diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
index 46097a1d..46a8a905 100644
--- a/.github/workflows/pypi-test.yml
+++ b/.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
diff --git a/docs/docs/cli/index.md b/docs/docs/cli/index.md
new file mode 100644
index 00000000..5fc13c77
--- /dev/null
+++ b/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
+```
diff --git a/docs/docs/index.md b/docs/docs/index.md
index 73c35423..cc8b5cb0 100644
--- a/docs/docs/index.md
+++ b/docs/docs/index.md
@@ -1,11 +1,11 @@

-# 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.
diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md
index f08fd3ae..fdea87bf 100644
--- a/docs/docs/installation-and-setup/index.md
+++ b/docs/docs/installation-and-setup/index.md
@@ -7,12 +7,11 @@ icon: material/cog-box
**EasyDiffraction** is a cross-platform Python library compatible with
**Python 3.12** through **3.14**.
-EasyDiffraction is a cross-platform Python library compatible with
-**Python 3.11 through 3.13**.
-Make sure Python is installed on your system before proceeding with the
-installation.
+To install and set up EasyDiffraction, we recommend using
+[**Pixi**](https://pixi.prefix.dev), a modern package manager for
+Windows, macOS, and Linux.
-## Environment Setup optional { #environment-setup data-toc-label="Environment Setup" }
+??? note "Main benefits of using Pixi"
- **Ease of use**: Pixi simplifies the installation process, making it
accessible even for users with limited experience in package management.
@@ -63,10 +62,22 @@ This section describes the simplest way to set up EasyDiffraction using
pixi init easydiffraction
cd easydiffraction
```
+- If you are on macOS, set the minimum system requirements:
+ ```txt
+ pixi project system-requirements add macos 14.0
+ ```
- Set the Python version for the Pixi environment (e.g., 3.14):
```txt
pixi add python=3.14
```
+- Add GNU Scientific Library (required for PDF calculations):
+ ```txt
+ pixi add gsl
+ ```
+- If you are on macOS, add libc++ (required for PDF calculations):
+ ```txt
+ pixi add --platform osx-arm64 libcxx
+ ```
- Add EasyDiffraction to the Pixi environment from PyPI:
```txt
pixi add --pypi easydiffraction
@@ -110,21 +121,21 @@ simply delete and recreate the environment.
- Create a new virtual environment:
- ```bash
+ ```txt
python3 -m venv venv
```
- Activate the environment:
=== ":material-apple: macOS"
- ```bash
+ ```txt
. venv/bin/activate
```
=== ":material-linux: Linux"
- ```bash
+ ```txt
. venv/bin/activate
```
=== ":fontawesome-brands-windows: Windows"
- ```bash
+ ```txt
. venv/Scripts/activate # Windows with Unix-like shells
.\venv\Scripts\activate.bat # Windows with CMD
.\venv\Scripts\activate.ps1 # Windows with PowerShell
@@ -140,198 +151,147 @@ simply delete and recreate the environment.
- Exit the environment:
- ```bash
+ ```txt
deactivate
```
- If this environment is no longer needed, delete it:
=== ":material-apple: macOS"
- ```bash
+ ```txt
rm -rf venv
```
=== ":material-linux: Linux"
- ```bash
+ ```txt
rm -rf venv
```
=== ":fontawesome-brands-windows: Windows"
- ```bash
+ ```txt
rmdir /s /q venv
```
-## Installation Guide
-
-### Installing from PyPI recommended { #from-pypi data-toc-label="Installing from PyPI" }
+### Installing from PyPI { #from-pypi }
EasyDiffraction is available on **PyPI (Python Package Index)** and can
-be installed using `pip`. We strongly recommend installing it within a
-virtual environment, as described in the
-[Environment Setup](#environment-setup) section.
-
-We recommend installing the latest release of EasyDiffraction with the
-`visualization` extras, which include optional dependencies used for
-simplified visualization of charts and tables. This can be especially
-useful for running the Jupyter Notebook examples. To do so, use the
-following command:
-
-```bash
-pip install 'easydiffraction[visualization]'
-```
-
-If only the core functionality is needed, the library can be installed
-simply with:
+be installed using `pip`. To do so, use the following command:
-```bash
+```txt
pip install easydiffraction
```
To install a specific version of EasyDiffraction, e.g., 1.0.3:
-```bash
+```txt
pip install 'easydiffraction==1.0.3'
```
To upgrade to the latest version:
-```bash
+```txt
+pip install --upgrade easydiffraction
+```
+
+To upgrade to the latest version and force reinstallation of all
+dependencies (useful if files are corrupted):
+
+```txt
pip install --upgrade --force-reinstall easydiffraction
```
To check the installed version:
-```bash
+```txt
pip show easydiffraction
```
-### Installing from GitHub
+### Installing from GitHub alternative { #from-github data-toc-label="Installing from GitHub" }
Installing unreleased versions is generally not recommended but may be
useful for testing.
-To install EasyDiffraction from, e.g., the `develop` branch of GitHub:
+To install EasyDiffraction from the `develop` branch of GitHub, for
+example:
-```bash
+```txt
pip install git+https://github.com/easyscience/diffraction-lib@develop
```
-To include extra dependencies (e.g., visualization):
+To include extra dependencies (e.g., dev):
-```bash
-pip install 'easydiffraction[visualization] @ git+https://github.com/easyscience/diffraction-lib@develop'
+```txt
+pip install 'easydiffraction[dev] @ git+https://github.com/easyscience/diffraction-lib@develop'
```
## How to Run Tutorials
EasyDiffraction includes a collection of **Jupyter Notebook examples**
that demonstrate key functionality. These tutorials serve as
-**step-by-step guides** to help users understand the diffraction data
-analysis workflow.
-
-They are available as **static HTML pages** in the
-[:material-school: Tutorials](../tutorials/index.md) section. You can
-also run them interactively in two ways:
+**step-by-step guides** to help users understand the data analysis
+workflow. They are available as **static HTML pages** in the
+[:material-school: Tutorials](../tutorials/index.md) section.
-- **Run Locally** – Download the notebook via the :material-download:
- **Download** button and run it on your computer.
-- **Run Online** – Use the :google-colab: **Open in Google Colab**
- button to run the tutorial directly in your browser (no setup
- required).
+In the next sections, we explain how to set up Jupyter and run the
+tutorials interactively in two different ways: locally or online via
+Google Colab.
-!!! note
+If you decide to run the tutorials locally, you need to download them
+first. This can be done individually via the :material-download:
+**Download Notebook** button available on each tutorial page, or all at
+once using the command line, as shown below.
- You can also download all Jupyter notebooks at once as a zip archive from the
- [EasyDiffraction Releases](https://github.com/easyscience/diffraction-lib/releases/latest).
+### Run Tutorials Locally with Pixi recommended { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" }
-### Run Tutorials Locally
+- Navigate to your existing Pixi project, created as described in the
+ [Installing with Pixi](#installing-with-pixi) section.
+- Add JupyterLab and the Pixi kernel for Jupyter:
+ ```txt
+ pixi add --pypi jupyterlab pixi-kernel
+ ```
+- Download all the EasyDiffraction tutorials to the `tutorials/`
+ directory:
+ ```txt
+ pixi run easydiffraction download-all-tutorials
+ ```
+- Start JupyterLab in the `tutorials/` directory to access the
+ notebooks:
+ ```txt
+ pixi run jupyter lab tutorials/
+ ```
+- Your web browser should open automatically. Click on one of the
+ `*.ipynb` files and select the `Python (Pixi)` kernel to get started.
-To run tutorials locally, install **Jupyter Notebook** or
-**JupyterLab**. Here are the steps to follow in the case of **Jupyter
-Notebook**:
+### Classical Run Tutorials Locally
- Install Jupyter Notebook and IPython kernel:
- ```bash
+ ```txt
pip install notebook ipykernel
```
-- Add the virtual environment as a Jupyter kernel
- ```bash
+- Add the virtual environment as a Jupyter kernel:
+ ```txt
python -m ipykernel install --user --name=venv --display-name "EasyDiffraction Python kernel"
```
-- Download the EasyDiffraction tutorials from GitHub Releases:
- ```bash
- python -m easydiffraction fetch-tutorials
+- Download all the EasyDiffraction tutorials to the `tutorials/`
+ directory:
+ ```txt
+ python -m easydiffraction download-all-tutorials
```
-- Launch the Jupyter Notebook server in the `examples/` directory:
- ```bash
+- Launch the Jupyter Notebook server (opens browser automatically at
+ `http://localhost:8888/`):
+ ```txt
jupyter notebook tutorials/
```
-- In your web browser, go to:
- ```bash
- http://localhost:8888/
- ```
- Open one of the `*.ipynb` files and select the
`EasyDiffraction Python kernel` to get started.
### Run Tutorials via Google Colab
**Google Colab** lets you run Jupyter Notebooks in the cloud without any
-local installation.
-
-To use Google Colab:
+local installation. This is the fastest way to start experimenting with
+EasyDiffraction.
- Ensure you have a **Google account**.
- Go to the **[:material-school: Tutorials](../tutorials/index.md)**
section.
- Click the :google-colab: **Open in Google Colab** button on any
tutorial.
-
-This is the fastest way to start experimenting with EasyDiffraction,
-without setting up Python on your system.
-
-## Installing with Pixi alternative { #installing-with-pixi data-toc-label="Installing with Pixi" }
-
-[Pixi](https://pixi.sh) is a modern package and environment manager for
-Python and Conda-compatible packages. It simplifies dependency
-management, environment isolation, and reproducibility.
-
-The following simple steps provide an alternative setup method for
-EasyDiffraction using Pixi, replacing the traditional virtual
-environment approach.
-
-
-
-- Install Pixi by following the instructions on the
- [official Pixi Installation Guide](https://pixi.sh/latest/installation).
-- Create a dedicated directory for the EasyDiffraction and navigate into it:
- ```bash
- mkdir easydiffraction
- cd easydiffraction
- ```
-- Download the pixi configuration file for EasyDiffraction:
-
- === "curl"
- ```bash
- curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi.toml
- ```
- === "wget"
- ```bash
- wget https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi.toml
- ```
-
-- Create the environment defined in `pixi.toml` and install all necessary
- dependencies:
- ```bash
- pixi install
- ```
-- Fetch the EasyDiffraction tutorials to the `tutorials/` directory:
- ```bash
- pixi run easydiffraction fetch-tutorials
- ```
-- Start JupyterLab in the `tutorials/` directory to access the notebooks:
- ```bash
- pixi run jupyter lab tutorials/
- ```
-- Your web browser should open automatically. Click on one of the `*.ipynb`
- files and select the `Python (Pixi)` kernel to get started.
-
-
diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md
index a2b42b59..ee1d2159 100644
--- a/docs/docs/introduction/index.md
+++ b/docs/docs/introduction/index.md
@@ -6,34 +6,30 @@ icon: material/information-slab-circle
## Description
-**EasyDiffraction** is scientific software for calculating diffraction
-patterns
-based on structural models and refining model parameters against
-experimental data.
+**EasyDiffraction** is a software for calculating neutron powder
+diffraction patterns based on a structural model and refining its
+parameters against experimental data.
-It is available as both a cross-platform desktop application and a
-Python library.
+**EasyDiffraction** is developed both as a Python library and as a
+cross-platform desktop application.
-This documentation covers the usage of the EasyDiffraction Python
-library.
-For the graphical user interface (GUI) version, refer to the
-[GUI documentation](https://docs.easydiffraction.org/app).
+Here, we focus on the Python library. For the graphical user interface
+(GUI), please see the corresponding
+[GUI resources](https://easyscience.github.io/diffraction-app).
-## EasyScience
-
-EasyDiffraction is developed using the
-[EasyScience framework](https://easyscience.software), which provides
-tools for
-building modular and flexible scientific libraries and applications.
+
## License
-EasyDiffraction is released under the
+**EasyDiffraction** library is released under the
[BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/diffraction-lib/master/LICENSE).
## Releases
-The latest version of the EasyDiffraction Python library is
+The latest version of the **EasyDiffraction** library is
[{{ vars.release_version }}](https://github.com/easyscience/diffraction-lib/releases/latest).
For a complete list of new features, bug fixes, and improvements, see
@@ -42,10 +38,10 @@ the
## Citation
-If you use EasyDiffraction in your work, please cite the specific
-version you used.
+If you use **EasyDiffraction** library in your work, please cite the
+specific version you used.
-All official releases of the EasyDiffraction library are archived on
+All official releases of the **EasyDiffraction** library are archived on
Zenodo, each with a version-specific Digital Object Identifier (DOI).
Citation details in various styles (e.g., APA, MLA) and formats (e.g.,
@@ -55,22 +51,24 @@ are available on the
## Contributing
-We welcome contributions from the community! EasyDiffraction is intended
-to be a community-driven, open-source project supported by a diverse
-group of contributors.
+We welcome contributions of any kind!
+
+**EasyDiffraction** is intended to be a community-driven, open-source
+project supported by a diverse group of contributors.
The project is maintained by the
[European Spallation Source (ESS)](https://ess.eu).
-To contribute, see our
+If you would like to report a bug or request a new feature, please use
+the
+[GitHub Issue Tracker](https://github.com/easyscience/diffraction-lib/issues)
+(A free GitHub account is required.)
+
+To contribute code, documentation, or tests, please see our
[:material-account-plus: Contributing Guidelines](https://github.com/easyscience/diffraction-lib/blob/master/CONTRIBUTING.md)
-on GitHub.
+for detailed development instructions.
## Get in Touch
-For general questions or feedback, contact us at
+For general questions or feedback, please contact us at
[support@easydiffraction.org](mailto:support@easydiffraction.org).
-
-To report bugs or request features, please use the
-[GitHub Issue Tracker](https://github.com/easyscience/diffraction-lib/issues)
-(free registration required).
diff --git a/docs/docs/tutorials/ed-1.ipynb b/docs/docs/tutorials/ed-1.ipynb
index 15b9f634..740e2c02 100644
--- a/docs/docs/tutorials/ed-1.ipynb
+++ b/docs/docs/tutorials/ed-1.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "9cc849f9",
+ "id": "b1e6b328",
"metadata": {
"tags": [
"hide-in-docs"
@@ -156,6 +156,27 @@
"id": "12",
"metadata": {},
"outputs": [],
+ "source": [
+ "# Define aliases and constraints for refinement. This is necessary to\n",
+ "# properly refine the isotropic displacement parameters of La and Ba,\n",
+ "# which are correlated due to their shared Wyckoff position.\n",
+ "project.analysis.aliases.create(\n",
+ " label='biso_La',\n",
+ " param=project.structures['lbco'].atom_sites['La'].b_iso,\n",
+ ")\n",
+ "project.analysis.aliases.create(\n",
+ " label='biso_Ba',\n",
+ " param=project.structures['lbco'].atom_sites['Ba'].b_iso,\n",
+ ")\n",
+ "project.analysis.constraints.create(expression='biso_Ba = biso_La')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "13",
+ "metadata": {},
+ "outputs": [],
"source": [
"# Start refinement. All parameters, which have standard uncertainties\n",
"# in the input CIF files, are refined by default.\n",
@@ -165,7 +186,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "13",
+ "id": "14",
"metadata": {},
"outputs": [],
"source": [
@@ -176,7 +197,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "14",
+ "id": "15",
"metadata": {},
"outputs": [],
"source": [
@@ -187,7 +208,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "15",
+ "id": "16",
"metadata": {},
"outputs": [],
"source": [
@@ -197,7 +218,7 @@
},
{
"cell_type": "markdown",
- "id": "16",
+ "id": "17",
"metadata": {},
"source": [
"## Step 5: Perform Analysis (crysfml)"
@@ -206,7 +227,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "17",
+ "id": "18",
"metadata": {},
"outputs": [],
"source": [
@@ -218,7 +239,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "18",
+ "id": "19",
"metadata": {},
"outputs": [],
"source": [
@@ -229,7 +250,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "19",
+ "id": "20",
"metadata": {},
"outputs": [],
"source": [
@@ -240,7 +261,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "20",
+ "id": "21",
"metadata": {},
"outputs": [],
"source": [
diff --git a/docs/docs/tutorials/ed-1.py b/docs/docs/tutorials/ed-1.py
index 92b98ecd..d74c7eea 100644
--- a/docs/docs/tutorials/ed-1.py
+++ b/docs/docs/tutorials/ed-1.py
@@ -57,6 +57,20 @@
# %% [markdown]
# ## Step 4: Perform Analysis (cryspy)
+# %%
+# Define aliases and constraints for refinement. This is necessary to
+# properly refine the isotropic displacement parameters of La and Ba,
+# which are correlated due to their shared Wyckoff position.
+project.analysis.aliases.create(
+ label='biso_La',
+ param=project.structures['lbco'].atom_sites['La'].b_iso,
+)
+project.analysis.aliases.create(
+ label='biso_Ba',
+ param=project.structures['lbco'].atom_sites['Ba'].b_iso,
+)
+project.analysis.constraints.create(expression='biso_Ba = biso_La')
+
# %%
# Start refinement. All parameters, which have standard uncertainties
# in the input CIF files, are refined by default.
diff --git a/docs/docs/tutorials/ed-10.ipynb b/docs/docs/tutorials/ed-10.ipynb
index 67524351..46489bd6 100644
--- a/docs/docs/tutorials/ed-10.ipynb
+++ b/docs/docs/tutorials/ed-10.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "0bc5d509",
+ "id": "307e00fa",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-11.ipynb b/docs/docs/tutorials/ed-11.ipynb
index fe700f34..c0bbdd68 100644
--- a/docs/docs/tutorials/ed-11.ipynb
+++ b/docs/docs/tutorials/ed-11.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "0fe3d93b",
+ "id": "2ab104e6",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-12.ipynb b/docs/docs/tutorials/ed-12.ipynb
index a411eb82..d0913cae 100644
--- a/docs/docs/tutorials/ed-12.ipynb
+++ b/docs/docs/tutorials/ed-12.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "214aa62c",
+ "id": "f188a46a",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-13.ipynb b/docs/docs/tutorials/ed-13.ipynb
index 0fa6f966..549d9167 100644
--- a/docs/docs/tutorials/ed-13.ipynb
+++ b/docs/docs/tutorials/ed-13.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "4116731d",
+ "id": "be0cfa00",
"metadata": {
"tags": [
"hide-in-docs"
@@ -969,7 +969,7 @@
"#### Show Free Parameters\n",
"\n",
"We can check which parameters are free to be refined by calling the\n",
- "`show_free_params` method of the `analysis` object of the project."
+ "`free_params` method of the `analysis.display` object of the project."
]
},
{
@@ -2647,7 +2647,7 @@
],
"metadata": {
"jupytext": {
- "cell_metadata_filter": "tags,title,-all",
+ "cell_metadata_filter": "title,tags,-all",
"main_language": "python",
"notebook_metadata_filter": "-all"
}
diff --git a/docs/docs/tutorials/ed-14.ipynb b/docs/docs/tutorials/ed-14.ipynb
index 6bf611fa..88c2077f 100644
--- a/docs/docs/tutorials/ed-14.ipynb
+++ b/docs/docs/tutorials/ed-14.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "bcfac86e",
+ "id": "f6f4b6a6",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-15.ipynb b/docs/docs/tutorials/ed-15.ipynb
index d4e97853..a6e4e7a0 100644
--- a/docs/docs/tutorials/ed-15.ipynb
+++ b/docs/docs/tutorials/ed-15.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "2e11e786",
+ "id": "ceaaff89",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-16.ipynb b/docs/docs/tutorials/ed-16.ipynb
index d3cd28f7..2fa0dd21 100644
--- a/docs/docs/tutorials/ed-16.ipynb
+++ b/docs/docs/tutorials/ed-16.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "2cfb7f0c",
+ "id": "c342992c",
"metadata": {
"tags": [
"hide-in-docs"
@@ -613,21 +613,11 @@
"cell_type": "code",
"execution_count": null,
"id": "56",
- "metadata": {
- "lines_to_next_cell": 2
- },
+ "metadata": {},
"outputs": [],
"source": [
"project.plotter.plot_meas_vs_calc(expt_name='nomad', show_residual=False)"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "57",
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
diff --git a/docs/docs/tutorials/ed-16.py b/docs/docs/tutorials/ed-16.py
index 214dfe25..4c224f9f 100644
--- a/docs/docs/tutorials/ed-16.py
+++ b/docs/docs/tutorials/ed-16.py
@@ -254,6 +254,3 @@
# %%
project.plotter.plot_meas_vs_calc(expt_name='nomad', show_residual=False)
-
-
-# %%
diff --git a/docs/docs/tutorials/ed-17.ipynb b/docs/docs/tutorials/ed-17.ipynb
index 189f93fe..3844add8 100644
--- a/docs/docs/tutorials/ed-17.ipynb
+++ b/docs/docs/tutorials/ed-17.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "9ec0f5a7",
+ "id": "47b804b0",
"metadata": {
"tags": [
"hide-in-docs"
@@ -540,6 +540,24 @@
"cell_type": "markdown",
"id": "41",
"metadata": {},
+ "source": [
+ "#### Compare measured and calculated patterns for the first fit."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "42",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "project.plotter.plot_meas_vs_calc(expt_name='d20', show_residual=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "43",
+ "metadata": {},
"source": [
"#### Run Sequential Fitting\n",
"\n",
@@ -550,7 +568,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "42",
+ "id": "44",
"metadata": {},
"outputs": [],
"source": [
@@ -559,7 +577,7 @@
},
{
"cell_type": "markdown",
- "id": "43",
+ "id": "45",
"metadata": {
"lines_to_next_cell": 2
},
@@ -571,7 +589,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "44",
+ "id": "46",
"metadata": {},
"outputs": [],
"source": [
@@ -585,7 +603,7 @@
},
{
"cell_type": "markdown",
- "id": "45",
+ "id": "47",
"metadata": {},
"source": [
"Run the sequential fit over all data files in the scan directory."
@@ -594,7 +612,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "46",
+ "id": "48",
"metadata": {},
"outputs": [],
"source": [
@@ -602,15 +620,36 @@
" data_dir=data_dir,\n",
" extract_diffrn=extract_diffrn,\n",
" max_workers='auto',\n",
+ " reverse=True,\n",
")"
]
},
{
"cell_type": "markdown",
- "id": "47",
+ "id": "49",
"metadata": {},
"source": [
"#### Replay a Dataset\n",
+ "\n",
+ "Apply fitted parameters from the first CSV row and plot the result."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "50",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "project.apply_params_from_csv(row_index=0)\n",
+ "project.plotter.plot_meas_vs_calc(expt_name='d20', show_residual=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "51",
+ "metadata": {},
+ "source": [
"\n",
"Apply fitted parameters from the last CSV row and plot the result."
]
@@ -618,7 +657,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "48",
+ "id": "52",
"metadata": {},
"outputs": [],
"source": [
@@ -628,7 +667,7 @@
},
{
"cell_type": "markdown",
- "id": "49",
+ "id": "53",
"metadata": {},
"source": [
"#### Plot Parameter Evolution\n",
@@ -639,7 +678,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "50",
+ "id": "54",
"metadata": {},
"outputs": [],
"source": [
@@ -648,7 +687,7 @@
},
{
"cell_type": "markdown",
- "id": "51",
+ "id": "55",
"metadata": {},
"source": [
"Plot unit cell parameters vs. temperature."
@@ -657,7 +696,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "52",
+ "id": "56",
"metadata": {},
"outputs": [],
"source": [
@@ -668,7 +707,7 @@
},
{
"cell_type": "markdown",
- "id": "53",
+ "id": "57",
"metadata": {},
"source": [
"Plot isotropic displacement parameters vs. temperature."
@@ -677,7 +716,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "54",
+ "id": "58",
"metadata": {},
"outputs": [],
"source": [
@@ -690,7 +729,7 @@
},
{
"cell_type": "markdown",
- "id": "55",
+ "id": "59",
"metadata": {},
"source": [
"Plot selected fractional coordinates vs. temperature."
@@ -699,7 +738,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "56",
+ "id": "60",
"metadata": {},
"outputs": [],
"source": [
diff --git a/docs/docs/tutorials/ed-18.ipynb b/docs/docs/tutorials/ed-18.ipynb
index 6285d966..082ab9ef 100644
--- a/docs/docs/tutorials/ed-18.ipynb
+++ b/docs/docs/tutorials/ed-18.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "2fec19b9",
+ "id": "15fcf6ce",
"metadata": {
"tags": [
"hide-in-docs"
@@ -161,24 +161,6 @@
"source": [
"project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)"
]
- },
- {
- "cell_type": "markdown",
- "id": "15",
- "metadata": {},
- "source": [
- "## Save Project"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "16",
- "metadata": {},
- "outputs": [],
- "source": [
- "project.save()"
- ]
}
],
"metadata": {
diff --git a/docs/docs/tutorials/ed-18.py b/docs/docs/tutorials/ed-18.py
index ee07a708..5b2c4b67 100644
--- a/docs/docs/tutorials/ed-18.py
+++ b/docs/docs/tutorials/ed-18.py
@@ -51,9 +51,3 @@
# %%
project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)
-
-# %% [markdown]
-# ## Save Project
-
-# %%
-project.save()
diff --git a/docs/docs/tutorials/ed-2.ipynb b/docs/docs/tutorials/ed-2.ipynb
index 11105e3c..0357de4a 100644
--- a/docs/docs/tutorials/ed-2.ipynb
+++ b/docs/docs/tutorials/ed-2.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "657acf7d",
+ "id": "15c2d211",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-3.ipynb b/docs/docs/tutorials/ed-3.ipynb
index 5d501391..8eade20f 100644
--- a/docs/docs/tutorials/ed-3.ipynb
+++ b/docs/docs/tutorials/ed-3.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "b7a584f7",
+ "id": "7be48772",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-4.ipynb b/docs/docs/tutorials/ed-4.ipynb
index c1bf91b3..e331438e 100644
--- a/docs/docs/tutorials/ed-4.ipynb
+++ b/docs/docs/tutorials/ed-4.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "902026e1",
+ "id": "05436c40",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-5.ipynb b/docs/docs/tutorials/ed-5.ipynb
index 7fc07c61..8c524eaf 100644
--- a/docs/docs/tutorials/ed-5.ipynb
+++ b/docs/docs/tutorials/ed-5.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "3169869f",
+ "id": "8ce91035",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-6.ipynb b/docs/docs/tutorials/ed-6.ipynb
index 4da37be2..f1b7ad5d 100644
--- a/docs/docs/tutorials/ed-6.ipynb
+++ b/docs/docs/tutorials/ed-6.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "bd23b3c8",
+ "id": "e53f4485",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-7.ipynb b/docs/docs/tutorials/ed-7.ipynb
index 3979677e..57e2d726 100644
--- a/docs/docs/tutorials/ed-7.ipynb
+++ b/docs/docs/tutorials/ed-7.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "521c03c7",
+ "id": "788753a7",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-8.ipynb b/docs/docs/tutorials/ed-8.ipynb
index 9012becf..7b9cf378 100644
--- a/docs/docs/tutorials/ed-8.ipynb
+++ b/docs/docs/tutorials/ed-8.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "0cd7ade3",
+ "id": "9e6c622d",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/ed-9.ipynb b/docs/docs/tutorials/ed-9.ipynb
index f49fc4e5..2de9787f 100644
--- a/docs/docs/tutorials/ed-9.ipynb
+++ b/docs/docs/tutorials/ed-9.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "bd91997f",
+ "id": "336ce5f0",
"metadata": {
"tags": [
"hide-in-docs"
diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md
index 06a9c69e..914bb859 100644
--- a/docs/docs/tutorials/index.md
+++ b/docs/docs/tutorials/index.md
@@ -7,13 +7,13 @@ icon: material/school
This section presents a collection of **Jupyter Notebook** tutorials
that demonstrate how to use EasyDiffraction for various tasks. These
tutorials serve as self-contained, step-by-step **guides** to help users
-grasp the workflow of diffraction data analysis using EasyDiffraction.
+grasp the workflow of data analysis using EasyDiffraction.
Instructions on how to run the tutorials are provided in the
[:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials)
section of the documentation.
-The tutorials are organized into the following categories.
+The tutorials are organized into the following categories:
## Getting Started
diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md
index 2ddc28b9..72978518 100644
--- a/docs/docs/user-guide/index.md
+++ b/docs/docs/user-guide/index.md
@@ -10,15 +10,15 @@ effectively.
Here is a brief overview of the User Guide sections:
-- [Glossary](glossary.md) – Defines common terms and labels used
- throughout the documentation.
-- [Concept](concept.md) – Introduces the overall idea behind diffraction
- data processing and where EasyDiffraction fits.
-- [Data Format](data-format.md) – Explains the Crystallographic
- Information File (CIF) and how it's used in EasyDiffraction.
-- [Parameters](parameters.md) – Describes how parameters are structured,
- named, and accessed within the EasyDiffraction library.
-- [First Steps](first-steps.md) – Shows how to begin using
- EasyDiffraction in Python or Jupyter notebooks.
-- [Analysis Workflow](analysis-workflow/index.md) – Breaks down the data
- analysis pipeline into practical, sequential steps.
+- [Glossary](#) – Defines common terms and labels used throughout the
+ documentation.
+- [Concept](#) – Introduces the overall idea behind data analysis in
+ EasyDiffraction.
+- [Data Format](#) – Explains the data structures and file formats used
+ by EasyDiffraction.
+- [Parameters](#) – Describes how parameters are structured, named, and
+ accessed within the EasyDiffraction.
+- [First Steps](#) – Shows how to begin using EasyDiffraction in Python
+ or Jupyter notebooks.
+- [Analysis Workflow](#) – Breaks down the data analysis pipeline into
+ practical, sequential steps.
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 5f2415c3..66265029 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -228,3 +228,5 @@ nav:
- project: api-reference/project.md
- summary: api-reference/summary.md
- utils: api-reference/utils.md
+ - Command-Line Interface:
+ - Command-Line Interface: cli/index.md
diff --git a/pixi.lock b/pixi.lock
index 0282155e..15c4b18e 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -33,7 +33,7 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py314h4a8dc5f_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.3-pyhe01879c_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.20-py314h42812f9_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
@@ -104,13 +104,13 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/mistune-3.2.0-pyhcf101f3_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/msgspec-0.20.0-py314h5bd0f2a_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.4-pyhd8ed1ab_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.17.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.17.1-pyhcf101f3_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.6.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/nodejs-25.8.2-he4ff34a_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.4-pyhd8ed1ab_1.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/overrides-7.7.0-pyhd8ed1ab_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2
@@ -126,10 +126,10 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyh29332c3_1.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.4-habeac84_100_cp314.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.21.2-pyhe01879c_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.7-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2026.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
@@ -184,7 +184,7 @@ environments:
- pypi: https://files.pythonhosted.org/packages/4a/57/3b7d4dd193ade4641c865bc2b93aeeb71162e81fc348b8dad020215601ed/build-1.4.2-py3-none-any.whl
- pypi: https://files.pythonhosted.org/packages/43/8e/278ea79cf8ee0c395a5ad74625b3465c2fc234bb277f171dd59dd203820d/bumps-1.0.3-py3-none-any.whl
- pypi: https://files.pythonhosted.org/packages/db/3c/33bac158f8ab7f89b2e59426d5fe2e4f63f7ed25df84c036890172b412b5/cfgv-3.5.0-py2.py3-none-any.whl
- - pypi: https://files.pythonhosted.org/packages/fb/b6/13cc503f45beeb1117fc9c83f294df16ebce5d75eac9f0cefb8cce4357a1/chardet-7.4.0.post2-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+ - pypi: https://files.pythonhosted.org/packages/e3/30/1af6666f34e3ced9a2dd2993743c1f70af7b52d5db4c4eba22c42a265eae/chardet-7.4.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
- pypi: https://files.pythonhosted.org/packages/e4/20/71885d8b97d4f3dde17b1fdb92dbd4908b00541c5a3379787137285f602e/click-8.3.2-py3-none-any.whl
- pypi: https://files.pythonhosted.org/packages/88/39/799be3f2f0f38cc727ee3b4f1445fe6d5e4133064ec2e4115069418a5bb6/cloudpickle-3.1.2-py3-none-any.whl
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- - libexpat >=2.7.3,<3.0a0
+ - libexpat >=2.7.5,<3.0a0
- libffi >=3.5.2,<3.6.0a0
- liblzma >=5.8.2,<6.0a0
- libmpdec >=4.0.0,<5.0a0
- - libsqlite >=3.51.2,<4.0a0
- - libzlib >=1.3.1,<2.0a0
+ - libsqlite >=3.52.0,<4.0a0
+ - libzlib >=1.3.2,<2.0a0
- ncurses >=6.5,<7.0a0
- - openssl >=3.5.5,<4.0a0
+ - openssl >=3.5.6,<4.0a0
- python_abi 3.14.* *_cp314
- readline >=8.3,<9.0a0
- tk >=8.6.13,<8.7.0a0
@@ -9672,8 +9671,8 @@ packages:
- zstd >=1.5.7,<1.6.0a0
license: Python-2.0
purls: []
- size: 13522698
- timestamp: 1770675365241
+ size: 13533346
+ timestamp: 1775616188373
python_site_packages_path: lib/python3.14/site-packages
- conda: https://conda.anaconda.org/conda-forge/win-64/python-3.12.13-h0159041_0_cpython.conda
sha256: a02b446d8b7b167b61733a3de3be5de1342250403e72a63b18dac89e99e6180e
@@ -9697,19 +9696,19 @@ packages:
purls: []
size: 15840187
timestamp: 1772728877265
-- conda: https://conda.anaconda.org/conda-forge/win-64/python-3.14.3-h4b44e0e_101_cp314.conda
- build_number: 101
- sha256: 3f99d83bfd95b9bdae64a42a1e4bf5131dc20b724be5ac8a9a7e1ac2c0f006d7
- md5: 7ec2be7eaf59f83f3e5617665f3fbb2e
+- conda: https://conda.anaconda.org/conda-forge/win-64/python-3.14.4-h4b44e0e_100_cp314.conda
+ build_number: 100
+ sha256: e258d626b0ba778abb319f128de4c1211306fe86fe0803166817b1ce2514c920
+ md5: 40b6a8f438afb5e7b314cc5c4a43cd84
depends:
- bzip2 >=1.0.8,<2.0a0
- - libexpat >=2.7.3,<3.0a0
+ - libexpat >=2.7.5,<3.0a0
- libffi >=3.5.2,<3.6.0a0
- liblzma >=5.8.2,<6.0a0
- libmpdec >=4.0.0,<5.0a0
- - libsqlite >=3.51.2,<4.0a0
- - libzlib >=1.3.1,<2.0a0
- - openssl >=3.5.5,<4.0a0
+ - libsqlite >=3.52.0,<4.0a0
+ - libzlib >=1.3.2,<2.0a0
+ - openssl >=3.5.6,<4.0a0
- python_abi 3.14.* *_cp314
- tk >=8.6.13,<8.7.0a0
- tzdata
@@ -9719,8 +9718,8 @@ packages:
- zstd >=1.5.7,<1.6.0a0
license: Python-2.0
purls: []
- size: 18273230
- timestamp: 1770675442998
+ size: 18055445
+ timestamp: 1775615317758
python_site_packages_path: Lib/site-packages
- conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda
sha256: d6a17ece93bbd5139e02d2bd7dbfa80bee1a4261dced63f65f679121686bf664
@@ -9735,10 +9734,10 @@ packages:
- pkg:pypi/python-dateutil?source=hash-mapping
size: 233310
timestamp: 1751104122689
-- pypi: https://files.pythonhosted.org/packages/67/0f/019d3949a40280f6193b62bc010177d4ce702d0fce424322286488569cd3/python_discovery-1.2.1-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/d8/db/795879cc3ddfe338599bddea6388cc5100b088db0a4caf6e6c1af1c27e04/python_discovery-1.2.2-py3-none-any.whl
name: python-discovery
- version: 1.2.1
- sha256: b6a957b24c1cd79252484d3566d1b49527581d46e789aaf43181005e56201502
+ version: 1.2.2
+ sha256: e1ae95d9af875e78f15e19aed0c6137ab1bb49c200f21f5061786490c9585c7a
requires_dist:
- filelock>=3.15.4
- platformdirs>=4.3.6,<5
@@ -9787,16 +9786,16 @@ packages:
purls: []
size: 46449
timestamp: 1772728979370
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.3-h4df99d1_101.conda
- sha256: 233aebd94c704ac112afefbb29cf4170b7bc606e22958906f2672081bc50638a
- md5: 235765e4ea0d0301c75965985163b5a1
+- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.4-h4df99d1_100.conda
+ sha256: 36ff7984e4565c85149e64f8206303d412a0652e55cf806dcb856903fa056314
+ md5: e4e60721757979d01d3964122f674959
depends:
- - cpython 3.14.3.*
+ - cpython 3.14.4.*
- python_abi * *_cp314
license: Python-2.0
purls: []
- size: 50062
- timestamp: 1770674497152
+ size: 49806
+ timestamp: 1775614307464
- conda: https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.7-pyhd8ed1ab_0.conda
sha256: 4790787fe1f4e8da616edca4acf6a4f8ed4e7c6967aa31b920208fc8f95efcca
md5: a61bf9ec79426938ff785eb69dbb1960
diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py
index a15b66ca..f0b5ab12 100644
--- a/src/easydiffraction/__main__.py
+++ b/src/easydiffraction/__main__.py
@@ -82,5 +82,26 @@ def download_all_tutorials(
ed.download_all_tutorials(destination=destination, overwrite=overwrite)
+@app.command('fit')
+def fit(
+ project_dir: str = typer.Argument(
+ ...,
+ help='Path to the project directory (must contain project.cif).',
+ ),
+ dry: bool = typer.Option(
+ False,
+ '--dry',
+ help='Run fitting without saving results back to the project directory.',
+ ),
+) -> None:
+ """Fit a saved project: easydiffraction fit PROJECT_DIR [--dry]."""
+ project = ed.Project.load(project_dir)
+ if dry:
+ project.info._path = None
+ project.analysis.fit()
+ project.analysis.display.fit_results()
+ project.summary.show_report()
+
+
if __name__ == '__main__':
app()
diff --git a/src/easydiffraction/analysis/calculators/crysfml.py b/src/easydiffraction/analysis/calculators/crysfml.py
index 3454ce28..aaaa537e 100644
--- a/src/easydiffraction/analysis/calculators/crysfml.py
+++ b/src/easydiffraction/analysis/calculators/crysfml.py
@@ -98,7 +98,7 @@ def calculate_pattern(
except KeyError:
print('[CrysfmlCalculator] Error: No calculated data')
y = []
- return y
+ return np.asarray(y)
def _adjust_pattern_length( # noqa: PLR6301
self,
@@ -122,8 +122,14 @@ def _adjust_pattern_length( # noqa: PLR6301
"""
# TODO: Check the origin of this discrepancy coming from
# PyCrysFML
+ # Safety guard: with the correct step formula (max-min)/(N-1+ε),
+ # pycrysfml should return exactly target_length points. Truncate
+ # if over-length; pad with the last value if under-length.
if len(pattern) > target_length:
return pattern[:target_length]
+ if len(pattern) < target_length:
+ pad = target_length - len(pattern)
+ return list(pattern) + [pattern[-1]] * pad
return pattern
def _crysfml_dict(
@@ -243,7 +249,13 @@ def _convert_experiment_to_dict( # noqa: PLR6301
else 0.0,
'_pd_meas_2theta_range_min': twotheta_min,
'_pd_meas_2theta_range_max': twotheta_max,
- '_pd_meas_2theta_range_inc': (twotheta_max - twotheta_min) / len(x_data),
+ # TODO: Check the origin of this discrepancy coming from
+ # PyCrysFML
+ # Divide by (N-1+ε) instead of (N-1) so that pycrysfml's
+ # internal floor((max-min)/step) is robustly N-1 despite
+ # floating-point rounding, producing exactly N points.
+ '_pd_meas_2theta_range_inc': (twotheta_max - twotheta_min)
+ / (len(x_data) - 1 + 1e-9),
}
}
diff --git a/tests/integration/fitting/test_switch-calculator.py b/tests/integration/fitting/test_switch-calculator.py
index 4ce7c18a..a195ac18 100644
--- a/tests/integration/fitting/test_switch-calculator.py
+++ b/tests/integration/fitting/test_switch-calculator.py
@@ -6,7 +6,6 @@
import pytest
from numpy.testing import assert_almost_equal
-
TEMP_DIR = tempfile.gettempdir()
diff --git a/tests/unit/easydiffraction/test___main__.py b/tests/unit/easydiffraction/test___main__.py
index 76ba7cec..88f08198 100644
--- a/tests/unit/easydiffraction/test___main__.py
+++ b/tests/unit/easydiffraction/test___main__.py
@@ -64,3 +64,90 @@ def test_cli_subcommands_call_utils(monkeypatch):
assert res2.exit_code == 0
assert res3.exit_code == 0
assert logs == ['LIST', 'DOWNLOAD_ALL', 'DOWNLOAD_1']
+
+
+def test_cli_fit_loads_and_fits(monkeypatch, tmp_path):
+ import easydiffraction.__main__ as main_mod
+ from easydiffraction.project.project import Project
+
+ calls = []
+
+ class FakeInfo:
+ _path = '/some/path'
+
+ class FakeProject:
+ info = FakeInfo()
+
+ class _analysis:
+ @staticmethod
+ def fit():
+ calls.append('FIT')
+
+ class display:
+ @staticmethod
+ def fit_results():
+ calls.append('DISPLAY')
+
+ analysis = _analysis()
+
+ class _summary:
+ @staticmethod
+ def show_report():
+ calls.append('SUMMARY')
+
+ summary = _summary()
+
+ fake_project = FakeProject()
+
+ # Create a minimal project directory so load doesn't fail on path check
+ proj_dir = tmp_path / 'proj'
+ proj_dir.mkdir()
+ (proj_dir / 'project.cif').write_text('_project.id test\n')
+
+ monkeypatch.setattr(Project, 'load', staticmethod(lambda dir_path: fake_project))
+
+ result = runner.invoke(main_mod.app, ['fit', str(proj_dir)])
+ assert result.exit_code == 0
+ assert calls == ['FIT', 'DISPLAY', 'SUMMARY']
+
+
+def test_cli_fit_dry_clears_path(monkeypatch, tmp_path):
+ import easydiffraction.__main__ as main_mod
+ from easydiffraction.project.project import Project
+
+ class FakeInfo:
+ _path = '/some/path'
+
+ class FakeProject:
+ info = FakeInfo()
+
+ class _analysis:
+ @staticmethod
+ def fit():
+ pass
+
+ class display:
+ @staticmethod
+ def fit_results():
+ pass
+
+ analysis = _analysis()
+
+ class _summary:
+ @staticmethod
+ def show_report():
+ pass
+
+ summary = _summary()
+
+ fake_project = FakeProject()
+
+ proj_dir = tmp_path / 'proj'
+ proj_dir.mkdir()
+ (proj_dir / 'project.cif').write_text('_project.id test\n')
+
+ monkeypatch.setattr(Project, 'load', staticmethod(lambda dir_path: fake_project))
+
+ result = runner.invoke(main_mod.app, ['fit', '--dry', str(proj_dir)])
+ assert result.exit_code == 0
+ assert fake_project.info._path is None
diff --git a/tmp/cli/lbco_hrpt/analysis/analysis.cif b/tmp/cli/lbco_hrpt/analysis/analysis.cif
new file mode 100644
index 00000000..6df5451c
--- /dev/null
+++ b/tmp/cli/lbco_hrpt/analysis/analysis.cif
@@ -0,0 +1,15 @@
+_analysis.fitting_engine lmfit
+_analysis.fit_mode single
+
+loop_
+_alias.label
+_alias.param_unique_name
+biso_La lbco.atom_site.La.b_iso
+biso_Ba lbco.atom_site.Ba.b_iso
+occ_La lbco.atom_site.La.occupancy
+occ_Ba lbco.atom_site.Ba.occupancy
+
+loop_
+_constraint.expression
+"biso_Ba = biso_La"
+"occ_Ba = 1 - occ_La"
diff --git a/tmp/cli/lbco_hrpt/experiments/hrpt.cif b/tmp/cli/lbco_hrpt/experiments/hrpt.cif
new file mode 100644
index 00000000..9af5e82c
--- /dev/null
+++ b/tmp/cli/lbco_hrpt/experiments/hrpt.cif
@@ -0,0 +1,3156 @@
+data_hrpt
+
+_expt_type.sample_form powder
+_expt_type.beam_mode "constant wavelength"
+_expt_type.radiation_probe neutron
+_expt_type.scattering_type bragg
+
+_diffrn.ambient_temperature 300
+_diffrn.ambient_pressure ?
+_diffrn.ambient_magnetic_field ?
+_diffrn.ambient_electric_field ?
+
+_peak.broad_gauss_u 0.10(1)
+_peak.broad_gauss_v -0.10(1)
+_peak.broad_gauss_w 0.10(1)
+_peak.broad_lorentz_x 0.0
+_peak.broad_lorentz_y 0.0(1)
+
+_instr.wavelength 1.494
+_instr.2theta_offset 0.0(1)
+
+loop_
+_pd_phase_block.id
+_pd_phase_block.scale
+lbco 10.0(1)
+
+loop_
+_excluded_region.id
+_excluded_region.start
+_excluded_region.end
+1 0.0 10.2
+2 164.7 180.0
+
+
+loop_
+_pd_background.id
+_pd_background.line_segment_X
+_pd_background.line_segment_intensity
+ 10 10.00000000 170.0(5)
+ 20 20.00000000 170.0(5)
+ 30 30.00000000 170.0(5)
+ 50 50.00000000 170.0(5)
+ 70 70.00000000 170.0(5)
+ 90 90.00000000 170.0(5)
+110 110.00000000 170.0(5)
+130 130.00000000 170.0(5)
+150 150.00000000 170.0(5)
+165 165.00000000 170.0(5)
+
+loop_
+_pd_proc.2theta_scan
+_pd_data.point_id
+_pd_proc.d_spacing
+_pd_meas.intensity_total
+_pd_meas.intensity_total_su
+_pd_calc.intensity_total
+_pd_calc.intensity_bkg
+_pd_data.refinement_status
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+162.05000000 3042 0.75625926 166.00000000 12.30000000 177.07081541 174.61655678 incl
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+162.55000000 3052 0.75574565 176.00000000 12.60000000 176.87771125 174.61030869 incl
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+162.80000000 3057 0.75549449 184.00000000 12.60000000 176.80053902 174.60718465 incl
+162.85000000 3058 0.75544471 179.00000000 12.70000000 176.78640937 174.60655984 incl
+162.90000000 3059 0.75539508 165.00000000 11.90000000 176.77268503 174.60593503 incl
+162.95000000 3060 0.75534561 146.00000000 11.50000000 176.75935438 174.60531022 incl
+163.00000000 3061 0.75529628 165.00000000 11.90000000 176.74640623 174.60468541 incl
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+163.20000000 3065 0.75510047 186.00000000 12.70000000 176.69823068 174.60218618 incl
+163.25000000 3066 0.75505189 182.00000000 13.00000000 176.68704263 174.60156137 incl
+163.30000000 3067 0.75500346 168.00000000 12.20000000 176.67617889 174.60093656 incl
+163.35000000 3068 0.75495518 193.00000000 13.50000000 176.66563103 174.60031175 incl
+163.40000000 3069 0.75490706 177.00000000 12.60000000 176.65539100 174.59968694 incl
+163.45000000 3070 0.75485908 180.00000000 13.10000000 176.64545102 174.59906213 incl
+163.50000000 3071 0.75481125 171.00000000 12.40000000 176.63580365 174.59843732 incl
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+163.65000000 3074 0.75466866 159.00000000 12.40000000 176.60854676 174.59656290 incl
+163.70000000 3075 0.75462143 165.00000000 12.40000000 176.60000074 174.59593809 incl
+163.75000000 3076 0.75457435 178.00000000 13.20000000 176.59171410 174.59531328 incl
+163.80000000 3077 0.75452742 150.00000000 11.80000000 176.58368091 174.59468847 incl
+163.85000000 3078 0.75448064 177.00000000 13.20000000 176.57589551 174.59406366 incl
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+163.95000000 3080 0.75438753 180.00000000 13.40000000 176.56104633 174.59281404 incl
+164.00000000 3081 0.75434120 184.00000000 13.20000000 176.55397223 174.59218924 incl
+164.05000000 3082 0.75429501 166.00000000 13.60000000 176.54712521 174.59156443 incl
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+164.15000000 3084 0.75420309 188.00000000 15.60000000 176.53409381 174.59031481 incl
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+164.35000000 3088 0.75402105 177.00000000 18.00000000 176.51056060 174.58781557 incl
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+164.45000000 3090 0.75393091 178.00000000 20.40000000 176.49999531 174.58656596 incl
+164.50000000 3091 0.75388607 153.00000000 18.00000000 176.49500025 174.58594115 incl
+164.55000000 3092 0.75384138 197.00000000 25.30000000 176.49019241 174.58531634 incl
+164.60000000 3093 0.75379684 153.00000000 20.70000000 176.48556858 174.58469153 incl
+164.65000000 3094 0.75375244 173.00000000 30.10000000 176.48112566 174.58406672 incl
+164.70000000 3095 0.00000000 187.00000000 27.90000000 0.00000000 0.00000000 excl
+164.75000000 3096 0.00000000 175.00000000 38.20000000 0.00000000 0.00000000 excl
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+164.85000000 3098 0.00000000 109.00000000 41.20000000 0.00000000 0.00000000 excl
diff --git a/tmp/cli/lbco_hrpt/project.cif b/tmp/cli/lbco_hrpt/project.cif
new file mode 100644
index 00000000..b03ee765
--- /dev/null
+++ b/tmp/cli/lbco_hrpt/project.cif
@@ -0,0 +1,5 @@
+_project.id lbco@hrpt
+_project.title 'Quick Start: LBCO Load Project'
+_project.description 'Most minimal example: load a saved project from a directory and run Rietveld refinement of La0.5Ba0.5CoO3'
+_project.created '03 Apr 2026 22:22:57'
+_project.last_modified '03 Apr 2026 22:22:57'
diff --git a/tmp/cli/lbco_hrpt/structures/lbco.cif b/tmp/cli/lbco_hrpt/structures/lbco.cif
new file mode 100644
index 00000000..5e11bb81
--- /dev/null
+++ b/tmp/cli/lbco_hrpt/structures/lbco.cif
@@ -0,0 +1,26 @@
+data_lbco
+
+_cell.length_a 3.88(1)
+_cell.length_b 3.88
+_cell.length_c 3.88
+_cell.angle_alpha 90.0
+_cell.angle_beta 90.0
+_cell.angle_gamma 90.0
+
+_space_group.name_H-M_alt "P m -3 m"
+_space_group.IT_coordinate_system_code 1
+
+loop_
+_atom_site.label
+_atom_site.type_symbol
+_atom_site.fract_x
+_atom_site.fract_y
+_atom_site.fract_z
+_atom_site.Wyckoff_letter
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.adp_type
+La La 0.00000000 0.00000000 0.00000000 a 0.5(1) 1.0(1) Biso
+Ba Ba 0.00000000 0.00000000 0.00000000 a 0.5 1.0 Biso
+Co Co 0.50000000 0.50000000 0.50000000 b 1.0 1.0(1) Biso
+O O 0.00000000 0.50000000 0.50000000 c 1.0 1.0(1) Biso
diff --git a/tmp/cli/lbco_hrpt/summary.cif b/tmp/cli/lbco_hrpt/summary.cif
new file mode 100644
index 00000000..ccc4df03
--- /dev/null
+++ b/tmp/cli/lbco_hrpt/summary.cif
@@ -0,0 +1 @@
+To be added...
\ No newline at end of file