scitex 2.7.3__py3-none-any.whl → 2.8.1__py3-none-any.whl

scitex/io/_zip_bundle.py

@@ -0,0 +1,439 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Timestamp: "2025-12-14 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-code/src/scitex/io/_zip_bundle.py
+
+"""
+SciTeX ZipBundle - In-memory zip archive handler with atomic writes.
+
+Provides efficient access to .figz, .pltz, .statsz bundles without extracting
+to disk. Supports:
+    - In-memory file reading
+    - Atomic writes using temp files
+    - Context manager protocol
+    - Dict-like access to files
+"""
+
+import io
+import json
+import os
+import shutil
+import tempfile
+import zipfile
+from pathlib import Path
+from typing import Any, BinaryIO, Dict, Iterator, List, Optional, Union
+
+import pandas as pd
+
+__all__ = [
+    "ZipBundle",
+    "open_bundle",
+    "create_bundle",
+]
+
+
+class ZipBundle:
+    """In-memory zip bundle handler.
+
+    Provides efficient read/write access to zip archives without extracting
+    to disk. Files are read into memory on demand and writes are atomic.
+
+    Usage:
+        # Reading
+        with ZipBundle("figure.figz") as bundle:
+            spec = bundle.read_json("spec.json")
+            csv_data = bundle.read_csv("data.csv")
+            png_bytes = bundle.read_bytes("exports/figure.png")
+
+        # Writing
+        with ZipBundle("output.pltz", mode="w") as bundle:
+            bundle.write_json("spec.json", spec_dict)
+            bundle.write_csv("data.csv", dataframe)
+            bundle.write_bytes("exports/plot.png", png_bytes)
+
+        # Modifying (read then write atomically)
+        with ZipBundle("figure.figz", mode="a") as bundle:
+            spec = bundle.read_json("spec.json")
+            spec["title"] = "Updated"
+            bundle.write_json("spec.json", spec)
+    """
+
+    def __init__(
+        self,
+        path: Union[str, Path],
+        mode: str = "r",
+        compression: int = zipfile.ZIP_DEFLATED,
+    ):
+        """Initialize ZipBundle.
+
+        Args:
+            path: Path to zip file (.figz, .pltz, .statsz)
+            mode: 'r' for read, 'w' for write, 'a' for append/modify
+            compression: ZIP compression method (default: ZIP_DEFLATED)
+        """
+        self.path = Path(path)
+        self.mode = mode
+        self.compression = compression
+        self._zipfile: Optional[zipfile.ZipFile] = None
+        self._cache: Dict[str, bytes] = {}  # Cache for read files
+        self._pending_writes: Dict[str, bytes] = {}  # Pending writes for atomic commit
+        self._temp_path: Optional[Path] = None
+        self._closed = False
+
+    def __enter__(self) -> "ZipBundle":
+        """Enter context manager."""
+        self.open()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb) -> None:
+        """Exit context manager with atomic commit on success."""
+        if exc_type is None and self.mode in ("w", "a"):
+            self._atomic_commit()
+        self.close()
+
+    def open(self) -> None:
+        """Open the zip bundle."""
+        if self.mode == "r":
+            if not self.path.exists():
+                raise FileNotFoundError(f"Bundle not found: {self.path}")
+            self._zipfile = zipfile.ZipFile(self.path, "r")
+        elif self.mode == "w":
+            # Create new archive (write to temp, commit on close)
+            self._temp_path = Path(tempfile.mktemp(suffix=self.path.suffix))
+            self._zipfile = zipfile.ZipFile(
+                self._temp_path, "w", self.compression
+            )
+        elif self.mode == "a":
+            # Append mode: read existing, write to temp, commit atomically
+            if self.path.exists():
+                # Load existing contents into cache
+                with zipfile.ZipFile(self.path, "r") as zf:
+                    for name in zf.namelist():
+                        self._cache[name] = zf.read(name)
+            self._temp_path = Path(tempfile.mktemp(suffix=self.path.suffix))
+            self._zipfile = zipfile.ZipFile(
+                self._temp_path, "w", self.compression
+            )
+        else:
+            raise ValueError(f"Invalid mode: {self.mode}")
+
+    def close(self) -> None:
+        """Close the zip bundle."""
+        if self._zipfile and not self._closed:
+            self._zipfile.close()
+            self._closed = True
+            # Clean up temp file if not committed (error case)
+            if self._temp_path and self._temp_path.exists():
+                if self.mode in ("w", "a") and not self.path.exists():
+                    # Commit wasn't called, clean up
+                    self._temp_path.unlink()
+
+    def _atomic_commit(self) -> None:
+        """Atomically commit writes by renaming temp file.
+
+        This ensures the bundle is never in an inconsistent state.
+        Either the old file exists completely, or the new one does.
+        """
+        if self._temp_path is None:
+            return
+
+        # Write all pending and cached content to the temp zip
+        self._zipfile.close()
+        self._closed = True
+
+        # Atomic rename (works on same filesystem)
+        # On Windows, we need to remove target first
+        if os.name == "nt" and self.path.exists():
+            backup_path = self.path.with_suffix(self.path.suffix + ".bak")
+            self.path.rename(backup_path)
+            try:
+                self._temp_path.rename(self.path)
+                backup_path.unlink()
+            except Exception:
+                # Restore backup on failure
+                backup_path.rename(self.path)
+                raise
+        else:
+            # Unix: atomic rename
+            self._temp_path.rename(self.path)
+
+    # =========================================================================
+    # File listing
+    # =========================================================================
+
+    def namelist(self) -> List[str]:
+        """List all files in the bundle."""
+        if self.mode == "r":
+            return self._zipfile.namelist()
+        else:
+            # Include both cached and pending writes
+            names = set(self._cache.keys())
+            names.update(self._pending_writes.keys())
+            return sorted(names)
+
+    def __contains__(self, name: str) -> bool:
+        """Check if file exists in bundle."""
+        return name in self.namelist()
+
+    def __iter__(self) -> Iterator[str]:
+        """Iterate over file names in bundle."""
+        return iter(self.namelist())
+
+    # =========================================================================
+    # Reading
+    # =========================================================================
+
+    def read_bytes(self, name: str) -> bytes:
+        """Read file as bytes.
+
+        Args:
+            name: File path within the zip (e.g., "spec.json", "exports/plot.png")
+
+        Returns:
+            File contents as bytes.
+        """
+        # Check cache first (for append mode)
+        if name in self._pending_writes:
+            return self._pending_writes[name]
+        if name in self._cache:
+            return self._cache[name]
+
+        # Read from zip
+        if self._zipfile is None:
+            raise RuntimeError("Bundle not opened")
+
+        # Handle files inside .d directory structure
+        # Try direct name first, then with .d prefix
+        try:
+            data = self._zipfile.read(name)
+            self._cache[name] = data
+            return data
+        except KeyError:
+            # Try with directory prefix (e.g., "bundle.pltz.d/spec.json")
+            # The path.name includes extension, so "foo.pltz" -> "foo.pltz.d"
+            dir_name = self.path.name + ".d"
+            full_name = f"{dir_name}/{name}"
+            try:
+                data = self._zipfile.read(full_name)
+                self._cache[name] = data
+                return data
+            except KeyError:
+                # Try to find the .d directory dynamically
+                # (handles case where pltz was renamed, e.g., panel_A.pltz -> A.pltz
+                # but internal structure is still panel_A.pltz.d/)
+                for arc_name in self._zipfile.namelist():
+                    if arc_name.endswith('.d/' + name) or arc_name.endswith('.d/' + name.replace('/', '/')):
+                        data = self._zipfile.read(arc_name)
+                        self._cache[name] = data
+                        return data
+                raise FileNotFoundError(f"File not found in bundle: {name}")
+
+    def read_text(self, name: str, encoding: str = "utf-8") -> str:
+        """Read file as text.
+
+        Args:
+            name: File path within the zip.
+            encoding: Text encoding (default: utf-8).
+
+        Returns:
+            File contents as string.
+        """
+        return self.read_bytes(name).decode(encoding)
+
+    def read_json(self, name: str = "spec.json") -> Dict[str, Any]:
+        """Read and parse JSON file.
+
+        Args:
+            name: JSON file path within the zip.
+
+        Returns:
+            Parsed JSON as dictionary.
+        """
+        return json.loads(self.read_text(name))
+
+    def read_csv(self, name: str = "data.csv", **kwargs) -> pd.DataFrame:
+        """Read CSV file as pandas DataFrame.
+
+        Args:
+            name: CSV file path within the zip.
+            **kwargs: Additional arguments passed to pd.read_csv.
+
+        Returns:
+            DataFrame with CSV contents.
+        """
+        data = self.read_bytes(name)
+        return pd.read_csv(io.BytesIO(data), **kwargs)
+
+    def read_image(self, name: str) -> bytes:
+        """Read image file as bytes.
+
+        Args:
+            name: Image file path (e.g., "exports/figure.png").
+
+        Returns:
+            Image bytes.
+        """
+        return self.read_bytes(name)
+
+    # =========================================================================
+    # Writing
+    # =========================================================================
+
+    def write_bytes(self, name: str, data: bytes) -> None:
+        """Write bytes to file in bundle.
+
+        Args:
+            name: File path within the zip.
+            data: Bytes to write.
+        """
+        if self.mode == "r":
+            raise RuntimeError("Cannot write in read mode")
+
+        self._pending_writes[name] = data
+        self._cache[name] = data  # Update cache
+
+        # Write to zip immediately
+        self._zipfile.writestr(name, data)
+
+    def write_text(self, name: str, text: str, encoding: str = "utf-8") -> None:
+        """Write text to file in bundle.
+
+        Args:
+            name: File path within the zip.
+            text: Text to write.
+            encoding: Text encoding (default: utf-8).
+        """
+        self.write_bytes(name, text.encode(encoding))
+
+    def write_json(
+        self, name: str, data: Dict[str, Any], indent: int = 2
+    ) -> None:
+        """Write dictionary as JSON file.
+
+        Args:
+            name: JSON file path within the zip.
+            data: Dictionary to serialize.
+            indent: JSON indentation (default: 2).
+        """
+        text = json.dumps(data, indent=indent, ensure_ascii=False)
+        self.write_text(name, text)
+
+    def write_csv(
+        self, name: str, df: pd.DataFrame, index: bool = False, **kwargs
+    ) -> None:
+        """Write pandas DataFrame as CSV.
+
+        Args:
+            name: CSV file path within the zip.
+            df: DataFrame to write.
+            index: Include index column (default: False).
+            **kwargs: Additional arguments passed to df.to_csv.
+        """
+        buffer = io.BytesIO()
+        df.to_csv(buffer, index=index, **kwargs)
+        self.write_bytes(name, buffer.getvalue())
+
+    def write_image(self, name: str, data: bytes) -> None:
+        """Write image bytes to bundle.
+
+        Args:
+            name: Image file path (e.g., "exports/figure.png").
+            data: Image bytes.
+        """
+        self.write_bytes(name, data)
+
+    # =========================================================================
+    # Convenience methods
+    # =========================================================================
+
+    @property
+    def spec(self) -> Optional[Dict[str, Any]]:
+        """Get bundle specification (spec.json)."""
+        try:
+            return self.read_json("spec.json")
+        except FileNotFoundError:
+            return None
+
+    @property
+    def style(self) -> Optional[Dict[str, Any]]:
+        """Get bundle style (style.json)."""
+        try:
+            return self.read_json("style.json")
+        except FileNotFoundError:
+            return None
+
+    @property
+    def data(self) -> Optional[pd.DataFrame]:
+        """Get bundle data (data.csv)."""
+        try:
+            return self.read_csv("data.csv")
+        except FileNotFoundError:
+            return None
+
+
+def open_bundle(
+    path: Union[str, Path], mode: str = "r"
+) -> ZipBundle:
+    """Open a bundle for reading or writing.
+
+    Args:
+        path: Path to bundle file.
+        mode: 'r' for read, 'w' for write, 'a' for append.
+
+    Returns:
+        ZipBundle instance (use as context manager).
+
+    Example:
+        with open_bundle("figure.figz") as bundle:
+            spec = bundle.spec
+            data = bundle.data
+    """
+    return ZipBundle(path, mode=mode)
+
+
+def create_bundle(
+    path: Union[str, Path],
+    spec: Dict[str, Any],
+    data: Optional[pd.DataFrame] = None,
+    style: Optional[Dict[str, Any]] = None,
+    exports: Optional[Dict[str, bytes]] = None,
+) -> Path:
+    """Create a new bundle with atomic write.
+
+    Args:
+        path: Output path (.figz, .pltz, or .statsz).
+        spec: Bundle specification dictionary.
+        data: Optional CSV data as DataFrame.
+        style: Optional style dictionary.
+        exports: Optional dict mapping export paths to bytes.
+
+    Returns:
+        Path to created bundle.
+
+    Example:
+        create_bundle(
+            "plot.pltz",
+            spec={"schema": {"name": "scitex.plt", "version": "1.0"}},
+            data=df,
+            exports={"exports/plot.png": png_bytes},
+        )
+    """
+    path = Path(path)
+
+    with ZipBundle(path, mode="w") as bundle:
+        bundle.write_json("spec.json", spec)
+
+        if data is not None:
+            bundle.write_csv("data.csv", data)
+
+        if style is not None:
+            bundle.write_json("style.json", style)
+
+        if exports:
+            for export_path, export_data in exports.items():
+                bundle.write_bytes(export_path, export_data)
+
+    return path
+
+
+# EOF

{scitex-2.7.3.dist-info → scitex-2.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scitex
-Version: 2.7.3
+Version: 2.8.1
 Summary: A comprehensive Python library for scientific computing and data analysis
 Project-URL: Homepage, https://github.com/ywatanabe1989/scitex-code
 Project-URL: Documentation, https://scitex.readthedocs.io

{scitex-2.7.3.dist-info → scitex-2.8.1.dist-info}/RECORD

@@ -1,7 +1,7 @@
 scitex/.mcp.json,sha256=ge1NDrBZkRIxJgx_tCS9QvcEa_P_ay8AAAafraZVRP4,1259
 scitex/__init__.py,sha256=ESpP5HKTZ34-xh1a2K_oJR3akM4hbkVVBfDb-A1CkrA,6083
 scitex/__main__.py,sha256=_7OnKtETkmRU1QhAGIUJaT2WrCdsYar0ggzgMJ-HyEI,489
-scitex/__version__.py,sha256=iQ0rp6rW9R0PfZp6PjAMyELi7pslATuNZUPRNUDqNvY,400
+scitex/__version__.py,sha256=NcPRlyVnKJaSOV7QCDikJE_oFfPtxPQDGpJ4tu0CgfA,400
 scitex/_optional_deps.py,sha256=dRLke1qnkOQ0RJBlKQ45ErfAphxjRcohpIjzYhnyylA,3607
 scitex/errors.py,sha256=R317_uneFtBWA8yYPOHq6CRi0menDk0NCooMLbCMBQs,15228
 scitex/units.py,sha256=lm2SH4PGXz-22tjUoBQhvKJDKmPD01ykSFWoCaFC384,10356
@@ -374,6 +374,13 @@ scitex/dev/plt/plot_stx_scatter.py,sha256=yJnZE0aL5Z0armnKyxCgdSIfmwSx0MO_BoDbzT
 scitex/dev/plt/plot_stx_shaded_line.py,sha256=Ss4RD0qxO_uH1h_NL_meSH1-_ZXfOKnV1MAT48tegnI,718
 scitex/dev/plt/plot_stx_violin.py,sha256=oEAWE4RwG7SQ3JlVuzfSbTFDF02VRb_vE4qBLU3tMu4,680
 scitex/dev/plt/plot_stx_violinplot.py,sha256=wafuzIKs9WJRfXcH4bxxuigqCh75nxcZDfFq-9P1zxA,687
+scitex/diagram/README.md,sha256=nJGYjSQRaQyecrs93Y5veiV9NYBI3BREC8VQRkja_fQ,4822
+scitex/diagram/__init__.py,sha256=JfT2X9-PNrUyUcvDiz_z7Na3ABzVUOftDV4aS9lGdHo,1488
+scitex/diagram/_compile.py,sha256=JPjVHEJPk884Qfrk9wpbxjQ0PB7AlzQxsi4Sv-osXHU,10282
+scitex/diagram/_diagram.py,sha256=lPTTjrPuAO0WJlTxluygzU7qaKL5cYIqK4yUSwO8NHI,10565
+scitex/diagram/_presets.py,sha256=X1bHVTxGeVHXGCUXJ1y-z7al9k_eh1TmuBnwogWPE20,5392
+scitex/diagram/_schema.py,sha256=moLs8yCthdDI9P4ehFPacGxdEUjeTJ0jAA1knkZtjWw,6173
+scitex/diagram/_split.py,sha256=EaLhK4X65luTx4Q0hPG-6kwESoQNbOAMdzUA3ekPlIY,8394
 scitex/dict/_DotDict.py,sha256=ES8FTu5icpyDimNEhCPybCKTvtmxiAb5qu2BvLdfGfA,14822
 scitex/dict/__init__.py,sha256=HX5JwsBeDp5mraVQrhSUOQz-KFead6fPDNBRAOkteVM,402
 scitex/dict/_flatten.py,sha256=S69tIfqeyhvsJU29FKrTKanWZ6mV-lal_aDGQ1dLElw,613
@@ -427,26 +434,74 @@ scitex/fig/backend/_export.py,sha256=WSHIDn_LjaScBoe0e27vCHgMLkuA3IVXw1I69DwdI_A
 scitex/fig/backend/_parser.py,sha256=WNPVW6peqeWBZRth0e4o6JWEFtREo6CAgyxhkKH7kjM,4490
 scitex/fig/backend/_render.py,sha256=_LEqJ2NmJxzDzi8FfgEWuT-Lvm_YlFRtNt3neKnQnXk,11138
 scitex/fig/docs/CANVAS_ARCHITECTURE.md,sha256=LF5GSiUA1ZWriZt1lAc0FNsGEjl__zgqDQLIp6HKkb8,10559
-scitex/fig/editor/__init__.py,sha256=WOTzc1pn-_GJb4WOATlI8T48_kbsPqUsLSnHgA3u4HM,578
-scitex/fig/editor/_dearpygui_editor.py,sha256=2ec6TuoPU_qNDn38C37YLk9pGbLzOWv_GrCTHzpmdhQ,76300
+scitex/fig/editor/__init__.py,sha256=FpsAFnNPTVeH_UudaRIMB_wHpO9MjYoqocLvzaFutkU,648
+scitex/fig/editor/_dearpygui_editor.py,sha256=9nKfqE45okVr6XbHwWdmJYqX-nAcuENIH5ElXeg_NaM,76299
 scitex/fig/editor/_defaults.py,sha256=4-oIZZmwkBTFJj7tKDCy7Ezp55GxbLFP8s_YTYvuFD0,9855
-scitex/fig/editor/_edit.py,sha256=VzSWGV7O3dtyGda77vojXLRa_3pQLPYEehxmAFf3Agw,23476
 scitex/fig/editor/_flask_editor.py,sha256=ZC_T-6zpB3SXO4I_p8rtEdSEfWckCGU-TsVh5IMf-Vs,848
-scitex/fig/editor/_mpl_editor.py,sha256=FzouErJ6gernrRDpXLXs0riWsKEC30YjH_uMJamkIzA,7909
-scitex/fig/editor/_qt_editor.py,sha256=AOMnlRzGOfIykvERc2QVJ1JaRQMHYQtosFktVGEwxKE,40688
-scitex/fig/editor/_tkinter_editor.py,sha256=MiiJCkNOUvYEvRn6ZqCaJWlc8hsTIZBV_9NEepKNFGM,19322
+scitex/fig/editor/_mpl_editor.py,sha256=HbcVkob-OTt4UcQtQXiGNkZ1iUOVyg8nlvGbV6jvzD4,7908
+scitex/fig/editor/_qt_editor.py,sha256=VS0PBC9VsXxRDrrNb5yFa42Cxc4Si9wsgNUGeBsRaHc,40687
+scitex/fig/editor/_tkinter_editor.py,sha256=JN2Oy2uyu0GB0fJjIQ8bb8YR9_gX2TQ_bhj4GQsSKP0,19321
+scitex/fig/editor/edit/__init__.py,sha256=T0L8PDwb7nO1myg-iR2Yy9qojTJdk0NI6uVVCKrawdw,1383
+scitex/fig/editor/edit/backend_detector.py,sha256=UN5Tc50UatJMafsdBypY0NBpRd01SxVv4DFCRTUVPIQ,2917
+scitex/fig/editor/edit/bundle_resolver.py,sha256=oMziNJPYvtIuEfXMeryLyYay9gEM8k3Ecq8pbjAU7k4,7476
+scitex/fig/editor/edit/editor_launcher.py,sha256=eQVVU7f2vWyuN78QZRX9ppbMVeyuO2LfFZE3L6XZoBQ,8135
+scitex/fig/editor/edit/manual_handler.py,sha256=5zKfn2T9ox4n_q5S351OY5r7bW1seOqZdTg1jB7o1_w,1249
+scitex/fig/editor/edit/panel_loader.py,sha256=cOf20nPtdGin35wNtNNleQwlctV9hplmD4uLQ0DMGV0,7099
+scitex/fig/editor/edit/path_resolver.py,sha256=9b1PCj9-ragRWvDNwW0oR733qTlvpjBp7zH2L7IUSTw,2056
 scitex/fig/editor/flask_editor/__init__.py,sha256=C-5iDsc5c2xSRhgexgB_XvQqJQBvNrGbzKzxOKSSMkA,531
-scitex/fig/editor/flask_editor/_bbox.py,sha256=EDm8OLtajxrX-eDAQ0HPuTzoyS77yTSVpN43ZUEaPAg,49546
-scitex/fig/editor/flask_editor/_core.py,sha256=bY71vAl2IZSxjCkOYpYk3oV4Vsi_L7OeD-wjeagSLhk,24673
+scitex/fig/editor/flask_editor/_bbox.py,sha256=o_hyh4ZFvV1-_ydf3UyRyp_DfJx5C4zICOywMNXlOck,50862
+scitex/fig/editor/flask_editor/_core.py,sha256=ZjYRiu_qDxgBJ_sBfh6fcYuqiniaWg0eJGlZFrtuOQc,62893
 scitex/fig/editor/flask_editor/_plotter.py,sha256=FUWHlGVac0mc3MmtuDWIfwe5jw47vGypL0Cbk0LvWPE,21221
-scitex/fig/editor/flask_editor/_renderer.py,sha256=O_HC8ysuWjzq41qC_r0_IF3c7w2jsKCqqmaO4IfSMJk,25216
+scitex/fig/editor/flask_editor/_renderer.py,sha256=m_8mvQjIo-r5rNmFt7qJ-mXqe6KGEW7Q_tamNB78FaE,27442
 scitex/fig/editor/flask_editor/_utils.py,sha256=V9wyfWy61tgnJIFshF2S-d7T8wiNdAgz_CIXCRfBkuI,2513
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