diff --git a/docs/api/gui.md b/docs/api/gui.md
new file mode 100644
index 0000000..3ef1f36
--- /dev/null
+++ b/docs/api/gui.md
@@ -0,0 +1,3 @@
+# API Documentation for the GUI
+
+::: rimsschemedrawer.gui
diff --git a/docs/api/index.md b/docs/api/index.md
index b9275db..616a2ca 100644
--- a/docs/api/index.md
+++ b/docs/api/index.md
@@ -1 +1,53 @@
# API Documentation
+
+The `RIMSSchemeDrawer` can be run without a GUI.
+Here you find some documentation on how to use the library itself.
+
+## Installation
+
+The package can be installed via `pip`:
+
+```bash
+pip install rimsschemedrawer
+```
+
+This will install the package without the GUI.
+If you want the GUI components as well,
+install the package as:
+
+```bash
+pip install rimsschemedrawer[gui]
+```
+
+## Create a figure
+
+In order to create a figure,
+you need to have an available dictionary that holds the information for a given scheme.
+Let us first look at an example, where a configuration file is available.
+You can find an example file
+[here](https://github.com/RIMS-Code/RIMSSchemeDrawer/blob/main/examples/example_titanium.json).
+
+The following code snippet will create a figure for you that you can save.
+
+```python
+from pathlib import Path
+
+from rimsschemedrawer import Plotter, json_reader
+
+# Load the configuration file
+config_file = Path("path_to_your_config_file.json")
+config = json_reader(config_file)
+
+# Plot the figure
+plotter = Plotter(config)
+fig = plotter.figure # returns a matplotlib figure
+
+# Save the figure
+outname = Path("path_to_your_output_file.pdf")
+fig.savefig(outname)
+```
+
+Of course, you can also create your own config dictionary.
+To do so, please have a look at the example file given above.
+If you need further examples,
+you can create them by using the GUI and then save the configuration.
diff --git a/docs/api/json_parser.md b/docs/api/json_parser.md
new file mode 100644
index 0000000..f4a05d2
--- /dev/null
+++ b/docs/api/json_parser.md
@@ -0,0 +1,3 @@
+# JSON parser
+
+::: rimsschemedrawer.json_parser
diff --git a/docs/api/plotter.md b/docs/api/plotter.md
new file mode 100644
index 0000000..ab5ac14
--- /dev/null
+++ b/docs/api/plotter.md
@@ -0,0 +1,3 @@
+# Plotter
+
+::: rimsschemedrawer.plotter
diff --git a/docs/api/utils.md b/docs/api/utils.md
new file mode 100644
index 0000000..08ebc38
--- /dev/null
+++ b/docs/api/utils.md
@@ -0,0 +1,3 @@
+# Utilities
+
+::: rimsschemedrawer.utils
diff --git a/docs/dev.md b/docs/dev.md
new file mode 100644
index 0000000..7106a66
--- /dev/null
+++ b/docs/dev.md
@@ -0,0 +1,81 @@
+# Development guide
+
+We welcome new contribution!
+Please feel free to open pull-requests and/or issues.
+If you are not sure what to do,
+file an [issue on GitHub](https://github.com/RIMS-Code/RIMSSchemeDrawer/issues)
+and we can discuss it there.
+
+Contributions do not only have to be in the form of code.
+We also welcome contributions in the form of documentation, etc.!
+
+Below are some guidelines/rough instructions on how this project is set up.
+If you have any questions, please raise them!
+
+## Configuration
+
+The `RIMSSchemeDrawer` package is configured to use
+[`rye`](https://rye-up.com/) for the development environment.
+If you have `rye` installed, clone the repo and then run
+
+```bash
+rye sync --aditional-features
+```
+
+to get the full development environment setup.
+
+## Pre-commit hooks
+
+We use [`pre-commit`](https://pre-commit.com/) hooks in order to ensure
+code formatting and linting prior to committing. To install the hooks, run
+
+```bash
+pre-commit install
+```
+
+!!! note
+ In order for this to work, you must have `pre-commit` itself installed.
+ If you use `rye`, you can simply install it by running
+
+ ```bash
+ rye install pre-commit
+ ```
+
+## Testing
+
+We use `pytest` for testing. To run the tests, simply run
+
+```bash
+rye run test
+```
+
+## Documentation
+
+Please ensure that all features, etc., are documented.
+The documentation is built using `mkdocs` and `mkdocstrings`.
+To check the documentation locally,
+run
+
+```bash
+rye run mkdocs serve
+```
+
+and then open your browser at `http://localhost:8000`.
+You should see the documentation there.
+
+Upon a pull-request,
+the documentation is also created using a readthedocs webhook.
+You can see the documentation by clicking on the appropriate check in the pull-request.
+
+## Formatting and linting
+
+We use [`ruff`](https://astral.sh/ruff) for formatting and linting.
+You can run `ruff` directly from `rye`:
+
+```bash
+rye fmt
+rye lint
+```
+
+This will run the formatter (first line)
+and the linter (second line).
diff --git a/docs/gui.md b/docs/gui.md
index 1720d05..47383fe 100644
--- a/docs/gui.md
+++ b/docs/gui.md
@@ -1 +1,119 @@
# Graphical user interface
+
+## Overview
+
+When starting the program, the user is presented with the following interface (minus the markings).
+
+
+
+The window is divided into several components:
+
+1. The main area to define the laser ionization scheme.
+2. Settings and configurations for how to display the plot. These are pre-filled with some reasonable defaults.
+3. The button to plot and show the figure.
+4. Buttons to load and save configurations.
+5. A button to set the formatting settings back to the default values.
+6. Buttons to get information about the program and to quit the program.
+
+An example of the filled in GUI can be seen here and is discussed further below.
+
+
+
+
+## Resonance ionization scheme
+
+The scheme can be set up in the left hand side of the program.
+The following shows a marked up version of this part:
+
+
+
+The sections are as follows:
+
+1. Unit selection: Please select if you want to enter the transitions in nm or in cm-1.
+2. Here you can enter the states / transitions.
+ The units that need to be entered are automatically updated if you change the selection in 1.
+3. In the left column, please give the term symbol of the state that should be displayed.
+ On the right, please enter the transition strength in s-1. Note that
+ To display the transition strength in the plot, the according box in the settings (see below) must be checked.
+4. If the ground state manifold contains low-lying states, please check the left box in this section.
+ The state must then be given in cm-1.
+ If a transition is forbidden, you can additionally check the "Forbidden?" box.
+5. As you can see for the IP level in 1, the ionization potential is automatically set.
+ We currently include all elements with IPs define in the
+ [NIST Atomic Spectra Database](https://physics.nist.gov/PhysRefData/ASD/levels_form.html).
+ Finally, please select the lasers that were used for this scheme.
+ While this is unimportant for the plot, it is used when submitting a scheme to the online database.
+
+## Settings of the plot
+
+The settings of the plot can be configured on the right-hand side of the program, labeled 2 in the overview image.
+The following settings from top to bottom in the left column are available.
+
+1. Width and height of the figure. This is set in inches, however, the actual units are fairly unimportant.
+2. Font size of the title (if set).
+3. Font size of the axes.
+4. Font size of the axes labels.
+5. Headspace in cm-1. This is the space above the IP that will be added.
+ This is one of the most frequent values changed in the settings.
+ For example, you might want to add additional space in order to display all labels nicely within the plot.
+6. Width of the arrow in arbitrary units. Mainly needs to be changed if the figure size is modified.
+7. Arrow head width in arbitrary units. Mainly needs to be changed if the figure size is modified.
+8. Precision of the wavelength: How many digits should be displayed for the wavelengths?
+9. Precision of the levels: How many digits should be displayed for the levels?
+10. Where should the IP be labeled: on top or on the bottom of the IP line?
+11. How do you want to show forbidden transitions? Cross them out ("x-out") or don't show them at all ("Don't show")?
+
+In the right column, the following options are available:
+
+1. Plot title: Here you can enter an optional title for the plot.
+2. Transition strengths? Checkbox to display the transition strengths in the plot.
+3. Line breaks? Checkbox to show line breaks between the levels and the term symbols.
+ This can be useful if you want a narrow figure or higher level precision.
+4. Show cm-1 axis labels? If unchecked, the left axis labels will disappear.
+5. Show eV axis labels? If unchecked, the right axis labels will disappear.
+6. Plot dark mode? If checked, the plot will be displayed in dark mode.
+ This can be useful, e.g., if you create slides with a dark background.
+
+!!! note
+ The filled GUI example image above shows a reasonable setup for a Ti resonance ionization scheme (plot shown below).
+ Note especially the setup for the low-lying states and the term symbols that were entered.
+
+
+!!! note "Show axis labels"
+ The "Show axis labels" as described above can be useful in case you need to combine multiple schemes into one figure.
+ In this case, create multiple figures with the same figure height.
+ Then, calculate the headspace for each figure, such that the cm-1 of the maximum height align in each figure.
+ The total height of the figure will always be IP level + headspace.
+ Finally, save the figure (see below), e.g., as an `svg` file and combine the figures with a vector graphics editor.
+
+## Plotting
+
+Once the scheme is filled out, hit the "Plot" button in order to display a figure.
+A window will open with the figure.
+Here's an example:
+
+
+
+This figure is for a Ti resonance ionization scheme,
+taken from [Trappitsch et al. (2018)](https://doi.org/10.1039/C8JA00269J).
+The setup of the GUI to create this scheme can be found above.
+
+To save this figure, you can use the [floppy disk](https://en.wikipedia.org/wiki/Floppy_disk)
+icon in the toolbar of the figure window.
+The available formats can be found [here](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html).
+Recommended saving formats are `png` for pixel graphics and `svg` or `pdf` for vector graphics.
+
+## Saving and loading configurations
+
+If you want to save a given configuration, you can use the "Save Config" button.
+The data will be saved as a `json` file.
+You can open a saved file with any text editor and have a look,
+but please note that bad things can happen if you change the file right there,
+unless of course you know what you're doing.
+The file should be fairly self-explanatory.
+
+To load a given configuration, you can use the "Load Config" button.
+This will open a file dialog where you can select the file to load.
+
+The configuration file for the example titanium scheme shown above can be found
+[here](https://github.com/RIMS-Code/RIMSSchemeDrawer/blob/main/examples/example_titanium.json).
diff --git a/docs/img/gui_overview.png b/docs/img/gui_overview.png
new file mode 100644
index 0000000..58d5422
Binary files /dev/null and b/docs/img/gui_overview.png differ
diff --git a/docs/img/gui_overview.svg b/docs/img/gui_overview.svg
new file mode 100644
index 0000000..3dd95bb
--- /dev/null
+++ b/docs/img/gui_overview.svg
@@ -0,0 +1,196 @@
+
+
+
+
diff --git a/docs/img/gui_scheme.png b/docs/img/gui_scheme.png
new file mode 100644
index 0000000..bfd5026
Binary files /dev/null and b/docs/img/gui_scheme.png differ
diff --git a/docs/img/gui_scheme.svg b/docs/img/gui_scheme.svg
new file mode 100644
index 0000000..9d99a20
--- /dev/null
+++ b/docs/img/gui_scheme.svg
@@ -0,0 +1,201 @@
+
+
+
+
diff --git a/docs/img/gui_ti_scheme.png b/docs/img/gui_ti_scheme.png
new file mode 100644
index 0000000..4a8111c
Binary files /dev/null and b/docs/img/gui_ti_scheme.png differ
diff --git a/docs/img/plot_window.png b/docs/img/plot_window.png
new file mode 100644
index 0000000..a26914d
Binary files /dev/null and b/docs/img/plot_window.png differ
diff --git a/examples/example_titanium.json b/examples/example_titanium.json
index 0673a16..bb38e1b 100644
--- a/examples/example_titanium.json
+++ b/examples/example_titanium.json
@@ -1,40 +1,66 @@
{
"scheme": {
- "gs_level": "0",
+ "element": "Ti",
+ "gs_level": "0.0",
"gs_term": "3F2",
- "ip_level": "55074",
"ip_term": "",
+ "lasers": "Ti:Sa",
+ "step_forbidden0": false,
+ "step_forbidden1": false,
+ "step_forbidden2": false,
+ "step_forbidden3": false,
+ "step_forbidden4": false,
+ "step_forbidden5": false,
+ "step_forbidden6": false,
"step_level0": "170.15",
"step_level1": "386.88",
"step_level2": "21469.5",
"step_level3": "45498.85",
"step_level4": "56844.45",
+ "step_level5": "",
+ "step_level6": "",
"step_lowlying0": true,
"step_lowlying1": true,
"step_lowlying2": false,
"step_lowlying3": false,
"step_lowlying4": false,
+ "step_lowlying5": false,
+ "step_lowlying6": false,
"step_term0": "3F3",
"step_term1": "3F4",
"step_term2": "3G3",
"step_term3": "3G4",
"step_term4": "",
+ "step_term5": "",
+ "step_term6": "",
+ "trans_strength0": "",
+ "trans_strength1": "",
+ "trans_strength2": "",
+ "trans_strength3": "",
+ "trans_strength4": "",
+ "trans_strength5": "",
+ "trans_strength6": "",
"unit": "cm-1"
},
"settings": {
"arrow_head_width": "0.6",
"arrow_width": "0.2",
- "fig_height": "8",
- "fig_width": "5",
- "fs_axes": "12",
- "fs_axes_labels": "14",
- "fs_labels": "12",
- "fs_title": "14",
- "headspace": "2700",
+ "fig_height": "8.0",
+ "fig_width": "5.0",
+ "fs_axes": "12.0",
+ "fs_axes_labels": "14.0",
+ "fs_labels": "12.0",
+ "fs_title": "14.0",
+ "headspace": "2700.0",
"ip_label_pos": "Top",
"line_breaks": false,
+ "plot_darkmode": false,
"plot_title": "",
"prec_level": "0",
- "prec_wavelength": "3"
+ "prec_wavelength": "3",
+ "show_cm-1_axis": true,
+ "show_eV_axis": true,
+ "show_forbidden_transitions": "x-out",
+ "show_transition_strength": true
}
-}
\ No newline at end of file
+}
diff --git a/mkdocs.yml b/mkdocs.yml
index d7355e7..dd8b6ac 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -39,10 +39,21 @@ markdown_extensions:
plugins:
- search
-
+ - mkdocstrings:
+ handlers:
+ python:
+ options:
+ docstring_style: sphinx
+ show_symbol_type_heading: true
+ show_symbol_type_toc: true
nav:
- Home: index.md
- Installation: install.md
- GUI: gui.md
+ - Development: dev.md
- API:
- Overview: api/index.md
+ - Plotter: api/plotter.md
+ - JSON Parser: api/json_parser.md
+ - Utilities: api/utils.md
+ - GUI: api/gui.md
diff --git a/pyproject.toml b/pyproject.toml
index 154b026..b266e4c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ gui = [
docs = [
"mkdocs>=1.5.3",
"mkdocs-material>=9.5.12",
+ "mkdocstrings[python]>=0.24.1",
]
[project.urls]
diff --git a/requirements-dev.lock b/requirements-dev.lock
index ef5ba9b..49bad37 100644
--- a/requirements-dev.lock
+++ b/requirements-dev.lock
@@ -18,7 +18,9 @@ charset-normalizer==3.3.2
# via requests
click==8.1.7
# via mkdocs
+ # via mkdocstrings
colorama==0.4.6
+ # via griffe
# via mkdocs-material
contourpy==1.2.0
# via matplotlib
@@ -30,6 +32,8 @@ fonttools==4.49.0
# via matplotlib
ghp-import==2.1.0
# via mkdocs
+griffe==0.41.3
+ # via mkdocstrings-python
hypothesis==6.98.13
idna==3.6
# via requests
@@ -38,26 +42,40 @@ iniconfig==2.0.0
jinja2==3.1.3
# via mkdocs
# via mkdocs-material
+ # via mkdocstrings
kiwisolver==1.4.5
# via matplotlib
markdown==3.5.2
# via mkdocs
+ # via mkdocs-autorefs
# via mkdocs-material
+ # via mkdocstrings
# via pymdown-extensions
markupsafe==2.1.5
# via jinja2
# via mkdocs
+ # via mkdocs-autorefs
+ # via mkdocstrings
matplotlib==3.8.3
# via rimsschemedrawer
mergedeep==1.3.4
# via mkdocs
mkdocs==1.5.3
+ # via mkdocs-autorefs
# via mkdocs-material
+ # via mkdocstrings
# via rimsschemedrawer
+mkdocs-autorefs==1.0.1
+ # via mkdocstrings
mkdocs-material==9.5.12
# via rimsschemedrawer
mkdocs-material-extensions==1.3.1
# via mkdocs-material
+mkdocstrings==0.24.1
+ # via mkdocstrings-python
+ # via rimsschemedrawer
+mkdocstrings-python==1.8.0
+ # via mkdocstrings
numpy==1.26.4
# via contourpy
# via matplotlib
@@ -75,12 +93,14 @@ pillow==10.2.0
# via matplotlib
platformdirs==4.2.0
# via mkdocs
+ # via mkdocstrings
pluggy==1.4.0
# via pytest
pygments==2.17.2
# via mkdocs-material
-pymdown-extensions==10.7
+pymdown-extensions==10.7.1
# via mkdocs-material
+ # via mkdocstrings
pyparsing==3.1.1
# via matplotlib
pyqt6==6.6.1
diff --git a/requirements.lock b/requirements.lock
index 549a499..bce7979 100644
--- a/requirements.lock
+++ b/requirements.lock
@@ -16,7 +16,9 @@ charset-normalizer==3.3.2
# via requests
click==8.1.7
# via mkdocs
+ # via mkdocstrings
colorama==0.4.6
+ # via griffe
# via mkdocs-material
contourpy==1.2.0
# via matplotlib
@@ -26,31 +28,47 @@ fonttools==4.49.0
# via matplotlib
ghp-import==2.1.0
# via mkdocs
+griffe==0.41.3
+ # via mkdocstrings-python
idna==3.6
# via requests
jinja2==3.1.3
# via mkdocs
# via mkdocs-material
+ # via mkdocstrings
kiwisolver==1.4.5
# via matplotlib
markdown==3.5.2
# via mkdocs
+ # via mkdocs-autorefs
# via mkdocs-material
+ # via mkdocstrings
# via pymdown-extensions
markupsafe==2.1.5
# via jinja2
# via mkdocs
+ # via mkdocs-autorefs
+ # via mkdocstrings
matplotlib==3.8.3
# via rimsschemedrawer
mergedeep==1.3.4
# via mkdocs
mkdocs==1.5.3
+ # via mkdocs-autorefs
# via mkdocs-material
+ # via mkdocstrings
# via rimsschemedrawer
+mkdocs-autorefs==1.0.1
+ # via mkdocstrings
mkdocs-material==9.5.12
# via rimsschemedrawer
mkdocs-material-extensions==1.3.1
# via mkdocs-material
+mkdocstrings==0.24.1
+ # via mkdocstrings-python
+ # via rimsschemedrawer
+mkdocstrings-python==1.8.0
+ # via mkdocstrings
numpy==1.26.4
# via contourpy
# via matplotlib
@@ -67,10 +85,12 @@ pillow==10.2.0
# via matplotlib
platformdirs==4.2.0
# via mkdocs
+ # via mkdocstrings
pygments==2.17.2
# via mkdocs-material
-pymdown-extensions==10.7
+pymdown-extensions==10.7.1
# via mkdocs-material
+ # via mkdocstrings
pyparsing==3.1.1
# via matplotlib
pyqt6==6.6.1