Belle II Software

https://software.belle2.org/development/sphinx/
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Belle II Software is a comprehensive physics analysis framework for the Belle II experiment,...
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### Set up experiment name

Source: https://software.belle2.org/development/sphinx/online_book/analysis/topoana.html

Sets up the experiment name for TopoAna. Use `./Setup Example` to try the program with examples under the examples directory.

```bash
./Setup Belle_II
```

--------------------------------

### Run RooFit example

Source: https://software.belle2.org/development/sphinx/_sources/zzz-fitting/doc/README.rst

Navigate to the roofit directory and run the simple 1D fit example. Assumes you run the script from the example directory.

```sh
cd roofit
python3 simple-1d-fit.py
```

--------------------------------

### Install zfit

Source: https://software.belle2.org/development/sphinx/_sources/zzz-fitting/doc/README.rst

Install zfit for the zfit examples, as it may not be included in the externals.

```sh
pip3 install --user zfit
```

--------------------------------

### Setup development version

Source: https://software.belle2.org/development/sphinx/_sources/build/tools_doc/cvmfs_setup.rst

Navigate to the development directory and run b2setup to configure the environment.

```bash
$ cd development
$ b2setup
```

--------------------------------

### Staging globaltag example

Source: https://software.belle2.org/development/sphinx/framework/doc/tools/06-b2conditionsdb.html

Example of a staging globaltag with new payloads. Payloads starting at (0,0) are interpreted as starting at the first valid run for the update. This is the second input to the b2conditionsdb tag runningupdate command.

```text
payload1, rev 3, valid from 0,0 to 1,8
payload1, rev 4, valid from 1,9 to 1,20
payload2, rev 2, valid from 1,5 to 1,20
payload3, rev 2, valid from 0,0 to -1,-1
payload4, rev 1, valid from 0,0 to 1,20
```

--------------------------------

### Create starterkit folder and my_file.py

Source: https://software.belle2.org/development/sphinx/_sources/online_book/prerequisites/python.rst

Bash commands to create a folder and a Python file, then open it in nano.

```bash
# Make sure we're in our home directory
cd ~
# Create a folder and change there
mkdir starterkit
cd starterkit
# Create your .py file
touch my_file.py
# Open your file to edit it in your editor of choice, e.g.
nano my_file.py
```

--------------------------------

### Job.setup_cmds

Source: https://software.belle2.org/development/sphinx/calibration/doc/caf.html

Property that returns the setup commands.

```APIDOC
## Job.setup_cmds

### Description
Returns the setup commands.

### Property
setup_cmds

```

--------------------------------

### Install externals v02-00-02b on Ubuntu 22.04

Source: https://software.belle2.org/development/sphinx/_sources/build/tools_doc/installation-local.rst

Example of installing externals v02-00-02b on an Ubuntu 22.04 machine by specifying the system as 'ubuntu2204'.

```bash
$ b2install-externals v02-00-02b ubuntu2204
```

--------------------------------

### Compile the example with make

Source: https://software.belle2.org/development/sphinx/zzz-fitting/doc/bat/Lifetime2DFit/README.html

Run make in the project directory to compile the code.

```bash
make

```

--------------------------------

### Compile fitting examples with CMake

Source: https://software.belle2.org/development/sphinx/_sources/zzz-fitting/doc/hydra/doc/README.rst

Builds all fitting examples from the hydra subdirectory. Requires ROOT installed and paths to Hydra and TCLAP include directories.

```sh
mkdir build
cd build
cmake -D HYDRA_INCLUDE_DIR=path_to_hydra_dir -D TCLAP_INCLUDE_DIR=path_to_tclap_dir ../
make
cd -
```

--------------------------------

### Set up a basf2 release in one step

Source: https://software.belle2.org/development/sphinx/_sources/online_book/basf2/introduction.rst

Combines the first and second steps by sourcing the full path to b2setup with the release name. Useful when you already know which release you want.

```bash
source /cvmfs/belle.cern.ch/tools/b2setup <your choice of release>
```

--------------------------------

### C++ Configuration Example

Source: https://software.belle2.org/development/sphinx/_sources/framework/doc/conditions-database.rst

Configures the conditions database in C++ by getting the singleton instance and prepending a global tag.

```c++
#include <framework/database/Configuration.h>

auto& config = Conditions::Configuration::getInstance();
config.prependGlobltag("some_tag");
```

--------------------------------

### b2install-data usage

Source: https://software.belle2.org/development/sphinx/_sources/build/tools_doc/installation-tools.rst

Installs or updates a given type of basf2 data. Supported data types are 'validation', 'examples', and 'starterkit'.

```text
Usage:: b2install-data datatype
```

--------------------------------

### b2setup usage (developer)

Source: https://software.belle2.org/development/sphinx/_sources/build/tools_doc/installation-tools.rst

Execute in a local release directory to set it up. If a centrally installed release with the same version exists, it is set up too. Optionally specify a release version for the central release.

```text
Usage: b2setup [release]
```

--------------------------------

### Example of documentation directory structure

Source: https://software.belle2.org/development/sphinx/framework/doc/atend-doctools.html

Shows the expected directory layout for documentation files in packages. Files not starting with 'index' in subdirectories are ignored.

```text
analysis/doc/
    index.rst
    variables.rst
    an_image.png
    variable_groups/01-Kinematics.rst
    variable_groups/02-PID.rst
calibration/doc/
    index_caf.rst
framework/doc/
    index-01-install.rst
    index-02-tools.rst

```

--------------------------------

### Run example executable with help flag

Source: https://software.belle2.org/development/sphinx/_sources/zzz-fitting/doc/hydra/doc/README.rst

Shows usage instructions for an example executable. The naming convention is example_{cpp,tbb,omp,cu} for different backends.

```sh
./bin/simple-1d-fit_cpp -h
```

--------------------------------

### b2file-check JSON output example

Source: https://software.belle2.org/development/sphinx/_sources/framework/doc/tools/02-b2file.rst

Example command and JSON output for the b2file-check tool using the --json parameter to get detailed machine-readable results for all consistency tests. The output includes checks_passed and stats fields such as events, compression, and file size.

```text
$ check_basf2_file --json framework/tests/root_input.root
{
  "checks_passed": {
    "all_entries_readable": true,
    "contains_persistent": true,
    "contains_tree": true,
    "entries_eq_filemetedata": true,
    "eventmetadata_readable": true,
    "file_readable": true,
    "filemetadata_readable": true
  },
  "stats": {
    "compression_algorithm": 0,
    "compression_factor": 2.591318368911743,
    "compression_level": 1,
    "events": 5,
    "filesize_kib": 61.8984375,
    "mcevents": 0,
    "size_per_event_kib": 12.3796875
  }
}
```

--------------------------------

### Set a setup function for all algorithms

Source: https://software.belle2.org/development/sphinx/_modules/caf/framework.html

Shows how to set a pre-algorithm function that runs before each algorithm.

```python
>>> cal.pre_algorithms = my_function_object
```

--------------------------------

### Run Python interactively and print math.pi

Source: https://software.belle2.org/development/sphinx/_sources/online_book/prerequisites/python.rst

Shows an interactive Python session started from the terminal. The example imports the math module and prints the value of pi.

```bash
python3
```

```python
>>> import math
>>> print(math.pi)
```

--------------------------------

### Set different setup functions for each algorithm

Source: https://software.belle2.org/development/sphinx/_modules/caf/framework.html

Shows how to set a list of pre-algorithm functions, one per algorithm.

```python
>>> cal.pre_algorithms = [my_function1, my_function2, ...]
```

--------------------------------

### Access PDG database with pdg.get

Source: https://software.belle2.org/development/sphinx/online_book/basf2/introduction.html

Use the basf2 python interface to the PDG database. This example gets the particle with PDG code 11 and prints its name and mass.

```python
In [1]: import pdg
In [2]: whatisthis = pdg.get(11)
In [3]: print(whatisthis.GetName(), whatisthis.Mass())

```

--------------------------------

### Path to FlavorTagger tutorial example

Source: https://software.belle2.org/development/sphinx/_sources/analysis/doc/FlavorTagger.rst

Path to the example tutorial for normal use of the FlavorTagger.

```text
analysis/examples/tutorials/B2A801-FlavorTagger.py
```

--------------------------------

### Encode skim name using Registry

Source: https://software.belle2.org/development/sphinx/skim/doc/04-experts.html

Use the Registry.encode_skim_name method to get the numeric skim code for a given skim name. The example shows that 'SinglePhotonDark' returns 18020100.

```python
>>> from skim.registry import Registry
>>> Registry.encode_skim_name("SinglePhotonDark")
18020100
```

--------------------------------

### get_object_with_name: Recursively get object from Belle2 namespace

Source: https://software.belle2.org/development/sphinx/_modules/b2test_utils.html

Resolves a dotted name by splitting on '.' and recursively calling itself. Uses getattr for the final lookup. Starts from the Belle2 namespace if no root is given.

```python
if root is None:
    from ROOT import Belle2  # noqa
    root = Belle2

if "." in object_name:
    namespace, object_name = object_name.split(".", 1)

    return get_object_with_name(object_name, get_object_with_name(namespace, root=root))

return getattr(root, object_name)
```

--------------------------------

### Set up isolated environment with uv and install dependencies

Source: https://software.belle2.org/development/sphinx/online_book/basf2/cs_onnx.html

Creates a virtual environment and installs the required packages for the tutorial, including scikit-learn, matplotlib, pandas, uproot, and ONNX-related tools. Run these commands in a terminal separate from the basf2 environment.

```bash
uv venv
source .venv/bin/activate
uv pip install scikit-learn matplotlib pandas uproot awkward-pandas \
    skl2onnx onnxmltools onnx onnxruntime netron jupyter

jupyter lab

```

--------------------------------

### BaseSkim.additional_setup

Source: https://software.belle2.org/development/sphinx/_modules/skim/core.html

Performs any setup steps necessary before running the skim. Standard particle lists should not be loaded here; use load_standard_lists instead.

```APIDOC
## BaseSkim.additional_setup

### Description
Perform any setup steps necessary before running the skim.

### Parameters
- **path** (basf2.Path) - Required - Skim path to be processed.

```

--------------------------------

### Run distributed.py FEI training on KEKCC

Source: https://software.belle2.org/development/sphinx/analysis/doc/FullEventInterpretation.html

Complete example of running the distributed.py script with the required parameters for training the FEI on the KEKCC cluster. Adjust the paths and number of jobs according to your setup.

```bash
python3 analysis/scripts/fei/distributed.py -s kekcc \
    -f analysis/examples/FEI/B_generic_train.py \
    -w /<local>/<path>/<to>/<project>/<directory>/ \
    -n 1000 -d /<local>/<path>/<to>/<input>/<mdst>/<files>/*.root

```

--------------------------------

### Configure package logging with logging.package()

Source: https://software.belle2.org/development/sphinx/framework/doc/logging.html

Shows how to get the LogConfig for a package and set its debug level and info mask. The example uses the 'svd' package and sets the info to show level, message, and file.

```python
>>> logging.package('svd').debug_level = 10
>>> logging.package('svd').set_info(LogLevel.INFO, LogInfo.LEVEL | LogInfo.MESSAGE | LogInfo.FILE)
```

--------------------------------

### Set up software with b2setup

Source: https://software.belle2.org/development/sphinx/build/tools_doc/installation-local.html

Attempts to set up the software version. If the required externals are missing, it prints an error indicating the needed externals version.

```bash
$ b2setup release-08-02-06

```
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