def setup(mocker, request):
"""Set up for diff function"""
local_packages = request.param["local_packages"]
local_logs = request.param["local_logs"]
local_actions = request.param["local_actions"]
env_name = request.param["env_name"]
remote_packages = request.param["remote_packages"]
remote_logs = request.param["remote_logs"]
remote_actions = request.param["remote_actions"]
dependencies = {
"conda": {
"pandas": Package("pandas", "pandas", version="0.23.0"),
"pytest": Package("pytest", "pytest", version="4.0.0"),
}
}
mocker.patch(
"conda_env_tracker.env.get_dependencies", mocker.Mock(return_value=dependencies)
)
history = History.create(
name=env_name,
packages=PackageRevision.create(local_packages, dependencies=dependencies),
channels=Channels(["conda-forge"]),
logs=Logs([log for log in local_logs]),
actions=local_actions,
diff=Diff(),
debug=Debug(),
)
env = Environment(name=env_name, history=history)
mocker.patch("conda_env_tracker.main.Environment.read", return_value=env)
mocker.patch(
"conda_env_tracker.gateways.io.EnvIO.get_remote_dir",
return_value="~/path/to/remote",
)
mocker.patch("pathlib.Path.is_dir", return_value=True)
history = History.create(
name=env_name,
channels=Channels(["conda-forge"]),
packages=PackageRevision.create(remote_packages, dependencies=dependencies),
logs=Logs([log for log in remote_logs]),
actions=remote_actions,
diff=Diff(),
debug=Debug(),
)
mocker.patch(
"conda_env_tracker.gateways.io.EnvIO.get_history", return_value=history
)
mocker.patch("pathlib.Path.write_text")
yield env, request.param["push_should_fail"]
if (USER_ENVS_DIR / env_name).exists():
shutil.rmtree(USER_ENVS_DIR / env_name)
def test_pull_no_new_action_in_local(setup_tests):
overwrite_mock = setup_tests["overwrite_mock"]
remote_history = setup_tests["remote_history"]
local_packages = (Package.from_spec("pandas"), )
local_logs = ["conda create --name pull_testing_environment pandas"]
local_actions = [
"conda create --name pull_testing_environment pandas=0.23=py36"
]
local_history = History(
name=ENV_NAME,
packages=HistoryPackages.create(local_packages),
channels=Channels(),
logs=Logs([log for log in local_logs]),
actions=Actions(local_actions),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
pull(env=env)
assert env.history.packages == remote_history.packages
assert env.history.logs == remote_history.logs
assert env.history.actions == remote_history.actions
overwrite_mock.called_once()
def test_pull_new_action_in_both(setup_tests, local_packages, local_logs,
local_actions):
overwrite_mock = setup_tests["overwrite_mock"]
remote_history = setup_tests["remote_history"]
packages_mock = setup_tests["get_dependencies"]
packages = HistoryPackages.create(local_packages["conda"])
if local_packages.get("pip"):
packages.update_packages(local_packages["pip"], source="pip")
local_history = History(
name=ENV_NAME,
channels=CHANNELS,
packages=packages,
logs=Logs([log for log in local_logs]),
actions=Actions(local_actions),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
if local_packages.get("pip") is not None:
packages_mock.configure_mock(
return_value={
"conda": {
"pandas": Package("pandas", "pandas", "0.23", "py36"),
"pytest": Package("pytest", "pytest", "0.1", "py36_3"),
},
"pip": {
"pylint": Package("pylint", "pylint", "1.11")
},
})
else:
packages_mock.configure_mock(
return_value={
"conda": {
"pandas": Package("pandas", "pandas", "0.23", "py36"),
"pytest": Package("pytest", "pytest", "0.1", "py36_3"),
"pylint": Package("pylint", "pylint", "1.11", "py36"),
},
"pip": {},
})
pull(env=env)
expected_packages = remote_history.packages
if local_packages.get("pip"):
expected_packages["pip"]["pylint"] = local_history.packages["pip"][
"pylint"]
elif "pylint" in local_history.packages["conda"]:
expected_packages["conda"]["pylint"] = local_history.packages["conda"][
"pylint"]
expected_logs = remote_history.logs
expected_actions = remote_history.actions
assert env.history.packages == expected_packages
assert env.history.logs == expected_logs
assert env.history.actions == expected_actions
assert env.history.logs[-1] == local_history.logs[-1]
assert env.history.actions[-1] == local_history.actions[-1]
overwrite_mock.called_once()
def test_get_packages_with_version_spec(mocker):
mocker.patch(
"conda_env_tracker.env.get_dependencies",
return_value={
"conda": {
"pandas": Package("pandas", "pandas", "0.23", "py_36"),
"numpy": Package("numpy", "numpy", "0.13", "py_36"),
},
"pip": {
"pytest": Package("pytest", "pytest", "4.0")
},
},
)
local_packages = HistoryPackages.create(
(Package.from_spec("pandas=0.23"), ))
local_packages.update_packages(
packages=(Package.from_spec("pytest==4.0"), ), source="pip")
local_history = History(
name=ENV_NAME,
packages=local_packages,
channels=Channels("defaults"),
logs=Logs([]),
actions=Actions(),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
expected = {
"conda": [Package("pandas", "pandas=0.23", "0.23", "py_36")],
"pip": [Package("pytest", "pytest==4.0", "4.0")],
}
actual = get_packages(env)
assert actual == expected
def infer(cls, name: str, packages: Packages, channels: ListLike = None):
"""create conda_env_tracker environment by inferring to existing conda environment"""
if name == "base":
raise CondaEnvTrackerCondaError(
"Environment can not be created using default name base"
)
if name not in get_all_existing_environment():
raise CondaEnvTrackerCondaError(
f"Environment {name} can not be inferred, does not exist"
)
existing_packages = get_dependencies(name=name)
if "r-base" in existing_packages["conda"]:
existing_r_packages = get_r_dependencies(name=name)
else:
existing_r_packages = {}
user_packages = {"conda": Packages(), "pip": Packages(), "r": Packages()}
for package in packages:
if package.name in existing_packages.get("conda", Packages()):
user_packages["conda"].append(package)
elif package.name in existing_packages.get("pip", Packages()):
user_packages["pip"].append(package)
elif package.name in existing_r_packages:
raise RError(
"Cannot infer R packages, must run follow-up R install command.\n"
f"Found '{package.name}' in installed R packages {existing_r_packages}."
)
else:
raise CondaEnvTrackerCondaError(
f"Environment {name} does not have {package.spec} installed"
)
conda_create_cmd = get_conda_create_command(
name, user_packages["conda"], channels
)
specs = Actions.get_package_specs(
packages=user_packages["conda"], dependencies=existing_packages["conda"]
)
history = History(
name=name,
channels=Channels(channels),
packages=HistoryPackages.create(user_packages["conda"]),
logs=Logs.create(conda_create_cmd),
actions=Actions.create(name=name, specs=specs, channels=Channels(channels)),
debug=Debug.create(name=name),
)
env = cls(name=name, history=history)
if user_packages["pip"]:
handler = PipHandler(env=env)
handler.update_history_install(packages=user_packages["pip"])
env = handler.env
env.export()
return env
def create(
cls,
name: str,
packages: Packages,
channels: ListLike = None,
yes: bool = False,
strict_channel_priority: bool = True,
):
"""Creating a conda environment from a list of packages."""
if name == "base":
raise CondaEnvTrackerCondaError(
"Environment can not be created using default name base"
)
if name in get_all_existing_environment():
raise CondaEnvTrackerCondaError(f"Environment {name} already exist")
logger.debug(f"creating conda env {name}")
conda_create(
name=name,
packages=packages,
channels=channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
create_cmd = get_conda_create_command(
name=name,
packages=packages,
channels=channels,
strict_channel_priority=strict_channel_priority,
)
specs = Actions.get_package_specs(
packages=packages, dependencies=get_dependencies(name=name)["conda"]
)
if not channels:
channels = get_conda_channels()
history = History(
name=name,
channels=Channels(channels),
packages=HistoryPackages.create(packages),
logs=Logs.create(create_cmd),
actions=Actions.create(
name=name,
specs=specs,
channels=Channels(channels),
strict_channel_priority=strict_channel_priority,
),
debug=Debug.create(name=name),
)
env = cls(name=name, history=history)
env.export()
return env
def setup_r_tests(mocker):
"""Set up for pull function with R packages"""
remote_packages = Packages.from_specs("r-base")
remote_logs = ["conda create --name pull_testing_environment r-base"]
remote_actions = [
"conda create --name pull_testing_environment r-base=3.5.1=h351"
]
remote_history = History(
name=ENV_NAME,
channels=CHANNELS,
packages=HistoryPackages.create(remote_packages),
logs=Logs([log for log in remote_logs]),
actions=Actions(remote_actions),
debug=Debug(),
)
mocker.patch("conda_env_tracker.conda.conda_install")
mocker.patch("conda_env_tracker.pip.pip_install")
mocker.patch("conda_env_tracker.history.get_pip_version")
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{"return_value.failed": False})
mocker.patch(
"conda_env_tracker.env.get_dependencies",
return_value={"conda": {
"r-base": "3.5.1"
}},
)
get_r_dependencies = mocker.patch(
"conda_env_tracker.env.get_r_dependencies")
overwrite_mock = mocker.patch(
"conda_env_tracker.pull.EnvIO.overwrite_local")
mocker.patch("conda_env_tracker.pull.EnvIO.get_remote_dir",
return_value="~/path/to/remote")
mocker.patch("conda_env_tracker.pull.EnvIO.get_history",
return_value=remote_history)
mocker.patch("conda_env_tracker.pull.prompt_yes_no", return_value=True)
mocker.patch("conda_env_tracker.pull.update_conda_environment")
mocker.patch("conda_env_tracker.pull.update_r_environment")
mocker.patch("conda_env_tracker.pull.Environment.export")
mocker.patch("conda_env_tracker.pull.Environment.validate")
yield {
"get_r_dependencies": get_r_dependencies,
"overwrite_mock": overwrite_mock,
"remote_history": remote_history,
}
env_dir = USER_ENVS_DIR / ENV_NAME
if env_dir.exists():
shutil.rmtree(env_dir)
def setup_tests(mocker):
"""Set up for pull function"""
remote_packages = (Package.from_spec("pandas"),
Package.from_spec("pytest"))
remote_logs = [
"conda create --name pull_testing_environment pandas",
"conda install --name pull_testing_environment pytest",
]
remote_actions = [
"conda create --name pull_testing_environment pandas=0.23=py36",
"conda install --name pull_testing_environment pytest=0.1=py36_3",
]
remote_history = History(
name=ENV_NAME,
channels=CHANNELS,
packages=HistoryPackages.create(remote_packages),
logs=Logs([log for log in remote_logs]),
actions=Actions(remote_actions),
debug=Debug(),
)
mocker.patch("conda_env_tracker.conda.conda_install")
mocker.patch("conda_env_tracker.conda.conda_update_all")
mocker.patch("conda_env_tracker.conda.conda_remove")
mocker.patch("conda_env_tracker.pip.pip_install")
mocker.patch("conda_env_tracker.pip.pip_remove")
mocker.patch("conda_env_tracker.history.get_pip_version")
get_dependencies = mocker.patch("conda_env_tracker.env.get_dependencies")
overwrite_mock = mocker.patch(
"conda_env_tracker.pull.EnvIO.overwrite_local")
mocker.patch("conda_env_tracker.pull.EnvIO.get_remote_dir",
return_value="~/path/to/remote")
mocker.patch("conda_env_tracker.pull.EnvIO.get_history",
return_value=remote_history)
mocker.patch("conda_env_tracker.pull.prompt_yes_no", return_value=True)
mocker.patch("conda_env_tracker.pull.update_conda_environment")
mocker.patch("conda_env_tracker.pull.update_r_environment")
mocker.patch("conda_env_tracker.pull.Environment.export")
mocker.patch("conda_env_tracker.pull.Environment.validate")
mocker.patch(
"conda_env_tracker.pull.Environment.validate_installed_packages")
yield {
"get_dependencies": get_dependencies,
"overwrite_mock": overwrite_mock,
"remote_history": remote_history,
}
env_dir = USER_ENVS_DIR / ENV_NAME
if env_dir.exists():
shutil.rmtree(env_dir)
def test_pull_remote_local_different_create_commands(setup_tests,
local_packages,
local_logs,
local_actions):
# pylint: disable=unused-argument
local_history = History(
name=ENV_NAME,
channels=CHANNELS,
packages=HistoryPackages.create(local_packages),
logs=Logs([log for log in local_logs]),
actions=Actions(local_actions),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
with pytest.raises(CondaEnvTrackerCreationError):
pull(env=env)
def test_get_packages_r(mocker):
mocker.patch(
"conda_env_tracker.env.get_dependencies",
return_value={
"conda": {
"r-base":
Package("r-base", "r-base", "3.5.1", "h539"),
"r-devtools":
Package("r-devtools", "r-devtools", "0.1.0", "r351_0"),
}
},
)
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
return_value={
"trelliscopejs": Package("trelliscopejs", "trelliscopejs"
"0.1.0")
},
)
local_packages = HistoryPackages.create(
Packages(
(Package.from_spec("r-base"), Package.from_spec("r-devtools"))))
local_packages.update_packages(
packages=(Package.from_spec("trelliscopejs"), ), source="r")
local_history = History(
name=ENV_NAME,
packages=local_packages,
channels=Channels("defaults"),
logs=Logs([]),
actions=Actions(),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
expected = {
"conda": [
Package("r-base", "r-base", "3.5.1", "h539"),
Package("r-devtools", "r-devtools", "0.1.0", "r351_0"),
],
"r": [Package("trelliscopejs", "trelliscopejs", "0.1.0")],
}
actual = get_packages(env)
assert actual == expected
def test_pull_actions_in_different_order(setup_tests):
overwrite_mock = setup_tests["overwrite_mock"]
remote_history = setup_tests["remote_history"]
new_log = "conda install --name pull_testing_environment pylint"
new_action = "conda install --name pull_testing_environment pylint=1.11=py36"
remote_history.packages["pylint"] = "*"
remote_history.logs.append(new_log)
remote_history.actions.append(new_action)
local_packages = (
Package.from_spec("pandas"),
Package.from_spec("pylint"),
Package.from_spec("pytest"),
)
local_logs = [
"conda create --name pull_testing_environment pandas",
new_log,
"conda install --name pull_testing_environment pytest",
]
local_actions = [
"conda create --name pull_testing_environment pandas=0.23=py36",
new_action,
"conda install --name pull_testing_environment pytest=0.1=py36_3",
]
local_history = History(
name=ENV_NAME,
channels=CHANNELS,
packages=HistoryPackages.create(local_packages),
logs=Logs([log for log in local_logs]),
actions=Actions(local_actions),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
pull(env=env)
assert env.history.packages == remote_history.packages
assert env.history.logs == remote_history.logs
assert env.history.actions == remote_history.actions
overwrite_mock.called_once()
def test_pull_no_new_action_in_remote(setup_tests, local_packages, local_logs,
local_actions):
overwrite_mock = setup_tests["overwrite_mock"]
local_history = History(
name=ENV_NAME,
packages=HistoryPackages.create(local_packages),
channels=Channels(),
logs=Logs([log for log in local_logs]),
actions=Actions(local_actions),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
pull(env=env)
assert env.history.packages == local_history.packages
assert env.history.logs == local_history.logs
assert env.history.actions == local_history.actions
overwrite_mock.assert_not_called()
def expected_update(mocker):
"""Set up for update function"""
packages = Packages.from_specs("pandas")
channel = "conda-forge"
create_cmd = "conda install pandas"
name = "test-update"
mocker.patch("conda_env_tracker.gateways.io.Path.mkdir")
mocker.patch("conda_env_tracker.gateways.io.Path.write_text")
mocker.patch("conda_env_tracker.gateways.io.Path.iterdir")
mocker.patch("conda_env_tracker.history.debug.get_pip_version",
return_value=None)
dependencies = {
"conda": {
"pandas": Package("pandas", "pandas", "0.23", "py36"),
"pytest": Package("pytest", "pytest", "0.1", "py36"),
},
"pip": {},
}
mocker.patch("conda_env_tracker.env.get_dependencies",
return_value=dependencies)
mocker.patch("conda_env_tracker.env.EnvIO.export_packages")
history = History.create(
name=name,
channels=Channels([channel]),
packages=PackageRevision.create(packages, dependencies=dependencies),
logs=Logs(create_cmd),
actions=Actions.create(name="test-update",
specs=["pandas"],
channels=Channels([channel])),
diff=Diff.create(packages, dependencies=dependencies),
debug=Debug(),
)
mocker.patch(
"conda_env_tracker.main.Environment.read",
return_value=Environment(name=name, history=history),
)
return history
def test_get_packages_conda(mocker):
mocker.patch(
"conda_env_tracker.env.get_dependencies",
return_value={
"conda": {
"pandas": Package("pandas", "pandas", "0.23", "py_36"),
"numpy": Package("numpy", "numpy", "0.13", "py_36"),
}
},
)
packages = (Package.from_spec("pandas"), )
local_history = History(
name=ENV_NAME,
packages=HistoryPackages.create(packages),
channels=Channels("defaults"),
logs=Logs([]),
actions=Actions(),
debug=Debug(),
)
env = Environment(name=ENV_NAME, history=local_history)
expected = {"conda": [Package("pandas", "pandas", "0.23", "py_36")]}
actual = get_packages(env)
assert actual == expected
def create(
cls,
name: str,
packages: Packages,
channels: ListLike = None,
yes: bool = False,
strict_channel_priority: bool = True,
):
"""Creating a conda environment from a list of packages."""
if name == "base":
raise CondaEnvTrackerCondaError(
"Environment can not be created using default name base"
)
if name in get_all_existing_environment():
message = (
f"This environment {name} already exists. Would you like to replace it"
)
if prompt_yes_no(prompt_msg=message, default=False):
delete_conda_environment(name=name)
local_io = EnvIO(env_directory=USER_ENVS_DIR / name)
if local_io.env_dir.exists():
local_io.delete_all()
else:
raise CondaEnvTrackerCondaError(f"Environment {name} already exists")
logger.debug(f"creating conda env {name}")
conda_create(
name=name,
packages=packages,
channels=channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
create_cmd = get_conda_create_command(
name=name,
packages=packages,
channels=channels,
strict_channel_priority=strict_channel_priority,
)
specs = Actions.get_package_specs(
packages=packages, dependencies=get_dependencies(name=name)["conda"]
)
if not channels:
channels = get_conda_channels()
dependencies = get_dependencies(name=name)
history = History.create(
name=name,
channels=Channels(channels),
packages=PackageRevision.create(packages, dependencies=dependencies),
logs=Logs(create_cmd),
actions=Actions.create(
name=name,
specs=specs,
channels=Channels(channels),
strict_channel_priority=strict_channel_priority,
),
diff=Diff.create(packages=packages, dependencies=dependencies),
debug=Debug.create(name=name),
)
env = cls(name=name, history=history, dependencies=dependencies)
env.export()
return env