Add fit functionality to command line interface (#145)

* Update save_as paths to include 'data/' directory and adjust test function to use temporary directory

* Add crysfml

* Update notebooks

* Clean up

* Add simple integration test for crysfml

* Bump pycrysfml to 0.2.1

* Add pytest marker to neutron_pd_cwl_lbco_crysfml test

* Extend package test script by adding pycrysfml

* Fix scipp integration test

* Move jupyterlab and pixi-kernel out from pyproject.toml

* Remove unnecessary libcxx addition for osx-64 in test.yml

* Add custom PyPI index support for pycrysfml in test.yml

* Update .gitignore to include data directory for tutorial runtime

* Apply latest templates

* Add temporary rule ignores for docstring and datetime checks in pyproject.toml

* Apply new templates

* Update index hash for data integrity in utils.py

* Add reverse flag to fit_sequential for reverse-order processing

* Update tutorials index

* Update tutorial

* Add initial structure and analysis configuration files

* Fix asymmetry and save/restore peak_profile_type in experiment CIF

* Refactor switchable-type restore into _restore_switchable_types

* Update test example

* Update data-index.json known hash in utils.py

* Return numpy array from CrysfmlCalculator and adjust pattern length handling

* Add aliases and constraints for isotropic displacement parameters refinement

* Add fit command to CLI

* Update notebooks

* Add CLI documentation to User Guide

* Update documentation to move Command-Line Interface section

* Bump dependencies

* Add back the lost doc file

* Re-copy templates

* Update installation instructions and CI workflow for macOS support

Author: AndrewSazonov

.github/workflows/pypi-test.yml

@@ -48,6 +48,9 @@ jobs:
       - name: Init pixi project
         run: pixi init easydiffraction
 
+      - name: Set the minimum system requirements
+        run: pixi project system-requirements add macos 14.0
+
       - name: Add Python 3.14 from Conda
         working-directory: easydiffraction
         run: pixi add "python=3.14"
@@ -58,22 +61,25 @@ jobs:
           pixi add gsl
           pixi add --platform osx-arm64 libcxx
 
-      - name: Add easydiffraction from PyPI
-        working-directory: easydiffraction
-        run: pixi add --pypi "easydiffraction"
-
-      - name: Add dev dependencies from PyPI
+      - name: Add pycrysfml calculator from custom PyPI index
         working-directory: easydiffraction
-        run: pixi add --pypi pytest pytest-xdist
+        run: |
+          echo '' >> pixi.toml
+          echo '[pypi-dependencies]' >> pixi.toml
+          echo 'pycrysfml = { version = ">=0.2.1", index = "https://easyscience.github.io/pypi/" }' >> pixi.toml
 
-      - name: Add Pixi task as a shortcut
+      - name: Add easydiffraction (with dev dependencies) from PyPI
         working-directory: easydiffraction
-        run: pixi task add easydiffraction "python -m easydiffraction"
+        run: pixi add --pypi "easydiffraction[dev]"
 
       - name: Run unit tests to verify the installation
         working-directory: easydiffraction
         run: pixi run python -m pytest ../tests/unit/ --color=yes -v
 
+      - name: Run functional tests to verify the installation
+        working-directory: easydiffraction
+        run: pixi run python -m pytest ../tests/functional/ --color=yes -v
+
       - name: Run integration tests to verify the installation
         working-directory: easydiffraction
         run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto

docs/docs/cli/index.md

@@ -0,0 +1,90 @@
+---
+icon: material/console
+---
+
+# :material-console: Command-Line Interface
+
+In addition to the Python API and Jupyter Notebooks, EasyDiffraction
+provides a **command-line interface (CLI)**. This is useful for basic
+operations without writing Python code.
+
+## Running the CLI
+
+The CLI is invoked as a Python module:
+
+```bash
+python -m easydiffraction [COMMAND] [OPTIONS]
+```
+
+If you use **Pixi** and have defined the `easydiffraction` task (see
+[Installation & Setup](../installation-and-setup/index.md)), you can
+use:
+
+```bash
+pixi run easydiffraction [COMMAND] [OPTIONS]
+```
+
+To see all available commands and options:
+
+```bash
+python -m easydiffraction --help
+```
+
+## Available Commands
+
+### Show Version
+
+Display the installed EasyDiffraction version:
+
+```bash
+python -m easydiffraction --version
+```
+
+### List Tutorials
+
+List all available tutorial notebooks:
+
+```bash
+python -m easydiffraction list-tutorials
+```
+
+### Download Tutorials
+
+Download a specific tutorial by ID:
+
+```bash
+python -m easydiffraction download-tutorial 1
+```
+
+Download all available tutorials:
+
+```bash
+python -m easydiffraction download-all-tutorials
+```
+
+Both commands accept `--destination` (`-d`) to specify the output
+directory (default: `tutorials/`) and `--overwrite` (`-o`) to replace
+existing files.
+
+### Fit a Project
+
+Load a saved project and run structural refinement:
+
+```bash
+python -m easydiffraction fit PROJECT_DIR
+```
+
+`PROJECT_DIR` is the path to a project directory previously created by
+`project.save_as()`. It must contain a `project.cif` file along with the
+`structures/`, `experiments/`, and `analysis/` subdirectories.
+
+After fitting, the command displays the fit results and a project
+summary. By default, updated parameter values are **saved back** to the
+project directory.
+
+Use the `--dry` flag to run the fit **without overwriting** the project
+files:
+
+```bash
+python -m easydiffraction fit PROJECT_DIR --dry
+```

docs/docs/index.md

@@ -1,11 +1,11 @@
 ![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only)
 
-# Diffraction data analysis library
+# Diffraction data analysis
 
 Here is a brief overview of the main documentation sections:
 
 - [:material-information-slab-circle: Introduction](introduction/index.md)
-  – Provides an overview of EasyDiffraction, including its purpose,
+  – Provides a description of EasyDiffraction, including its purpose,
   licensing, latest release details, and contact information.
 - [:material-cog-box: Installation & Setup](installation-and-setup/index.md)
   – Guides users through system requirements, environment configuration,
@@ -19,3 +19,6 @@ Here is a brief overview of the main documentation sections:
 - [:material-code-braces-box: API Reference](api-reference/index.md) –
   An auto-generated reference detailing the available functions and
   modules in EasyDiffraction.
+- [:material-console: Command-Line Interface](cli/index.md) – Describes
+  how to use EasyDiffraction from the terminal for batch fitting and
+  other tasks.