dcmspec 0.2.1__tar.gz → 0.2.3__tar.gz

dcmspec-0.2.3/CHANGELOG.md

@@ -0,0 +1,51 @@
+# Release Notes
+
+These release notes summarize key changes, improvements, and breaking updates for each version of **dcmspec**.
+
+## [0.2.3] - 2025-09-29
+
+### Fixed
+
+- Hotfix: Force UTF-8 decoding for DICOM standard XHTML downloads to prevent mojibake when server omits charset ([#85](https://github.com/dwikler/dcmspec/issues/85)).
+- Hotfix: Add missing `progress_observer` argument to `CSVTableSpecParser.parse` for interface compatibility and to prevent `TypeError` when used with `SpecFactory` ([#86](https://github.com/dwikler/dcmspec/issues/86)).
+
+## [0.2.2] - 2025-09-25
+
+### Fixed
+
+- Fix CONTRIBUTING.md link in README for PyPI compatibility
+- Remove focus border and misleading text cursor in iod-explorer details panel
+
+### Changed
+
+- Update README: add PyPI and Python version badges
+- Replace Unicode ▶ with ASCII > in status bar for compatibility
+- Improve DICOM Modules usage condition parsing using regex for robustness to missing spaces
+- Add PR template to remind contributors to check the target branch and check tests and docs were updated
+- Move detailed table parsing logs to DEBUG level for less verbose INFO output
+
+## [0.2.1] - 2025-09-19
+
+### Fixed
+
+- Sanitize node and attribute names to remove "/" in DOMTableSpecParser ([#56](https://github.com/dwikler/dcmspec/issues/56))
+
+### Changed
+
+- Major project restructure: move CLI and UI apps to new `apps/cli` and `apps/ui` folders
+- Improve installation instructions and documentation
+- Prepare and publish the package to [PyPI](https://pypi.org/project/dcmspec/)
+
+## [0.2.0] - 2025-09-13
+
+### Changed
+
+- **Breaking change:** `IODSpecBuilder.build_from_url` now returns a tuple `(iod_model, module_models)` instead of just the IOD model. All callers must be updated to unpack the tuple
+- Update CLI and UI applications to support new return value
+- Add registry mode to `IODSpecBuilder` for efficient module model sharing
+
+## [0.1.0] - 2025-05-25
+
+### Added
+
+- Initial release

{dcmspec-0.2.1 → dcmspec-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcmspec
-Version: 0.2.1
+Version: 0.2.3
 Summary: Toolkit for extracting, parsing, and processing DICOM specifications.
 License: Apache-2.0
 License-File: LICENSE
@@ -43,6 +43,9 @@ Project-URL: Source, https://github.com/dwikler/dcmspec
 Description-Content-Type: text/markdown
 
 [![tests](https://github.com/dwikler/dcmspec/actions/workflows/test.yml/badge.svg)](https://github.com/dwikler/dcmspec/actions/workflows/test.yml)
+[![PyPI version](https://badge.fury.io/py/dcmspec.svg)](https://badge.fury.io/py/dcmspec)
+[![Python versions](https://img.shields.io/pypi/pyversions/dcmspec.svg)](https://pypi.org/project/dcmspec/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17233195.svg)](https://doi.org/10.5281/zenodo.17233195)
 
 # dcmspec
 
@@ -112,7 +115,7 @@ See [Configuration & Caching](https://dwikler.github.io/dcmspec/configuration/)
 
 ## Contributing
 
-See [CONTRIBUTING.md](./CONTRIBUTING.md) for guidelines and instructions on how to contribute to the project.
+See [CONTRIBUTING.md](https://github.com/dwikler/dcmspec/blob/main/CONTRIBUTING.md) for guidelines and instructions on how to contribute to the project.
 
 ## Similar Projects
 

{dcmspec-0.2.1 → dcmspec-0.2.3}/README.md

@@ -1,4 +1,7 @@
 [![tests](https://github.com/dwikler/dcmspec/actions/workflows/test.yml/badge.svg)](https://github.com/dwikler/dcmspec/actions/workflows/test.yml)
+[![PyPI version](https://badge.fury.io/py/dcmspec.svg)](https://badge.fury.io/py/dcmspec)
+[![Python versions](https://img.shields.io/pypi/pyversions/dcmspec.svg)](https://pypi.org/project/dcmspec/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17233195.svg)](https://doi.org/10.5281/zenodo.17233195)
 
 # dcmspec
 
@@ -68,7 +71,7 @@ See [Configuration & Caching](https://dwikler.github.io/dcmspec/configuration/)
 
 ## Contributing
 
-See [CONTRIBUTING.md](./CONTRIBUTING.md) for guidelines and instructions on how to contribute to the project.
+See [CONTRIBUTING.md](https://github.com/dwikler/dcmspec/blob/main/CONTRIBUTING.md) for guidelines and instructions on how to contribute to the project.
 
 ## Similar Projects
 

{dcmspec-0.2.1 → dcmspec-0.2.3}/pyproject.toml

@@ -1,11 +1,9 @@
 [project]
 name = "dcmspec"
-version = "0.2.1"
+version = "0.2.3"
 description = "Toolkit for extracting, parsing, and processing DICOM specifications."
-authors = [
-    {name = "David Wikler",email = "david.wikler@ulb.be"}
-]
-license = {text = "Apache-2.0"}
+authors = [{ name = "David Wikler", email = "david.wikler@ulb.be" }]
+license = { text = "Apache-2.0" }
 readme = "README.md"
 requires-python = ">=3.10,<4.0"
 keywords = ["DICOM", "python"]
@@ -51,23 +49,15 @@ pdf = [
 gui = ["tkhtmlview (>=0.3.1,<0.4.0)"]
 
 [tool.poetry]
-packages = [{include = "dcmspec", from = "src"}]
-include = [
-    "README.md",
-    "LICENSE",
-    "CHANGELOG.md",
-    "src/dcmspec/*"
-]
-exclude = [
-    "src/dcmspec/tests/*",
-    "src/dcmspec/.DS_Store",
-]
+packages = [{ include = "dcmspec", from = "src" }]
+include = ["README.md", "LICENSE", "CHANGELOG.md", "src/dcmspec/*"]
+exclude = ["src/dcmspec/tests/*", "src/dcmspec/.DS_Store"]
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.5"
 pytest-cov = "^6.1.1"
 mkdocs = "^1.6.1"
-mkdocstrings = {extras = ["python"], version = "^0.29.1"}
+mkdocstrings = { extras = ["python"], version = "^0.29.1" }
 mkdocs-material = "^9.6.14"
 
 [build-system]
@@ -87,4 +77,8 @@ iod-explorer = "dcmspec.apps.ui.iod_explorer.iod_explorer:main"
 
 [tool.ruff]
 line-length = 120
-select = ["E", "F", "D"]  # E includes line-too-long (E501), D includes docstrings checks
+select = [
+    "E",
+    "F",
+    "D",
+] # E includes line-too-long (E501), D includes docstrings checks

{dcmspec-0.2.1 → dcmspec-0.2.3}/src/dcmspec/apps/ui/iod_explorer/iod_explorer.py

@@ -28,36 +28,6 @@ PART3_TOC_URL = "https://dicom.nema.org/medical/dicom/current/output/chtml/part0
 # Canonical DICOM Part 3 HTML URL
 PART3_HTML_URL = "https://dicom.nema.org/medical/dicom/current/output/html/part03.html"
 
-
-class StatusManager:
-    """Handles status bar messaging with consistent logic."""
-    
-    def __init__(self, status_var):
-        """Initialize the StatusManager.
-
-        Args:
-            status_var: A tkinter StringVar or similar object used to update the status bar text.
-
-        """
-        self.status_var = status_var
-    
-    def show_count_status(self, count: int):
-        """Show count-based status when no selection."""
-        message = f"Showing {count} IODs"
-        self.status_var.set(message)
-    
-    def show_selection_status(self, title: str, iod_type: str, is_iod: bool = True):
-        """Show selection-based status when item selected."""
-        if is_iod:
-            self.status_var.set(f"{title} {iod_type} • Click ▶ to expand")
-        else:
-            self.status_var.set(f"{iod_type}: {title}")
-
-    def show_loading_status(self, message: str):
-        """Show loading status."""
-        self.status_var.set(message)
-
-
 def load_app_config() -> Config:
     """Load app-specific configuration with priority search order.
     
@@ -78,8 +48,6 @@ def load_app_config() -> Config:
         Config: Configuration object with app-specific settings.
         
     """
-    import os
-
     # Look for app-specific config file in several locations (highest priority)
     app_config_locations = [
         "iod_explorer_config.json",  # Current directory
@@ -142,6 +110,34 @@ def setup_logger(config: Config) -> logging.Logger:
     
     return logger
 
+class StatusManager:
+    """Handles status bar messaging with consistent logic."""
+    
+    def __init__(self, status_var):
+        """Initialize the StatusManager.
+
+        Args:
+            status_var: A tkinter StringVar or similar object used to update the status bar text.
+
+        """
+        self.status_var = status_var
+    
+    def show_count_status(self, count: int):
+        """Show count-based status when no selection."""
+        message = f"Showing {count} IODs"
+        self.status_var.set(message)
+    
+    def show_selection_status(self, title: str, iod_type: str, is_iod: bool = True):
+        """Show selection-based status when item selected."""
+        if is_iod:
+            self.status_var.set(f"{title} {iod_type} • Click > to expand")
+        else:
+            self.status_var.set(f"{iod_type}: {title}")
+
+    def show_loading_status(self, message: str):
+        """Show loading status."""
+        self.status_var.set(message)
+
 
 class IODExplorer:
     """Main window for the IOD Explorer application."""
@@ -207,7 +203,7 @@ class IODExplorer:
         y = (screen_height - window_height) // 2
         self.root.geometry(f"{window_width}x{window_height}+{x}+{y}")
     
-    def setup_ui(self):
+    def setup_ui(self): 
         """Set up the user interface."""
         # Create main frame
         main_frame = ttk.Frame(self.root)
@@ -248,7 +244,7 @@ class IODExplorer:
         details_label_header.pack(side=tk.LEFT)
         
         # Left frame for treeview
-        left_frame = ttk.Frame(left_panel)
+        left_frame = ttk.Frame(left_panel)  # sourcery skip: extract-duplicate-method
         left_frame.pack(fill=tk.BOTH, expand=True)
         
         # Configure grid for treeview area
@@ -329,11 +325,14 @@ class IODExplorer:
                 f'</div>'
             ),
             width=50,
-            height=30
-        )
+            height=30,
+            highlightthickness=0,
+            )
+        
         self.details_text.grid(row=0, column=0, sticky="nsew")
         self.details_font_family = selected_font  # Store for later use
         self.details_font_size = 10
+        self.details_text.config(cursor="arrow")
 
         # Add scrollbars that match the treeview style
         details_scroll_y = ttk.Scrollbar(right_frame, orient=tk.VERTICAL, command=self.details_text.yview)
@@ -710,11 +709,12 @@ class IODExplorer:
         elif usage.startswith("U"):
             return "User Optional (U)"
         elif usage.startswith("C"):
-            if len(usage) > 1 and " - " in usage:
-                conditional_part = usage[usage.find(" - ") + 3:]
-                return f"Conditional (C) - {conditional_part}"
+            match = re.match(r"^C\s*-?\s*(.*)$", usage)
+            condition = match[1].strip() if match and match[1] else ""
+            if condition:
+                return f"Conditional (C) - {condition}"
             else:
-                return "Conditional (C)"
+                return "Conditional (C) - Condition not found"
         else:
             return usage
 

{dcmspec-0.2.1 → dcmspec-0.2.3}/src/dcmspec/csv_table_spec_parser.py

@@ -3,10 +3,11 @@
 Provides the CSVTableSpecParser class for parsing DICOM specification tables in CSV format,
 converting them into structured in-memory representations using anytree.
 """
-from typing import Tuple
+from typing import Dict, List, Tuple, Optional
 from anytree import Node
 
 from dcmspec.spec_parser import SpecParser
+from dcmspec.progress import ProgressObserver
 
 class CSVTableSpecParser(SpecParser):
     """Base parser for DICOM Specification IHE tables in CSV-like format."""
@@ -14,10 +15,11 @@ class CSVTableSpecParser(SpecParser):
     def parse(
         self,
         table: dict,
-        column_to_attr,
-        name_attr="elem_name",
-        table_id=None,
-        include_depth=None,
+        column_to_attr: dict,
+        name_attr: str = "elem_name",
+        table_id: Optional[str] = None,
+        include_depth: Optional[int] = None,
+        progress_observer: Optional[ProgressObserver] = None,
     ) -> Tuple[Node, Node]:
         """Parse specification metadata and content from a single table dict.
 
@@ -27,11 +29,18 @@ class CSVTableSpecParser(SpecParser):
             name_attr (str): The attribute to use for node names.
             table_id (str, optional): Table identifier for model parsing.
             include_depth (int, optional): The depth to which included tables should be parsed.
+            progress_observer (Optional[ProgressObserver]): 
+                Accepted for interface compatibility, but ignored in this parser.
+                Included so that this method can be called with the same arguments as other table parsers.
 
         Returns:
             tuple: (metadata_node, content_node)
 
         """
+        if progress_observer is not None and hasattr(self, "logger"):
+            self.logger.debug(
+                "Progress reporting is not supported yet for CSV parsing and will be ignored."
+            )
         # Use the header and data from the grouped table dict
         header = table.get("header", [])
         data = table.get("data", [])
@@ -47,8 +56,8 @@ class CSVTableSpecParser(SpecParser):
 
     def parse_table(
         self,
-        tables: list,  # List of tables, each a list of rows (list of str)
-        column_to_attr: dict,
+        tables: List[List[List[str]]],  # List of tables, each a list of rows (list of str)
+        column_to_attr: Dict[int, str],
         name_attr: str = "elem_name",
     ) -> Node:
         """Build a tree from tables using column mapping and '>' nesting logic.

{dcmspec-0.2.1 → dcmspec-0.2.3}/src/dcmspec/doc_handler.py

@@ -94,6 +94,8 @@ class DocHandler:
         try:
             with requests.get(url, timeout=30, stream=True, headers={"Accept-Encoding": "identity"}) as response:
                 response.raise_for_status()
+                self._set_response_encoding(response)
+
                 total = int(response.headers.get('content-length', 0))
                 chunk_size = 8192
                 if binary:
@@ -109,6 +111,19 @@ class DocHandler:
             self.logger.error(f"Failed to save file {file_path}: {e}")
             raise RuntimeError(f"Failed to save file {file_path}: {e}") from e
 
+    def _set_response_encoding(self, response):
+        """Set response.encoding to UTF-8 only if the Content-Type header does not specify a charset.
+        
+        Force utf-8 decoding if the web server does not specify the charset in the HTTP response
+        Content-Type header (DICOM standard XHTML files are always UTF-8 encoded).  
+        """
+        content_type = response.headers.get("Content-Type", "")
+        if "charset=" not in content_type.lower():
+            response.encoding = "utf-8"
+            self.logger.debug("No charset in Content-Type header; forcing UTF-8 decoding.")
+        else:
+            self.logger.debug(f"Using server-specified encoding from Content-Type: {content_type}")
+            
     def _report_progress(self, downloaded, total, progress_observer, last_percent):
         """Report progress if percent changed.
 

{dcmspec-0.2.1 → dcmspec-0.2.3}/src/dcmspec/dom_table_spec_parser.py

@@ -13,7 +13,7 @@ from typing import Any, Dict, Optional, Union
 from dcmspec.spec_parser import SpecParser
 
 from dcmspec.dom_utils import DOMUtils
-from dcmspec.progress import Progress, ProgressStatus, calculate_percent
+from dcmspec.progress import Progress, ProgressObserver, ProgressStatus, calculate_percent
 
 class DOMTableSpecParser(SpecParser):
     """Parser for DICOM specification tables in XHTML DOM format.
@@ -43,7 +43,7 @@ class DOMTableSpecParser(SpecParser):
         column_to_attr: Dict[int, str],
         name_attr: str,
         include_depth: Optional[int] = None,  # None means unlimited
-        progress_observer: Optional[Any] = None,
+        progress_observer: Optional[ProgressObserver] = None,
         skip_columns: Optional[list[int]] = None,
         unformatted: Optional[Union[bool, Dict[int, bool]]] = True,
     ) -> tuple[Node, Node]:
@@ -59,7 +59,7 @@ class DOMTableSpecParser(SpecParser):
             name_attr (str): The attribute name to use for building node names.
             include_depth (Optional[int], optional): The depth to which included tables should be parsed. 
                 None means unlimited.
-            progress_observer (Optional[object], optional): Optional observer to report download progress.
+            progress_observer (Optional[ProgressObserver]): Optional observer to report parsing progress.
             skip_columns (Optional[list[int]]): List of column indices to skip if the row is missing a column.
                 This argument is typically set via `parser_kwargs` when using SpecFactory.
             unformatted (Optional[Union[bool, Dict[int, bool]]]): 
@@ -132,7 +132,7 @@ class DOMTableSpecParser(SpecParser):
         name_attr: str,
         table_nesting_level: int = 0,
         include_depth: Optional[int] = None,  # None means unlimited
-        progress_observer: Optional[Any] = None,
+        progress_observer: Optional[ProgressObserver] = None,
         skip_columns: Optional[list[int]] = None,
         visited_tables: Optional[set] = None,
         unformatted_list: Optional[list[bool]] = None,
@@ -151,7 +151,7 @@ class DOMTableSpecParser(SpecParser):
             name_attr: tree node attribute name to use to build node name
             table_nesting_level: The nesting level of the table (used for recursion call only).
             include_depth: The depth to which included tables should be parsed.
-            progress_observer (Optional[object], optional): Optional observer to report download progress.
+            progress_observer (Optional[ProgressObserver]): Optional observer to report parsing progress.
             skip_columns (Optional[list[int]]): List of column indices to skip if the row is missing a column.
             visited_tables (Optional[set]): Set of table IDs that have been visited to prevent infinite recursion.
             unformatted_list (Optional[list[bool]]): List of booleans indicating whether to extract each column as 
@@ -161,7 +161,7 @@ class DOMTableSpecParser(SpecParser):
             root: The root node of the tree representation of the specification table.
 
         """
-        self.logger.info(f"Nesting Level: {table_nesting_level}, Parsing table with id {table_id}")
+        self.logger.debug(f"Nesting Level: {table_nesting_level}, Parsing table with id {table_id}")
 
         if unformatted_list is None:
             num_columns = max(column_to_attr.keys()) + 1
@@ -208,7 +208,7 @@ class DOMTableSpecParser(SpecParser):
                 progress_observer=progress_observer if table_nesting_level == 0 else None,
             )
 
-            self.logger.info(f"Nesting Level: {table_nesting_level}, Table parsed successfully")
+            self.logger.debug(f"Nesting Level: {table_nesting_level}, Table parsed successfully")
 
             return root
 
@@ -287,7 +287,7 @@ class DOMTableSpecParser(SpecParser):
         unformatted_list: list[bool],
         level_nodes: Dict[int, Node],
         root: Node,
-        progress_observer: Optional[Any] = None
+        progress_observer: Optional[ProgressObserver] = None
     ) -> None:
         """Process all rows in the table, handling recursion, nesting, and node creation."""
         rows = table.find_all("tr")[1:]
@@ -777,7 +777,7 @@ class DOMTableSpecParser(SpecParser):
             for col_idx in column_to_attr
             if col_idx < len(cells)
         )
-        self.logger.info(f"Extracted Header: {header}")
+        self.logger.debug(f"Extracted Header: {header}")
         return header
 
     def _clean_extracted_text(self, text: str) -> str:

dcmspec-0.2.1/CHANGELOG.md

@@ -1,29 +0,0 @@
-# Release Notes
-
-These release notes summarize key changes, improvements, and breaking updates for each version of **dcmspec**.
-
-## [0.2.1] - 2025-09-19
-
-### Fixed
-
-- Sanitize node and attribute names to remove "/" in DOMTableSpecParser ([#56](https://github.com/dwikler/dcmspec/issues/56))
-
-### Changed
-
-- Major project restructure: moved CLI and UI apps to new `apps/cli` and `apps/ui` folders
-- Improved installation instructions and documentation
-- Prepared and published the package to [PyPI](https://pypi.org/project/dcmspec/)
-
-## [0.2.0] - 2025-09-13
-
-### Changed
-
-- **Breaking change:** `IODSpecBuilder.build_from_url` now returns a tuple `(iod_model, module_models)` instead of just the IOD model. All callers must be updated to unpack the tuple.
-- Updated CLI and UI applications to support new return value.
-- Added registry mode to `IODSpecBuilder` for efficient module model sharing.
-
-## [0.1.0] - 2025-05-25
-
-### Added
-
-- Initial release.