two version of R2R are here HEAD master

5 files changed, 598 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/openpyxl/reader/__init__.py b/.venv/lib/python3.12/site-packages/openpyxl/reader/__init__.py
new file mode 100644
index 00000000..ab6cdead
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/openpyxl/reader/__init__.py
@@ -0,0 +1 @@
+# Copyright (c) 2010-2024 openpyxl
diff --git a/.venv/lib/python3.12/site-packages/openpyxl/reader/drawings.py b/.venv/lib/python3.12/site-packages/openpyxl/reader/drawings.py
new file mode 100644
index 00000000..caaa8570
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/openpyxl/reader/drawings.py
@@ -0,0 +1,71 @@
+
+# Copyright (c) 2010-2024 openpyxl
+
+
+from io import BytesIO
+from warnings import warn
+
+from openpyxl.xml.functions import fromstring
+from openpyxl.xml.constants import IMAGE_NS
+from openpyxl.packaging.relationship import (
+    get_rel,
+    get_rels_path,
+    get_dependents,
+)
+from openpyxl.drawing.spreadsheet_drawing import SpreadsheetDrawing
+from openpyxl.drawing.image import Image, PILImage
+from openpyxl.chart.chartspace import ChartSpace
+from openpyxl.chart.reader import read_chart
+
+
+def find_images(archive, path):
+    """
+    Given the path to a drawing file extract charts and images
+
+    Ignore errors due to unsupported parts of DrawingML
+    """
+
+    src = archive.read(path)
+    tree = fromstring(src)
+    try:
+        drawing = SpreadsheetDrawing.from_tree(tree)
+    except TypeError:
+        warn("DrawingML support is incomplete and limited to charts and images only. Shapes and drawings will be lost.")
+        return [], []
+
+    rels_path = get_rels_path(path)
+    deps = []
+    if rels_path in archive.namelist():
+        deps = get_dependents(archive, rels_path)
+
+    charts = []
+    for rel in drawing._chart_rels:
+        try:
+            cs = get_rel(archive, deps, rel.id, ChartSpace)
+        except TypeError as e:
+            warn(f"Unable to read chart {rel.id} from {path} {e}")
+            continue
+        chart = read_chart(cs)
+        chart.anchor = rel.anchor
+        charts.append(chart)
+
+    images = []
+    if not PILImage: # Pillow not installed, drop images
+        return charts, images
+
+    for rel in drawing._blip_rels:
+        dep = deps.get(rel.embed)
+        if dep.Type == IMAGE_NS:
+            try:
+                image = Image(BytesIO(archive.read(dep.target)))
+            except OSError:
+                msg = "The image {0} will be removed because it cannot be read".format(dep.target)
+                warn(msg)
+                continue
+            if image.format.upper() == "WMF": # cannot save
+                msg = "{0} image format is not supported so the image is being dropped".format(image.format)
+                warn(msg)
+                continue
+            image.anchor = rel.anchor
+            images.append(image)
+    return charts, images
diff --git a/.venv/lib/python3.12/site-packages/openpyxl/reader/excel.py b/.venv/lib/python3.12/site-packages/openpyxl/reader/excel.py
new file mode 100644
index 00000000..dfd8eeac
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/openpyxl/reader/excel.py
@@ -0,0 +1,349 @@
+# Copyright (c) 2010-2024 openpyxl
+
+
+"""Read an xlsx file into Python"""
+
+# Python stdlib imports
+from zipfile import ZipFile, ZIP_DEFLATED
+from io import BytesIO
+import os.path
+import warnings
+
+from openpyxl.pivot.table import TableDefinition
+
+# Allow blanket setting of KEEP_VBA for testing
+try:
+    from ..tests import KEEP_VBA
+except ImportError:
+    KEEP_VBA = False
+
+# package imports
+from openpyxl.utils.exceptions import InvalidFileException
+from openpyxl.xml.constants import (
+    ARC_CORE,
+    ARC_CUSTOM,
+    ARC_CONTENT_TYPES,
+    ARC_WORKBOOK,
+    ARC_THEME,
+    COMMENTS_NS,
+    SHARED_STRINGS,
+    XLTM,
+    XLTX,
+    XLSM,
+    XLSX,
+)
+from openpyxl.cell import MergedCell
+from openpyxl.comments.comment_sheet import CommentSheet
+
+from .strings import read_string_table, read_rich_text
+from .workbook import WorkbookParser
+from openpyxl.styles.stylesheet import apply_stylesheet
+
+from openpyxl.packaging.core import DocumentProperties
+from openpyxl.packaging.custom import CustomPropertyList
+from openpyxl.packaging.manifest import Manifest, Override
+
+from openpyxl.packaging.relationship import (
+    RelationshipList,
+    get_dependents,
+    get_rels_path,
+)
+
+from openpyxl.worksheet._read_only import ReadOnlyWorksheet
+from openpyxl.worksheet._reader import WorksheetReader
+from openpyxl.chartsheet import Chartsheet
+from openpyxl.worksheet.table import Table
+from openpyxl.drawing.spreadsheet_drawing import SpreadsheetDrawing
+
+from openpyxl.xml.functions import fromstring
+
+from .drawings import find_images
+
+
+SUPPORTED_FORMATS = ('.xlsx', '.xlsm', '.xltx', '.xltm')
+
+
+def _validate_archive(filename):
+    """
+    Does a first check whether filename is a string or a file-like
+    object. If it is a string representing a filename, a check is done
+    for supported formats by checking the given file-extension. If the
+    file-extension is not in SUPPORTED_FORMATS an InvalidFileException
+    will raised. Otherwise the filename (resp. file-like object) will
+    forwarded to zipfile.ZipFile returning a ZipFile-Instance.
+    """
+    is_file_like = hasattr(filename, 'read')
+    if not is_file_like:
+        file_format = os.path.splitext(filename)[-1].lower()
+        if file_format not in SUPPORTED_FORMATS:
+            if file_format == '.xls':
+                msg = ('openpyxl does not support the old .xls file format, '
+                       'please use xlrd to read this file, or convert it to '
+                       'the more recent .xlsx file format.')
+            elif file_format == '.xlsb':
+                msg = ('openpyxl does not support binary format .xlsb, '
+                       'please convert this file to .xlsx format if you want '
+                       'to open it with openpyxl')
+            else:
+                msg = ('openpyxl does not support %s file format, '
+                       'please check you can open '
+                       'it with Excel first. '
+                       'Supported formats are: %s') % (file_format,
+                                                       ','.join(SUPPORTED_FORMATS))
+            raise InvalidFileException(msg)
+
+    archive = ZipFile(filename, 'r')
+    return archive
+
+
+def _find_workbook_part(package):
+    workbook_types = [XLTM, XLTX, XLSM, XLSX]
+    for ct in workbook_types:
+        part = package.find(ct)
+        if part:
+            return part
+
+    # some applications reassign the default for application/xml
+    defaults = {p.ContentType for p in package.Default}
+    workbook_type = defaults & set(workbook_types)
+    if workbook_type:
+        return Override("/" + ARC_WORKBOOK, workbook_type.pop())
+
+    raise IOError("File contains no valid workbook part")
+
+
+class ExcelReader:
+
+    """
+    Read an Excel package and dispatch the contents to the relevant modules
+    """
+
+    def __init__(self, fn, read_only=False, keep_vba=KEEP_VBA,
+                 data_only=False, keep_links=True, rich_text=False):
+        self.archive = _validate_archive(fn)
+        self.valid_files = self.archive.namelist()
+        self.read_only = read_only
+        self.keep_vba = keep_vba
+        self.data_only = data_only
+        self.keep_links = keep_links
+        self.rich_text = rich_text
+        self.shared_strings = []
+
+
+    def read_manifest(self):
+        src = self.archive.read(ARC_CONTENT_TYPES)
+        root = fromstring(src)
+        self.package = Manifest.from_tree(root)
+
+
+    def read_strings(self):
+        ct = self.package.find(SHARED_STRINGS)
+        reader = read_string_table
+        if self.rich_text:
+            reader = read_rich_text
+        if ct is not None:
+            strings_path = ct.PartName[1:]
+            with self.archive.open(strings_path,) as src:
+                self.shared_strings = reader(src)
+
+
+    def read_workbook(self):
+        wb_part = _find_workbook_part(self.package)
+        self.parser = WorkbookParser(self.archive, wb_part.PartName[1:], keep_links=self.keep_links)
+        self.parser.parse()
+        wb = self.parser.wb
+        wb._sheets = []
+        wb._data_only = self.data_only
+        wb._read_only = self.read_only
+        wb.template = wb_part.ContentType in (XLTX, XLTM)
+
+        # If are going to preserve the vba then attach a copy of the archive to the
+        # workbook so that is available for the save.
+        if self.keep_vba:
+            wb.vba_archive = ZipFile(BytesIO(), 'a', ZIP_DEFLATED)
+            for name in self.valid_files:
+                wb.vba_archive.writestr(name, self.archive.read(name))
+
+        if self.read_only:
+            wb._archive = self.archive
+
+        self.wb = wb
+
+
+    def read_properties(self):
+        if ARC_CORE in self.valid_files:
+            src = fromstring(self.archive.read(ARC_CORE))
+            self.wb.properties = DocumentProperties.from_tree(src)
+
+
+    def read_custom(self):
+        if ARC_CUSTOM in self.valid_files:
+            src = fromstring(self.archive.read(ARC_CUSTOM))
+            self.wb.custom_doc_props = CustomPropertyList.from_tree(src)
+
+
+    def read_theme(self):
+        if ARC_THEME in self.valid_files:
+            self.wb.loaded_theme = self.archive.read(ARC_THEME)
+
+
+    def read_chartsheet(self, sheet, rel):
+        sheet_path = rel.target
+        rels_path = get_rels_path(sheet_path)
+        rels = []
+        if rels_path in self.valid_files:
+            rels = get_dependents(self.archive, rels_path)
+
+        with self.archive.open(sheet_path, "r") as src:
+            xml = src.read()
+        node = fromstring(xml)
+        cs = Chartsheet.from_tree(node)
+        cs._parent = self.wb
+        cs.title = sheet.name
+        self.wb._add_sheet(cs)
+
+        drawings = rels.find(SpreadsheetDrawing._rel_type)
+        for rel in drawings:
+            charts, images = find_images(self.archive, rel.target)
+            for c in charts:
+                cs.add_chart(c)
+
+
+    def read_worksheets(self):
+        comment_warning = """Cell '{0}':{1} is part of a merged range but has a comment which will be removed because merged cells cannot contain any data."""
+        for sheet, rel in self.parser.find_sheets():
+            if rel.target not in self.valid_files:
+                continue
+
+            if "chartsheet" in rel.Type:
+                self.read_chartsheet(sheet, rel)
+                continue
+
+            rels_path = get_rels_path(rel.target)
+            rels = RelationshipList()
+            if rels_path in self.valid_files:
+                rels = get_dependents(self.archive, rels_path)
+
+            if self.read_only:
+                ws = ReadOnlyWorksheet(self.wb, sheet.name, rel.target, self.shared_strings)
+                ws.sheet_state = sheet.state
+                self.wb._sheets.append(ws)
+                continue
+            else:
+                fh = self.archive.open(rel.target)
+                ws = self.wb.create_sheet(sheet.name)
+                ws._rels = rels
+                ws_parser = WorksheetReader(ws, fh, self.shared_strings, self.data_only, self.rich_text)
+                ws_parser.bind_all()
+                fh.close()
+
+            # assign any comments to cells
+            for r in rels.find(COMMENTS_NS):
+                src = self.archive.read(r.target)
+                comment_sheet = CommentSheet.from_tree(fromstring(src))
+                for ref, comment in comment_sheet.comments:
+                    try:
+                        ws[ref].comment = comment
+                    except AttributeError:
+                        c = ws[ref]
+                        if isinstance(c, MergedCell):
+                            warnings.warn(comment_warning.format(ws.title, c.coordinate))
+                            continue
+
+            # preserve link to VML file if VBA
+            if self.wb.vba_archive and ws.legacy_drawing:
+                ws.legacy_drawing = rels.get(ws.legacy_drawing).target
+            else:
+                ws.legacy_drawing = None
+
+            for t in ws_parser.tables:
+                src = self.archive.read(t)
+                xml = fromstring(src)
+                table = Table.from_tree(xml)
+                ws.add_table(table)
+
+            drawings = rels.find(SpreadsheetDrawing._rel_type)
+            for rel in drawings:
+                charts, images = find_images(self.archive, rel.target)
+                for c in charts:
+                    ws.add_chart(c, c.anchor)
+                for im in images:
+                    ws.add_image(im, im.anchor)
+
+            pivot_rel = rels.find(TableDefinition.rel_type)
+            pivot_caches = self.parser.pivot_caches
+            for r in pivot_rel:
+                pivot_path = r.Target
+                src = self.archive.read(pivot_path)
+                tree = fromstring(src)
+                pivot = TableDefinition.from_tree(tree)
+                pivot.cache = pivot_caches[pivot.cacheId]
+                ws.add_pivot(pivot)
+
+            ws.sheet_state = sheet.state
+
+
+    def read(self):
+        action = "read manifest"
+        try:
+            self.read_manifest()
+            action = "read strings"
+            self.read_strings()
+            action = "read workbook"
+            self.read_workbook()
+            action = "read properties"
+            self.read_properties()
+            action = "read custom properties"
+            self.read_custom()
+            action = "read theme"
+            self.read_theme()
+            action = "read stylesheet"
+            apply_stylesheet(self.archive, self.wb)
+            action = "read worksheets"
+            self.read_worksheets()
+            action = "assign names"
+            self.parser.assign_names()
+            if not self.read_only:
+                self.archive.close()
+        except ValueError as e:
+            raise ValueError(
+                f"Unable to read workbook: could not {action} from {self.archive.filename}.\n"
+                "This is most probably because the workbook source files contain some invalid XML.\n"
+                "Please see the exception for more details."
+                ) from e
+
+
+def load_workbook(filename, read_only=False, keep_vba=KEEP_VBA,
+                  data_only=False, keep_links=True, rich_text=False):
+    """Open the given filename and return the workbook
+
+    :param filename: the path to open or a file-like object
+    :type filename: string or a file-like object open in binary mode c.f., :class:`zipfile.ZipFile`
+
+    :param read_only: optimised for reading, content cannot be edited
+    :type read_only: bool
+
+    :param keep_vba: preserve vba content (this does NOT mean you can use it)
+    :type keep_vba: bool
+
+    :param data_only: controls whether cells with formulae have either the formula (default) or the value stored the last time Excel read the sheet
+    :type data_only: bool
+
+    :param keep_links: whether links to external workbooks should be preserved. The default is True
+    :type keep_links: bool
+
+    :param rich_text: if set to True openpyxl will preserve any rich text formatting in cells. The default is False
+    :type rich_text: bool
+
+    :rtype: :class:`openpyxl.workbook.Workbook`
+
+    .. note::
+
+        When using lazy load, all worksheets will be :class:`openpyxl.worksheet.iter_worksheet.IterableWorksheet`
+        and the returned workbook will be read-only.
+
+    """
+    reader = ExcelReader(filename, read_only, keep_vba,
+                         data_only, keep_links, rich_text)
+    reader.read()
+    return reader.wb
diff --git a/.venv/lib/python3.12/site-packages/openpyxl/reader/strings.py b/.venv/lib/python3.12/site-packages/openpyxl/reader/strings.py
new file mode 100644
index 00000000..5168f201
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/openpyxl/reader/strings.py
@@ -0,0 +1,44 @@
+# Copyright (c) 2010-2024 openpyxl
+
+from openpyxl.cell.text import Text
+
+from openpyxl.xml.functions import iterparse
+from openpyxl.xml.constants import SHEET_MAIN_NS
+from openpyxl.cell.rich_text import CellRichText
+
+
+def read_string_table(xml_source):
+    """Read in all shared strings in the table"""
+
+    strings = []
+    STRING_TAG = '{%s}si' % SHEET_MAIN_NS
+
+    for _, node in iterparse(xml_source):
+        if node.tag == STRING_TAG:
+            text = Text.from_tree(node).content
+            text = text.replace('x005F_', '')
+            node.clear()
+
+            strings.append(text)
+
+    return strings
+
+
+def read_rich_text(xml_source):
+    """Read in all shared strings in the table"""
+
+    strings = []
+    STRING_TAG = '{%s}si' % SHEET_MAIN_NS
+
+    for _, node in iterparse(xml_source):
+        if node.tag == STRING_TAG:
+            text = CellRichText.from_tree(node)
+            if len(text) == 0:
+                text = ''
+            elif len(text) == 1 and isinstance(text[0], str):
+                text = text[0]
+            node.clear()
+
+            strings.append(text)
+
+    return strings
diff --git a/.venv/lib/python3.12/site-packages/openpyxl/reader/workbook.py b/.venv/lib/python3.12/site-packages/openpyxl/reader/workbook.py
new file mode 100644
index 00000000..2afbfddb
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/openpyxl/reader/workbook.py
@@ -0,0 +1,133 @@
+# Copyright (c) 2010-2024 openpyxl
+
+from warnings import warn
+
+from openpyxl.xml.functions import fromstring
+
+from openpyxl.packaging.relationship import (
+    get_dependents,
+    get_rels_path,
+    get_rel,
+)
+from openpyxl.packaging.workbook import WorkbookPackage
+from openpyxl.workbook import Workbook
+from openpyxl.workbook.defined_name import DefinedNameList
+from openpyxl.workbook.external_link.external import read_external_link
+from openpyxl.pivot.cache import CacheDefinition
+from openpyxl.pivot.record import RecordList
+from openpyxl.worksheet.print_settings import PrintTitles, PrintArea
+
+from openpyxl.utils.datetime import CALENDAR_MAC_1904
+
+
+class WorkbookParser:
+
+    _rels = None
+
+    def __init__(self, archive, workbook_part_name, keep_links=True):
+        self.archive = archive
+        self.workbook_part_name = workbook_part_name
+        self.defined_names = DefinedNameList()
+        self.wb = Workbook()
+        self.keep_links = keep_links
+        self.sheets = []
+
+
+    @property
+    def rels(self):
+        if self._rels is None:
+            self._rels = get_dependents(self.archive, get_rels_path(self.workbook_part_name)).to_dict()
+        return self._rels
+
+
+    def parse(self):
+        src = self.archive.read(self.workbook_part_name)
+        node = fromstring(src)
+        package = WorkbookPackage.from_tree(node)
+        if package.properties.date1904:
+            self.wb.epoch = CALENDAR_MAC_1904
+
+        self.wb.code_name = package.properties.codeName
+        self.wb.active = package.active
+        self.wb.views = package.bookViews
+        self.sheets = package.sheets
+        self.wb.calculation = package.calcPr
+        self.caches = package.pivotCaches
+
+        # external links contain cached worksheets and can be very big
+        if not self.keep_links:
+            package.externalReferences = []
+
+        for ext_ref in package.externalReferences:
+            rel = self.rels.get(ext_ref.id)
+            self.wb._external_links.append(
+                read_external_link(self.archive, rel.Target)
+            )
+
+        if package.definedNames:
+            self.defined_names = package.definedNames
+
+        self.wb.security = package.workbookProtection
+
+
+    def find_sheets(self):
+        """
+        Find all sheets in the workbook and return the link to the source file.
+
+        Older XLSM files sometimes contain invalid sheet elements.
+        Warn user when these are removed.
+        """
+
+        for sheet in self.sheets:
+            if not sheet.id:
+                msg = f"File contains an invalid specification for {0}. This will be removed".format(sheet.name)
+                warn(msg)
+                continue
+            yield sheet, self.rels[sheet.id]
+
+
+    def assign_names(self):
+        """
+        Bind defined names and other definitions to worksheets or the workbook
+        """
+
+        for idx, names in self.defined_names.by_sheet().items():
+            if idx == "global":
+                self.wb.defined_names = names
+                continue
+
+            try:
+                sheet = self.wb._sheets[idx]
+            except IndexError:
+                warn(f"Defined names for sheet index {idx} cannot be located")
+                continue
+
+            for name, defn in names.items():
+                reserved = defn.is_reserved
+                if reserved is None:
+                    sheet.defined_names[name] = defn
+
+                elif reserved == "Print_Titles":
+                    titles = PrintTitles.from_string(defn.value)
+                    sheet._print_rows = titles.rows
+                    sheet._print_cols = titles.cols
+                elif reserved == "Print_Area":
+                    try:
+                        sheet._print_area = PrintArea.from_string(defn.value)
+                    except TypeError:
+                        warn(f"Print area cannot be set to Defined name: {defn.value}.")
+                        continue
+
+    @property
+    def pivot_caches(self):
+        """
+        Get PivotCache objects
+        """
+        d = {}
+        for c in self.caches:
+            cache = get_rel(self.archive, self.rels, id=c.id, cls=CacheDefinition)
+            if cache.deps:
+                records = get_rel(self.archive, cache.deps, cache.id, RecordList)
+                cache.records = records
+            d[c.cacheId] = cache
+        return d