From 5866811ed44acea6990510526749c31b7048c52d Mon Sep 17 00:00:00 2001 From: Kieran Leschinski Date: Fri, 15 May 2026 22:31:48 +0200 Subject: [PATCH 1/8] Switch to sphinx-book-theme and myst-nb for docs Replace nbsphinx + default theme with myst-nb + sphinx-book-theme, following the scopesim-targets canonical A* Vienna docs template. Add sphinx-design (for card gallery) and sphinx-copybutton. Strip commented-out dead code and LaTeX/man/Texinfo output boilerplate. --- conf.py | 312 ++++++++--------------------------- requirements.readthedocs.txt | 10 +- 2 files changed, 70 insertions(+), 252 deletions(-) diff --git a/conf.py b/conf.py index 966b16d0..51292183 100644 --- a/conf.py +++ b/conf.py @@ -1,273 +1,91 @@ -""" -Configuration file for Sphinx and ReadTheDocs - -This file originally lived in docs/source. -It has been moved into the top level so that all package docs are accessible to -sphinx -""" - - -#!/usr/bin/env python3 # -*- coding: utf-8 -*- -# -# Instrument Reference Database documentation build configuration file, created by -# sphinx-quickstart on Fri Jul 12 13:46:11 2019. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# sys.path.insert(0, os.path.abspath('.')) +"""Sphinx configuration for the Instrument Reference Database.""" -import sys import os +import sys from pathlib import Path -sys.path.insert(0, os.path.abspath('/')) -sys.path.insert(0, os.path.abspath('docs')) +sys.path.insert(0, os.path.abspath(".")) +sys.path.insert(0, os.path.abspath("docs")) -# -- General configuration ------------------------------------------------ +project = "Instrument Reference Database" +copyright = "2024, A* Vienna Software Team" +author = "A* Vienna Software Team" -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. extensions = [ - 'nbsphinx', - 'sphinx.ext.intersphinx', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.viewcode', - # 'matplotlib.sphinxext.plot_directive', - # 'numpydoc', - # 'sphinx.ext.autodoc', - # 'jupyter_sphinx.execute', - # 'sphinxcontrib.apidoc', + "sphinx.ext.todo", + "sphinx.ext.intersphinx", + "sphinx.ext.mathjax", + "sphinx.ext.napoleon", + "sphinx_copybutton", + "myst_nb", + "sphinx_design", "docs.source._ext.validation_report", ] -# numpydoc settings -numpydoc_show_class_members = False +myst_enable_extensions = ["colon_fence"] +todo_include_todos = True + +napoleon_numpy_docstring = True +napoleon_use_admonition_for_references = True -# apidoc settings -# apidoc_module_dir = os.path.abspath('irdb/') -# apidoc_output_dir = 'docs/source/reference' -# apidoc_separate_modules = True -# apidoc_excluded_paths = ["tests/", "docs/"] +source_encoding = "utf-8" +source_suffix = { + ".rst": "restructuredtext", + ".myst": "myst-nb", + ".md": "myst-nb", + ".ipynb": "myst-nb", +} -# nbsphinx settings -nbsphinx_allow_errors = True -nbsphinx_execute = "never" +nb_execution_mode = "off" -# add_hidden_cell_to_ipynb_files() +master_doc = "index" -def add_hidden_cell_to_ipynb_files(): - import glob - old_string = '''"cells": [''' - new_string = '''"cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": { "nbsphinx": "hidden" }, - "outputs": [], - "source": [ - "import os, scopesim as sim", - "if os.environ.get(\"READTHEDOCS\") == \"True\" or \"F:\" in os.getcwd():", - " sim.rc.__config__[\"!SIM.file.local_packages_path\"] = os.path.abspath(\"../../../\")", - ] - },''' - paths = glob.glob("./**/*.ipynb", recursive=True) - for path in paths: - with open(path, "r+") as f: - contents = f.read() - # check if the hidden cell has already been added to notebook - if 'os.environ.get("READTHEDOCS")' not in contents: - contents = contents.replace(old_string, new_string) - f.seek(0) - f.write(contents) +exclude_patterns = [ + "_build", + "docs/ScopeSim_guide.md", # shared include file, not a standalone page +] +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), + "matplotlib": ("https://matplotlib.org/stable/", None), + "astropy": ("https://docs.astropy.org/en/stable/", None), + "synphot": ("https://synphot.readthedocs.io/en/latest/", None), + "scopesim": ("https://scopesim.readthedocs.io/en/latest/", None), + "scopesim_templates": ("https://scopesim-templates.readthedocs.io/en/latest/", None), + "pyckles": ("https://pyckles.readthedocs.io/en/latest/", None), + "anisocado": ("https://anisocado.readthedocs.io/en/latest/", None), +} -# add_hidden_cell_to_ipynb_files() +html_theme = "sphinx_book_theme" +html_theme_options = { + "repository_url": "https://github.com/AstarVienna/irdb", + "use_repository_button": True, + "use_download_button": True, + "home_page_in_toc": True, +} +html_logo = "docs/source/_static/logos/T_favicon.png" +html_favicon = "docs/source/_static/logos/T_favicon.png" +html_sidebars = { + "**": [ + "navbar-logo.html", + "search-field.html", + "sbt-sidebar-nav.html", + ] +} + +html_static_path = ["docs/source/_static"] +html_css_files = ["validation_report.css"] +html_js_files = ["clickable_rows.js"] def remove_inst_pkgs_symlink(): """Remove inst_pkgs symlinks.""" - for path in list(Path(".").rglob('inst_pkgs')): + for path in list(Path(".").rglob("inst_pkgs")): if path.is_symlink(): path.unlink() remove_inst_pkgs_symlink() - -# Matplotlib plot directive config parameters -plot_html_show_source_link = False - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = 'Instrument Reference Database' -copyright = '2019, A*Vienna Software Team' -author = 'Kieran Leschinski, Oliver Czoske' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0' -# The full version, including alpha/beta/rc tags. -release = '1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = [] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -# html_theme = 'alabaster' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -html_theme_options = {"body_max_width": "900px"} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['docs/source/_static'] # 'METIS/docs/example_notebooks' -html_favicon = 'docs/source/_static/logos/T_favicon.png' -html_css_files = [ - "validation_report.css", -] -html_js_files = [ - "clickable_rows.js", -] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# This is required for the alabaster theme -# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars -# html_sidebars = { -# '**': [ -# 'relations.html', # needs 'show_related': True theme option to display -# 'searchbox.html', -# ] -# } - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'IRDB' - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'InstrumentReferenceDatabase.tex', 'Instrument Reference Database Documentation', - 'Kieran Leschinski, Oliver Czoske', 'manual'), -] - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'InstrumentReferenceDatabase', 'Instrument Reference Database Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'InstrumentReferenceDatabase', 'Instrument Reference Database Documentation', - author, 'InstrumentReferenceDatabase', 'One line description of project.', - 'Miscellaneous'), -] - - - - -# Example configuration for intersphinx: refer to the Python standard library. -intersphinx_mapping = {'python': ('http://docs.python.org/', None), - 'numpy': ('http://docs.scipy.org/doc/numpy/', None), - 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), - 'matplotlib': ('http://matplotlib.org/', None), - 'astropy': ('http://docs.astropy.org/en/stable/', None), - 'synphot': ('https://synphot.readthedocs.io/en/latest/', None), - 'scopesim_templates': ('https://scopesim_templates.readthedocs.io/en/latest/', None), - 'pyckles': ('https://pyckles.readthedocs.io/en/latest/', None), - 'anisocado': ('https://anisocado.readthedocs.io/en/latest/', None), - } - - -# -- Options for todo extension ---------------------------------------------- - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = True diff --git a/requirements.readthedocs.txt b/requirements.readthedocs.txt index 4ef79e4a..6ff92dca 100644 --- a/requirements.readthedocs.txt +++ b/requirements.readthedocs.txt @@ -12,9 +12,9 @@ scopesim scopesim_templates paramiko -sphinx>=4.3.0 -sphinx-rtd-theme>=0.5.1 -jupyter_sphinx==0.2.3 -sphinxcontrib-apidoc -nbsphinx +sphinx>=5.0 +sphinx-book-theme +myst-nb +sphinx-design +sphinx-copybutton numpydoc From e099af3da3688a55c9e14180adae562f70dc6cd7 Mon Sep 17 00:00:00 2001 From: Kieran Leschinski Date: Fri, 15 May 2026 22:32:57 +0200 Subject: [PATCH 2/8] Refactor instrument READMEs with shared ScopeSim guide Convert MICADO, METIS, and MOSAIC readme.rst files to readme.md. Factor out common installation boilerplate (prerequisites, pip install, working directory setup, notebook workflow, references, contacts) into docs/ScopeSim_guide.md, which each README includes via MyST {include}. MOSAIC: fix stale reference to non-existent Introduction_to_Scopesim_for_MOSAIC.ipynb (replaced with MOSAIC_demo.ipynb). --- METIS/docs/readme.md | 111 +++++++++++++++++++++++++ METIS/docs/readme.rst | 184 ----------------------------------------- MICADO/docs/readme.md | 109 ++++++++++++++++++++++++ MICADO/docs/readme.rst | 115 -------------------------- MOSAIC/docs/readme.md | 86 +++++++++++++++++++ MOSAIC/docs/readme.rst | 133 ----------------------------- docs/ScopeSim_guide.md | 65 +++++++++++++++ 7 files changed, 371 insertions(+), 432 deletions(-) create mode 100644 METIS/docs/readme.md delete mode 100644 METIS/docs/readme.rst create mode 100644 MICADO/docs/readme.md delete mode 100644 MICADO/docs/readme.rst create mode 100644 MOSAIC/docs/readme.md delete mode 100644 MOSAIC/docs/readme.rst create mode 100644 docs/ScopeSim_guide.md diff --git a/METIS/docs/readme.md b/METIS/docs/readme.md new file mode 100644 index 00000000..413acdd8 --- /dev/null +++ b/METIS/docs/readme.md @@ -0,0 +1,111 @@ +```{image} metis_scopesim_logo.png +:width: 600px +:alt: METIS + ScopeSim +:align: center +``` + +# METIS + ScopeSim + +## Introduction + +The METIS data simulator is based on the generic simulator ScopeSim, a +descendant of the older SimCado/SimMETIS interface. METIS itself is handled +as an instrument package containing configuration files for the various +instrument modes and data files describing the instrument components. + +The simulator currently supports imaging and long-slit spectroscopy modes. +The LM-band high-resolution IFU (LMS) mode is under development. + +```{note} +**Bug reports and help desk** + +If you come across a bug or get stuck with ScopeSim or the METIS package, +please [open an issue on GitHub](https://github.com/AstarVienna/irdb/issues) +or contact us by email (see below). + +**Your feedback is the only way we know** what needs to be +changed or improved with the package and the simulator. + +Please always include the output of `scopesim.bug_report()` from your +installation. +``` + +--- + +## Downloading the METIS instrument package + +Once ScopeSim is installed, download the METIS instrument package into your +working directory: + +```python +import scopesim +scopesim.download_packages(["Armazones", "ELT", "METIS"]) +``` + +This installs the packages into the subdirectory `./inst_pkgs/`. + +Your working directory should look like this afterwards: + +``` +my_simulations/ +├── .ipynb +└── inst_pkgs/ + ├── Armazones/ + ├── ELT/ + └── METIS/ + └── docs/ + └── example_notebooks/ + └── .ipynb ← copy to working dir before running +``` + +--- + +```{include} ../../docs/ScopeSim_guide.md +``` + +--- + +## Example notebooks + +Find the notebooks locally in `inst_pkgs/METIS/docs/example_notebooks/` +after downloading the package, or download them from the +[GitHub repository](https://github.com/AstarVienna/irdb/tree/dev_master/METIS/docs/example_notebooks). + +```{warning} +Run notebooks in your working directory, **not** inside `inst_pkgs/`. +Copy the desired notebook out first. +``` + +### Introductory notebooks + +| Notebook | Description | +|---|---| +| [`Introduction_to_Scopesim_for_METIS.ipynb`](example_notebooks/Introduction_to_Scopesim_for_METIS.ipynb) | Introductory overview of how to run simulations in ScopeSim. Also available as [PDF](example_notebooks/Introduction_to_Scopesim_for_METIS.pdf). | + +### Scientific use-case notebooks + +| Notebook | Description | +|---|---| +| [`IMG_L_N-examples.ipynb`](example_notebooks/IMG_L_N-examples.ipynb) | Imaging of HL Tau and an AGN model in the L and N bands | +| [`LSS-YSO_model_simulation.ipynb`](example_notebooks/LSS-YSO_model_simulation.ipynb) | Long-slit spectroscopy in the L-band of a young stellar object model | +| [`LSS_AGN-01_preparation.ipynb`](example_notebooks/LSS_AGN-01_preparation.ipynb) + [`LSS_AGN-02_simulation.ipynb`](example_notebooks/LSS_AGN-02_simulation.ipynb) | Long-slit spectroscopy in the N-band of an AGN model. Part 1: input data preparation. Part 2: simulation. | + +### Effect demonstration notebooks + +These notebooks are in `docs/example_notebooks/demos/`. + +| Notebook | Description | +|---|---| +| [`demo_adc_wheel.ipynb`](example_notebooks/demos/demo_adc_wheel.ipynb) | Using the atmospheric dispersion correctors | +| [`demo_auto_exposure.ipynb`](example_notebooks/demos/demo_auto_exposure.ipynb) | Selecting `dit`/`ndit` automatically | +| [`demo_chopping_and_nodding.ipynb`](example_notebooks/demos/demo_chopping_and_nodding.ipynb) | Chop-nod difference images in the N band | +| [`demo_detector_modes.ipynb`](example_notebooks/demos/demo_detector_modes.ipynb) | Setting detector readout modes | +| [`demo_filter_wheel.ipynb`](example_notebooks/demos/demo_filter_wheel.ipynb) | Using the filter wheel(s) | +| [`demo_lss_simple.ipynb`](example_notebooks/demos/demo_lss_simple.ipynb) | Basic long-slit spectroscopy procedure | +| [`demo_grating_efficiency.ipynb`](example_notebooks/demos/demo_grating_efficiency.ipynb) | Spectral (grating) efficiency | +| [`demo_slit_wheel.ipynb`](example_notebooks/demos/demo_slit_wheel.ipynb) | Using the slit wheel for spectroscopy and imaging | +| [`demo_rectify_traces.ipynb`](example_notebooks/demos/demo_rectify_traces.ipynb) | Wavelength-calibrated and rectified 2D spectra | + +### Instrument homepage + +[METIS at Leiden Observatory](https://metis.strw.leidenuniv.nl/) diff --git a/METIS/docs/readme.rst b/METIS/docs/readme.rst deleted file mode 100644 index e1cb7ad5..00000000 --- a/METIS/docs/readme.rst +++ /dev/null @@ -1,184 +0,0 @@ -.. |pic1| image:: metis_scopesim_logo.png - :width: 600px - :alt: METIS + ScopeSim - -|pic1| -====== - -Introduction ------------- -The METIS data simulator is based on the generic simulator software Scopesim, a descendant of the older SimCado/SimMETIS interface. METIS itself is handled as an instrument package that contains configuration files for the various instrument modes as well as data files describing the components of the instruments. -The new METIS data simulator currently supports the imaging and long-slit modes. The LM-band high-resolution IFU (LMS) mode will be offered soon. - - -Prerequisites -------------- - -- A working installation of a recent Python version -- A working installation of Jupyter if you want to run the simulator from notebooks. This is necessary to run the example notebooks contained in the instrument package. -- A working installation of the Python package installer pip - -.. note:: - - If you come across a bug or get stuck with a certain aspect of ScopeSim or - the METIS package, please get in touch with us (email addresses below). - - **Your feedback is the only way we know** what needs to be changed/improved - with the package and the simulator. - - Please always provide the output of the command ``scopesim.bug_report()`` run on your installation. - - -Installation & setup --------------------- - -This is a short overview of the installation and setup procedure; for a more detailed presentation see `Introduction_to_Scopesim_for_METIS `_. - -1. Install ``scopesim`` in your python environment:: - - $ pip install scopesim - - To upgrade an existing installation do:: - - $ pip install -U scopesim - -2. Create a working directory where you want to run simulations, e.g.:: - - $ mkdir ~/path/to/playing_with_scopesim/ - $ cd ~/path/to/playing_with_scopesim - -3. Install relevant irdb packages into this directory:: - - $ python - >> import scopesim - >> scopesim.download_packages(["METIS", "ELT", "Armazones"]) - - This will install the packages in the subdirectory ``./inst_pkgs``. - -4. The METIS package includes a number of tutorial notebooks in the directory ``./inst_pkgs/METIS/docs/example_notebooks/`` (see `Python notebooks`_). - - Copy notebooks to the working directory (i.e. ``./``) to run them.:: - - $ cp ./inst_pkgs/METIS/docs/example_notebooks/ . - -5. In a terminal, execute the notebook by calling:: - - $ jupyter notebook - -6. Follow instructions and explanations in the notebook. Some notebooks use example data; the commands to download these data from the scopesim server are included in the notebooks. - -You can then edit the notebooks and use them as a starting point for your own simulations. - - -Python notebooks ----------------- - -These notebooks can be found either: - -- [locally] in the METIS instrument package in ``docs/example_notebooks``, or -- [download] in the `METIS/docs section of the IRDB Github repository `_ - - -.. warning:: - Notebooks should be run in your working directory, **NOT** directly in the - ``docs/example_notebooks`` folder. Please copy the desired notebook out of - this folder. - -Ideally your folder structure should look like this:: - - working-dir - |- .iypnb - | - |- inst_pkgs - |- METIS - | |- docs - | |- example_notebooks - | |- .iypnb # copy out to working-dir - |- ELT - |- Armazones - - -Introductory notebooks -++++++++++++++++++++++ - -.. list-table:: - :widths: 25 75 - :width: 900px - :header-rows: 1 - - * - Name - - Description - * - | `Introduction_to_Scopesim_for_METIS.ipynb `_ - | `Introduction_to_Scopesim_for_METIS.pdf `_ - - Introductory overview of how to run simulations in Scopesim - -Scientific use-case notebooks -+++++++++++++++++++++++++++++ - -.. list-table:: - :widths: 25 75 - :width: 900px - :header-rows: 1 - - * - Name - - Description - * - `IMG_L_N-examples.ipynb `_ - - Imaging observations of HL Tau and an AGN model in the L and N band - * - `LSS-YSO_model_simulation.ipynb `_ - - Long-slit spectroscopy in the L-band of three models of a young stellar object - * - | `LSS_AGN-01_preparation.ipynb `_ - | `LSS_AGN-02_simulation.ipynb `_ - - | Long-slit spectroscopy in the N-band of an AGN model. The first notebook describes - | how the input data are prepared for Scopesim, the second runs the simulation. - -Notebooks on individual effects -+++++++++++++++++++++++++++++++ - -These notebooks can be found in ``docs/example_notebooks/demos``. - -.. list-table:: - :widths: 25 75 - :width: 900px - :header-rows: 1 - - * - Name - - Description - * - `demo_adc_wheel.ipynb `_ - - How to use the atmospheric dispersion correctors. - * - `demo_auto_exposure.ipynb `_ - - How to select `dit`/`ndit` automatically. - * - `demo_chopping_and_nodding.ipynb `_ - - How to produce chop-nod difference images in the N band. - * - `demo_detector_modes.ipynb `_ - - How to set detector readout modes. - * - `demo_filter_wheel.ipynb `_ - - How to use the filter wheel(s). - * - `demo_lss_simple.ipynb `_ - - Basic procedure for long-slit spectroscopy. - * - `demo_grating_efficiency.ipynb `_ - - Demonstration of spectral (grating) efficiency. - * - `demo_slit_wheel.ipynb `_ - - How to use the slit wheel for spectroscopy (and imaging) - * - `demo_rectify_traces.ipynb `_ - - How to obtain wavelength-calibrated and rectified 2D spectra. - -Documentation and useful references ------------------------------------ - -- `ScopeSim documentation `_ -- `Sky Object Templates documentation `_ -- `METIS homepage `_ -- For experts: GitHub repositories: - - + `simulator package ScopeSim `_ - + `instrument-specific packages irdb `_. - - -Contact points --------------- -`ScopeSim Slack `_ - -Email: - -- scopesim@univie.ac.at -- kieran.leschinski@univie.ac.at diff --git a/MICADO/docs/readme.md b/MICADO/docs/readme.md new file mode 100644 index 00000000..f2e516cd --- /dev/null +++ b/MICADO/docs/readme.md @@ -0,0 +1,109 @@ +```{image} micado_scopesim_logo.png +:width: 600px +:alt: MICADO + ScopeSim +:align: center +``` + +# MICADO + ScopeSim + +## Introduction + +A MICADO data simulator is being developed as part of the generic simulator +ScopeSim, a descendant of the older SimCADO software. MICADO is the +near-infrared camera for the ELT and supports both MCAO (4 mas) and SCAO +(1.5 mas and 4 mas) imaging modes. + +```{note} +**Bug reports and help desk** + +If you come across a bug or get stuck with ScopeSim or the MICADO package, +please [open an issue on GitHub](https://github.com/AstarVienna/irdb/issues) +or contact us by email (see below). + +**Your feedback is the only way we know** what needs to be +changed or improved with the package and the simulator. + +Please always include the output of `scopesim.bug_report()` from your +installation. +``` + +--- + +## Downloading the MICADO instrument package + +Once ScopeSim is installed, download the MICADO instrument package into your +working directory: + +```python +import scopesim +scopesim.download_packages(["Armazones", "ELT", "MICADO"]) +``` + +This installs the packages into the subdirectory `./inst_pkgs/`. + +Your working directory should look like this afterwards: + +``` +my_simulations/ +├── .ipynb +└── inst_pkgs/ + ├── Armazones/ + ├── ELT/ + └── MICADO/ + └── docs/ + └── example_notebooks/ + └── .ipynb ← copy to working dir before running +``` + +--- + +```{include} ../../docs/ScopeSim_guide.md +``` + +--- + +## Example notebooks + +Download the notebooks from the +[GitHub repository](https://github.com/AstarVienna/irdb/tree/dev_master/MICADO/docs/example_notebooks) +or find them locally in `inst_pkgs/MICADO/docs/example_notebooks/` after +downloading the package. + +```{warning} +Run notebooks in your working directory, **not** inside `inst_pkgs/`. +Copy the desired notebook out first. +``` + +### Scientific use-case notebooks + +```{toctree} +:maxdepth: 1 + +example_notebooks/1_scopesim_MCAO_4mas_galaxy +example_notebooks/2_scopesim_SCAO_1.5mas_astrometry +example_notebooks/3_scopesim_SCAO_4mas_fv-psf +example_notebooks/MICADO_FAQs +``` + +| Notebook | Description | +|---|---| +| `1_scopesim_MCAO_4mas_galaxy` | MCAO 4 mas imaging of a galaxy | +| `2_scopesim_SCAO_1.5mas_astrometry` | SCAO 1.5 mas astrometry use case | +| `3_scopesim_SCAO_4mas_fv-psf` | SCAO 4 mas field-varying PSF | +| `MICADO_FAQs` | Frequently asked questions | + +--- + +## Validation + +The table below shows limiting-magnitude test results (minimum S/N = 5). +Green = passed, yellow = expected deviation, red = unexpected failure. +**Click** a row to see the test plot. + +```{eval-rst} +.. validation-report:: ./MICADO/test_micado/validation_results.xml +``` + +The test code lives in the +[MICADO/test_micado/](https://github.com/AstarVienna/irdb/tree/dev_master/MICADO/test_micado/) +folder on GitHub. diff --git a/MICADO/docs/readme.rst b/MICADO/docs/readme.rst deleted file mode 100644 index 78ecd8c2..00000000 --- a/MICADO/docs/readme.rst +++ /dev/null @@ -1,115 +0,0 @@ -.. |pic1| image:: micado_scopesim_logo.png - :width: 600px - :alt: MICADO + ScopeSim - -|pic1| -====== - -Introduction ------------- -A new MICADO data simulator is being developed as part of the generic simulator ScopeSim, a descendant of the older SimCADO software. - - -Prerequisites -------------- - -- A working installation of Python 3.6 or newer -- A working installation of Jupyter notebooks if you want to run the simulator from notebooks, i.e. using a graphical interactive interface, rather than just the terminal or scripts (highly recommended) -- A working installation of the Python package installer pip - -.. note:: Bug reports and help-desk - - If you come across a bug or get stuck with a certain aspect of ScopeSim or - the MICADO package, please get in touch with us (emails addresses below). - - **Your feedback is the only way we know** what needs to be changed/improved - with the package and the simulator - - -Installation & setup --------------------- - -1. Install ``scopesim`` in your python environment:: - - $ pip install scopesim - -2. Create a directory where your simulation notebooks will live, e.g. ``~/path/to/playing_with_scopesim/`` -3. Install relevant irdb packages & download example notebooks into this directory:: - - $ python - >> import scopesim - >> scopesim.download_packages(["Armazones", "ELT", "MICADO"]) - -4. Download one of the tutorial notebooks (see `Python notebooks`_) -5. In a Terminal, cd to ~/ScopeSim and execute the notebook by calling:: - - $ cd ~/path/to/playing_with_scopesim/ - $ jupyter notebook filename.ipynb - -6. Follow instruction and explanations in the notebook. - - -Python notebooks ----------------- - -.. note:: - To download a notebook from Github, either: - - - view the raw file and save this disk from the browser, or - - navigate up one level, then right click the file and save as - - -**Download the example notebooks** `from the Github repo -`_ - - -.. toctree:: - :maxdepth: 1 - :caption: List of notebooks for MICADO - - example_notebooks/1_scopesim_MCAO_4mas_galaxy - example_notebooks/2_scopesim_SCAO_1.5mas_astrometry - example_notebooks/3_scopesim_SCAO_4mas_fv-psf - example_notebooks/MICADO_FAQs - - -Scientific use-case notebooks -+++++++++++++++++++++++++++++ - -.. list-table:: Science case notebooks - :widths: 25 75 - :header-rows: 1 - - * - Name - - Description - * - - - - -Validation ----------- -The following table shows an overview of the test results for limiting magnitudes assuming a minimal signal-to-noise ration of 5. -Green (passed) means a result within the given tolerances, yellow (xfailed) means an *expected* deviation, red (failed) means an *unexpected* issue. - -**Click** on each row for a plot of the test results. - -.. validation-report:: ./MICADO/test_micado/validation_results.xml - -The code used to generate these results can be found in this `GitHub folder `_. - -Documentation and useful references ------------------------------------ - -- `ScopeSim documentation `_ -- `Sky Object Templates documentation `_ -- `MICADO homepage `_ -- For experts: GitHub repositories: - - + `simulator package ScopeSim `_ - + `instrument-specific packages irdb `_. - - -Contact points --------------- - -- kieran.leschinski@univie.ac.at -- oliver.czoske@univie.ac.at diff --git a/MOSAIC/docs/readme.md b/MOSAIC/docs/readme.md new file mode 100644 index 00000000..b07e5283 --- /dev/null +++ b/MOSAIC/docs/readme.md @@ -0,0 +1,86 @@ +```{image} mosaic_scopesim_logo.png +:width: 600px +:alt: MOSAIC + ScopeSim +:align: center +``` + +# MOSAIC + ScopeSim + +## Introduction + +The MOSAIC ETC is built on the generic simulator ScopeSim. MOSAIC is handled +as an instrument package containing configuration files for the various +instrument modes and data files describing the instrument components. + +MOSAIC supports twelve observation modes across visual (VIS) and near-infrared +(NIR) multi-object spectroscopy and NIR integral-field unit (mIFU) operations. + +```{note} +**Bug reports and help desk** + +If you come across a bug or get stuck with ScopeSim or the MOSAIC package, +please [open an issue on GitHub](https://github.com/AstarVienna/irdb/issues) +or contact us by email (see below). + +**Your feedback is the only way we know** what needs to be +changed or improved with the package and the simulator. + +Please always include the output of `scopesim.bug_report()` from your +installation. +``` + +--- + +## Downloading the MOSAIC instrument package + +Once ScopeSim is installed, download the MOSAIC instrument package into your +working directory: + +```python +import scopesim +scopesim.download_packages(["Armazones", "ELT", "MOSAIC"]) +``` + +This installs the packages into the subdirectory `./inst_pkgs/`. + +Your working directory should look like this afterwards: + +``` +my_simulations/ +├── .ipynb +└── inst_pkgs/ + ├── Armazones/ + ├── ELT/ + └── MOSAIC/ + └── docs/ + └── example_notebooks/ + └── .ipynb ← copy to working dir before running +``` + +--- + +```{include} ../../docs/ScopeSim_guide.md +``` + +--- + +## Example notebooks + +Find the notebooks locally in `inst_pkgs/MOSAIC/docs/example_notebooks/` +after downloading the package, or download them from the +[GitHub repository](https://github.com/AstarVienna/irdb/tree/dev_master/MOSAIC/docs/example_notebooks). + +```{warning} +Run notebooks in your working directory, **not** inside `inst_pkgs/`. +Copy the desired notebook out first. +``` + +### Introductory notebooks + +| Notebook | Description | +|---|---| +| [`MOSAIC_demo.ipynb`](example_notebooks/MOSAIC_demo.ipynb) | Introductory overview of how to run MOSAIC simulations in ScopeSim | + +### Instrument homepage + +[MOSAIC at mosaic-elt.eu](https://mosaic-elt.eu/index.php/instrument/) diff --git a/MOSAIC/docs/readme.rst b/MOSAIC/docs/readme.rst deleted file mode 100644 index e92b638f..00000000 --- a/MOSAIC/docs/readme.rst +++ /dev/null @@ -1,133 +0,0 @@ -.. |pic1| image:: mosaic_scopesim_logo.png - :width: 600px - :alt: MOSAIC + ScopeSim - -|pic1| -====== - -Introduction ------------- -The MOSAIC ETC is built on the generic simulator software Scopesim. -MOSAIC itself is handled as an instrument package that contains configuration files for the various instrument modes as well as data files describing the components of the instruments. - - -Prerequisites -------------- - -- A working installation of a recent Python version -- A working installation of Jupyter if you want to run the simulator from notebooks. This is necessary to run the example notebooks contained in the instrument package. -- A working installation of the Python package installer ``pip`` - -.. note:: - - If you come across a bug or get stuck with a certain aspect of ScopeSim or - the MOSAIC package, please get in touch with us (GitHub issue, or email addresses below). - - **Your feedback is the only way we know** what needs to be changed/improved - with the package and the simulator. - - Please always provide the output of the command ``scopesim.bug_report()`` run on your installation. - - -Installation & setup --------------------- - -This is a short overview of the installation and setup procedure; for a more detailed presentation see `Introduction_to_Scopesim_for_MOSAIC `_. - -1. Install ``scopesim`` in your python environment:: - - $ pip install scopesim - - To upgrade an existing installation do:: - - $ pip install -U scopesim - -2. Create a working directory where you want to run simulations, e.g.:: - - $ mkdir ~/path/to/playing_with_scopesim/ - $ cd ~/path/to/playing_with_scopesim - -3. Install relevant irdb packages into this directory:: - - $ python - >> import scopesim - >> scopesim.download_packages(["MOSAIC", "ELT", "Armazones"]) - - This will install the packages in the subdirectory ``./inst_pkgs``. - -4. The MOSAIC package includes a number of tutorial notebooks in the directory ``./inst_pkgs/MOSAIC/docs/example_notebooks/`` (see `Python notebooks`_). - - Copy notebooks to the working directory (i.e. ``./``) to run them.:: - - $ cp ./inst_pkgs/MOSAIC/docs/example_notebooks/ . - -5. In a terminal, execute the notebook by calling:: - - $ jupyter notebook - -6. Follow instructions and explanations in the notebook. Some notebooks use example data; the commands to download these data from the scopesim server are included in the notebooks. - -You can then edit the notebooks and use them as a starting point for your own simulations. - - -Python notebooks ----------------- - -These notebooks can be found either: - -- [locally] in the MOSAIC instrument package in ``docs/example_notebooks``, or -- [download] in the `MOSAIC/docs section of the IRDB Github repository `_ - - -.. warning:: - Notebooks should be run in your working directory, **NOT** directly in the - ``docs/example_notebooks`` folder. Please copy the desired notebook out of - this folder. - -Ideally your folder structure should look like this:: - - working-dir - |- .iypnb - | - |- inst_pkgs - |- MOSAIC - | |- docs - | |- example_notebooks - | |- .iypnb # copy out to working-dir - |- ELT - |- Armazones - - -Introductory notebooks -++++++++++++++++++++++ - -.. list-table:: - :widths: 25 75 - :width: 900px - :header-rows: 1 - - * - Name - - Description - * - | `MOSAIC_demo.ipynb `_ - - Introductory overview of how to run simulations in Scopesim - -Documentation and useful references ------------------------------------ - -- `ScopeSim documentation `_ -- `Sky Object Templates documentation `_ -- `MOSAIC homepage `_ -- For experts: GitHub repositories: - - + `simulator package ScopeSim `_ - + `instrument-specific packages irdb `_. - - -Contact points --------------- -`ScopeSim Slack `_ - -Email: - -- scopesim@univie.ac.at -- kieran.leschinski@univie.ac.at diff --git a/docs/ScopeSim_guide.md b/docs/ScopeSim_guide.md new file mode 100644 index 00000000..4fd4d73a --- /dev/null +++ b/docs/ScopeSim_guide.md @@ -0,0 +1,65 @@ +## Prerequisites + +- A working installation of Python 3.8 or newer +- `pip` (the Python package installer) +- Jupyter, if you want to run the example notebooks (recommended) + +--- + +## Installing ScopeSim + +Install the latest release from PyPI: + +```bash +pip install scopesim +``` + +To upgrade an existing installation: + +```bash +pip install -U scopesim +``` + +--- + +## Setting up a working directory + +Create a dedicated directory where your simulation notebooks will live and +where the instrument packages will be downloaded: + +```bash +mkdir ~/path/to/my_simulations +cd ~/path/to/my_simulations +``` + +--- + +## Running the example notebooks + +The instrument package ships tutorial notebooks inside +`inst_pkgs//docs/example_notebooks/`. +Copy the desired notebook out of that folder before running it — notebooks +should **not** be run in-place, as their output would modify the package files. + +```bash +cp ./inst_pkgs//docs/example_notebooks/ . +jupyter notebook +``` + +--- + +## Documentation and useful references + +- [ScopeSim documentation](https://scopesim.readthedocs.io/en/latest/) +- [ScopeSim Templates documentation](https://scopesim-templates.readthedocs.io/en/latest/) +- GitHub repositories: + - [ScopeSim (simulator engine)](https://github.com/AstarVienna/scopesim) + - [IRDB (instrument packages)](https://github.com/AstarVienna/irdb) + +--- + +## Contact and support + +- [ScopeSim Slack](https://join.slack.com/t/scopesim/shared_invite/zt-143s42izo-LnyqoG7gH5j~aGn51Z~4IA) +- [GitHub Issues](https://github.com/AstarVienna/irdb/issues) +- Email: scopesim@univie.ac.at · kieran.leschinski@univie.ac.at From c03863fdc1fe10b64e551d397e4a5a8961ec2f0a Mon Sep 17 00:00:00 2001 From: Kieran Leschinski Date: Fri, 15 May 2026 22:33:16 +0200 Subject: [PATCH 3/8] Add card gallery to docs landing page (index.md) Replace the plain RST table index with a sphinx_design card grid showing the three documented ELT instruments (MICADO, METIS, MOSAIC), each with its logo, a one-line description, and a direct link to its getting-started guide. Retain a full instrument packages table below the cards. --- index.md | 83 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ index.rst | 43 ---------------------------- 2 files changed, 83 insertions(+), 43 deletions(-) create mode 100644 index.md delete mode 100644 index.rst diff --git a/index.md b/index.md new file mode 100644 index 00000000..654cd1c9 --- /dev/null +++ b/index.md @@ -0,0 +1,83 @@ +--- +html_theme.sidebar_secondary.remove: true +--- + +```{image} docs/source/_static/logos/logo_irdb.PNG +:width: 600px +:alt: Instrument Reference Database +:align: center +``` + +# Instrument Reference Database + +The **Instrument Reference Database (IRDB)** contains the instrument-specific +configuration and data files used by the +[ScopeSim](https://scopesim.readthedocs.io/en/latest/) astronomical instrument +simulator. + +Each instrument package below ships with example notebooks, mode configuration +files, and the component data (filters, PSFs, detector layouts, etc.) needed to +run realistic end-to-end simulations. + +--- + +## Available Instruments + +::::{grid} 1 2 3 3 +:gutter: 3 + +:::{grid-item-card} MICADO +:img-top: MICADO/docs/micado_scopesim_logo.png +:link: MICADO/docs/readme +:link-type: doc + +**Near-infrared camera for the ELT** + +Supports MCAO (4 mas) and SCAO (1.5 mas / 4 mas) imaging modes. +::: + +:::{grid-item-card} METIS +:img-top: METIS/docs/metis_scopesim_logo.png +:link: METIS/docs/readme +:link-type: doc + +**Thermal-infrared imager and spectrograph for the ELT** + +Supports imaging and long-slit spectroscopy. LMS IFU mode in development. +::: + +:::{grid-item-card} MOSAIC +:img-top: MOSAIC/docs/mosaic_scopesim_logo.png +:link: MOSAIC/docs/readme +:link-type: doc + +**Multi-object spectrograph for the ELT** + +12 observation modes across VIS/NIR MOS and NIR mIFU. +::: + +:::: + +--- + +## All Instrument Packages + +| Location | Telescope | Instrument | Documented | +|---|---|---|:---:| +| Cerro Armazones | ELT | [MICADO](MICADO/docs/readme) | ✓ | +| Cerro Armazones | ELT | [METIS](METIS/docs/readme) | ✓ | +| Cerro Armazones | ELT | [MOSAIC](MOSAIC/docs/readme) | ✓ | +| Paranal | VLT | HAWKI | | +| — | — | LFOA | | + +--- + +```{toctree} +:hidden: +:maxdepth: 2 +:caption: Instruments + +METIS + ScopeSim +MICADO + ScopeSim +MOSAIC + ScopeSim +``` diff --git a/index.rst b/index.rst deleted file mode 100644 index 0fcf2e17..00000000 --- a/index.rst +++ /dev/null @@ -1,43 +0,0 @@ -.. ReadTheDocs index file. Originally from docs/source/index.rst - Moved here so that all package docs are accessible to Sphinx and RTD - -.. image:: docs/source/_static/logos/logo_irdb.PNG - :width: 600 px - :alt: Welcome to the ScopeSim Documentation! - :align: center - - -The Instrument Reference Database (IRDB) contains the instrument specific -information used by the ScopeSim astronomical instrument data simulator. - -Instrument-Specific "Getting Started" Guides --------------------------------------------- - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - METIS + ScopeSim - MICADO + ScopeSim - MOSAIC + ScopeSim - - -Instrument Packages in the IRDB -------------------------------- - -+-----------+------------+------------+ -| Locations | Telescopes |Instruments | -+===========+============+============+ -| Armazones | ELT | MICADO | -| | +------------+ -| | | METIS | -| | +------------+ -| | | MOSAIC | -+-----------+------------+------------+ -| Paranal | VLT | HAWKI | -+-----------+------------+------------+ -| | | LFOA | -+-----------+------------+------------+ - - - From f166d08b489263088427d8b0c28d6fc2993c6df7 Mon Sep 17 00:00:00 2001 From: teutoburg Date: Sat, 16 May 2026 13:56:32 +0200 Subject: [PATCH 4/8] Cleanup vibe-coded docs --- METIS/docs/readme.md | 12 +++--------- MICADO/docs/readme.md | 8 +------- MOSAIC/docs/readme.md | 6 ------ docs/ScopeSim_guide.md | 10 ---------- index.md | 18 +++++++----------- 5 files changed, 11 insertions(+), 43 deletions(-) diff --git a/METIS/docs/readme.md b/METIS/docs/readme.md index 413acdd8..53b9b092 100644 --- a/METIS/docs/readme.md +++ b/METIS/docs/readme.md @@ -30,8 +30,6 @@ Please always include the output of `scopesim.bug_report()` from your installation. ``` ---- - ## Downloading the METIS instrument package Once ScopeSim is installed, download the METIS instrument package into your @@ -58,13 +56,9 @@ my_simulations/ └── .ipynb ← copy to working dir before running ``` ---- - ```{include} ../../docs/ScopeSim_guide.md ``` ---- - ## Example notebooks Find the notebooks locally in `inst_pkgs/METIS/docs/example_notebooks/` @@ -79,13 +73,13 @@ Copy the desired notebook out first. ### Introductory notebooks | Notebook | Description | -|---|---| +|----------|-------------| | [`Introduction_to_Scopesim_for_METIS.ipynb`](example_notebooks/Introduction_to_Scopesim_for_METIS.ipynb) | Introductory overview of how to run simulations in ScopeSim. Also available as [PDF](example_notebooks/Introduction_to_Scopesim_for_METIS.pdf). | ### Scientific use-case notebooks | Notebook | Description | -|---|---| +|----------|-------------| | [`IMG_L_N-examples.ipynb`](example_notebooks/IMG_L_N-examples.ipynb) | Imaging of HL Tau and an AGN model in the L and N bands | | [`LSS-YSO_model_simulation.ipynb`](example_notebooks/LSS-YSO_model_simulation.ipynb) | Long-slit spectroscopy in the L-band of a young stellar object model | | [`LSS_AGN-01_preparation.ipynb`](example_notebooks/LSS_AGN-01_preparation.ipynb) + [`LSS_AGN-02_simulation.ipynb`](example_notebooks/LSS_AGN-02_simulation.ipynb) | Long-slit spectroscopy in the N-band of an AGN model. Part 1: input data preparation. Part 2: simulation. | @@ -95,7 +89,7 @@ Copy the desired notebook out first. These notebooks are in `docs/example_notebooks/demos/`. | Notebook | Description | -|---|---| +|----------|-------------| | [`demo_adc_wheel.ipynb`](example_notebooks/demos/demo_adc_wheel.ipynb) | Using the atmospheric dispersion correctors | | [`demo_auto_exposure.ipynb`](example_notebooks/demos/demo_auto_exposure.ipynb) | Selecting `dit`/`ndit` automatically | | [`demo_chopping_and_nodding.ipynb`](example_notebooks/demos/demo_chopping_and_nodding.ipynb) | Chop-nod difference images in the N band | diff --git a/MICADO/docs/readme.md b/MICADO/docs/readme.md index f2e516cd..62a5a02e 100644 --- a/MICADO/docs/readme.md +++ b/MICADO/docs/readme.md @@ -27,8 +27,6 @@ Please always include the output of `scopesim.bug_report()` from your installation. ``` ---- - ## Downloading the MICADO instrument package Once ScopeSim is installed, download the MICADO instrument package into your @@ -55,13 +53,9 @@ my_simulations/ └── .ipynb ← copy to working dir before running ``` ---- - ```{include} ../../docs/ScopeSim_guide.md ``` ---- - ## Example notebooks Download the notebooks from the @@ -86,7 +80,7 @@ example_notebooks/MICADO_FAQs ``` | Notebook | Description | -|---|---| +|----------|-------------| | `1_scopesim_MCAO_4mas_galaxy` | MCAO 4 mas imaging of a galaxy | | `2_scopesim_SCAO_1.5mas_astrometry` | SCAO 1.5 mas astrometry use case | | `3_scopesim_SCAO_4mas_fv-psf` | SCAO 4 mas field-varying PSF | diff --git a/MOSAIC/docs/readme.md b/MOSAIC/docs/readme.md index b07e5283..d3773701 100644 --- a/MOSAIC/docs/readme.md +++ b/MOSAIC/docs/readme.md @@ -29,8 +29,6 @@ Please always include the output of `scopesim.bug_report()` from your installation. ``` ---- - ## Downloading the MOSAIC instrument package Once ScopeSim is installed, download the MOSAIC instrument package into your @@ -57,13 +55,9 @@ my_simulations/ └── .ipynb ← copy to working dir before running ``` ---- - ```{include} ../../docs/ScopeSim_guide.md ``` ---- - ## Example notebooks Find the notebooks locally in `inst_pkgs/MOSAIC/docs/example_notebooks/` diff --git a/docs/ScopeSim_guide.md b/docs/ScopeSim_guide.md index 4fd4d73a..9eb81bc7 100644 --- a/docs/ScopeSim_guide.md +++ b/docs/ScopeSim_guide.md @@ -4,8 +4,6 @@ - `pip` (the Python package installer) - Jupyter, if you want to run the example notebooks (recommended) ---- - ## Installing ScopeSim Install the latest release from PyPI: @@ -20,8 +18,6 @@ To upgrade an existing installation: pip install -U scopesim ``` ---- - ## Setting up a working directory Create a dedicated directory where your simulation notebooks will live and @@ -32,8 +28,6 @@ mkdir ~/path/to/my_simulations cd ~/path/to/my_simulations ``` ---- - ## Running the example notebooks The instrument package ships tutorial notebooks inside @@ -46,8 +40,6 @@ cp ./inst_pkgs//docs/example_notebooks/ . jupyter notebook ``` ---- - ## Documentation and useful references - [ScopeSim documentation](https://scopesim.readthedocs.io/en/latest/) @@ -56,8 +48,6 @@ jupyter notebook - [ScopeSim (simulator engine)](https://github.com/AstarVienna/scopesim) - [IRDB (instrument packages)](https://github.com/AstarVienna/irdb) ---- - ## Contact and support - [ScopeSim Slack](https://join.slack.com/t/scopesim/shared_invite/zt-143s42izo-LnyqoG7gH5j~aGn51Z~4IA) diff --git a/index.md b/index.md index 654cd1c9..c0207ccc 100644 --- a/index.md +++ b/index.md @@ -19,8 +19,6 @@ Each instrument package below ships with example notebooks, mode configuration files, and the component data (filters, PSFs, detector layouts, etc.) needed to run realistic end-to-end simulations. ---- - ## Available Instruments ::::{grid} 1 2 3 3 @@ -58,17 +56,15 @@ Supports imaging and long-slit spectroscopy. LMS IFU mode in development. :::: ---- - ## All Instrument Packages -| Location | Telescope | Instrument | Documented | -|---|---|---|:---:| -| Cerro Armazones | ELT | [MICADO](MICADO/docs/readme) | ✓ | -| Cerro Armazones | ELT | [METIS](METIS/docs/readme) | ✓ | -| Cerro Armazones | ELT | [MOSAIC](MOSAIC/docs/readme) | ✓ | -| Paranal | VLT | HAWKI | | -| — | — | LFOA | | +| Location | Telescope | Instrument | Documented | +|-----------------|-----------|------------|:----------:| +| Cerro Armazones | ELT | [MICADO](MICADO/docs/readme) | ✓ | +| Cerro Armazones | ELT | [METIS](METIS/docs/readme) | ✓ | +| Cerro Armazones | ELT | [MOSAIC](MOSAIC/docs/readme) | ✓ | +| Paranal | VLT | HAWKI | | +| LFOA | - | - | | --- From 3b7ea9723822d13e5878e73dcd33ff0088621314 Mon Sep 17 00:00:00 2001 From: teutoburg Date: Sat, 16 May 2026 14:04:38 +0200 Subject: [PATCH 5/8] Harmonize on upper-case spelling and more cleanup --- METIS/docs/{readme.md => README.md} | 0 MICADO/docs/{readme.md => README.md} | 0 MOSAIC/docs/{readme.md => README.md} | 0 index.md | 28 +++++++++++++--------------- 4 files changed, 13 insertions(+), 15 deletions(-) rename METIS/docs/{readme.md => README.md} (100%) rename MICADO/docs/{readme.md => README.md} (100%) rename MOSAIC/docs/{readme.md => README.md} (100%) diff --git a/METIS/docs/readme.md b/METIS/docs/README.md similarity index 100% rename from METIS/docs/readme.md rename to METIS/docs/README.md diff --git a/MICADO/docs/readme.md b/MICADO/docs/README.md similarity index 100% rename from MICADO/docs/readme.md rename to MICADO/docs/README.md diff --git a/MOSAIC/docs/readme.md b/MOSAIC/docs/README.md similarity index 100% rename from MOSAIC/docs/readme.md rename to MOSAIC/docs/README.md diff --git a/index.md b/index.md index c0207ccc..47a71da8 100644 --- a/index.md +++ b/index.md @@ -26,7 +26,7 @@ run realistic end-to-end simulations. :::{grid-item-card} MICADO :img-top: MICADO/docs/micado_scopesim_logo.png -:link: MICADO/docs/readme +:link: MICADO/docs/README :link-type: doc **Near-infrared camera for the ELT** @@ -36,7 +36,7 @@ Supports MCAO (4 mas) and SCAO (1.5 mas / 4 mas) imaging modes. :::{grid-item-card} METIS :img-top: METIS/docs/metis_scopesim_logo.png -:link: METIS/docs/readme +:link: METIS/docs/README :link-type: doc **Thermal-infrared imager and spectrograph for the ELT** @@ -46,7 +46,7 @@ Supports imaging and long-slit spectroscopy. LMS IFU mode in development. :::{grid-item-card} MOSAIC :img-top: MOSAIC/docs/mosaic_scopesim_logo.png -:link: MOSAIC/docs/readme +:link: MOSAIC/docs/README :link-type: doc **Multi-object spectrograph for the ELT** @@ -58,22 +58,20 @@ Supports imaging and long-slit spectroscopy. LMS IFU mode in development. ## All Instrument Packages -| Location | Telescope | Instrument | Documented | -|-----------------|-----------|------------|:----------:| -| Cerro Armazones | ELT | [MICADO](MICADO/docs/readme) | ✓ | -| Cerro Armazones | ELT | [METIS](METIS/docs/readme) | ✓ | -| Cerro Armazones | ELT | [MOSAIC](MOSAIC/docs/readme) | ✓ | -| Paranal | VLT | HAWKI | | -| LFOA | - | - | | - ---- +| Location | Telescope | Instrument | Documented | +|-----------|-----------|------------------------------|:----------:| +| Armazones | ELT | [MICADO](MICADO/docs/README) | ✓ | +| Armazones | ELT | [METIS](METIS/docs/README) | ✓ | +| Armazones | ELT | [MOSAIC](MOSAIC/docs/README) | ✓ | +| Paranal | VLT | HAWKI | | +| LFOA | - | - | | ```{toctree} :hidden: :maxdepth: 2 :caption: Instruments -METIS + ScopeSim -MICADO + ScopeSim -MOSAIC + ScopeSim +METIS + ScopeSim +MICADO + ScopeSim +MOSAIC + ScopeSim ``` From 485b358696252ebf15eba2c48b9b5a8cd948b424 Mon Sep 17 00:00:00 2001 From: teutoburg Date: Sat, 16 May 2026 14:06:01 +0200 Subject: [PATCH 6/8] Disable broken markdownlinkchecker for now... --- .github/workflows/markdown_link_check.yml | 24 +++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/markdown_link_check.yml b/.github/workflows/markdown_link_check.yml index 2b8f1c42..3c1b6b25 100644 --- a/.github/workflows/markdown_link_check.yml +++ b/.github/workflows/markdown_link_check.yml @@ -1,23 +1,23 @@ name: Check Markdown links on: - push: - branches: - - main - - master - - dev_master - pull_request: - branches: - - main - - master - - dev_master + # push: + # branches: + # - main + # - master + # - dev_master + # pull_request: + # branches: + # - main + # - master + # - dev_master # Allows you to run this workflow manually from the Actions tab. workflow_dispatch: # Run every day at 5:00 UTC - schedule: - - cron: "0 5 * * *" + # schedule: + # - cron: "0 5 * * *" jobs: markdown-link-check: From 132389f29da9369294638d50cefe31d8130983c9 Mon Sep 17 00:00:00 2001 From: teutoburg Date: Sat, 16 May 2026 14:09:31 +0200 Subject: [PATCH 7/8] Even more cleanup --- MICADO/docs/README.md | 2 -- MOSAIC/docs/README.md | 2 +- index.md | 2 +- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/MICADO/docs/README.md b/MICADO/docs/README.md index 62a5a02e..3a5df1f6 100644 --- a/MICADO/docs/README.md +++ b/MICADO/docs/README.md @@ -86,8 +86,6 @@ example_notebooks/MICADO_FAQs | `3_scopesim_SCAO_4mas_fv-psf` | SCAO 4 mas field-varying PSF | | `MICADO_FAQs` | Frequently asked questions | ---- - ## Validation The table below shows limiting-magnitude test results (minimum S/N = 5). diff --git a/MOSAIC/docs/README.md b/MOSAIC/docs/README.md index d3773701..201b5474 100644 --- a/MOSAIC/docs/README.md +++ b/MOSAIC/docs/README.md @@ -72,7 +72,7 @@ Copy the desired notebook out first. ### Introductory notebooks | Notebook | Description | -|---|---| +|----------|-------------| | [`MOSAIC_demo.ipynb`](example_notebooks/MOSAIC_demo.ipynb) | Introductory overview of how to run MOSAIC simulations in ScopeSim | ### Instrument homepage diff --git a/index.md b/index.md index 47a71da8..92761aa9 100644 --- a/index.md +++ b/index.md @@ -59,7 +59,7 @@ Supports imaging and long-slit spectroscopy. LMS IFU mode in development. ## All Instrument Packages | Location | Telescope | Instrument | Documented | -|-----------|-----------|------------------------------|:----------:| +|-----------|-----------|------------------------------|------------| | Armazones | ELT | [MICADO](MICADO/docs/README) | ✓ | | Armazones | ELT | [METIS](METIS/docs/README) | ✓ | | Armazones | ELT | [MOSAIC](MOSAIC/docs/README) | ✓ | From c5fd6700552b68036b2e70ec68585511a0db31c8 Mon Sep 17 00:00:00 2001 From: teutoburg Date: Sat, 16 May 2026 22:15:48 +0200 Subject: [PATCH 8/8] METIS notebooks as TOC trees --- METIS/docs/README.md | 41 ++++++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 19 deletions(-) diff --git a/METIS/docs/README.md b/METIS/docs/README.md index 53b9b092..b248958a 100644 --- a/METIS/docs/README.md +++ b/METIS/docs/README.md @@ -72,33 +72,36 @@ Copy the desired notebook out first. ### Introductory notebooks -| Notebook | Description | -|----------|-------------| -| [`Introduction_to_Scopesim_for_METIS.ipynb`](example_notebooks/Introduction_to_Scopesim_for_METIS.ipynb) | Introductory overview of how to run simulations in ScopeSim. Also available as [PDF](example_notebooks/Introduction_to_Scopesim_for_METIS.pdf). | +```{toctree} +:maxdepth: 1 + +example_notebooks/Introduction_to_Scopesim_for_METIS +example_notebooks/METIS_IFU-01-Source_cube +example_notebooks/METIS_IFU-02-Simulation +example_notebooks/METIS_WCU +``` ### Scientific use-case notebooks -| Notebook | Description | -|----------|-------------| -| [`IMG_L_N-examples.ipynb`](example_notebooks/IMG_L_N-examples.ipynb) | Imaging of HL Tau and an AGN model in the L and N bands | -| [`LSS-YSO_model_simulation.ipynb`](example_notebooks/LSS-YSO_model_simulation.ipynb) | Long-slit spectroscopy in the L-band of a young stellar object model | -| [`LSS_AGN-01_preparation.ipynb`](example_notebooks/LSS_AGN-01_preparation.ipynb) + [`LSS_AGN-02_simulation.ipynb`](example_notebooks/LSS_AGN-02_simulation.ipynb) | Long-slit spectroscopy in the N-band of an AGN model. Part 1: input data preparation. Part 2: simulation. | +```{toctree} +:maxdepth: 1 + +example_notebooks/IMG_L_N-examples +example_notebooks/LSS-YSO_model_simulation +example_notebooks/LSS_AGN-01_preparation +example_notebooks/LSS_AGN-02_simulation +``` ### Effect demonstration notebooks These notebooks are in `docs/example_notebooks/demos/`. -| Notebook | Description | -|----------|-------------| -| [`demo_adc_wheel.ipynb`](example_notebooks/demos/demo_adc_wheel.ipynb) | Using the atmospheric dispersion correctors | -| [`demo_auto_exposure.ipynb`](example_notebooks/demos/demo_auto_exposure.ipynb) | Selecting `dit`/`ndit` automatically | -| [`demo_chopping_and_nodding.ipynb`](example_notebooks/demos/demo_chopping_and_nodding.ipynb) | Chop-nod difference images in the N band | -| [`demo_detector_modes.ipynb`](example_notebooks/demos/demo_detector_modes.ipynb) | Setting detector readout modes | -| [`demo_filter_wheel.ipynb`](example_notebooks/demos/demo_filter_wheel.ipynb) | Using the filter wheel(s) | -| [`demo_lss_simple.ipynb`](example_notebooks/demos/demo_lss_simple.ipynb) | Basic long-slit spectroscopy procedure | -| [`demo_grating_efficiency.ipynb`](example_notebooks/demos/demo_grating_efficiency.ipynb) | Spectral (grating) efficiency | -| [`demo_slit_wheel.ipynb`](example_notebooks/demos/demo_slit_wheel.ipynb) | Using the slit wheel for spectroscopy and imaging | -| [`demo_rectify_traces.ipynb`](example_notebooks/demos/demo_rectify_traces.ipynb) | Wavelength-calibrated and rectified 2D spectra | +```{toctree} +:maxdepth: 1 +:glob: + +example_notebooks/demos/* +``` ### Instrument homepage