diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 9a6b9b44..60e42dc4 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,9 +1,16 @@ # Change Log +## 0.3.10 + +- ⬆️ Upgrade xqute to 0.1.3 +- ⬆️ Upgrade datar to 0.11 and format test files +- ✨ Add cli command version to show versions of deps +- ➖ Remove rich as it is required by xqute already + ## 0.3.9 -- ⬆️ Pump pipda to 0.11 -- ⬆️ Pump xqute to 0.1.2 +- ⬆️ Bump pipda to 0.11 +- ⬆️ Bump xqute to 0.1.2 ## 0.3.8 diff --git a/docs/cli.md b/docs/cli.md index e7f85bec..161ba9e4 100644 --- a/docs/cli.md +++ b/docs/cli.md @@ -2,7 +2,7 @@ To run it: -``` +```shell ❯ pipen DESCRIPTION: @@ -15,6 +15,7 @@ OPTIONAL OPTIONS: -h, --help - Print help information for the CLI tool. COMMANDS: + version - Print versions of pipen and its dependencies profile - List available profiles. plugins - List installed plugins help - Print help for commands @@ -57,6 +58,9 @@ It is used to list the configurations/profiles in current directory. Run `pipen This subcommand is used to list the plugins for `pipen` itself, templates, scheduler and cli. Run `pipen plugins` or `pipen help plugins` to get more information. +## The `version` subcommand + +This command prints the versions of `pipen` and its dependencies. [1]: https://github.com/pwwang/pyparam [2]: ../plugin diff --git a/pipen/cli/version.py b/pipen/cli/version.py new file mode 100644 index 00000000..a58a91c4 --- /dev/null +++ b/pipen/cli/version.py @@ -0,0 +1,61 @@ +"""Print help for commands""" +from typing import Any, Mapping + +from rich import print +from pyparam import Params + +from ._hooks import CLIPlugin + +__all__ = ("CLIVersionPlugin",) + + +def get_pkg_version(pkg: str) -> str: + try: + from importlib.metadata import version + return version(pkg) + except ImportError: # pragma: no cover + from pkg_resources import get_distribution # type: ignore + return get_distribution(pkg).version + + +class CLIVersionPlugin(CLIPlugin): + """Print versions of pipen and its dependencies""" + + name = "version" + + @property + def params(self) -> Params: + """Define the params""" + pms = Params( + desc=self.__class__.__doc__, + help_on_void=False, + ) + return pms + + def exec_command(self, args: Mapping[str, Any]) -> None: + """Run the command""" + import sys + from .. import __version__ + + versions = {"python": sys.version, "pipen": __version__} + + for pkg in ( + "liquidpy", + "pandas", + "python-slugify", + "enlighten", + "pyparam", + "xqute", + "python-simpleconf", + "pipda", + "varname", + ): + versions[pkg] = get_pkg_version(pkg) + + keylen = max(map(len, versions)) + for key in versions: + ver = versions[key] + verlines = ver.splitlines() + print(f"{key.ljust(keylen)}: {verlines.pop(0)}") + for verline in verlines: + print(f"{' ' * keylen} {verline}") diff --git a/pipen/proc.py b/pipen/proc.py index 4bfa5b28..d0e3eeb9 100644 --- a/pipen/proc.py +++ b/pipen/proc.py @@ -503,7 +503,7 @@ def _compute_requires( # req.nexts my_nexts = None if cls.nexts is None else cls.nexts[:] for req in requires: # type: ignore - if req.nexts is None: + if not req.nexts: req.nexts = [cls] else: req.nexts.append(cls) # type: ignore diff --git a/pipen/version.py b/pipen/version.py index 0f6db007..6c5f331b 100644 --- a/pipen/version.py +++ b/pipen/version.py @@ -1,3 +1,3 @@ """Provide version of pipen""" -__version__ = "0.3.9" +__version__ = "0.3.10" diff --git a/poetry.lock b/poetry.lock index bffe3eed..efe4c538 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry and should not be changed by hand. + [[package]] name = "aiofiles" version = "0.8.0" @@ -5,6 +7,10 @@ description = "File support for asyncio." category = "main" optional = false python-versions = ">=3.6,<4.0" +files = [ + {file = "aiofiles-0.8.0-py3-none-any.whl", hash = "sha256:7a973fc22b29e9962d0897805ace5856e6a566ab1f0c8e5c91ff6c866519c937"}, + {file = "aiofiles-0.8.0.tar.gz", hash = "sha256:8334f23235248a3b2e83b2c3a78a22674f39969b96397126cc93664d9a901e59"}, +] [[package]] name = "ansicon" @@ -13,20 +19,29 @@ description = "Python wrapper for loading Jason Hood's ANSICON" category = "main" optional = false python-versions = "*" +files = [ + {file = "ansicon-1.89.0-py2.py3-none-any.whl", hash = "sha256:f1def52d17f65c2c9682cf8370c03f541f410c1752d6a14029f97318e4b9dfec"}, + {file = "ansicon-1.89.0.tar.gz", hash = "sha256:e4d039def5768a47e4afec8e89e83ec3ae5a26bf00ad851f914d1240b444d2b1"}, +] [[package]] name = "attrs" -version = "22.1.0" +version = "22.2.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" +files = [ + {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"}, + {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"}, +] [package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", 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making terminal apps, by providing an category = "main" optional = false python-versions = ">=2.7" +files = [ + {file = "blessed-1.19.1-py2.py3-none-any.whl", hash = "sha256:63b8554ae2e0e7f43749b6715c734cc8f3883010a809bf16790102563e6cf25b"}, + {file = "blessed-1.19.1.tar.gz", hash = "sha256:9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc"}, +] [package.dependencies] jinxed = {version = ">=1.1.0", markers = "platform_system == \"Windows\""} @@ -48,6 +67,10 @@ description = "A decorator for caching properties in classes." category = "main" optional = false python-versions = "*" +files = [ + {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"}, + {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, +] [[package]] name = "colorama" @@ -56,6 +79,10 @@ description = "Cross-platform colored terminal text." category = "dev" 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-16,7 +16,6 @@ repository = "https://github.com/pwwang/pipen" python = "^3.7.1" # align with datar/pandas liquidpy = "^0.7" pandas = "^1.3" -rich = "^12" python-slugify = "^6" enlighten = "^1" cached-property = "^1" @@ -24,6 +23,7 @@ more-itertools = "^8" pyparam = "^0.5" xqute = "^0.1" ## included in xqute +# rich = "^12" # diot = "^0.1" # simplug = "^0.0" ## including rtoml @@ -35,17 +35,20 @@ varname = "^0.10" openpyxl = "^3" pytest = "^7" pytest-cov = "^4" -pytest-xdist = "^2" -datar = { version = "^0.10", extras = ["pandas"] } +pytest-xdist = "^3" +datar = { version = "^0.11", extras = ["pandas"] } [tool.poetry.scripts] pipen = "pipen.cli:main" [tool.pytest.ini_options] -addopts = "-vv -n auto -p no:asyncio -W error::UserWarning --cov-config=.coveragerc --cov=pipen --cov-report xml:.coverage.xml --cov-report term-missing" +addopts = "-vv -n auto -p no:asyncio -p no:benchmark -W error::UserWarning --cov-config=.coveragerc --cov=pipen --cov-report xml:.coverage.xml --cov-report term-missing" # addopts = "-vv -n auto -p no:asyncio -W error::UserWarning" console_output_style = "progress" junit_family = "xunit1" +filterwarnings = [ + "ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning", +] [tool.mypy] ignore_missing_imports = true diff --git a/tests/conftest.py b/tests/conftest.py index e69de29b..2fd365cd 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -0,0 +1,3 @@ +import datar + +datar.options(backends=["numpy", "pandas"]) diff --git a/tests/helpers.py b/tests/helpers.py index f707d0bd..20addbcd 100644 --- a/tests/helpers.py +++ b/tests/helpers.py @@ -1,9 +1,9 @@ import sys -import signal +# import signal from tempfile import gettempdir from pathlib import Path -from shutil import rmtree -from multiprocessing import Process +# from shutil import rmtree +# from multiprocessing import Process import pytest from pipen import Proc, Pipen, plugin @@ -76,7 +76,10 @@ class RetryProc(ErrorProc): error_strategy = "retry" num_retries = 10 lang = sys.executable # python - script = "import sys, time; sys.exit(1 if time.time() < {{in.starttime}} + 3 else 0)" + script = """ + import sys, time + sys.exit(1 if time.time() < {{in.starttime}} + 3 else 0) + """ class OutputRenderErrorProc(Proc): @@ -124,6 +127,7 @@ class FileInputProc(Proc): output = "out:file:{{in.in.split('/')[-1]}}" script = "cat {{in.in}} > {{out.out}}" + class OutputNotGeneratedProc(Proc): """Process with output file not generated intentionally""" @@ -157,11 +161,11 @@ class DirOutputProc(Proc): class SimplePlugin: - @plugin.impl async def on_init(pipen): print("SimplePlugin") + @pytest.fixture def pipen(tmp_path): """Get a simple Pipen object each time""" @@ -177,6 +181,7 @@ def pipen(tmp_path): return pipen_simple + @pytest.fixture def pipen_with_plugin(tmp_path): """Get a simple Pipen object each time""" diff --git a/tests/test_channel.py b/tests/test_channel.py index c86f5ba5..8a504b58 100644 --- a/tests/test_channel.py +++ b/tests/test_channel.py @@ -1,53 +1,58 @@ from io import StringIO from pathlib import Path from math import ceil -import pytest -from pipen.channel import * -from datar.all import * + +import pytest # noqa +from pipen.channel import Channel, expand_dir, collapse_files +from datar.tibble import tibble from pandas import DataFrame + def test_create(): assert isinstance(Channel.create(DataFrame([[1]])), DataFrame) + def test_from_glob(): - glob = Path(__file__).parent / 'test_*.py' - glob_files = list(Path(__file__).parent.glob('test_*.py')) + glob = Path(__file__).parent / "test_*.py" + glob_files = list(Path(__file__).parent.glob("test_*.py")) ch = Channel.from_glob(glob) assert ch.shape == (len(glob_files), 1) + def test_from_pairs(): - glob = Path(__file__).parent / 'test_*.py' - glob_files = list(Path(__file__).parent.glob('test_*.py')) + glob = Path(__file__).parent / "test_*.py" + glob_files = list(Path(__file__).parent.glob("test_*.py")) ch = Channel.from_pairs(glob) assert ch.shape == (ceil(len(glob_files) / 2.0), 2) + def test_expand_dir_collapse_files(): ch0 = Channel.create([(Path(__file__).parent.as_posix(), 1)]) - ch1 = ch0 >> expand_dir(pattern='test_*.py') - glob_files = list(Path(__file__).parent.glob('test_*.py')) + ch1 = ch0 >> expand_dir(pattern="test_*.py") + glob_files = list(Path(__file__).parent.glob("test_*.py")) assert ch1.shape == (len(glob_files), 2) ch2 = ch1 >> collapse_files() assert ch2.equals(ch0) + def test_from_csv(tmp_path): - df = tibble(a=[1,2], b=[3,4]) - df.to_csv(tmp_path / 'input.csv', index=False) - ch = Channel.from_csv(tmp_path / 'input.csv') + df = tibble(a=[1, 2], b=[3, 4]) + df.to_csv(tmp_path / "input.csv", index=False) + ch = Channel.from_csv(tmp_path / "input.csv") assert ch.equals(df) + def test_from_excel(tmp_path): - df = tibble(a=[1,2], b=[3,4]) - df.to_excel(tmp_path / 'input.xls', index=False) - ch = Channel.from_excel(tmp_path / 'input.xls') + df = tibble(a=[1, 2], b=[3, 4]) + df.to_excel(tmp_path / "input.xls", index=False) + ch = Channel.from_excel(tmp_path / "input.xls") assert ch.equals(df) + def test_from_table(): - df = StringIO("""a b -1 3 -2 4 -""") + df = StringIO("a b\n1 3\n2 4\n") ch = Channel.from_table(df, sep=" ") - exp = tibble(a=[1,2], b=[3,4]) - assert ch.equals(exp) \ No newline at end of file + exp = tibble(a=[1, 2], b=[3, 4]) + assert ch.equals(exp) diff --git a/tests/test_cli.py b/tests/test_cli.py index f9bcba96..32311528 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,5 +1,6 @@ from subprocess import check_output, CalledProcessError -import pytest +import pytest # noqa: F401 + def cmdoutput(cmd): try: @@ -15,16 +16,19 @@ def test_main(): out = cmdoutput(["pipen", "--help"]) assert "CLI Tool for pipen" in out + def test_nosuch_command(): out = cmdoutput(["pipen", "x"]) assert "No such command" in out + def test_help(): out = cmdoutput(["pipen", "help", "x"]) assert "No such command" in out out = cmdoutput(["pipen", "help", "profile"]) assert "List available profiles" in out + def test_profile_all(): out = cmdoutput(["pipen", "profile"]) assert "Note:" in out @@ -38,3 +42,10 @@ def test_profile_default(): def test_profile_nosuch(): out = cmdoutput(["pipen", "profile", "-n", "nosuch"]) assert "Profile: nosuch" not in out + + +def test_version(): + out = cmdoutput(["pipen", "version"]) + assert "pipen" in out + assert "python" in out + assert "liquidpy" in out diff --git a/tests/test_job.py b/tests/test_job.py index c62f3f0c..28bd226c 100644 --- a/tests/test_job.py +++ b/tests/test_job.py @@ -117,7 +117,7 @@ def test_check_cached_input_or_output_different( caplog.clear() pipen.set_starts(proc_io_diff2).run() - pipen.build_proc_relationships() # not redoing it. + pipen.build_proc_relationships() # not redoing it. assert "Not cached (input or output is different)" in caplog.text @@ -175,7 +175,9 @@ def test_check_cached_force_cache(caplog, pipen, infile): def test_check_cached_infile_newer(caplog, pipen, infile): - proc_infile_newer = Proc.from_proc(MixedInputProc, input_data=[(1, infile)]) + proc_infile_newer = Proc.from_proc( + MixedInputProc, input_data=[(1, infile)] + ) pipen.set_starts(proc_infile_newer).run() caplog.clear() diff --git a/tests/test_pipen.py b/tests/test_pipen.py index 29b01e81..26addaaa 100644 --- a/tests/test_pipen.py +++ b/tests/test_pipen.py @@ -58,8 +58,10 @@ def test_cyclic_dependency(pipen): def test_not_cyclic_for_subclass_of_proc_in_pipeline(pipen): proc1 = Proc.from_proc(NormalProc, input_data=[1]) proc2 = Proc.from_proc(NormalProc, requires=proc1) + class proc3(proc1): requires = proc2 + pipen.set_starts(proc1).run() assert pipen.procs == [proc1, proc2, proc3] diff --git a/tests/test_plugin.py b/tests/test_plugin.py index da4db551..bbcfb141 100644 --- a/tests/test_plugin.py +++ b/tests/test_plugin.py @@ -7,6 +7,7 @@ from .helpers import pipen, OutputNotGeneratedProc + def test_job_succeeded(pipen, caplog): out = pipen.set_starts(OutputNotGeneratedProc).run() diff --git a/tests/test_proc.py b/tests/test_proc.py index 7a990048..227a3273 100644 --- a/tests/test_proc.py +++ b/tests/test_proc.py @@ -114,13 +114,12 @@ def test_proc_with_input_data(pipen): def test_proc_with_input_callable(pipen): proc = Proc.from_proc(NormalProc, input_data=[1]) proc2 = Proc.from_proc( - NormalProc, - requires=proc, - input_data=lambda ch: ch >> mutate(output=2) + NormalProc, requires=proc, input_data=lambda ch: ch >> mutate(output=2) ) pipen.set_starts(proc).run() assert proc2.output_data.equals(pandas.DataFrame({"output": ["2"]})) + def test_proc_is_singleton(pipen): pipen.workdir = ".pipen/" os.makedirs(pipen.workdir, exist_ok=True) @@ -128,6 +127,7 @@ def test_proc_is_singleton(pipen): p2 = SimpleProc(pipen) assert p1 is p2 + def test_ignore_input_data_of_start_proc(caplog, pipen): proc = Proc.from_proc(NormalProc, input_data=[1]) proc2 = Proc.from_proc(NormalProc, requires=proc, input_data=[2]) @@ -135,6 +135,7 @@ def test_ignore_input_data_of_start_proc(caplog, pipen): assert "Ignoring input data" in caplog.text assert proc2.output_data.equals(pandas.DataFrame({"output": ["1"]})) + def test_proc_wasted_input_columns(caplog, pipen): proc1 = Proc.from_proc(NormalProc, input_data=[1]) proc2 = Proc.from_proc(NormalProc, input_data=[1]) @@ -142,6 +143,7 @@ def test_proc_wasted_input_columns(caplog, pipen): pipen.set_starts(proc1, proc2).run() assert "Wasted 1 column" in caplog.text + def test_proc_not_enough_input_columns(caplog, pipen): proc1 = Proc.from_proc(NormalProc, input_data=[1]) proc2 = Proc.from_proc(In2Out1Proc, requires=proc1) @@ -149,11 +151,13 @@ def test_proc_not_enough_input_columns(caplog, pipen): assert "No data column for input: ['in2'], using None" in caplog.text assert proc2.output_data.equals(pandas.DataFrame({"out": ["1_None"]})) + def test_proc_relative_path_script(pipen): pipen.set_starts(RelPathScriptProc).run() script = RelPathScriptProc().script.render() assert "AbCdEf" in script + def test_script_file_exists(pipen): with pytest.raises(ProcScriptFileNotFound): pipen.set_starts(ScriptNotExistsProc).run() diff --git a/tests/test_scheduler.py b/tests/test_scheduler.py index 639de50c..4548251b 100644 --- a/tests/test_scheduler.py +++ b/tests/test_scheduler.py @@ -2,13 +2,13 @@ from pipen.scheduler import * + def test_get_scheduler(): - sge = get_scheduler('sge') + sge = get_scheduler("sge") assert sge is SgeScheduler sge = get_scheduler(sge) assert sge is SgeScheduler with pytest.raises(NoSuchSchedulerError): - get_scheduler('nosuchscheduler') - + get_scheduler("nosuchscheduler") diff --git a/tests/test_template.py b/tests/test_template.py index 373d0295..2d83a76c 100644 --- a/tests/test_template.py +++ b/tests/test_template.py @@ -3,12 +3,13 @@ from pipen.template import * from pipen.template import NoSuchTemplateEngineError + def test_update_envs(): - jinja = get_template_engine('jinja2') + jinja = get_template_engine("jinja2") jinja2 = get_template_engine(jinja) assert jinja is jinja2 - jinja_tpl = jinja('abc') - assert jinja_tpl.render() == 'abc' + jinja_tpl = jinja("abc") + assert jinja_tpl.render() == "abc" with pytest.raises(NoSuchTemplateEngineError): - get_template_engine('nosuchtemplate') + get_template_engine("nosuchtemplate") diff --git a/tests/test_utils.py b/tests/test_utils.py index ab86bcab..bc9d163c 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,36 +1,52 @@ import pytest from pathlib import Path import pipen -from pipen.utils import brief_list, desc_from_docstring, get_logger, get_mtime, get_plugin_context, get_shebang, ignore_firstline_dedent, strsplit, truncate_text, update_dict +from pipen.utils import ( + brief_list, + desc_from_docstring, + get_logger, + get_mtime, + get_plugin_context, + get_shebang, + ignore_firstline_dedent, + strsplit, + truncate_text, + update_dict, +) from pipen.exceptions import ConfigurationError from pipen.pluginmgr import plugin + def test_get_logger(caplog): - logger = get_logger('test', 'info') - logger.debug('debug message') - assert 'debug message' not in caplog.text + logger = get_logger("test", "info") + logger.debug("debug message") + assert "debug message" not in caplog.text + def test_plugin_context(): with pytest.raises(ConfigurationError): - get_plugin_context(['a', 'no:b']) + get_plugin_context(["a", "no:b"]) - plugin.get_plugin('main').enable() - context = get_plugin_context(['no:main']) + plugin.get_plugin("main").enable() + context = get_plugin_context(["no:main"]) with context: - assert plugin.get_plugin('main').enabled is False + assert plugin.get_plugin("main").enabled is False + + assert plugin.get_plugin("main").enabled is True - assert plugin.get_plugin('main').enabled is True def test_brief_list(): - assert brief_list([1]) == '1' - assert brief_list([1,2,3]) == '1-3' + assert brief_list([1]) == "1" + assert brief_list([1, 2, 3]) == "1-3" + def test_get_mtime_dir(): package_dir = Path(pipen.__file__).parent mtime = get_mtime(package_dir, 2) assert mtime > 0 + def test_desc_from_docstring(): def obj1(): """ @@ -43,21 +59,25 @@ def obj1(): desc = desc_from_docstring(obj1) assert desc == "abc def" + def test_update_dict(): assert update_dict(None, None) is None assert update_dict({}, None) == {} assert update_dict(None, {}) == {} + def test_strsplit(): assert strsplit("a ,b ", ",", trim=None) == ["a ", "b "] assert strsplit("a , b", ",", trim="left") == ["a ", "b"] assert strsplit("a , b", ",", trim="right") == ["a", " b"] + def test_get_shebang(): assert get_shebang("") is None assert get_shebang("#!bash") == "bash" assert get_shebang("#!bash \n") == "bash" + def test_ignore_firstline_dedent(): text = """ @@ -65,5 +85,6 @@ def test_ignore_firstline_dedent(): """ assert ignore_firstline_dedent(text) == "a\n" + def test_truncate_text(): assert truncate_text("abcd", 2) == "a…" diff --git a/tests/test_xqute_pars.py b/tests/test_xqute_pars.py index 0ce79be7..8ca811da 100644 --- a/tests/test_xqute_pars.py +++ b/tests/test_xqute_pars.py @@ -5,6 +5,7 @@ import time from .helpers import RetryProc, pipen + def test_retry(caplog, pipen): proc = Proc.from_proc(RetryProc) rc = pipen.set_starts(proc).set_data([time.time()]).run()