to_list(io) - io_section += io_list - proc_section += io_section - block_section += proc_section + # Try to convert each definition to a node + for block_type, block_docs in docstrings.items(): + block_section = nodes.section() + block_section += nodes.title(text=block_type) + for proc_name, proc_docs in block_docs.items(): + proc_section = nodes.section() + proc_section += nodes.title(text=proc_name) + proc_section += nodes.paragraph(text=proc_docs["summary"]) + io_methods = ["input", "output"] + for met in io_methods: + if met in proc_docs.keys(): + io_section = nodes.section() + io_section += nodes.title(text=met) + io_list = nodes.bullet_list() + for io in proc_docs[met]: + io_list += self.params_to_list(io) + io_section += io_list + proc_section += io_section + block_section += proc_section - return_nodes.append(block_section) + return_nodes.append(block_section) - print(return_nodes) + return return_nodes