Use the new module name in tests etc

multimeric · multimeric · commit 76fd89a26288 · 2020-09-16T16:05:16.000+10:00
diff --git a/aclimatise/__init__.py b/aclimatise/__init__.py
@@ -17,7 +17,7 @@
 from aclimatise.model import Command, Flag
 from aclimatise.usage_parser.parser import UsageParser
 
-logger = logging.getLogger("acclimatise")
+logger = logging.getLogger("aclimatise")
 
 default_executor = LocalExecutor()
 
diff --git a/aclimatise/cli.py b/aclimatise/cli.py
@@ -1,5 +1,5 @@
 """
-Code relating to the command line interface to acclimatise
+Code relating to the command line interface to aCLImatise
 """
 import sys
 from pathlib import Path
diff --git a/aclimatise/converter/__init__.py b/aclimatise/converter/__init__.py
@@ -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(
diff --git a/setup.py b/setup.py
@@ -22,7 +22,7 @@
         "dataclasses",
     ],
     python_requires=">=3.6",
-    entry_points={"console_scripts": ["acclimatise = acclimatise.cli:main"]},
+    entry_points={"console_scripts": ["aclimatise = aclimatise.cli:main"]},
     extras_require={
         "dev": [
             "pytest",
diff --git a/test/conftest.py b/test/conftest.py
@@ -3,11 +3,11 @@
 import pytest
 from pkg_resources import resource_filename
 
-from acclimatise.converter.yml import YmlGenerator
-from acclimatise.execution.local import LocalExecutor
-from acclimatise.flag_parser.parser import CliParser
-from acclimatise.usage_parser.parser import UsageParser
-from acclimatise.yaml import yaml
+from aclimatise.converter.yml import YmlGenerator
+from aclimatise.execution.local import LocalExecutor
+from aclimatise.flag_parser.parser import CliParser
+from aclimatise.usage_parser.parser import UsageParser
+from aclimatise.yaml import yaml
 
 
 @pytest.fixture()
diff --git a/test/executors/test_docker.py b/test/executors/test_docker.py
@@ -1,7 +1,7 @@
 import docker
 import pytest
 
-from acclimatise.execution.docker import DockerExecutor
+from aclimatise.execution.docker import DockerExecutor
 
 
 def test_docker(bwamem_help):
diff --git a/test/executors/test_local.py b/test/executors/test_local.py
@@ -1,4 +1,4 @@
-from acclimatise.execution.local import LocalExecutor
+from aclimatise.execution.local import LocalExecutor
 
 from ..util import skip_not_installed
 
diff --git a/test/flags/conftest.py b/test/flags/conftest.py
@@ -1,6 +1,6 @@
 import pytest
 
-from acclimatise.flag_parser.parser import CliParser
+from aclimatise.flag_parser.parser import CliParser
 
 
 @pytest.fixture
diff --git a/test/flags/test_bwa.py b/test/flags/test_bwa.py
@@ -3,9 +3,9 @@
 
 import pytest
 
-from acclimatise import parse_help
-from acclimatise.flag_parser import elements
-from acclimatise.model import Flag, FlagSynonym, OptionalFlagArg
+from aclimatise import parse_help
+from aclimatise.flag_parser import elements
+from aclimatise.model import Flag, FlagSynonym, OptionalFlagArg
 
 
 def test_flag_arg(parser):
diff --git a/test/flags/test_gth.py b/test/flags/test_gth.py
@@ -1,4 +1,4 @@
-from acclimatise.model import Flag
+from aclimatise.model import Flag
 
 
 def test_unindented_flags(parser):
diff --git a/test/flags/test_htseq.py b/test/flags/test_htseq.py
@@ -6,8 +6,8 @@
 
 import pytest
 
-from acclimatise.flag_parser import elements
-from acclimatise.model import EmptyFlagArg, FlagSynonym, RepeatFlagArg
+from aclimatise.flag_parser import elements
+from aclimatise.model import EmptyFlagArg, FlagSynonym, RepeatFlagArg
 
 
 def test_short(parser):
diff --git a/test/flags/test_pisces.py b/test/flags/test_pisces.py
@@ -2,9 +2,9 @@
 
 from pkg_resources import resource_filename
 
-from acclimatise.flag_parser import elements
-from acclimatise.flag_parser.parser import CliParser
-from acclimatise.model import SimpleFlagArg
+from aclimatise.flag_parser import elements
+from aclimatise.flag_parser.parser import CliParser
+from aclimatise.model import SimpleFlagArg
 
 
 def test_pisces_flag(parser):
diff --git a/test/flags/test_podchecker.py b/test/flags/test_podchecker.py
@@ -1,4 +1,4 @@
-from acclimatise.model import Flag
+from aclimatise.model import Flag
 
 
 def test_podchecker_flags(parser):
diff --git a/test/flags/test_samtools.py b/test/flags/test_samtools.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from acclimatise.model import Flag
+from aclimatise.model import Flag
 
 
 def test_samtools_bedcov_j(parser):
diff --git a/test/flags/test_singularity.py b/test/flags/test_singularity.py
@@ -2,7 +2,7 @@
 
 import pytest
 
-from acclimatise.flag_parser.parser import CliParser
+from aclimatise.flag_parser.parser import CliParser
 
 
 def test_singularity_style_flags(parser):
diff --git a/test/name_generation/conftest.py b/test/name_generation/conftest.py
@@ -1,6 +1,6 @@
 import pytest
 
-from acclimatise.converter import WrapperGenerator
+from aclimatise.converter import WrapperGenerator
 
 
 @pytest.fixture()
diff --git a/test/name_generation/test_batch.py b/test/name_generation/test_batch.py
@@ -4,7 +4,7 @@
 import pytest
 from pkg_resources import resource_filename
 
-from acclimatise import WrapperGenerator, parse_help
+from aclimatise import WrapperGenerator, parse_help
 
 from ..util import HelpText, all_tests, convert_validate, validate_cwl, validate_wdl
 
diff --git a/test/name_generation/test_case.py b/test/name_generation/test_case.py
@@ -3,8 +3,8 @@
 """
 import pytest
 
-from acclimatise.converter import WrapperGenerator
-from acclimatise.model import EmptyFlagArg, Flag
+from aclimatise.converter import WrapperGenerator
+from aclimatise.model import EmptyFlagArg, Flag
 
 
 def test_camel_short(camel_gen):
diff --git a/test/name_generation/test_description.py b/test/name_generation/test_description.py
@@ -1,7 +1,7 @@
 """
 Tests the generate_name function, which converts a paragraph of text into a variable name
 """
-from acclimatise.name_generation import generate_name, preprocess
+from aclimatise.name_generation import generate_name, preprocess
 
 
 def test_bwa_mem_t():
diff --git a/test/name_generation/test_group.py b/test/name_generation/test_group.py
@@ -1,8 +1,8 @@
 """
 Tests certain groups of flags used together
 """
-from acclimatise.converter import WrapperGenerator
-from acclimatise.model import EmptyFlagArg, Flag, SimpleFlagArg
+from aclimatise.converter import WrapperGenerator
+from aclimatise.model import EmptyFlagArg, Flag, SimpleFlagArg
 
 
 def test_bedtools_window_sm():
diff --git a/test/name_generation/test_single_flag.py b/test/name_generation/test_single_flag.py
@@ -1,8 +1,8 @@
 """
 Tests for the name generation of single flags
 """
-from acclimatise.converter.wdl import WdlGenerator
-from acclimatise.model import EmptyFlagArg, Flag, Positional, SimpleFlagArg
+from aclimatise.converter.wdl import WdlGenerator
+from aclimatise.model import EmptyFlagArg, Flag, Positional, SimpleFlagArg
 
 
 def test_samtools_dict_output():
diff --git a/test/test_cli.py b/test/test_cli.py
@@ -8,7 +8,7 @@
 from click.testing import CliRunner
 from packaging import version
 
-from acclimatise.cli import main
+from aclimatise.cli import main
 
 from .util import validate_cwl, validate_wdl
 
diff --git a/test/test_convert.py b/test/test_convert.py
@@ -2,7 +2,7 @@
 import tempfile
 from pathlib import Path
 
-from acclimatise import explore_command
+from aclimatise import explore_command
 
 from .util import convert_validate, skip_not_installed
 
diff --git a/test/test_explore_e2e.py b/test/test_explore_e2e.py
@@ -5,8 +5,8 @@
 
 import pytest
 
-from acclimatise import explore_command
-from acclimatise.model import Command, Positional
+from aclimatise import explore_command
+from aclimatise.model import Command, Positional
 
 from .util import (
     HelpText,
@@ -75,8 +75,8 @@ def test_repeat_positionals():
     )
     child = Command(command=[])
 
-    with patch("acclimatise.explore_command", new=lambda *args, **kwargs: child):
-        with patch("acclimatise.best_cmd", new=Mock(return_value=parent)) as mocked:
+    with patch("aclimatise.explore_command", new=lambda *args, **kwargs: child):
+        with patch("aclimatise.best_cmd", new=Mock(return_value=parent)) as mocked:
             explore_command([])
 
             # We should only call best_command once, since there's only one unique positional
diff --git a/test/test_parse_e2e.py b/test/test_parse_e2e.py
@@ -4,7 +4,7 @@
 import pytest
 from pkg_resources import resource_filename
 
-from acclimatise import parse_help
+from aclimatise import parse_help
 
 from .util import (
     HelpText,
diff --git a/test/test_type_inference.py b/test/test_type_inference.py
@@ -1,6 +1,6 @@
 import pytest
 
-from acclimatise.cli_types import (
+from aclimatise.cli_types import (
     CliBoolean,
     CliDir,
     CliFile,
@@ -9,7 +9,7 @@
     CliString,
     CliType,
 )
-from acclimatise.model import CliArgument, EmptyFlagArg, Flag, SimpleFlagArg, infer_type
+from aclimatise.model import CliArgument, EmptyFlagArg, Flag, SimpleFlagArg, infer_type
 
 
 @pytest.mark.parametrize(
diff --git a/test/test_yaml_dump.py b/test/test_yaml_dump.py
@@ -1,7 +1,7 @@
 from io import StringIO
 
-from acclimatise import parse_help
-from acclimatise.yaml import yaml
+from aclimatise import parse_help
+from aclimatise.yaml import yaml
 
 
 def test_round_trip(bwamem_help):
diff --git a/test/usage/test_usage.py b/test/usage/test_usage.py
@@ -2,18 +2,14 @@
 
 import pytest
 
-from acclimatise.flag_parser.elements import (
-    arg_expression,
-    flag_with_arg,
-    list_type_arg,
-)
-from acclimatise.model import Flag, RepeatFlagArg, SimpleFlagArg
-from acclimatise.usage_parser.elements import (  # short_flag_list,
+from aclimatise.flag_parser.elements import arg_expression, flag_with_arg, list_type_arg
+from aclimatise.model import Flag, RepeatFlagArg, SimpleFlagArg
+from aclimatise.usage_parser.elements import (  # short_flag_list,
     stack,
     usage,
     usage_element,
 )
-from acclimatise.usage_parser.model import UsageElement
+from aclimatise.usage_parser.model import UsageElement
 
 
 def test_bwa():
diff --git a/test/util.py b/test/util.py
@@ -14,10 +14,10 @@
 from dataclasses import dataclass, field
 from WDL import Error, parse_document
 
-from acclimatise import Command, Flag, WrapperGenerator, cli_types
-from acclimatise.model import CliArgument
-from acclimatise.name_generation import NameGenerationError
-from acclimatise.yaml import yaml
+from aclimatise import Command, Flag, WrapperGenerator, cli_types
+from aclimatise.model import CliArgument
+from aclimatise.name_generation import NameGenerationError
+from aclimatise.yaml import yaml
 
 logging.getLogger("cwltool").setLevel(30)
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-from acclimatise.execution.local import LocalExecutor`
	`1`	`+from aclimatise.execution.local import LocalExecutor`
`2`	`2`
`3`	`3`	`from ..util import skip_not_installed`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-from acclimatise.model import Flag`
	`1`	`+from aclimatise.model import Flag`
`2`	`2`
`3`	`3`
`4`	`4`	`def test_unindented_flags(parser):`