finalcif 159__tar.gz → 161__tar.gz

finalcif-161/.githooks/pre-push

@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+# pre-push hook: rejects pushing a version tag whose version
+# does not match VERSION in finalcif/__init__.py.
+#
+# Activate with:
+#   git config core.hooksPath .githooks
+
+INIT_FILE="finalcif/__init__.py"
+
+# Extract VERSION from source (pure shell, no Python dependency)
+get_source_version() {
+    grep -m1 '^VERSION' "$INIT_FILE" | sed 's/^VERSION[[:space:]]*=[[:space:]]*\([0-9]*\).*/\1/'
+}
+
+# Read stdin for refs being pushed
+while read -r local_ref local_sha remote_ref remote_sha; do
+    # Only check version tags (refs/tags/*)
+    if [[ "$local_ref" == refs/tags/* ]]; then
+        tag_version="${local_ref#refs/tags/}"
+        tag_version="${tag_version#v}" # remove leading v if any
+
+        # Only process if tag is an integer
+        if [[ "$tag_version" =~ ^[0-9]+$ ]]; then
+            source_version=$(get_source_version)
+            if [ $? -ne 0 ] || [ -z "$source_version" ]; then
+                echo "ERROR: Could not extract VERSION from ${INIT_FILE}" >&2
+                exit 1
+            fi
+            if [ "$tag_version" != "$source_version" ]; then
+                echo "ERROR: Tag ${tag_version} does not match VERSION = ${source_version} in ${INIT_FILE}" >&2
+                echo "Update VERSION before tagging, or fix the tag name." >&2
+                exit 1
+            fi
+        fi
+    fi
+done
+
+exit 0
+

{finalcif-159 → finalcif-161}/.run/compile_ui_files.run.xml

@@ -1,6 +1,6 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="compile_ui_files" type="PythonConfigurationType" factoryName="Python" activateToolWindowBeforeRun="false" nameIsGenerated="true">
-    <module name="FinalCif" />
+    <module name="finalcif" />
     <option name="ENV_FILES" value="" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />

finalcif-161/AGENTS.md

@@ -0,0 +1,58 @@
+# FinalCif AI Developer Instructions
+
+## General Principles
+- **No Assumptions:** If information or code is missing, ask for it. Do not make assumptions.
+- **Refuse over Guessing:** Prefer refusing over guessing. If you don't know how to complete the code, say you don't know.
+- **Require Specifications:** If the user asks you to write code, ask for a detailed specification first. Do not write code until you have a detailed specification.
+- **Quality Standards:** Follow the rules of 'Refactoring' and 'Clean Code' as described by Martin Fowler and Robert C. Martin, respectively.
+
+## Core Setup Conventions
+- **Language/Runtime:** Use Python >=3.12 (`pyproject.toml`), with CI tested on 3.12/3.13/3.14 (`.github/workflows/python_tests.yml`).
+- **UI Framework:** Assume PySide6. UI imports in the codebase are typically routed through `qtpy` (note that UI files are compiled locally via bindings).
+- **Qt Binding Selection:** Set `QT_API=pyside6` before `qtpy` imports (see `finalcif/finalcif_start.py`).
+
+## Architecture
+- **Desktop Application:** FinalCif is a crystallographic information file (CIF) editor built with a Qt frontend.
+- **Entry Point:** The application starts from `finalcif/finalcif_start.py` (registered as `finalcif` in `pyproject.toml`).
+- **Main Window:** `AppWindow` (QMainWindow) in `finalcif/appwindow.py` is the orchestrator wiring all subsystems; UI defined in `finalcif/gui/finalcif_gui_ui.ui`.
+- **Subpackage Map:**
+  - `finalcif/cif/` — CIF I/O via `gemmi.cif` wrapped in `CifContainer` (`cif_file_io.py`); dict definitions (core/powder/modulation/twin/restraints); subpackages `checkcif/` (IUCr CheckCIF HTML/PDF parsing) and `cod/` (COD/CCDC deposition: `deposit.py`, `upload.py`, `doi.py`, `website_parser.py`).
+  - `finalcif/ciforder/` — CIF key ordering dialog.
+  - `finalcif/datafiles/` — raw instrument data importers: Bruker (`bruker_data.py`, `bruker_frame.py`), SAINT, SADABS, SHELX `.lst` (`shelx_lst.py`), `.p4p`, CCDC deposition mail parser (`ccdc_mail.py`).
+  - `finalcif/displaymol/` — 3D molecular display (`vtk_molecule.py`) is not used; 2D rendering is provided by the external `fastmolwidget` package (custom widget in `finalcif_gui_ui.ui`).
+  - `finalcif/equip_property/` — Equipment/Properties/AuthorLoops template tables (`equipment.py`, `properties.py`, `author_loop_templates.py`).
+  - `finalcif/gui/` — Qt widgets; `.ui` files compiled to sibling `*_ui.py` modules.
+  - `finalcif/report/` — DOCX report generation via `docxtpl` (`DocxTemplate`, `RichText`, `InlineImage`) in `templated_report.py`; also archive reports, tables, references, symmetry.
+  - `finalcif/template/` — Report template infrastructure (`ReportTemplates`).
+  - `finalcif/tools/` — cross-cutting helpers: `platon.py` (`PlatonRunner`), `shred.py`, `space_groups.py`, `sumformula.py`, `settings.py` (`FinalCifSettings` QSettings wrapper), `download.py`, `pupdate.py` (auto-updater), `statusbar.py`, `chemparse.py`, `dsrmath.py`.
+- **External Tool Integration:**
+  - Offline CheckCIF uses PLATON via `finalcif/tools/platon.py`; executable resolution checks bundled `platon/platon_special.exe`, then `C:\pwt\platon.exe` (Windows), then `platon` on `PATH`.
+  - Online CheckCIF (IUCr) via HTTP in `finalcif/cif/checkcif/checkcif.py`.
+  - CCDC/COD deposition in `finalcif/cif/cod/` (`deposit.py`, `upload.py`, `deposit_check.py`); deposition email parsing in `finalcif/datafiles/ccdc_mail.py`.
+  - DOI / CrossRef lookups via `crossrefapi` (see `finalcif/cif/cod/doi.py`).
+  - SHELX parsing via the external `shelxfile` package (used in `report/templated_report.py`); in-tree `.lst` parser in `datafiles/shelx_lst.py`.
+- **CIF Parsing:** Standardized on `gemmi` (>=0.7.5); `gemmi.set_leak_warnings(False)` is set at startup.
+
+## Conventions
+- **UI Files:** Edit `.ui` files in Qt Designer (`scripts/designer.py`), then regenerate via `python scripts/compile_ui_files.py`. Never hand-edit generated `*_ui.py`.
+- **qtpy Imports:** `from qtpy import QtCore, QtGui, QtWebEngineWidgets, QtWidgets, compat` — `QtWebEngine` is used and requires `PySide6-Addons`.
+- **App Bootstrap:** `appwindow.py` uses `QApplication.instance() or QApplication([])` with `app.setStyle("windowsvista")`. A `DEBUG` flag in `finalcif_start.py` toggles the crash hook; crash reports are written to `~/finalcif-crash.txt` by `my_exception_hook`.
+- **Settings:** Persisted via `FinalCifSettings` (QSettings wrapper) in `finalcif/tools/settings.py`.
+
+## Workflow & Commands
+- **Dependency Management:** The project uses `uv` for package management (`uv.lock`, `pylock.toml`, `pyproject.toml`).
+  - *Setup:* `uv sync --all-extras --dev`
+- **Testing:** 
+  - *Command:* `uv run pytest tests`
+  - *CI/Linux Headless:* run tests with `QT_QPA_PLATFORM=offscreen` (see `.github/workflows/python_tests.yml`).
+  - *Network-Gated Tests:* set `NO_NETWORK=1` to skip network-dependent checks (CheckCIF/DOI/deposit/PLATON; see `tests/test_checkcif.py`, `tests/test_doi.py`).
+  - *Helpers:* shared base class `AppWindowTestCase` and `processevents()` in `tests/helpers.py`; `get_platon_exe()` resolves `C:\pwt\platon.exe` on Windows or `which('platon')`. Fixtures live in `tests/examples/`, `tests/statics/`, `tests/checkcif_results/`, and top-level `test-data/`.
+- **Linting:** 
+  - *Command (local):* `ruff check .` — configured via `.ruff.toml` (line-length 120, target py312).
+  - *CI Lint:* GitHub Actions runs `flake8` in `.github/workflows/python_tests.yml` (ruff is not invoked in CI).
+- **UI Compilation:** 
+  - *Command:* `python scripts/compile_ui_files.py` (discovers `.ui` files, compiles them, and hot-fixes imports to `qtpy`).
+- **Build/Releases:**
+  - Packaged with `hatchling`; tag pushes trigger `.github/workflows/python-dist.yml` which runs `uv build` and publishes to PyPI via trusted publishing.
+  - Desktop installers built with PyInstaller specs (`Finalcif_installer_win.spec`, `Finalcif_linux_onefile.spec`, `Finalcif_mac.spec`) plus `scripts/_make_win_release.py`, `scripts/make_win_release.bat`, and Inno Setup `scripts/finalcif-install_win64.iss`.
+  - Dev launchers: `run_finalcif.bat` / `run_finalcif` / `scripts/finalcif-start.sh`.

{finalcif-159 → finalcif-161}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 159
+Version: 161
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -17,11 +17,11 @@ Requires-Dist: chardet
 Requires-Dist: charset-normalizer
 Requires-Dist: crossrefapi
 Requires-Dist: docxtpl[subdoc]>=0.20.2
-Requires-Dist: fastmolwidget
+Requires-Dist: fastmolwidget>=0.9.5
 Requires-Dist: gemmi>=0.7.5
 Requires-Dist: hatchling
 Requires-Dist: html2text
-Requires-Dist: lxml==6.0.2
+Requires-Dist: lxml==6.1.0
 Requires-Dist: numpy<2.4,>=2.3.5
 Requires-Dist: packaging
 Requires-Dist: pefile
@@ -75,6 +75,6 @@ You only need them if you want to make report tables that differ from the defaul
 
 ![FinalCif CheckCIF](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_checkcif.png)
 
-![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_responses.png)
+![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/docs/pics/finalcif_responses.png)
 
-![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_loops.png)
+![FinalCif loops](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_loops.png)

{finalcif-159 → finalcif-161}/README.md

@@ -35,6 +35,6 @@ You only need them if you want to make report tables that differ from the defaul
 
 ![FinalCif CheckCIF](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_checkcif.png)
 
-![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_responses.png)
+![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/docs/pics/finalcif_responses.png)
 
-![FinalCif responses](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_loops.png)
+![FinalCif loops](https://github.com/dkratzert/FinalCif/raw/master/screenshots/finalcif_loops.png)

finalcif-161/finalcif/__init__.py

@@ -0,0 +1,3 @@
+
+VERSION = 161
+__version__ = VERSION

{finalcif-159 → finalcif-161}/finalcif/appwindow.py

@@ -18,6 +18,8 @@ from math import sin, radians
 from pathlib import Path, WindowsPath
 from typing import cast
 
+from fastmolwidget import Atomtuple
+from fastmolwidget.part_combo import PartFilterWidget
 from fastmolwidget.sdm import SDM
 
 from finalcif.gui.vzs_viewer import VZSImageViewer
@@ -113,6 +115,10 @@ class AppWindow(QMainWindow):
         self.ui = Ui_FinalCifWindow()
         self.ui.setupUi(self)
         self.ui.page_MainTable.setParent(self.ui.MainStackedWidget)
+        # Parts selector widget – inserted after adpCheckBox in horizontalLayout_7
+        self.parts_combo = PartFilterWidget(parent=self.ui.molGroupBox, label=' ', min_combo_width=90)
+        self.parts_combo.setObjectName('partsFilterWidget')
+        self.ui.horizontalLayout_7.insertWidget(3, self.parts_combo)
         # Inject the Author Editor tab (defined in the .ui file) into LoopsPage
         self.ui.loops_page.set_author_editor_tab(self.ui.author_editor_widget)
         self.fixfont = QtGui.QFontDatabase.systemFont(QtGui.QFontDatabase.SystemFont.FixedFont)
@@ -204,7 +210,7 @@ class AppWindow(QMainWindow):
         self.ui.PictureWidthDoubleSpinBox.setRange(0.0, 25)
         self.ui.PictureWidthDoubleSpinBox.setSingleStep(0.5)
         # Just too slow for large structures:
-        self.ui.growCheckBox.setChecked(False)
+        self.ui.growCheckBox.setChecked(True)
         self.ui.CheckcifButton.setDisabled(True)
         self.ui.CheckcifStartButton.setDisabled(True)
         self.ui.ReportPicPushButton.setDisabled(True)
@@ -419,6 +425,7 @@ class AppWindow(QMainWindow):
         self.ui.growCheckBox.toggled.connect(lambda: self.redraw_molecule(reset_view=False))
         self.ui.labelsCheckBox.toggled.connect(self.show_labels)
         self.ui.adpCheckBox.toggled.connect(self.show_adp)
+        self.parts_combo.selectionChanged.connect(self._on_parts_selection_changed)
         self.ui.SourcesPushButton.clicked.connect(self.show_sources)
         self.ui.BackSourcesPushButton.clicked.connect(self.back_to_main_noload)
         self.ui.BackFromOptionspPushButton.clicked.connect(self.back_to_main_noload)
@@ -1314,6 +1321,11 @@ class AppWindow(QMainWindow):
                 ok = t.make_templated_html_report(output_filename=str(report_filename),
                                                   template_path=template_path.parent,
                                                   template_file=template_path.name)
+            elif template_path.suffix in ('.tex', '.latex'):
+                t = TemplatedReport(format=ReportFormat.LATEX, options=self.options, cif=self.cif)
+                ok = t.make_templated_latex_report(output_filename=str(report_filename),
+                                                   template_path=template_path.parent,
+                                                   template_file=template_path.name)
             if not ok:
                 return None
         except FileNotFoundError as e:
@@ -1965,14 +1977,15 @@ class AppWindow(QMainWindow):
             atoms = self.cif.atoms_orth
 
         with suppress(Exception):
+            atom_tuples = self._atoms_with_adps(atoms)
+            self._update_parts_combo(atom_tuples)
             if reset_view:
-                self.ui.render_widget.open_molecule(atoms,
+                self.ui.render_widget.open_molecule(atom_tuples,
                                                     cell=self.cif.cell[:6],
-                                                    adps=self.get_adps(), keep_view=not reset_view)
+                                                    keep_view=not reset_view)
             else:
-                self.ui.render_widget.grow_molecule(atoms,
-                                                    cell=self.cif.cell[:6],
-                                                    adps=self.get_adps())
+                self.ui.render_widget.grow_molecule(atom_tuples,
+                                                    cell=self.cif.cell[:6])
 
     def _calc_grown_atoms(self):
         """Helper to generate the symmetry expanded atoms without drawing them."""
@@ -1991,6 +2004,35 @@ class AppWindow(QMainWindow):
                                   to_float(dp.U23), to_float(dp.U13), to_float(dp.U12))
         return adp_dict
 
+    def _atoms_with_adps(self, atoms) -> list[Atomtuple]:
+        """Convert atom objects to Atomtuple instances with ADP data embedded directly."""
+        adp_dict = self.get_adps()
+        result = []
+        for at in atoms:
+            adp = adp_dict.get(at.label)
+            if isinstance(at, Atomtuple):
+                result.append(at._replace(adp=adp))
+            else:
+                result.append(Atomtuple(label=at.label, type=at.type,
+                                        x=at.x, y=at.y, z=at.z,
+                                        part=at.part, adp=adp))
+        return result
+
+    def _update_parts_combo(self, atoms: list[Atomtuple]) -> None:
+        """Repopulate the parts selector with the unique disorder parts present in *atoms*.
+
+        The widget is shown only when more than one distinct part is found (i.e. disorder exists).
+        """
+        parts = frozenset(at.part for at in atoms)
+        self.parts_combo.update_parts(parts)
+
+    def _on_parts_selection_changed(self) -> None:
+        """Forward the current parts selection to the molecule widget."""
+        checked = self.parts_combo.checked_values()
+        visible: set[int] | None = set(checked) if checked else None
+        with suppress(Exception):
+            self.ui.render_widget.set_visible_parts(visible)
+
     def redraw_molecule(self, reset_view: bool = False) -> None:
         try:
             self.view_molecule(reset_view=reset_view)

{finalcif-159 → finalcif-161}/finalcif/cif/text.py

@@ -12,6 +12,7 @@ from html import unescape
 import gemmi
 
 
+
 def quote(string: str, wrapping=80) -> str:
     """
     Quotes a cif string and wraps it. The shorter strings are directly handled by cif.quote().
@@ -28,56 +29,56 @@ def quote(string: str, wrapping=80) -> str:
 
 
 characters = {
-    '—'      : r'--',
-    '±'      : r'+-',
-    '×'      : r'\\times',  # noqa: RUF001
-    '≠'      : r'\\neq',
-    '→'      : r'\\rightarrow',
-    '←'      : r'\\leftarrow',
-    '∞'      : r'\\infty',
-    '≃'      : r'\\simeq',
-    '≈'      : r'\\sim',
-    'ß'      : r'\&s',
-    'ü'      : r'\"u',
-    'Ü'      : r'\"U',
-    'ö'      : r'\"o',  # 'LATIN SMALL LETTER O WITH DIAERESIS'
-    'Ö'      : r'\"O',
-    'ä'      : r'\"a',
-    'Ä'      : r'\"A',
-    'é'      : r"\'e",
-    'É'      : r"\'E",
-    'è'      : r'\`e',
-    'È'      : r'\`E',
-    'ì'      : r'\`i',
-    'Ì'      : r'\`I',
-    'í'      : r'\'i',
-    'Í'      : r'\'I',
-    'ó'      : r"\'o",
-    'Ó'      : r"\'O",
-    'ò'      : r'\`o',
-    'Ò'      : r'\`O',
-    'ȯ'      : r'\.o',
-    'ø'      : r'\/o',
-    'á'      : r'\'a',
-    'Á'      : r'\'A',
-    'à'      : r'\`a',
-    'À'      : r'\`A',
-    'â'      : r'\^a',
-    'Â'      : r'\^A',
-    'å'      : r'\%a',
-    'ê'      : r'\^e',
-    'î'      : r'\^i',
-    'Î'      : r'\^I',
-    'ô'      : r'\^o',
-    'Ô'      : r'\^O',
-    'û'      : r'\^u',
-    'Û'      : r'\^U',
-    'ç'      : r'\,c',
-    'ñ'      : r'\~n',
-    'ł'      : r'\/l',
-    'đ'      : r'\/d',
-    'Å'      : r'\%A',  # 'LATIN CAPITAL LETTER A WITH RING ABOVE'
-    'Å'      : r'\%A',  # unicodedata.name('Å'): 'ANGSTROM SIGN'
+    '—'     : r'--',
+    '±'     : r'+-',
+    '×'     : r'\\times',  # noqa: RUF001
+    '≠'     : r'\\neq',
+    '→'     : r'\\rightarrow',
+    '←'     : r'\\leftarrow',
+    '∞'     : r'\\infty',
+    '≃'     : r'\\simeq',
+    '≈'     : r'\\sim',
+    'ß'     : r'\&s',
+    'ü'     : r'\"u',
+    'Ü'     : r'\"U',
+    'ö'     : r'\"o',  # 'LATIN SMALL LETTER O WITH DIAERESIS'
+    'Ö'     : r'\"O',
+    'ä'     : r'\"a',
+    'Ä'     : r'\"A',
+    'é'     : r"\'e",
+    'É'     : r"\'E",
+    'è'     : r'\`e',
+    'È'     : r'\`E',
+    'ì'     : r'\`i',
+    'Ì'     : r'\`I',
+    'í'     : r'\'i',
+    'Í'     : r'\'I',
+    'ó'     : r"\'o",
+    'Ó'     : r"\'O",
+    'ò'     : r'\`o',
+    'Ò'     : r'\`O',
+    'ȯ'     : r'\.o',
+    'ø'     : r'\/o',
+    'á'     : r'\'a',
+    'Á'     : r'\'A',
+    'à'     : r'\`a',
+    'À'     : r'\`A',
+    'â'     : r'\^a',
+    'Â'     : r'\^A',
+    'å'     : r'\%a',
+    'ê'     : r'\^e',
+    'î'     : r'\^i',
+    'Î'     : r'\^I',
+    'ô'     : r'\^o',
+    'Ô'     : r'\^O',
+    'û'     : r'\^u',
+    'Û'     : r'\^U',
+    'ç'     : r'\,c',
+    'ñ'     : r'\~n',
+    'ł'     : r'\/l',
+    'đ'     : r'\/d',
+    'Å'     : r'\%A',  # 'LATIN CAPITAL LETTER A WITH RING ABOVE'
+    'Å'     : r'\%A',  # unicodedata.name('Å'): 'ANGSTROM SIGN'
     '\u2079': r'^9^',
     '\u2078': r'^8^',
     '\u2077': r'^7^',
@@ -149,7 +150,7 @@ characters = {
     "\u03A9": r'\W',
     "\u03D5": r'\f',
     "\u00B0": r"\%",
-    '·'      : r"{middle dot}",
+    '·'     : r"{middle dot}",
     # "1̄": r'\=1',  # Does not work in QT?
 }
 
@@ -199,6 +200,17 @@ def string_to_utf8(txt: str) -> str:
     return retranslate_delimiter(txt)
 
 
+def string_to_latex(cif_string: str) -> str:
+    from finalcif.template.unicode2latex.u2l import uni2tex
+    utf8_string = string_to_utf8(cif_string)
+    return uni2tex(utf8_string, add_font_modifiers=False, prefer_unicode_math=False, convert_accents=True)
+
+
+def utf8_to_latex(utf8_string: str) -> str:
+    from finalcif.template.unicode2latex.u2l import uni2tex
+    return uni2tex(utf8_string, add_font_modifiers=False, prefer_unicode_math=False, convert_accents=True)
+
+
 def retranslate_delimiter(txt: str, no_html_unescape: bool = False) -> str:
     """
     Translates delimited cif characters back to Unicode characters.
@@ -219,3 +231,26 @@ def utf8_to_html_ascii(text: str) -> str:
 
 def html_ascii_to_utf8(text: str) -> str:
     return unescape(text)
+
+
+def escape_for_latex(text: str) -> str:
+    """
+    Escapes special characters in text so that it can be safely used in LaTeX.
+    """
+    latex_special_chars = {
+        '\\': r'\textbackslash{}',
+        '{' : r'\{',
+        '}' : r'\}',
+        '$' : r'\$',
+        '&' : r'\&',
+        '#' : r'\#',
+        '_' : r'\_',
+        '%' : r'\%',
+        '~' : r'\textasciitilde{}',
+        '^' : r'\textasciicircum{}',
+        '[' : r'\[',
+        ']' : r'\]',
+    }
+    regex = re.compile('|'.join(re.escape(key) for key in latex_special_chars))
+    escaped_text = regex.sub(lambda match: latex_special_chars[match.group()], text)
+    return string_to_latex(escaped_text)

{finalcif-159 → finalcif-161}/finalcif/equip_property/author_loop_templates.py

@@ -13,7 +13,8 @@ from pathlib import Path
 from typing import TYPE_CHECKING
 
 import gemmi.cif
-from qtpy.QtWidgets import QListWidgetItem
+from qtpy import QtCore
+from qtpy.QtWidgets import QListWidgetItem, QMenu
 from gemmi.cif import Loop, as_string
 
 from finalcif.cif.cif_file_io import CifContainer
@@ -54,6 +55,8 @@ class AuthorLoops:
         self.ui = ui
         self.cif = cif
         self.app = app
+        self._rename_old_name: str = ''
+        self._rename_menu: QMenu | None = None
         self.cif_key = '_publ_author'
         self.keys_list = [f'{self.cif_key}_name', f'{self.cif_key}_address', f'{self.cif_key}_email',
                           f'{self.cif_key}_phone', f'{self.cif_key}_id_orcid', f'{self.cif_key}_id_iucr',
@@ -86,6 +89,11 @@ class AuthorLoops:
         self.ui.ImportAuthorPushButton.clicked.connect(self.import_author)
         self.ui.FullNameLineEdit.textChanged.connect(self.make_sure_to_save_only_when_name_field_has_text)
         self.ui.FullNameLineEdit_cif.textChanged.connect(self.make_sure_to_save_only_when_name_field_has_text)
+        self.ui.LoopTemplatesListWidget.setContextMenuPolicy(
+            QtCore.Qt.ContextMenuPolicy.CustomContextMenu)
+        self.ui.LoopTemplatesListWidget.customContextMenuRequested.connect(
+            self.show_author_rename_menu)
+        self.ui.LoopTemplatesListWidget.itemChanged.connect(self.on_author_item_renamed)
 
     def set_author_state(self) -> None:
         if self.ui.authorEditTabWidget.currentWidget().objectName() == 'page_publication':
@@ -242,16 +250,30 @@ class AuthorLoops:
         self.general_author_save(author)
         self.clear_fields()
 
-    def general_author_save(self, author: Author) -> None:
+    def _author_template_name(self, author: Author) -> str:
+        """Return the default template-list name for an author."""
+        if author.contact_author:
+            return f'{string_to_utf8(as_string(author.name))} (contact author)'
+        return string_to_utf8(as_string(author.name))
+
+    def _unique_author_name(self, base_name: str) -> str:
+        """Return a name not yet in the authors list, appending a counter if necessary."""
+        existing = set(self.authors_list())
+        if base_name not in existing:
+            return base_name
+        counter = 2
+        while f'{base_name} {counter}' in existing:
+            counter += 1
+        return f'{base_name} {counter}'
+
+    def general_author_save(self, author: Author, template_name: str | None = None) -> None:
         if not author.name:
             return
-        if author.contact_author:
-            itemtext = f'{string_to_utf8(as_string(author.name))} (contact author)'
-        else:
-            itemtext = string_to_utf8(as_string(author.name))
-        if not itemtext:
+        if template_name is None:
+            template_name = self._author_template_name(author)
+        if not template_name:
             return
-        self.settings.save_settings_dict(property='authors_list', name=itemtext, items=author)
+        self.settings.save_settings_dict(property='authors_list', name=template_name, items=author)
         self.show_authors_list()
 
     def export_author_template(self, filename: str | None = None) -> None:
@@ -341,7 +363,8 @@ class AuthorLoops:
                     author_type=AuthorType.publ,
                     contact_author=True
                 )
-                self.general_author_save(author)
+                unique_name = self._unique_author_name(self._author_template_name(author))
+                self.general_author_save(author, template_name=unique_name)
 
             names = list(block.find_values('_publ_author_name'))
             if names:
@@ -368,7 +391,8 @@ class AuthorLoops:
                         author_type=AuthorType.publ,
                         contact_author=False
                     )
-                    self.general_author_save(author)
+                    unique_name = self._unique_author_name(self._author_template_name(author))
+                    self.general_author_save(author, template_name=unique_name)
 
         self.show_authors_list()
 
@@ -401,6 +425,58 @@ class AuthorLoops:
             if author:
                 self.ui.LoopTemplatesListWidget.addItem(QListWidgetItem(author))
 
+    def show_author_rename_menu(self, pos: QtCore.QPoint) -> None:
+        """Show a context menu with a Rename action for the author loop templates list."""
+        listw = self.ui.LoopTemplatesListWidget
+        item = listw.itemAt(pos)
+        if item is None:
+            return
+        menu = QMenu(listw)
+        rename_action = menu.addAction('Rename')
+        # Keep a strong Python reference so PySide6 does not garbage-collect the
+        # menu wrapper (and thereby drop the triggered signal connection) before
+        # the user selects an action.  Clear it whenever the menu closes so the
+        # reference is not held indefinitely if the user dismisses without action.
+        self._rename_menu = menu
+        menu.aboutToHide.connect(lambda: setattr(self, '_rename_menu', None))
+
+        def _on_triggered(action) -> None:
+            if action == rename_action:
+                # Set flags first so the spurious itemChanged signal (fired by
+                # setFlags) finds _rename_old_name still empty and returns early.
+                item.setFlags(
+                    QtCore.Qt.ItemFlag.ItemIsEditable
+                    | QtCore.Qt.ItemFlag.ItemIsEnabled
+                    | QtCore.Qt.ItemFlag.ItemIsSelectable
+                )
+                self._rename_old_name = item.text()
+                # Defer editItem() to the next event-loop tick so that all
+                # menu-close events are processed before Qt starts the editor.
+                QtCore.QTimer.singleShot(0, lambda: listw.editItem(item))
+
+        menu.triggered.connect(_on_triggered)
+        menu.popup(listw.viewport().mapToGlobal(pos))
+
+    def on_author_item_renamed(self, item: QListWidgetItem) -> None:
+        """Persist an author template rename when the user finishes editing."""
+        if not self._rename_old_name:
+            return
+        new_name = item.text().strip()
+        old_name = self._rename_old_name
+        self._rename_old_name = ''
+        # Remove the editable flag so items cannot be renamed by accident
+        item.setFlags(QtCore.Qt.ItemFlag.ItemIsEnabled | QtCore.Qt.ItemFlag.ItemIsSelectable)
+        if not new_name:
+            item.setText(old_name)
+            return
+        if new_name != old_name:
+            if new_name in self.authors_list():
+                show_general_warning(self.app, f'A template named "{new_name}" already exists.')
+                item.setText(old_name)
+                return
+            self.settings.rename_template('authors_list', old_name, new_name)
+            self.show_authors_list()
+
     def export_raw_data(self) -> list[Author]:
         """
         Export all authors in order to export them all"""
@@ -415,7 +491,8 @@ class AuthorLoops:
         Import all authors from an external file"""
         for author in authors_data:
             if author and isinstance(author, Author):
-                self.general_author_save(author)
+                unique_name = self._unique_author_name(self._author_template_name(author))
+                self.general_author_save(author, template_name=unique_name)
 
     def authors_list(self) -> list[str]:
         return self.settings.list_saved_items(property='authors_list')