bioelectea 0.1.0__tar.gz

bioelectea-0.1.0/.gitignore

@@ -0,0 +1,6 @@
+.venv/
+build/
+dist/
+*.egg-info/
+__pycache__/
+.pytest_cache/

bioelectea-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+      - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        args: [--fix]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea/__init__.py

@@ -0,0 +1,2 @@
+__all__ = ["__version__"]
+__version__ = "0.1.0"

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea/__main__.py

@@ -0,0 +1,4 @@
+from .cli import main
+
+if __name__ == "__main__":
+    main()

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea/cli.py

@@ -0,0 +1,2 @@
+def main():
+    print("bioelectea: hello, world! CLI stub is alive.")

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea-0.1.0.dist-info/INSTALLER

@@ -0,0 +1 @@
+pip

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea-0.1.0.dist-info/METADATA

@@ -0,0 +1,19 @@
+Metadata-Version: 2.4
+Name: bioelectea
+Version: 0.1.0
+Summary: BioElecTEA: TEA/LCA toolkit for bioelectrochemical & microfluidic processes
+Author-email: Sunghoon Kim <rlatjdgns456@naver.com>
+License: MIT
+Keywords: LCA,TEA,bioelectrochemistry,microfluidics
+Requires-Python: >=3.11
+Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# bioelectea
+Quickstart for BioElecTEA package.

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea-0.1.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+../../Scripts/bioelectea.exe,sha256=tThEzDCn9fhH7SZokYTvFVETN1Uf6dsgkj95mDMHNm8,108396
+bioelectea-0.1.0.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4
+bioelectea-0.1.0.dist-info/METADATA,sha256=wQ4IXUD2uTEuoZflp6naBWiO2HN0xfdZVMg25ZmUIMg,618
+bioelectea-0.1.0.dist-info/RECORD,,
+bioelectea-0.1.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+bioelectea-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+bioelectea-0.1.0.dist-info/entry_points.txt,sha256=HK1ogjSOhfUb_H8kBIXvkaZ2XyPJHakSHd5tKuqxTEc,51
+bioelectea/__init__.py,sha256=sca3B8hAtmHVH9qxtqZusd9a0Kzov3VtgHnvq8_ZJY8,49
+bioelectea/__main__.py,sha256=HrbCy8Q6qXHtsbU7_WIsmGfH9P4jRqYv8vsXdQdiozw,62
+bioelectea/__pycache__/__init__.cpython-312.pyc,,
+bioelectea/__pycache__/__main__.cpython-312.pyc,,
+bioelectea/__pycache__/cli.cpython-312.pyc,,
+bioelectea/cli.py,sha256=DvdPH4SnlIRYKI4IQmR1W9fHE77VdAr30gUKp6POjWU,71

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

bioelectea-0.1.0/.venv-test/Lib/site-packages/bioelectea-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+bioelectea = bioelectea.cli:main

bioelectea-0.1.0/.venv-test/Lib/site-packages/pip/__init__.py

@@ -0,0 +1,13 @@
+from typing import List, Optional
+
+__version__ = "25.0.1"
+
+
+def main(args: Optional[List[str]] = None) -> int:
+    """This is an internal API only meant for use by pip's own console scripts.
+
+    For additional details, see https://github.com/pypa/pip/issues/7498.
+    """
+    from pip._internal.utils.entrypoints import _wrapper
+
+    return _wrapper(args)

bioelectea-0.1.0/.venv-test/Lib/site-packages/pip/__main__.py

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+import os
+import sys
+
+# Remove '' and current working directory from the first entry
+# of sys.path, if present to avoid using current directory
+# in pip commands check, freeze, install, list and show,
+# when invoked as python -m pip <command>
+if sys.path[0] in ("", os.getcwd()):
+    sys.path.pop(0)
+
+# If we are running from a wheel, add the wheel to sys.path
+# This allows the usage python pip-*.whl/pip install pip-*.whl
+if __package__ == "":
+    # __file__ is pip-*.whl/pip/__main__.py
+    # first dirname call strips of '/__main__.py', second strips off '/pip'
+    # Resulting path is the name of the wheel itself
+    # Add that to sys.path so we can import pip
+    path = os.path.dirname(os.path.dirname(__file__))
+    sys.path.insert(0, path)
+
+if __name__ == "__main__":
+    from pip._internal.cli.main import main as _main
+
+    sys.exit(_main())

bioelectea-0.1.0/.venv-test/Lib/site-packages/pip/__pip-runner__.py

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+"""Execute exactly this copy of pip, within a different environment.
+
+This file is named as it is, to ensure that this module can't be imported via
+an import statement.
+"""
+
+# /!\ This version compatibility check section must be Python 2 compatible. /!\
+
+import sys
+
+# Copied from pyproject.toml
+PYTHON_REQUIRES = (3, 8)
+
+
+def version_str(version):  # type: ignore
+    return ".".join(str(v) for v in version)
+
+
+if sys.version_info[:2] < PYTHON_REQUIRES:
+    raise SystemExit(
+        "This version of pip does not support python {} (requires >={}).".format(
+            version_str(sys.version_info[:2]), version_str(PYTHON_REQUIRES)
+        )
+    )
+
+# From here on, we can use Python 3 features, but the syntax must remain
+# Python 2 compatible.
+
+import runpy  # noqa: E402
+from importlib.machinery import PathFinder  # noqa: E402
+from os.path import dirname  # noqa: E402
+
+PIP_SOURCES_ROOT = dirname(dirname(__file__))
+
+
+class PipImportRedirectingFinder:
+    @classmethod
+    def find_spec(self, fullname, path=None, target=None):  # type: ignore
+        if fullname != "pip":
+            return None
+
+        spec = PathFinder.find_spec(fullname, [PIP_SOURCES_ROOT], target)
+        assert spec, (PIP_SOURCES_ROOT, fullname)
+        return spec
+
+
+sys.meta_path.insert(0, PipImportRedirectingFinder())
+
+assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module"
+runpy.run_module("pip", run_name="__main__", alter_sys=True)

bioelectea-0.1.0/.venv-test/Lib/site-packages/pip/_internal/__init__.py

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+from typing import List, Optional
+
+from pip._internal.utils import _log
+
+# init_logging() must be called before any call to logging.getLogger()
+# which happens at import of most modules.
+_log.init_logging()
+
+
+def main(args: Optional[List[str]] = None) -> int:
+    """This is preserved for old console scripts that may still be referencing
+    it.
+
+    For additional details, see https://github.com/pypa/pip/issues/7498.
+    """
+    from pip._internal.utils.entrypoints import _wrapper
+
+    return _wrapper(args)

bioelectea-0.1.0/.venv-test/Lib/site-packages/pip/_internal/build_env.py

@@ -0,0 +1,322 @@
+"""Build Environment used for isolation during sdist building
+"""
+
+import logging
+import os
+import pathlib
+import site
+import sys
+import textwrap
+from collections import OrderedDict
+from types import TracebackType
+from typing import TYPE_CHECKING, Iterable, List, Optional, Set, Tuple, Type, Union
+
+from pip._vendor.packaging.version import Version
+
+from pip import __file__ as pip_location
+from pip._internal.cli.spinners import open_spinner
+from pip._internal.locations import get_platlib, get_purelib, get_scheme
+from pip._internal.metadata import get_default_environment, get_environment
+from pip._internal.utils.logging import VERBOSE
+from pip._internal.utils.packaging import get_requirement
+from pip._internal.utils.subprocess import call_subprocess
+from pip._internal.utils.temp_dir import TempDirectory, tempdir_kinds
+
+if TYPE_CHECKING:
+    from pip._internal.index.package_finder import PackageFinder
+
+logger = logging.getLogger(__name__)
+
+
+def _dedup(a: str, b: str) -> Union[Tuple[str], Tuple[str, str]]:
+    return (a, b) if a != b else (a,)
+
+
+class _Prefix:
+    def __init__(self, path: str) -> None:
+        self.path = path
+        self.setup = False
+        scheme = get_scheme("", prefix=path)
+        self.bin_dir = scheme.scripts
+        self.lib_dirs = _dedup(scheme.purelib, scheme.platlib)
+
+
+def get_runnable_pip() -> str:
+    """Get a file to pass to a Python executable, to run the currently-running pip.
+
+    This is used to run a pip subprocess, for installing requirements into the build
+    environment.
+    """
+    source = pathlib.Path(pip_location).resolve().parent
+
+    if not source.is_dir():
+        # This would happen if someone is using pip from inside a zip file. In that
+        # case, we can use that directly.
+        return str(source)
+
+    return os.fsdecode(source / "__pip-runner__.py")
+
+
+def _get_system_sitepackages() -> Set[str]:
+    """Get system site packages
+
+    Usually from site.getsitepackages,
+    but fallback on `get_purelib()/get_platlib()` if unavailable
+    (e.g. in a virtualenv created by virtualenv<20)
+
+    Returns normalized set of strings.
+    """
+    if hasattr(site, "getsitepackages"):
+        system_sites = site.getsitepackages()
+    else:
+        # virtualenv < 20 overwrites site.py without getsitepackages
+        # fallback on get_purelib/get_platlib.
+        # this is known to miss things, but shouldn't in the cases
+        # where getsitepackages() has been removed (inside a virtualenv)
+        system_sites = [get_purelib(), get_platlib()]
+    return {os.path.normcase(path) for path in system_sites}
+
+
+class BuildEnvironment:
+    """Creates and manages an isolated environment to install build deps"""
+
+    def __init__(self) -> None:
+        temp_dir = TempDirectory(kind=tempdir_kinds.BUILD_ENV, globally_managed=True)
+
+        self._prefixes = OrderedDict(
+            (name, _Prefix(os.path.join(temp_dir.path, name)))
+            for name in ("normal", "overlay")
+        )
+
+        self._bin_dirs: List[str] = []
+        self._lib_dirs: List[str] = []
+        for prefix in reversed(list(self._prefixes.values())):
+            self._bin_dirs.append(prefix.bin_dir)
+            self._lib_dirs.extend(prefix.lib_dirs)
+
+        # Customize site to:
+        # - ensure .pth files are honored
+        # - prevent access to system site packages
+        system_sites = _get_system_sitepackages()
+
+        self._site_dir = os.path.join(temp_dir.path, "site")
+        if not os.path.exists(self._site_dir):
+            os.mkdir(self._site_dir)
+        with open(
+            os.path.join(self._site_dir, "sitecustomize.py"), "w", encoding="utf-8"
+        ) as fp:
+            fp.write(
+                textwrap.dedent(
+                    """
+                import os, site, sys
+
+                # First, drop system-sites related paths.
+                original_sys_path = sys.path[:]
+                known_paths = set()
+                for path in {system_sites!r}:
+                    site.addsitedir(path, known_paths=known_paths)
+                system_paths = set(
+                    os.path.normcase(path)
+                    for path in sys.path[len(original_sys_path):]
+                )
+                original_sys_path = [
+                    path for path in original_sys_path
+                    if os.path.normcase(path) not in system_paths
+                ]
+                sys.path = original_sys_path
+
+                # Second, add lib directories.
+                # ensuring .pth file are processed.
+                for path in {lib_dirs!r}:
+                    assert not path in sys.path
+                    site.addsitedir(path)
+                """
+                ).format(system_sites=system_sites, lib_dirs=self._lib_dirs)
+            )
+
+    def __enter__(self) -> None:
+        self._save_env = {
+            name: os.environ.get(name, None)
+            for name in ("PATH", "PYTHONNOUSERSITE", "PYTHONPATH")
+        }
+
+        path = self._bin_dirs[:]
+        old_path = self._save_env["PATH"]
+        if old_path:
+            path.extend(old_path.split(os.pathsep))
+
+        pythonpath = [self._site_dir]
+
+        os.environ.update(
+            {
+                "PATH": os.pathsep.join(path),
+                "PYTHONNOUSERSITE": "1",
+                "PYTHONPATH": os.pathsep.join(pythonpath),
+            }
+        )
+
+    def __exit__(
+        self,
+        exc_type: Optional[Type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[TracebackType],
+    ) -> None:
+        for varname, old_value in self._save_env.items():
+            if old_value is None:
+                os.environ.pop(varname, None)
+            else:
+                os.environ[varname] = old_value
+
+    def check_requirements(
+        self, reqs: Iterable[str]
+    ) -> Tuple[Set[Tuple[str, str]], Set[str]]:
+        """Return 2 sets:
+        - conflicting requirements: set of (installed, wanted) reqs tuples
+        - missing requirements: set of reqs
+        """
+        missing = set()
+        conflicting = set()
+        if reqs:
+            env = (
+                get_environment(self._lib_dirs)
+                if hasattr(self, "_lib_dirs")
+                else get_default_environment()
+            )
+            for req_str in reqs:
+                req = get_requirement(req_str)
+                # We're explicitly evaluating with an empty extra value, since build
+                # environments are not provided any mechanism to select specific extras.
+                if req.marker is not None and not req.marker.evaluate({"extra": ""}):
+                    continue
+                dist = env.get_distribution(req.name)
+                if not dist:
+                    missing.add(req_str)
+                    continue
+                if isinstance(dist.version, Version):
+                    installed_req_str = f"{req.name}=={dist.version}"
+                else:
+                    installed_req_str = f"{req.name}==={dist.version}"
+                if not req.specifier.contains(dist.version, prereleases=True):
+                    conflicting.add((installed_req_str, req_str))
+                # FIXME: Consider direct URL?
+        return conflicting, missing
+
+    def install_requirements(
+        self,
+        finder: "PackageFinder",
+        requirements: Iterable[str],
+        prefix_as_string: str,
+        *,
+        kind: str,
+    ) -> None:
+        prefix = self._prefixes[prefix_as_string]
+        assert not prefix.setup
+        prefix.setup = True
+        if not requirements:
+            return
+        self._install_requirements(
+            get_runnable_pip(),
+            finder,
+            requirements,
+            prefix,
+            kind=kind,
+        )
+
+    @staticmethod
+    def _install_requirements(
+        pip_runnable: str,
+        finder: "PackageFinder",
+        requirements: Iterable[str],
+        prefix: _Prefix,
+        *,
+        kind: str,
+    ) -> None:
+        args: List[str] = [
+            sys.executable,
+            pip_runnable,
+            "install",
+            "--ignore-installed",
+            "--no-user",
+            "--prefix",
+            prefix.path,
+            "--no-warn-script-location",
+            "--disable-pip-version-check",
+            # The prefix specified two lines above, thus
+            # target from config file or env var should be ignored
+            "--target",
+            "",
+        ]
+        if logger.getEffectiveLevel() <= logging.DEBUG:
+            args.append("-vv")
+        elif logger.getEffectiveLevel() <= VERBOSE:
+            args.append("-v")
+        for format_control in ("no_binary", "only_binary"):
+            formats = getattr(finder.format_control, format_control)
+            args.extend(
+                (
+                    "--" + format_control.replace("_", "-"),
+                    ",".join(sorted(formats or {":none:"})),
+                )
+            )
+
+        index_urls = finder.index_urls
+        if index_urls:
+            args.extend(["-i", index_urls[0]])
+            for extra_index in index_urls[1:]:
+                args.extend(["--extra-index-url", extra_index])
+        else:
+            args.append("--no-index")
+        for link in finder.find_links:
+            args.extend(["--find-links", link])
+
+        if finder.proxy:
+            args.extend(["--proxy", finder.proxy])
+        for host in finder.trusted_hosts:
+            args.extend(["--trusted-host", host])
+        if finder.custom_cert:
+            args.extend(["--cert", finder.custom_cert])
+        if finder.client_cert:
+            args.extend(["--client-cert", finder.client_cert])
+        if finder.allow_all_prereleases:
+            args.append("--pre")
+        if finder.prefer_binary:
+            args.append("--prefer-binary")
+        args.append("--")
+        args.extend(requirements)
+        with open_spinner(f"Installing {kind}") as spinner:
+            call_subprocess(
+                args,
+                command_desc=f"pip subprocess to install {kind}",
+                spinner=spinner,
+            )
+
+
+class NoOpBuildEnvironment(BuildEnvironment):
+    """A no-op drop-in replacement for BuildEnvironment"""
+
+    def __init__(self) -> None:
+        pass
+
+    def __enter__(self) -> None:
+        pass
+
+    def __exit__(
+        self,
+        exc_type: Optional[Type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[TracebackType],
+    ) -> None:
+        pass
+
+    def cleanup(self) -> None:
+        pass
+
+    def install_requirements(
+        self,
+        finder: "PackageFinder",
+        requirements: Iterable[str],
+        prefix_as_string: str,
+        *,
+        kind: str,
+    ) -> None:
+        raise NotImplementedError()