Remove doit support (Now using snakemake instead)

dodo.py

@@ -1,184 +0,0 @@
-#!/usr/bin/env doit -f
-# -*- coding: utf-8; -*-
-
-from collections import Iterable, Mapping  # in Python 3 use from collections.abc
-from distutils.spawn import find_executable
-from fnmatch import fnmatch
-from kwonly import kwonly
-from subprocess import check_output
-from types import StringTypes
-import os.path
-import regex
-
-try:
-    from os import scandir, walk
-except ImportError:
-    from scandir import scandir, walk
-
-DOIT_CONFIG = {
-    'default_tasks': ['publish'],
-}
-
-def unnest(*args):
-    """Un-nest list- and tuple-like elements in arguments.
-
-"List-like" means anything with a len() and whose elments can be
-accessed with numeric indexing, except for string-like elements. It
-must also be an instance of the collections.Iterable abstract class.
-Dict-like elements and iterators/generators are not affected.
-
-This function always returns a list, even if it is passed a single
-scalar argument.
-
-    """
-    result = []
-    for arg in args:
-        if isinstance(arg, StringTypes):
-            # String
-            result.append(arg)
-        elif isinstance(arg, Mapping):
-            # Dict-like
-            result.append(arg)
-        elif isinstance(arg, Iterable):
-            try:
-                # Duck-typing test for list-ness (a stricter condition
-                # than just "iterable")
-                for i in xrange(len(arg)):
-                    result.append(arg[i])
-            except TypeError:
-                # Iterable but not list-like
-                result.append(arg)
-        else:
-            # Not iterable
-            result.append(arg)
-    return result
-
-def find_mac_app(name):
-    try:
-        return check_output(
-            ["mdfind",
-             "kMDItemDisplayName=={name}&&kMDItemKind==Application".format(name=name)]).split("\n")[0]
-    except Exception:
-        return None
-
-def glob_recursive(pattern, top=".", include_hidden=False, *args, **kwargs):
-    """Combination of glob.glob and os.walk.
-
-Reutrns the relative path to every file or directory matching the
-pattern anywhere in the specified directory hierarchy. Defaults to the
-current working directory. Any additional arguments are passed to
-os.walk."""
-    for (path, dirs, files) in walk(top, *args, **kwargs):
-        for f in dirs + files:
-            if include_hidden or f.startswith("."):
-                continue
-            if fnmatch(f, pattern):
-                yield os.path.normpath(os.path.join(path, f))
-
-LYXPATH = find_executable("lyx") or \
-    os.path.join(find_mac_app("LyX"), "Contents/MacOS/lyx") or \
-    '/bin/false'
-
-@kwonly(0)
-def rsync_list_files(extra_rsync_args=(), include_dirs=False, *paths):
-    """Iterate over the files in path that rsync would copy.
-
-By default, only files are listed, not directories, since doit doesn't
-like dependencies on directories because it can't hash them.
-
-This uses "rsync --list-only" to make rsync directly indicate which
-files it would copy, so any exclusion/inclusion rules are taken into
-account.
-
-    """
-    rsync_list_cmd = [ 'rsync', '-r', "--list-only" ] + unnest(extra_rsync_args) + unnest(paths) + [ "." ]
-    rsync_out = check_output(rsync_list_cmd).splitlines()
-    for line in rsync_out:
-        s = regex.search("^(-|d)(?:\S+\s+){4}(.*)", line)
-        if s is not None:
-            if include_dirs or s.group(1) == '-':
-                yield s.group(2)
-
-rsync_common_args = ["-rL", "--size-only", "--delete", "--delete-excluded",
-                     "--exclude", ".DS_Store", "--exclude", ".#*" ]
-
-def task_lyx2pdf():
-    yield {
-        'name': None,
-        'doc': "Convert LyX file to PDF."
-    }
-    for lyxfile in glob_recursive("*.lyx"):
-        pdffile = lyxfile[:-3] + "pdf"
-        lyx_cmd = [LYXPATH, "--export-to", "pdf4" , pdffile, lyxfile]
-        yield {
-            'name': lyxfile,
-            'actions': [lyx_cmd],
-            # Assume every bib file is a dependency of any LaTeX
-            # operation
-            'file_dep': [lyxfile] + list(glob_recursive('*.bib')),
-            'targets': [pdffile],
-            'verbosity': 0,
-            'clean': True,
-        }
-
-def task_readme2index():
-    yield {
-        'name': None,
-        'doc': "Convert README.mkdn files to index.html."
-    }
-    for mkdnfile in glob_recursive("README.mkdn", top="examples"):
-        htmlfile = os.path.join(os.path.dirname(mkdnfile), "index.html")
-        yield {
-            'name': mkdnfile,
-            'actions': [["pandoc", "-t", "html", "-o", htmlfile, mkdnfile]],
-            'file_dep': [mkdnfile],
-            'targets': [htmlfile],
-            'clean': True,
-        }
-
-def task_publish():
-    yield {
-        'name': None,
-        'doc': "Sync resume and supporting files to my web server."
-    }
-    # Resume PDF file
-    rsync_src = "ryan_thompson_resume.pdf"
-    rsync_dest = "mneme:public_html/resume/"
-    file_deps = [rsync_src]
-    rsync_xfer_cmd = ["rsync"] + rsync_common_args + [ rsync_src, rsync_dest ]
-    yield {
-        'name': rsync_src,
-        'actions': [rsync_xfer_cmd],
-        'file_dep': file_deps,
-        'task_dep': [ 'lyx2pdf' ],
-        'doc': "rsync resume PDF file to my web server.",
-        'verbosity': 2,
-    }
-    # Examples directory
-    rsync_src = "examples"
-    rsync_dest = "mneme:public_html/resume/"
-    file_deps = list(rsync_list_files(rsync_src, extra_rsync_args=rsync_common_args))
-    # Ensure the generated html files are in file_deps
-    for f in file_deps:
-        if os.path.basename(f) == "README.mkdn":
-            htmlfile = os.path.join(os.path.dirname(f), "index.html")
-            if htmlfile not in file_deps:
-                file_deps.append(htmlfile)
-    file_deps = sorted(file_deps)
-    rsync_xfer_cmd = ["rsync"] + rsync_common_args + [ rsync_src, rsync_dest ]
-    yield {
-        'name': rsync_src,
-        'actions': [rsync_xfer_cmd],
-        'file_dep': file_deps,
-        'task_dep': [ 'readme2index' ],
-        'doc': "rsync examples directory to my web server.",
-        'verbosity': 2,
-    }
-
-# Dummy target if you just want to build everything but not publish
-def task_build():
-    return {
-        'doc': 'Build resume and supporting files.',
-        'task_dep': [ 'lyx2pdf', 'readme2index' ],
-        'actions': [],
-    }