gammasimtools 0.17.0__tar.gz → 0.18.0__tar.gz

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/.github/workflows/CI-docs.yml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches: [main]
     types: [opened, closed, synchronize]
+  release:
+    types: [published]
 
 jobs:
 

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/.github/workflows/CI-linter.yml

@@ -34,13 +34,19 @@ jobs:
         with:
           python-version: "3.12"
 
-
       - name: Check for non-ASCII characters
         run: |
-          output=$(find . -type f \
-          \( -name "*.py" -o -name "*.rst" -o -name "*.yml" -o -name "*.toml" \) \
-          -exec perl -ne 'print if /[^[:ascii:]]/ && !/latin/i' {} \;)
-          if [ -n "$output" ]; then
+          found=0
+          while IFS= read -r file; do
+            matches=$(perl -ne 'print if /[^[:ascii:]]/ && !/latin/i' "$file")
+            if [ -n "$matches" ]; then
+              echo "File: $file"
+              echo "$matches"
+              found=1
+            fi
+          done < <(find . -type f \( -name "*.py" -o -name "*.rst" -o -name "*.yml" -o -name "*.toml" \))
+
+          if [ "$found" -eq 1 ]; then
             echo "Non-ASCII characters found in documentation."
             exit 1
           fi

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 repos:
 # Ruff
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.12
+  rev: v0.12.1
   hooks:
   - id: ruff
     args: ["--fix"]
@@ -29,6 +29,7 @@ repos:
   - id: end-of-file-fixer
   - id: check-added-large-files
     args: ['--maxkb=500']
+  - id: check-json
 # https://github.com/HunterMcGushion/docstr_coverage
 - repo: https://github.com/HunterMcGushion/docstr_coverage
   rev: v2.3.2  # most recent docstr-coverage release or commit sha

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/CHANGELOG.md

@@ -7,6 +7,35 @@ This changelog is generated using [Towncrier](https://towncrier.readthedocs.io/)
 
 <!-- towncrier release notes start -->
 
+## [v0.18.0](https://github.com/gammasim/simtools/tree/v0.18.0) - 2025-07-08
+
+### Bugfixes
+
+- Run documentation generation CI on release to obtain current version of docs. ([#1607](https://github.com/gammasim/simtools/pull/1607))
+- Fix authentication errors in script to setup a local mongoDB. ([#1610](https://github.com/gammasim/simtools/pull/1610))
+
+### Documentation
+
+- Reorganisation and improvement of the documentation in the GitHub pages. ([#1611](https://github.com/gammasim/simtools/pull/1611))
+
+### New Features
+
+- Use CTAO telescope names when writing out telescope list in reduced event data tables. ([#1616](https://github.com/gammasim/simtools/pull/1616))
+- Allow CORSIKA limits to use layouts defined in simulation models database. ([#1619](https://github.com/gammasim/simtools/pull/1619))
+- Add application / API to plot tabulated model parameters using default plotting configurations defined in model parameters schemas. ([#1628](https://github.com/gammasim/simtools/pull/1628))
+- Allow to use current prod6 simulations for reduced event data generation. ([#1631](https://github.com/gammasim/simtools/pull/1631))
+- Add common array elements ID. Add list with triggered common telescope IDs to reduced event data tables. ([#1637](https://github.com/gammasim/simtools/pull/1637))
+
+### Maintenance
+
+- Removed unused ‘critical’ log level. ([#1604](https://github.com/gammasim/simtools/pull/1604))
+- Add JSON checker to pre-commit linter. ([#1615](https://github.com/gammasim/simtools/pull/1615))
+- Update test files with proton simulations (simtel output) and add provenance information. ([#1617](https://github.com/gammasim/simtools/pull/1617))
+- Improve linter CI to print file containing non-ascii characters. ([#1620](https://github.com/gammasim/simtools/pull/1620))
+- Replace file lists `tests/resources/simtel_output_files.txt` used for testing by explicitly listing of files. ([#1629](https://github.com/gammasim/simtools/pull/1629))
+- Add default plotting configuration for tabular data. Introduce consistent lower-cases for keys in plotting configuration schema. ([#1635](https://github.com/gammasim/simtools/pull/1635))
+
+
 ## [0.17.0](https://github.com/gammasim/simtools/tree/0.17.0) - 2025-06-10
 
 ### Bugfixes

{gammasimtools-0.17.0/src/gammasimtools.egg-info → gammasimtools-0.18.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gammasimtools
-Version: 0.17.0
+Version: 0.18.0
 Summary: Tools for the Simulation System of the CTA Observatory
 Author-email: simtools developers <simtools-developer@desy.de>
 License-Expression: BSD-3-Clause
@@ -42,6 +42,7 @@ Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: numpydoc; extra == "doc"
 Requires-Dist: pydata-sphinx-theme; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
 Requires-Dist: towncrier; extra == "doc"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/database_scripts/setup_local_db.sh

@@ -17,14 +17,14 @@ else
     exit 1
 fi
 
-echo "Create network $SIMTOOLS_NETWORK"
+echo "Creating network $SIMTOOLS_NETWORK"
 $CMD network create $SIMTOOLS_NETWORK
 
-echo "Data directory ./mongo-data"
+echo "Creating data directory ./mongo-data"
 mkdir -p "$(pwd)"/mongo-data
 chmod 755 "$(pwd)"/mongo-data
 
-# Start mongoDB
+echo "Starting MongoDB container..."
 $CMD run -d \
   --name $CONTAINER_NAME \
   --network $SIMTOOLS_NETWORK \
@@ -33,31 +33,25 @@ $CMD run -d \
   -e MONGO_INITDB_ROOT_PASSWORD=example \
   -p 27017:27017 \
   -v "$(pwd)"/mongo-data:/data/db \
-  mongo:latest
+  mongo:8.0.10
 
-echo "Waiting for MongoDB to start..."
-sleep 5
-# Loop until MongoDB is ready
+echo "Waiting for MongoDB to be fully ready and root user to be available..."
 RETRIES=30
-until $CMD exec $CONTAINER_NAME mongosh --eval "db.runCommand({ ping: 1 })" >/dev/null 2>&1 || [ $RETRIES -eq 0 ]; do
-  echo "Waiting for MongoDB to be ready... ($((RETRIES--)) retries left)"
+until $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "db.runCommand({ connectionStatus: 1 })" >/dev/null 2>&1 || [ $RETRIES -eq 0 ]; do
+  echo "Waiting for MongoDB to be ready and root authable... ($((RETRIES--)) retries left)"
   sleep 2
 done
 if [ $RETRIES -eq 0 ]; then
   echo "MongoDB did not start in time."
-  exit 1
-fi
-
-# Verify root authentication
-echo "Verifying root authentication..."
-if ! $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "db.runCommand({ connectionStatus: 1 })"; then
-  echo "Error: Root authentication failed."
   $CMD logs $CONTAINER_NAME
   exit 1
 fi
+echo "MongoDB is ready and root authentication is working."
 
-echo "Create admin user"
-$CMD exec -it $CONTAINER_NAME mongosh admin -u root -p example --eval "
+echo "Creating 'api' user..."
+# This command *requires* the root user to be able to authenticate and have userAdminAnyDatabase role.
+# If this fails, the root setup was indeed the problem.
+if ! $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "
 db.createUser({
   user: 'api',
   pwd: 'password',
@@ -67,4 +61,9 @@ db.createUser({
     { role: 'userAdminAnyDatabase', db: 'admin' },
   ]
 });
-"
+"; then
+  echo "Error: Failed to create 'api' user. Check root credentials or MongoDB logs."
+  $CMD logs $CONTAINER_NAME
+  exit 1
+fi
+echo "'api' user created successfully."

gammasimtools-0.18.0/docs/source/changelog.md

@@ -0,0 +1 @@
+```{include} ../../CHANGELOG.md

gammasimtools-0.18.0/docs/source/components/corsika.md

@@ -0,0 +1,8 @@
+# Air shower simulations with CORSIKA
+
+- [CORSIKA 7](https://www.iap.kit.edu/corsika/): Simulates extensive air showers.
+- [corsika-opt-patches](https://gitlab.cta-observatory.org/cta-computing/dpps/simpipe/corsika-opt-patches): Vectorized performance-optimized patches for Cherenkov light generation in propagation in CORSIKA.
+
+```{warning}
+Incomplete documentation - missing references
+```

{gammasimtools-0.17.0/docs/source/user-guide → gammasimtools-0.18.0/docs/source/components}/databases.md

@@ -1,20 +1,14 @@
 # Databases
 
-The simtools package uses a prototype MongoDB database to store the simulation model parameters.
-Access to the DB is handled via a dedicated API module ([db_handler](#dbhandler)).
+Simulation model parameters and production configurations are stored in databases (see the [Simulation Model](model_parameters.md#simulation-model) section) and synced with the [CTAO model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models).
+The simtools package uses a MongoDB database to store production tables and simulation model parameters.
 
-Simulation model parameters are stored in databases (see the [Simulation Model](model_parameters.md#simulation-model) section) and synced with the [CTAO model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models).
-
-## Database structure
-
-Several different databases are used in simtools.
-
-:::{Important}
-The structure of the database is currently under revisions and will change in near future.
-This documentation is therefore incomplete.
-:::
+```{important}
+No direct write access to the simulation model database is allowed.
+Updates to the simulation models should be done via merge requests to the [CTAO model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models).
+```
 
-### Model parameters DB
+## Simulation Models Database
 
 The name of the model parameter database needs to be indicated by `$SIMTOOLS_DB_SIMULATION_MODEL` environmental variable and defined e.g., in the `.env` file. Use `CTAO-Simulation-ModelParameters-LATEST` to use the latest version of the CTAO simulation model database (simtools will replace `LATEST` with the latest version number).
 
@@ -28,21 +22,26 @@ Collections:
 * `metadata` containing tables describing the model versions
 * `fs.files` with all file type entries for the model parameters (e.g., the quantum-efficiency tables)
 
-### Other databases
+### Update the Simulation Models Database
+
+Model parameters should first be reviewed and accepted in the [model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models) before they are uploaded to the database.
+To update the database, release a new version of the simulation models repository and the CI will automatically update the database with the new model parameters.
+
+## Other Databases
 
 All other currently available databases are not in use and kept for historical reasons.
 
-## Using the remote database located at DESY
+## Using the Simulation Models Database located at DESY
 
-A prototype remote database is located at DESY. Access to the database is restricted, please contact the developers in order to obtain access.
+A simulation models database is located at DESY. Access to the database is restricted, please contact the developers in order to obtain access.
 
 Database and access configuration is given in the `.env` file, see the [.env_template](../../.env_template) file as example:
 
 ```console
-SIMTOOLS_DB_API_PORT=27017 #Port on the MongoDB server
-SIMTOOLS_DB_SERVER='cta-simpipe-protodb.zeuthen.desy.de' # MongoDB server
-SIMTOOLS_DB_API_USER=YOUR_USERNAME # username for MongoDB: ask the responsible person
-SIMTOOLS_DB_API_PW=YOUR_PASSWORD # Password for MongoDB: ask the responsible person
+SIMTOOLS_DB_API_PORT=27017 # Port on the database server
+SIMTOOLS_DB_SERVER='cta-simpipe-protodb.zeuthen.desy.de' # MongodatabaseDB server
+SIMTOOLS_DB_API_USER=YOUR_USERNAME # username for database: ask the responsible person
+SIMTOOLS_DB_API_PW=YOUR_PASSWORD # Password for database: ask the responsible person
 SIMTOOLS_DB_API_AUTHENTICATION_DATABASE='admin'
 SIMTOOLS_DB_SIMULATION_MODEL='CTAO-Simulation-ModelParameters-LATEST'
 SIMTOOLS_SIMTEL_PATH='/workdir/sim_telarray'
@@ -52,26 +51,10 @@ SIMTOOLS_SIMTEL_PATH='/workdir/sim_telarray'
 
 The mongoDB database can be accessed via the command-line interface `mongo` or via a GUI tool like `Robo 3T` or `Studio 3T`.
 
-## Update the database
-
-Model parameters should first be reviewed and accepted in the [model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models) before they are uploaded to the database (see the following sections on how to set up a local copy of the model parameter database for testing and development).
-
-:::{Danger}
-Updating the database is for experts only.
-Note that updating the databases might have impact on workflows of others.
-Best to define a new database when adding new values or files.
-:::
-
-The following applications are important:
-
-* update or define a single model parameter from a json file (as defined in the model parameter repository): [db_add_value_from_json_to_db.py](db_add_value_from_json_to_db)
-* upload a model parameter file: [db_add_file_to_db.py](db_add_file_to_db)
-* upload all model parameters and files from the model parameter repository: [db_add_simulation_model_from_repository_to_db.py](db_add_simulation_model_from_repository_to_db)
-
-## Configure and use a local copy of the model parameter database
+## Setup a local copy of the model parameter database
 
 The production version of model-parameter database is a mongoDB instance running on a server at DESY.
-For testing and development, it might be useful to work with a local copy of the database.
+For testing and development, it is recommend to work with a local copy of the database.
 The following scripts allow to setup and fill a local database running in a container.
 
 All scripts to setup and fill a local database instance are located in the [database_scripts](../../database_scripts/) directory.
@@ -87,44 +70,34 @@ The script [setup_local_db.sh](../../database_scripts/setup_local_db.sh) generat
 
 ### Fill the local database instance
 
-#### Option 1: Fill local database from remote DB dump
-
-Access to a database dump of the production database is required. It is assumed that the dumps
-are located in the directory `database_scripts/dumps`.
-
-The script `./dump_remote_db.sh` can be used to create a dump of the production database (requires access to this DB and the `mongodump` tool).
-
-Use then the `upload_dump_to_local_db.sh` to upload this dump to the local database instance.
-
-Note that database names are hardcoded in the scripts and need to be adjusted accordingly.
-
-#### Option 2: Fill local database from model parameter repository
+#### Option 1 (preferred): Fill local database from model parameter repository
 
 The script `upload_from_model_repository_to_db.sh` uses the [model repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models) from the CTAO gitlab and
 uploads its contents to the local database instance.
 
 Note that repository branches are hardcoded in the scripts and need to be adjusted accordingly.
 
-**If you get timeout errors, try to run it run from within the simtools container**
+#### Option 2: Fill local database from remote DB dump
 
-### Purge the local database instance and all networks, images, containers
+Access to a database dump of the production database is required. It is assumed that the dumps
+are located in the directory `database_scripts/dumps`.
 
-The script `purge_local_db.sh` stops and removes the container and deletes all networks, images, and containers.
+The script `./dump_remote_db.sh` can be used to create a dump of the production database (requires access to this DB and the `mongodump` tool).
 
-:::{Danger}
-Attention: this script removes all local docker containers, images, and networks without awaiting confirmation.
-:::
+Use then the `upload_dump_to_local_db.sh` to upload this dump to the local database instance.
+
+Note that database names are hardcoded in the scripts and need to be adjusted accordingly.
 
-### Use the local database instance (with and without docker)
+### Use the local database instance
 
 This requires the following changes to the settings of the environmental variables in `.evn`:
 
 ```console
 # Environmental variables
-SIMTOOLS_DB_API_PORT=27017 #Port on the MongoDB server
+SIMTOOLS_DB_API_PORT=27017 # Port on the database server
 SIMTOOLS_DB_SERVER='localhost'
-SIMTOOLS_DB_API_USER='api' # username for MongoDB
-SIMTOOLS_DB_API_PW='password' # Password for MongoDB
+SIMTOOLS_DB_API_USER='api' # username for database
+SIMTOOLS_DB_API_PW='password' # Password for database
 SIMTOOLS_DB_API_AUTHENTICATION_DATABASE='admin'
 SIMTOOLS_DB_SIMULATION_MODEL='STAGING-CTA-Simulation-Model-LATEST'
 ```
@@ -144,11 +117,19 @@ For completeness, here the full `.env` file to be used with a container:
 
 ```console
 # Environmental variables
-SIMTOOLS_DB_API_PORT=27017 #Port on the MongoDB server
+SIMTOOLS_DB_API_PORT=27017 # Port on the database server
 SIMTOOLS_DB_SERVER='simtools-mongodb'
-SIMTOOLS_DB_API_USER='api' # username for MongoDB
-SIMTOOLS_DB_API_PW='password' # Password for MongoDB
+SIMTOOLS_DB_API_USER='api' # username for database
+SIMTOOLS_DB_API_PW='password' # Password for database
 SIMTOOLS_DB_API_AUTHENTICATION_DATABASE='admin'
 SIMTOOLS_DB_SIMULATION_MODEL='CTAO-Simulation-ModelParameters-LATEST'
 SIMTOOLS_SIMTEL_PATH='/workdir/sim_telarray'
 ```
+
+### Purge the local database instance
+
+The script `purge_local_db.sh` stops and removes the container and deletes all networks, images, and containers.
+
+:::{Danger}
+Attention: this script removes all local docker containers, images, and networks without awaiting confirmation.
+:::

gammasimtools-0.18.0/docs/source/components/index.md

@@ -0,0 +1,51 @@
+# Components
+
+simtools provides tools to configure, run, and analyze simulations and to manage simulation model parameters. It integrates the components listed below into a modular simulation framework.
+
+The main components are:
+
+- simulation software like CORSIKA and sim_telarray
+- simulation models and parameters, associated databases, setting and validation procedures
+- reading and writing simulation data
+
+## Simulation Software
+
+```{warning}
+Incomplete Documentation.
+```
+
+The following simulation software packages are used by simtools:
+
+- [CORSIKA](corsika.md): Air shower simulation software.
+- [sim_telarray](sim_telarray.md): Telescope simulation software for ray tracing, triggering, and camera-level simulation.
+- ROBAST
+
+```{note}
+Simulation software is external to simtools and developed by the respective teams. The integration of these components into simtools is done through interfaces, allowing for flexibility and future updates.
+```
+
+## Simulation Models
+
+[Simulation models and parameters](simulation_models.md) describe the properties of all relevant elements of the observatory, including site, telescopes, and calibration devices.
+[Databases](databases.md) are used to store simulation model parameters for efficient querying and management.
+
+```{toctree}
+:hidden:
+:maxdepth: 1
+corsika.md
+sim_telarray.md
+simulation_models.md
+databases.md
+```
+
+## I/O using pyeventio
+
+[pyeventio](https://github.com/cta-observatory/pyeventio) is a python library for reading the output of the simulation software (EventIO data format used by sim_telarray). *pyeventio* is external to simtools, but an essential component for reading simulation output data by the CTAO pipelines.
+
+## Additional Components
+
+```{warning}
+Incomplete documentation
+```
+
+- software tool for geomagnetic field determination

gammasimtools-0.18.0/docs/source/components/sim_telarray.md

@@ -0,0 +1,17 @@
+# Telescope simulations with sim_telarray
+
+sim_telarray ([MPIK site](https://www.mpi-hd.mpg.de/hfm/~bernlohr/sim_telarray), [CTAO gitlab repository](https://gitlab.cta-observatory.org/Konrad.Bernloehr/sim_telarray)) is used for telescope simulations, including ray tracing, triggering, readout, and camera-level simulation.
+
+The following executables from the `sim_telarray` package are used by `simtools`:
+
+- `sim_telarray`: Main ray-tracing and detector simulation executable.
+- `testeff`: Computes telescope and camera optical/electronic efficiency.
+- `rx`: Calculates the optical point spread function (PSF) (optional use).
+- `corsika_autoinputs`: Generates input parameters for CORSIKA.
+- `pfp`: Preprocessor for `sim_telarray`.
+- `xyzls`: Simulates a calibration light source at a specified position.
+- `ls-beam`: Simulates a laser beam calibration light source.
+
+```{warning}
+Incomplete documentation - missing references
+```

gammasimtools-0.18.0/docs/source/components/simulation_models.md

@@ -0,0 +1,31 @@
+# Simulation Models
+
+```{warning}
+Incomplete Documentation.
+Note also overlap with model parameters section in [data model](../data-model/index.md).
+```
+
+Simulation model parameters describe properties of all relevant elements of the observatory. This includes site,
+telescopes, and calibration devices.
+The management, definition, derivation, verification, and validation of the simulation model is central to simtools.
+
+Model parameters describe for example:
+
+- Atmospheric model parameters (profile, transmission)
+- Geomagnetic field characteristics
+- Optical and mechanical telescope properties
+- Detector plane settings
+- Trigger configurations
+- Camera readout parameters
+- Simulation production related software parameters
+
+The major components of the simulation model are:
+
+1. **Model parameter schema files:** The schema files define the model parameters and their properties. Every model parameter is defined in a schema file, see the corresponding [data model section](../data-model/model_parameters.md) for details.
+2. **Model parameter repository:** The simulation model is stored in a [gitlab repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-models). Review and revision control of the simulation model is done using this repository.
+3. **Model parameter databases:** The simulation models are stored in the simulation models database to ensure query efficiency for simtools applications, see the [databases section](databases.md) for details.
+4. **Simulation model setting workflows**: Parameter derivation and validation pipelines implemented in through workflows consisting of simtools applications. Maintained in [simulation model setting repository](https://gitlab.cta-observatory.org/cta-science/simulations/simulation-model/simulation-model-parameter-setting).
+
+```{note}
+Simulation models are at the core of the CTAO Simulation Pipeline. The responsibility for the values and the correctness of the simulation model parameters is with the CTAO Simulation Team.
+```

{gammasimtools-0.17.0 → gammasimtools-0.18.0}/docs/source/conf.py

@@ -48,7 +48,7 @@ def get_python_version_from_pyproject():
 # -- Project information -----------------------------------------------------
 
 project = "simtools"
-copyright = "2024, gammasim-tools, simtools developers"  # noqa A001
+copyright = "2024-2025, gammasim-tools, simtools developers"  # noqa A001
 author = get_authors_from_citation_file()
 rst_epilog = f"""
 .. |author| replace:: {author}
@@ -81,6 +81,7 @@ extensions = [
     "sphinx.ext.githubpages",
     "myst_parser",
     "numpydoc",
+    "sphinx_design",
 ]
 
 # Display todos by setting to True
@@ -99,11 +100,7 @@ source_suffix = [".rst"]
 # The master toctree document.
 master_doc = "index"
 
-# 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.
+# The language for content autogenerated by Sphinx.
 language = "en"
 
 # List of patterns, relative to source directory, that match files and
@@ -127,25 +124,17 @@ html_title = f"{project}"
 # 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_logo = "../_static/simtools_logo.png"
 html_theme_options = {
-    "navbar_start": ["navbar-logo", "version-switcher"],
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["version-switcher", "navbar-icon-links"],
     "show_toc_level": 1,
-    "announcement": (
-        "simtools is under rapid development with continuous changes. "
-        "Please contact the developers before using it."
-    ),
     "icon_links": [
         {
             "name": "GitHub",
             "url": "https://github.com/gammasim/simtools",
             "icon": "fa-brands fa-github",
         },
-        {
-            "name": "PyPI",
-            "url": "https://pypi.org/project/gammasimtools/",
-            "icon": "https://badge.fury.io/py/gammasimtools.svg",
-            "type": "url",
-        },
     ],
     "navigation_with_keys": False,
     "switcher": {
@@ -153,6 +142,9 @@ html_theme_options = {
         "version_match": "latest",
     },
     "check_switcher": True,
+    "logo": {
+        "alt_text": "simtools",
+    },
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -177,9 +169,16 @@ locale_dirs = []
 
 # myst (markdown options)
 myst_heading_anchors = 3
-myst_enable_extensions = {
+myst_enable_extensions = [
     "colon_fence",
+    "deflist",
+    "html_admonition",
+    "html_image",
     "substitution",
-}
+    "tasklist",
+    "attrs_block",
+    "attrs_inline",
+]
+
 
 suppress_warnings = ["myst.*", "myst.duplicate_def"]

gammasimtools-0.18.0/docs/source/data-model/index.md

@@ -0,0 +1,15 @@
+# Data Model
+
+- Description of [simulation model parameters](model_parameters.md) through schema files
+- description of simulation data format
+- description of metadata
+
+:::{warning}
+Incomplete Documentation.
+:::
+
+```{toctree}
+:hidden:
+:maxdepth: 1
+model_parameters.md
+```