Merge pull request #50 from aCLImatise/rename-aclimatise

Rename acclimatise to aclimatise

Author: multimeric

acclimatise/__init__.py aclimatise/__init__.pyacclimatise/__init__.py renamed to aclimatise/__init__.py

@@ -7,17 +7,17 @@
 import psutil
 from pyparsing import ParseBaseException
 
-from acclimatise.converter import WrapperGenerator
-from acclimatise.converter.cwl import CwlGenerator
-from acclimatise.converter.wdl import WdlGenerator
-from acclimatise.converter.yml import YmlGenerator
-from acclimatise.execution import Executor
-from acclimatise.execution.local import LocalExecutor
-from acclimatise.flag_parser.parser import CliParser
-from acclimatise.model import Command, Flag
-from acclimatise.usage_parser.parser import UsageParser
-
-logger = logging.getLogger("acclimatise")
+from aclimatise.converter import WrapperGenerator
+from aclimatise.converter.cwl import CwlGenerator
+from aclimatise.converter.wdl import WdlGenerator
+from aclimatise.converter.yml import YmlGenerator
+from aclimatise.execution import Executor
+from aclimatise.execution.local import LocalExecutor
+from aclimatise.flag_parser.parser import CliParser
+from aclimatise.model import Command, Flag
+from aclimatise.usage_parser.parser import UsageParser
+
+logger = logging.getLogger("aclimatise")
 
 default_executor = LocalExecutor()
 

acclimatise/cli.py aclimatise/cli.pyacclimatise/cli.py renamed to aclimatise/cli.py

@@ -1,14 +1,14 @@
 """
-Code relating to the command line interface to acclimatise
+Code relating to the command line interface to aCLImatise
 """
 import sys
 from pathlib import Path
 from typing import Iterable, Tuple
 
 import click
 
-from acclimatise import WrapperGenerator, best_cmd, explore_command, parse_help
-from acclimatise.flag_parser.parser import CliParser
+from aclimatise import WrapperGenerator, best_cmd, explore_command, parse_help
+from aclimatise.flag_parser.parser import CliParser
 
 # Some common options
 opt_pos = click.option(

acclimatise/cli_types.py aclimatise/cli_types.pyacclimatise/cli_types.py renamed to aclimatise/cli_types.py

@@ -6,8 +6,8 @@
 
 from dataclasses import dataclass
 
-from acclimatise.model import CliArgument, Command, Flag
-from acclimatise.name_generation import (
+from aclimatise.model import CliArgument, Command, Flag
+from aclimatise.name_generation import (
     NameGenerationError,
     choose_unique_name,
     generate_name,
@@ -117,7 +117,7 @@ def choose_variable_names(
         """
         Choose names for a list of flags. This needs to be done in one go because there is a risk of duplicate
         variable names otherwise
-        :param length: See :py:func:`acclimatise.name_generation.generate_name`
+        :param length: See :py:func:`from aclimatise.name_generation.generate_name`
         """
         options = list(
             zip_longest(

acclimatise/converter/__init__.py aclimatise/converter/__init__.pyacclimatise/converter/__init__.py renamed to aclimatise/converter/__init__.py

@@ -14,10 +14,10 @@
 )
 from dataclasses import dataclass
 
-from acclimatise import cli_types
-from acclimatise.converter import NamedArgument, WrapperGenerator
-from acclimatise.model import CliArgument, Command, Flag, Positional
-from acclimatise.yaml import yaml
+from aclimatise import cli_types
+from aclimatise.converter import NamedArgument, WrapperGenerator
+from aclimatise.model import CliArgument, Command, Flag, Positional
+from aclimatise.yaml import yaml
 
 
 @dataclass

acclimatise/converter/cwl.py aclimatise/converter/cwl.pyacclimatise/converter/cwl.py renamed to aclimatise/converter/cwl.py

@@ -19,10 +19,10 @@
     WdlType,
 )
 
-from acclimatise import cli_types, model
-from acclimatise.converter import NamedArgument, WrapperGenerator
-from acclimatise.model import CliArgument, Command, Flag, Positional
-from acclimatise.nlp import wordsegment
+from aclimatise import cli_types, model
+from aclimatise.converter import NamedArgument, WrapperGenerator
+from aclimatise.model import CliArgument, Command, Flag, Positional
+from aclimatise.nlp import wordsegment
 
 #: A regex, borrowed from MiniWDL, that ma
 WDL_IDENT = re.compile(r"[a-zA-Z][a-zA-Z0-9_]*")

acclimatise/converter/wdl.py aclimatise/converter/wdl.pyacclimatise/converter/wdl.py renamed to aclimatise/converter/wdl.py

@@ -5,9 +5,9 @@
 
 from dataclasses import dataclass
 
-from acclimatise.converter import WrapperGenerator
-from acclimatise.model import Command
-from acclimatise.yaml import yaml
+from aclimatise.converter import WrapperGenerator
+from aclimatise.model import Command
+from aclimatise.yaml import yaml
 
 
 @dataclass