finalcif 157__tar.gz → 159__tar.gz

{finalcif-157 → finalcif-159}/.gitignore

@@ -235,3 +235,5 @@ finalcif_keys_order.cif
 /tests/examples/work/cu_BruecknerJK_153F40_0m-finalcif-2.zip
 /tests/examples/work/cu_BruecknerJK_153F40_0m_video-finalcif.png
 /tests/examples/work/report_cu_BruecknerJK_153F40_0m-finalcif.html
+/test-data/checkcif-DK_Zucker2_0m-finalcif.html
+/test-data/report_DK_Zucker2_0m-finalcif.html

{finalcif-157 → finalcif-159}/.run/compile_ui_files.run.xml

@@ -1,6 +1,7 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="compile_ui_files" type="PythonConfigurationType" factoryName="Python" activateToolWindowBeforeRun="false" nameIsGenerated="true">
     <module name="FinalCif" />
+    <option name="ENV_FILES" value="" />
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +12,9 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
+    <option name="DEBUG_JUST_MY_CODE" value="true" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <option name="RUN_TOOL" value="true" />
     <option name="SCRIPT_NAME" value="scripts/compile_ui_files.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />

finalcif-159/AGENTS.md

@@ -0,0 +1,31 @@
+# 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`).
+- **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`.
+
+## Workflow & Commands
+- **Dependency Management:** The project uses `uv` for package management (e.g., `uv.lock`, `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 (see `tests/test_checkcif.py`, `tests/test_doi.py`).
+- **Linting:** 
+  - *Command:* `ruff check .`
+  - *CI Lint:* GitHub Actions currently runs `flake8` in `.github/workflows/python_tests.yml`.
+- **UI Compilation:** 
+  - *Command:* `python scripts/compile_ui_files.py` (this discovers `.ui` files, compiles them, and hot-fixes imports to `qtpy`).
+- **Build/Releases:** Packaged with `hatchling`. Desktop releases use scripts in the `scripts/` directory (like `make_win_release.bat`).

{finalcif-157 → finalcif-159}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 157
+Version: 159
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -11,17 +11,18 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Requires-Dist: certifi
 Requires-Dist: chardet
 Requires-Dist: charset-normalizer
 Requires-Dist: crossrefapi
 Requires-Dist: docxtpl[subdoc]>=0.20.2
+Requires-Dist: fastmolwidget
 Requires-Dist: gemmi>=0.7.5
 Requires-Dist: hatchling
 Requires-Dist: html2text
 Requires-Dist: lxml==6.0.2
-Requires-Dist: numpy
+Requires-Dist: numpy<2.4,>=2.3.5
 Requires-Dist: packaging
 Requires-Dist: pefile
 Requires-Dist: pybind11
@@ -37,8 +38,8 @@ Requires-Dist: urllib3
 Requires-Dist: wheel
 Description-Content-Type: text/markdown
 
-![Lates Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
-[![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python-app_windows.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python-app_windows.yml)
+![Latest Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
+[![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml)
 ![Contributions](https://img.shields.io/badge/contributions-welcome-blue)
 [![PyPI package](https://repology.org/badge/version-for-repo/pypi/python:finalcif.svg)](https://repology.org/project/python:finalcif/versions)
 <a href="https://repology.org/project/finalcif/versions">
@@ -48,7 +49,7 @@ Description-Content-Type: text/markdown
 
 # FinalCif
 
-FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-xrystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
+FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-crystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
 
 For tables from multiple CIF files, you may want to use the program [multitable](https://github.com/dkratzert/multitable).
 

{finalcif-157 → finalcif-159}/README.md

@@ -1,5 +1,5 @@
-![Lates Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
-[![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python-app_windows.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python-app_windows.yml)
+![Latest Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
+[![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml)
 ![Contributions](https://img.shields.io/badge/contributions-welcome-blue)
 [![PyPI package](https://repology.org/badge/version-for-repo/pypi/python:finalcif.svg)](https://repology.org/project/python:finalcif/versions)
 <a href="https://repology.org/project/finalcif/versions">
@@ -9,7 +9,7 @@
 
 # FinalCif
 
-FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-xrystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
+FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-crystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
 
 For tables from multiple CIF files, you may want to use the program [multitable](https://github.com/dkratzert/multitable).
 

finalcif-159/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 159