bioelectea 0.1.0__tar.gz → 0.1.3__tar.gz

bioelectea-0.1.3/.github/workflows/ci.yml

@@ -0,0 +1,39 @@
+name: ci
+
+on:
+  push:
+    branches: ["main", "develop"]
+  pull_request:
+    branches: ["main", "develop"]
+
+jobs:
+  build-test-lint:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]  # <= 3.10 제거
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Upgrade pip
+        run: python -m pip install -U pip
+
+      - name: Install dev deps
+        run: pip install -e .[dev]
+
+      - name: Lint (ruff)
+        run: ruff check .
+
+      - name: Type check (mypy)
+        run: mypy src
+
+      - name: Test (pytest)
+        run: pytest -q

bioelectea-0.1.3/.github/workflows/release.yml

@@ -0,0 +1,31 @@
+name: release
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi          # 👈 이 줄 추가 (PyPI에 등록한 Environment name과 정확히 동일해야 합니다)
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build package
+        run: |
+          python -m pip install -U pip build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

bioelectea-0.1.3/.gitignore

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

bioelectea-0.1.3/.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+      - id: ruff-format
+
+  - repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        # 🔑 venv/배포 산출물은 제외
+        exclude: ^(\.venv.*|venv|\.vscode|dist|build|\.eggs|\.pytest_cache|\.mypy_cache|docs/|scripts/|notebooks/)
+        # 🔑 파일 범위: src/와 tests/만
+        files: ^(src/|tests/)
+        args:
+          - --config-file=pyproject.toml
+          - --install-types
+          - --non-interactive
+        additional_dependencies: []

bioelectea-0.1.3/.venv-prod/Lib/site-packages/bioelectea/__init__.py

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

bioelectea-0.1.3/.venv-prod/Lib/site-packages/bioelectea/__main__.py

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

bioelectea-0.1.3/.venv-prod/Lib/site-packages/bioelectea/cli.py

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

bioelectea-0.1.3/.venv-prod/Lib/site-packages/bioelectea-0.1.0.dist-info/RECORD

@@ -0,0 +1,13 @@
+../../Scripts/bioelectea.exe,sha256=hYlpLwyYQcY4sfYTxSGkoj7QiwmV0mLlRAYRBPD8MEA,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-0.1.3/.venv-prod/Lib/site-packages/pip/_internal/build_env.py

@@ -0,0 +1,316 @@
+"""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()

bioelectea-0.1.3/.venv-prod/Lib/site-packages/pip/_internal/cli/autocompletion.py

@@ -0,0 +1,167 @@
+"""Logic that powers autocompletion installed by ``pip completion``.
+"""
+
+import optparse
+import os
+import sys
+from itertools import chain
+from typing import Any, Iterable, List, Optional
+
+from pip._internal.cli.main_parser import create_main_parser
+from pip._internal.commands import commands_dict, create_command
+from pip._internal.metadata import get_default_environment
+
+
+def autocomplete() -> None:
+    """Entry Point for completion of main and subcommand options."""
+    # Don't complete if user hasn't sourced bash_completion file.
+    if "PIP_AUTO_COMPLETE" not in os.environ:
+        return
+    # Don't complete if autocompletion environment variables
+    # are not present
+    if not os.environ.get("COMP_WORDS") or not os.environ.get("COMP_CWORD"):
+        return
+    cwords = os.environ["COMP_WORDS"].split()[1:]
+    cword = int(os.environ["COMP_CWORD"])
+    try:
+        current = cwords[cword - 1]
+    except IndexError:
+        current = ""
+
+    parser = create_main_parser()
+    subcommands = list(commands_dict)
+    options = []
+
+    # subcommand
+    subcommand_name: Optional[str] = None
+    for word in cwords:
+        if word in subcommands:
+            subcommand_name = word
+            break
+    # subcommand options
+    if subcommand_name is not None:
+        # special case: 'help' subcommand has no options
+        if subcommand_name == "help":
+            sys.exit(1)
+        # special case: list locally installed dists for show and uninstall
+        should_list_installed = not current.startswith("-") and subcommand_name in [
+            "show",
+            "uninstall",
+        ]
+        if should_list_installed:
+            env = get_default_environment()
+            lc = current.lower()
+            installed = [
+                dist.canonical_name
+                for dist in env.iter_installed_distributions(local_only=True)
+                if dist.canonical_name.startswith(lc) and dist.canonical_name not in cwords[1:]
+            ]
+            # if there are no dists installed, fall back to option completion
+            if installed:
+                for dist in installed:
+                    print(dist)
+                sys.exit(1)
+
+        should_list_installables = not current.startswith("-") and subcommand_name == "install"
+        if should_list_installables:
+            for path in auto_complete_paths(current, "path"):
+                print(path)
+            sys.exit(1)
+
+        subcommand = create_command(subcommand_name)
+
+        for opt in subcommand.parser.option_list_all:
+            if opt.help != optparse.SUPPRESS_HELP:
+                options += [(opt_str, opt.nargs) for opt_str in opt._long_opts + opt._short_opts]
+
+        # filter out previously specified options from available options
+        prev_opts = [x.split("=")[0] for x in cwords[1 : cword - 1]]
+        options = [(x, v) for (x, v) in options if x not in prev_opts]
+        # filter options by current input
+        options = [(k, v) for k, v in options if k.startswith(current)]
+        # get completion type given cwords and available subcommand options
+        completion_type = get_path_completion_type(
+            cwords,
+            cword,
+            subcommand.parser.option_list_all,
+        )
+        # get completion files and directories if ``completion_type`` is
+        # ``<file>``, ``<dir>`` or ``<path>``
+        if completion_type:
+            paths = auto_complete_paths(current, completion_type)
+            options = [(path, 0) for path in paths]
+        for option in options:
+            opt_label = option[0]
+            # append '=' to options which require args
+            if option[1] and option[0][:2] == "--":
+                opt_label += "="
+            print(opt_label)
+    else:
+        # show main parser options only when necessary
+
+        opts = [i.option_list for i in parser.option_groups]
+        opts.append(parser.option_list)
+        flattened_opts = chain.from_iterable(opts)
+        if current.startswith("-"):
+            for opt in flattened_opts:
+                if opt.help != optparse.SUPPRESS_HELP:
+                    subcommands += opt._long_opts + opt._short_opts
+        else:
+            # get completion type given cwords and all available options
+            completion_type = get_path_completion_type(cwords, cword, flattened_opts)
+            if completion_type:
+                subcommands = list(auto_complete_paths(current, completion_type))
+
+        print(" ".join([x for x in subcommands if x.startswith(current)]))
+    sys.exit(1)
+
+
+def get_path_completion_type(cwords: List[str], cword: int, opts: Iterable[Any]) -> Optional[str]:
+    """Get the type of path completion (``file``, ``dir``, ``path`` or None)
+
+    :param cwords: same as the environmental variable ``COMP_WORDS``
+    :param cword: same as the environmental variable ``COMP_CWORD``
+    :param opts: The available options to check
+    :return: path completion type (``file``, ``dir``, ``path`` or None)
+    """
+    if cword < 2 or not cwords[cword - 2].startswith("-"):
+        return None
+    for opt in opts:
+        if opt.help == optparse.SUPPRESS_HELP:
+            continue
+        for o in str(opt).split("/"):
+            if cwords[cword - 2].split("=")[0] == o:
+                if not opt.metavar or any(
+                    x in ("path", "file", "dir") for x in opt.metavar.split("/")
+                ):
+                    return opt.metavar
+    return None
+
+
+def auto_complete_paths(current: str, completion_type: str) -> Iterable[str]:
+    """If ``completion_type`` is ``file`` or ``path``, list all regular files
+    and directories starting with ``current``; otherwise only list directories
+    starting with ``current``.
+
+    :param current: The word to be completed
+    :param completion_type: path completion type(``file``, ``path`` or ``dir``)
+    :return: A generator of regular files and/or directories
+    """
+    directory, filename = os.path.split(current)
+    current_path = os.path.abspath(directory)
+    # Don't complete paths if they can't be accessed
+    if not os.access(current_path, os.R_OK):
+        return
+    filename = os.path.normcase(filename)
+    # list all files that start with ``filename``
+    file_list = (x for x in os.listdir(current_path) if os.path.normcase(x).startswith(filename))
+    for f in file_list:
+        opt = os.path.join(current_path, f)
+        comp_file = os.path.normcase(os.path.join(directory, f))
+        # complete regular files when there is not ``<dir>`` after option
+        # complete directories when there is ``<file>``, ``<path>`` or
+        # ``<dir>``after option
+        if completion_type != "dir" and os.path.isfile(opt):
+            yield comp_file
+        elif os.path.isdir(opt):
+            yield os.path.join(comp_file, "")