From 84019bdce1492bfcafb0acaf543580a9212c73ee Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 23 Jul 2025 09:01:01 +0200
Subject: [PATCH 01/22] chore: add missing links to changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2c78d30..fdc4e68 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -871,6 +871,7 @@ returns `None` instead. Fixes [#11]
 ## [0.5.3] - 2022-08-22
 
 <!-- markdownlint-disable-file MD024 -->
+[1.0.0rc3]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc2...1.0.0rc3
 [1.0.0rc2]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc1...1.0.0rc2
 [1.0.0rc1]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a7...1.0.0rc1
 [1.0.0.a7]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a6...1.0.0.a7
@@ -931,6 +932,7 @@ returns `None` instead. Fixes [#11]
 [#70]: https://github.com/lycosystem/lyscripts/issues/70
 [#72]: https://github.com/lycosystem/lyscripts/issues/72
 [#74]: https://github.com/lycosystem/lyscripts/issues/74
+[#75]: https://github.com/lycosystem/lyscripts/issues/75
 
 [`emcee`]: https://emcee.readthedocs.io/en/stable/
 [`rich`]: https://rich.readthedocs.io/en/latest/

From da05e7345fb4bab16a200560e9f2268debee4dde Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 24 Jul 2025 16:53:44 +0200
Subject: [PATCH 02/22] change: make compatible with new lydata version

---
 CHANGELOG.md                         |  2 +-
 README.md                            |  2 +-
 pyproject.toml                       |  2 +-
 schemas/ly.json                      |  2 +-
 src/lyscripts/compute/prevalences.py |  3 ++-
 src/lyscripts/data/__init__.py       |  2 +-
 src/lyscripts/data/enhance.py        | 37 +++++++++++-----------------
 src/lyscripts/data/filter.py         |  4 +--
 src/lyscripts/data/join.py           |  2 +-
 9 files changed, 25 insertions(+), 31 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fdc4e68..cfdd3f0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -356,7 +356,7 @@ over diagnosis times cannot be converted to a `DistributionConfig`.
   BREAKING CHANGES: `generate` command is better configurable
 - (**config**) Merge sample/sampling configs.
 - Use lydata's `ModalityConfig`.\
-  Since the [lydata](https://github.com/rmnldwg/lydata) package is
+  Since the [lydata](https://github.com/lycosystem/lydata) package is
   evolving quickly, I added it as a dependency and moved the first bit of
   code over there.
 - Enable use of lydata to load patient data.
diff --git a/README.md b/README.md
index e757f19..9621e28 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 
 ## What are these `lyscripts`?
 
-This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/lycosystem/lymph) library and the [lydata](https://github.com/rmnldwg/lydata) repository that stores lymphatic progression data.
+This package provides convenient scripts for performing inference and learning regarding the lymphatic spread of head & neck cancer. Essentially, it provides a *command line interface* (CLI) to the [lymph](https://github.com/lycosystem/lymph) library and the [lydata](https://github.com/lycosystem/lydata) repository that stores lymphatic progression data.
 
 We are making these "convenience" scripts public, because doing so is one necessary requirement to making our research easily and fully reproducible. There exists another repository, [lynference](https://github.com/lycosystem/lynference), where we stored the pipelines that produced our published results in a persistent way.
 
diff --git a/pyproject.toml b/pyproject.toml
index f3f409b..705fa9e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,7 +50,7 @@ dependencies = [
     "pydantic",
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
-    "lydata >= 0.3.3",
+    "lydata >= 0.4.0",
     "loguru",
 ]
 dynamic = ["version"]
diff --git a/schemas/ly.json b/schemas/ly.json
index d14eb3f..6bb3ca1 100644
--- a/schemas/ly.json
+++ b/schemas/ly.json
@@ -308,7 +308,7 @@
           "type": "string"
         },
         "repo_name": {
-          "default": "rmnldwg/lydata",
+          "default": "lycosystem/lydata",
           "description": "GitHub `repository/owner`.",
           "minLength": 1,
           "title": "Repo Name",
diff --git a/src/lyscripts/compute/prevalences.py b/src/lyscripts/compute/prevalences.py
index 8771eb9..f48ea0a 100644
--- a/src/lyscripts/compute/prevalences.py
+++ b/src/lyscripts/compute/prevalences.py
@@ -13,7 +13,8 @@
 import pandas as pd
 from loguru import logger
 from lydata import C, Q
-from lydata.accessor import NoneQ, QueryPortion
+from lydata.accessor import QueryPortion
+from lydata.querier import NoneQ
 from lydata.utils import is_old
 from lymph import models
 from pydantic import Field
diff --git a/src/lyscripts/data/__init__.py b/src/lyscripts/data/__init__.py
index cd1fb8d..c9863ec 100644
--- a/src/lyscripts/data/__init__.py
+++ b/src/lyscripts/data/__init__.py
@@ -11,7 +11,7 @@
 .. _DVC: https://dvc.org
 .. _LyProX: https://lyprox.org
 .. _lydata: https://lydata.readthedocs.io
-.. _GitHub repository: https://github.com/rmnldwg/lydata
+.. _GitHub repository: https://github.com/lycosystem/lydata
 """
 
 from pydantic_settings import BaseSettings, CliApp, CliSubCommand
diff --git a/src/lyscripts/data/enhance.py b/src/lyscripts/data/enhance.py
index 0662072..a8a795a 100644
--- a/src/lyscripts/data/enhance.py
+++ b/src/lyscripts/data/enhance.py
@@ -1,13 +1,15 @@
 """Enhance the dataset by inferring additional columns from the data.
 
-This is a command-line interface to the
-:py:func:`~lydata.utils.infer_and_combine_levels` function.
+This is a command-line interface to the methods
+:py:meth:`~lydata.accessor.LyDataAccessor.combine` and
+:py:meth:`~lydata.accessor.LyDataAccessor.augment` of the
+:py:class:`~lydata.accessor.LyDataAccessor` class.
 """
 
 from typing import Literal
 
 from loguru import logger
-from lydata import infer_and_combine_levels
+from lydata.accessor import LyDataFrame
 from lydata.utils import ModalityConfig
 
 from lyscripts.cli import assemble_main
@@ -21,7 +23,6 @@ class EnhanceCLI(BaseCLI):
     input: DataConfig
     modalities: dict[str, ModalityConfig] | None = None
     method: Literal["max_llh", "rank"] = "max_llh"
-    sides: list[Literal["ipsi", "contra"]] = ["ipsi", "contra"]
     lnl_subdivisions: dict[str, list[str]] = {
         "I": ["a", "b"],
         "II": ["a", "b"],
@@ -33,29 +34,21 @@ def cli_cmd(self) -> None:
         """Infer additional columns from the data and save the enhanced dataset.
 
         This basically provides a CLI to the
-        :py:func:`~lydata.utils.infer_and_combine_levels` function. See its docs for
+        :py:func:`~lydata.accessor.LyDataAccessor.augment` function. See its docs for
         more details on what exactly is happening here.
         """
         logger.debug(self.model_dump_json(indent=2))
 
-        data = self.input.load()
-        modality_names = list(self.modalities.keys()) if self.modalities else None
-
-        infer_lvls_kwargs = {
-            "modalities": modality_names,
-            "sides": self.sides,
-            "subdivisions": self.lnl_subdivisions,
-        }
-        enhanced = infer_and_combine_levels(
-            dataset=data,
-            infer_superlevels_kwargs=infer_lvls_kwargs,
-            infer_sublevels_kwargs=infer_lvls_kwargs,
-            combine_kwargs={
-                "modalities": self.modalities,
-                "method": self.method,
-            },
+        data: LyDataFrame = self.input.load()
+        data[self.method] = data.ly.combine(
+            modalities=self.modalities,
+            method=self.method,
         )
-        save_table_to_csv(file_path=self.output_file, table=enhanced)
+        data[self.method] = data.ly.augment(
+            modality=self.method,
+            subdivisions=self.lnl_subdivisions,
+        )
+        save_table_to_csv(file_path=self.output_file, table=data)
 
 
 if __name__ == "__main__":
diff --git a/src/lyscripts/data/filter.py b/src/lyscripts/data/filter.py
index bf64566..3e09fe8 100644
--- a/src/lyscripts/data/filter.py
+++ b/src/lyscripts/data/filter.py
@@ -1,7 +1,7 @@
 """Filter a dataset according to some common criteria.
 
 This is essentially a command line interface to building a
-:py:class:`query object <lydata.accessor.Q>` and applying it to the dataset.
+:py:class:`query object <lydata.querier.Q>` and applying it to the dataset.
 """
 
 from pathlib import Path
@@ -68,7 +68,7 @@ def model_post_init(self, __context):
     def cli_cmd(self):
         """Execute the ``filter`` command.
 
-        This command uses the :py:class:`~lydata.accessor.Q` objects of the `lydata`_
+        This command uses the :py:class:`~lydata.querier.Q` objects of the `lydata`_
         library to filter the dataset according to the given criteria.
 
         .. _lydata: https://lydata.readthedocs.io
diff --git a/src/lyscripts/data/join.py b/src/lyscripts/data/join.py
index 6ecd8df..d7eb62e 100644
--- a/src/lyscripts/data/join.py
+++ b/src/lyscripts/data/join.py
@@ -55,7 +55,7 @@ def cli_cmd(self) -> None:
             lyscripts data join --configs datasets.ly.yaml --output-file joined.csv
 
         .. _pydantic: https://docs.pydantic.dev/latest/
-        .. _lydata Github repo: https://github.com/rmnldwg/lydata
+        .. _lydata Github repo: https://github.com/lycosystem/lydata
         """
         joined = None
 

From 66a7c96eab916e92bb5c56b118d74b74347372ac Mon Sep 17 00:00:00 2001
From: noemibuehrer <nritzmann@student.ethz.ch>
Date: Mon, 28 Jul 2025 12:39:18 +0200
Subject: [PATCH 03/22] feat: add `integrate` command for thermodynamic
 integration

---
 src/lyscripts/__init__.py  |   3 +-
 src/lyscripts/configs.py   |  30 +++++++-
 src/lyscripts/integrate.py | 154 +++++++++++++++++++++++++++++++++++++
 src/lyscripts/sample.py    |   7 +-
 4 files changed, 191 insertions(+), 3 deletions(-)
 create mode 100644 src/lyscripts/integrate.py

diff --git a/src/lyscripts/__init__.py b/src/lyscripts/__init__.py
index f6b7de8..6727547 100644
--- a/src/lyscripts/__init__.py
+++ b/src/lyscripts/__init__.py
@@ -17,7 +17,7 @@
     CliSubCommand,
 )
 
-from lyscripts import compute, data, sample, schedule  # noqa: F401
+from lyscripts import compute, data, sample, schedule, integrate  # noqa: F401
 from lyscripts._version import version
 from lyscripts.cli import assemble_main, configure_logging
 from lyscripts.utils import console
@@ -51,6 +51,7 @@ class LyscriptsCLI(BaseSettings):
     sample: CliSubCommand[sample.SampleCLI]
     compute: CliSubCommand[compute.ComputeCLI]
     schedule: CliSubCommand[schedule.ScheduleCLI]
+    integrate: CliSubCommand[integrate.IntegrateCLI]
 
     def __init__(self, **kwargs):
         """Add logging configuration to the lyscripts CLI."""
diff --git a/src/lyscripts/configs.py b/src/lyscripts/configs.py
index f76726e..ed9ffb5 100644
--- a/src/lyscripts/configs.py
+++ b/src/lyscripts/configs.py
@@ -18,7 +18,7 @@
 from collections.abc import Callable, Sequence
 from copy import deepcopy
 from pathlib import Path
-from typing import Annotated, Any, Literal
+from typing import Annotated, Any, Literal, Optional
 
 import numpy as np
 import pandas as pd
@@ -432,6 +432,12 @@ class SamplingConfig(BaseModel):
         default=0.05,
         description="Relative threshold for convergence.",
     )
+    burnin_steps: int | None = Field(
+        default=None,
+        description=(
+            "Number of burn-in steps to take. If None, burn-in runs until convergence."
+        )
+    )
     num_steps: int | None = Field(
         default=100,
         description=("Number of steps to take in the MCMC sampling."),
@@ -460,6 +466,28 @@ def load(self, thin: int = 1) -> np.ndarray:
             thin=thin,
         )
 
+class ScheduleConfig(BaseModel):
+        """Configuration for generating a schedule of inverse temperatures."""
+
+        method: Literal["geometric", "linear", "power"] = Field(
+            default="power",
+            description="Method to generate the inverse temperature schedule.",
+        )
+        num: int = Field(
+            default=32,
+            description="Number of inverse temperatures in the schedule.",
+        )
+        power: float = Field(
+            default=4.0,
+            description="If a power schedule is chosen, use this as power.",
+        )
+        values: list[float] | None = Field(
+            default=None,
+            description=(
+                "List of inverse temperatures to use instead of generating a schedule. "
+                "If a list is provided, the other parameters are ignored."
+            ),
+        )
 
 def map_to_optional_bool(value: Any) -> Any:
     """Try to convert the options in the `PatternType` to a boolean value."""
diff --git a/src/lyscripts/integrate.py b/src/lyscripts/integrate.py
new file mode 100644
index 0000000..d54a9d6
--- /dev/null
+++ b/src/lyscripts/integrate.py
@@ -0,0 +1,154 @@
+"""
+Perform thermodynamic integration to evaluate the model evidence.
+"""
+
+from __future__ import annotations
+
+import os
+from typing import Any
+from loguru import logger
+
+import emcee
+import numpy as np
+import h5py
+
+from lyscripts.cli import assemble_main
+from pydantic import Field
+
+from lydata.utils import ModalityConfig
+
+from lyscripts.configs import (
+    BaseCLI,
+    DataConfig,
+    DistributionConfig,
+    GraphConfig,
+    ModelConfig,
+    SamplingConfig,
+    ScheduleConfig,
+    construct_model,
+    add_distributions,
+    add_modalities,
+)
+
+import lyscripts.sample as sample_module  # Import the module to set its global MODEL
+from lyscripts.schedule import SCHEDULES
+
+from lyscripts.utils import get_hdf5_backend
+
+def init_ti_sampler(
+    settings: IntegrateCLI, 
+    temp_idx: int, 
+    ndim: int, 
+    inv_temp: float, 
+    pool: Any    
+) -> emcee.EnsembleSampler:
+    """Initialize the ``emcee.EnsembleSampler``with the given ``settings''."""
+    nwalkers = ndim * settings.sampling.walkers_per_dim
+    backend = get_hdf5_backend(
+                    file_path=settings.sampling.storage_file,
+                    dataset=f"ti/{temp_idx+1:0>2d}",
+                    nwalkers=nwalkers,
+                    ndim=ndim,
+                )
+    return emcee.EnsembleSampler(
+        nwalkers=nwalkers,
+        ndim=ndim,
+        log_prob_fn=sample_module.log_prob_fn,
+        kwargs={"inverse_temp": inv_temp},
+        moves=[(emcee.moves.DEMove(), 0.8), (emcee.moves.DESnookerMove(), 0.2)],
+        backend=backend,
+        pool=pool,
+        blobs_dtype=[("log_prob", np.float64)],
+        parameter_names=list(MODEL.get_named_params().keys()),
+    )
+
+class IntegrateCLI(BaseCLI):
+    """Perform thermodynamic integration to compute the model evidence."""
+
+    graph: GraphConfig
+    model: ModelConfig = ModelConfig()
+    distributions: dict[str, DistributionConfig] = Field(
+        default={},
+        description=(
+            "Mapping of model T-categories to predefined distributions over "
+            "diagnose times."
+        ),
+    )
+    modalities: dict[str, ModalityConfig] = Field(
+        default={},
+        description=(
+            "Maps names of diagnostic modalities to their specificity/sensitivity."
+        ),
+    )
+    data: DataConfig
+    sampling: SamplingConfig
+    schedule: ScheduleConfig = Field(
+        description="Configuration for generating inverse temperature schedule."
+    )
+
+
+    def cli_cmd(self) -> None:
+        """Start the thermodynamic integration process."""
+        # as recommended in https://emcee.readthedocs.io/en/stable/tutorials/parallel/#
+        os.environ["OMP_NUM_THREADS"] = "1"
+
+        logger.debug(self.model_dump_json(indent=2))
+
+        # ugly, but necessary for pickling  
+        global MODEL
+        MODEL = construct_model(self.model, self.graph)
+        MODEL = add_distributions(MODEL, self.distributions)
+        MODEL = add_modalities(MODEL, self.modalities)
+        MODEL.load_patient_data(**self.data.get_load_kwargs())
+        ndim = MODEL.get_num_dims()
+        
+        # set MODEL in the sample module's namespace so log_prob_fn can access it
+        sample_module.MODEL = MODEL
+
+        # temperature schedule: use direct list or generate
+        if self.schedule.values is not None:
+            temp_schedule = np.array(self.schedule.values)
+            logger.info(f"Using direct temperature values: {temp_schedule}")
+        else:
+            func = SCHEDULES[self.schedule.method]
+            temp_schedule = func(self.schedule.num, self.schedule.power)
+            logger.info(f"Generated {self.schedule.method} schedule: {temp_schedule}")
+        
+        # emcee does not support numpy's new random number generator yet.
+        np.random.seed(self.sampling.seed) # noqa: NPY002
+
+        with sample_module.get_pool(self.sampling.cores) as pool:
+            for idx, inv_temp in enumerate(temp_schedule):
+                sampler = init_ti_sampler(
+                    settings=self,
+                    temp_idx=idx,
+                    ndim=ndim,
+                    inv_temp=inv_temp,
+                    pool=pool
+                )
+
+                sample_module.run_sampling(
+                    description=f"Burn-in phase: TI step {idx+1}/{len(temp_schedule)}",
+                    sampler=sampler,
+                    num_steps=self.sampling.burnin_steps,
+                    check_interval=self.sampling.check_interval,
+                    trust_factor=self.sampling.trust_factor,
+                    relative_thresh=self.sampling.relative_thresh,
+                    history_file=self.sampling.history_file,
+                )
+
+                sample_module.run_sampling(
+                    description=f"Sampling phase: TI step {idx+1}/{len(temp_schedule)}",
+                    sampler=sampler,
+                    num_steps=self.sampling.num_steps,
+                    reset_backend=True,
+                    check_interval=self.sampling.num_steps,
+                    thin_by=self.sampling.thin_by,
+                )
+            # copy last sampling round over to a group in the HDF5 file called "mcmc"
+            with h5py.File(self.sampling.storage_file, mode="r+") as h5_file:
+                h5_file.copy(f"ti/{len(temp_schedule):0>2d}", h5_file, name=self.sampling.dataset)
+
+if __name__ == "__main__":
+    main = assemble_main(settings_cls=IntegrateCLI, prog_name="integrate")
+    main()
\ No newline at end of file
diff --git a/src/lyscripts/sample.py b/src/lyscripts/sample.py
index d154dfb..083b16d 100644
--- a/src/lyscripts/sample.py
+++ b/src/lyscripts/sample.py
@@ -129,7 +129,10 @@ def log_prob_fn(theta: ParamsType, inverse_temp: float = 1.0) -> tuple[float, fl
     An inverse temperature ``inverse_temp`` can be provided for thermodynamic
     integration.
     """
-    return inverse_temp * MODEL.likelihood(given_params=theta), inverse_temp
+    llh = MODEL.likelihood(given_params=theta)
+    if np.isinf(llh):  # to prevent the case of 0 * inf = NaN
+        return -np.inf, -np.inf
+    return inverse_temp * llh, llh
 
 
 def ensure_initial_state(sampler: emcee.EnsembleSampler) -> np.ndarray:
@@ -402,6 +405,7 @@ def cli_cmd(self) -> None:
             run_sampling(
                 description="Burn-in phase",
                 sampler=sampler,
+                num_steps=self.sampling.burnin_steps,
                 check_interval=self.sampling.check_interval,
                 trust_factor=self.sampling.trust_factor,
                 relative_thresh=self.sampling.relative_thresh,
@@ -411,6 +415,7 @@ def cli_cmd(self) -> None:
                 description="Sampling phase",
                 sampler=sampler,
                 num_steps=self.sampling.num_steps,
+                check_interval=self.sampling.num_steps,
                 reset_backend=True,
                 thin_by=self.sampling.thin_by,
             )

From 0b27d3796f2f8e18722dd4463b0a2b789a504425 Mon Sep 17 00:00:00 2001
From: noemibuehrer <nritzmann@student.ethz.ch>
Date: Tue, 29 Jul 2025 11:05:19 +0200
Subject: [PATCH 04/22] feat (compute): add `evidence` command for computing
 model evidence with TI samples

---
 src/lyscripts/compute/__init__.py |   5 +-
 src/lyscripts/compute/evidence.py | 193 ++++++++++++++++++++++++++++++
 src/lyscripts/sample.py           |   2 +-
 3 files changed, 197 insertions(+), 3 deletions(-)
 create mode 100644 src/lyscripts/compute/evidence.py

diff --git a/src/lyscripts/compute/__init__.py b/src/lyscripts/compute/__init__.py
index 84f0e1a..c2bbdff 100644
--- a/src/lyscripts/compute/__init__.py
+++ b/src/lyscripts/compute/__init__.py
@@ -5,16 +5,17 @@
 
 from pydantic_settings import BaseSettings, CliApp, CliSubCommand
 
-from lyscripts.compute import posteriors, prevalences, priors, risks
+from lyscripts.compute import posteriors, prevalences, priors, risks, evidence
 
 
 class ComputeCLI(BaseSettings):
-    """Compute priors, posteriors, risks, and prevalences from model samples."""
+    """Compute priors, posteriors, risks, prevalences and model evidence from model samples."""
 
     priors: CliSubCommand[priors.PriorsCLI]
     posteriors: CliSubCommand[posteriors.PosteriorsCLI]
     risks: CliSubCommand[risks.RisksCLI]
     prevalences: CliSubCommand[prevalences.PrevalencesCLI]
+    evidence: CliSubCommand[evidence.EvidenceCLI]
 
     def cli_cmd(self) -> None:
         """Start the ``compute`` subcommand."""
diff --git a/src/lyscripts/compute/evidence.py b/src/lyscripts/compute/evidence.py
new file mode 100644
index 0000000..8959d46
--- /dev/null
+++ b/src/lyscripts/compute/evidence.py
@@ -0,0 +1,193 @@
+"""Given samples drawn during thermodynamic integration, compute the model log evidence."""
+
+from __future__ import annotations
+import numpy as np
+import json
+import pandas as pd
+from loguru import logger
+from pydantic import Field
+
+import h5py
+import emcee
+from pathlib import Path
+
+from lyscripts.cli import assemble_main
+from lyscripts.configs import (
+    BaseCLI,
+    DataConfig,
+    SamplingConfig,
+    ScheduleConfig,
+)
+from lyscripts.schedule import SCHEDULES
+
+from scipy.integrate import trapezoid
+
+RNG = np.random.default_rng()
+
+def comp_bic(log_probs: np.ndarray, num_params: int, num_data: int) -> float:
+    r"""Compute the negative one half of the Bayesian Information Criterion (BIC).
+
+    The BIC is defined as [^1]
+    $$ BIC = k \\ln{n} - 2 \\ln{\\hat{L}} $$
+    where $k$ is the number of parameters ``num_params``, $n$ the number of datapoints
+    ``num_data`` and $\\hat{L}$ the maximum likelihood estimate of the ``log_prob``.
+    It is constructed such that the following is an
+    approximation of the model evidence:
+    $$ p(D \\mid m) \\approx \\exp{\\left( - BIC / 2 \\right)} $$
+    which is why this function returns the negative one half of it.
+
+    [^1]: https://en.wikipedia.org/wiki/Bayesian_information_criterion
+    """
+    return np.max(log_probs) - num_params * np.log(num_data) / 2.0
+
+
+def compute_evidence(
+    temp_schedule: np.ndarray,
+    log_probs: np.ndarray,
+    num: int = 1000,
+) -> tuple[float, float]:
+    """Compute the evidence and its standard deviation.
+
+    Given a ``temp_schedule`` of inverse temperatures and corresponding sets of
+    ``log_probs``, draw ``num`` "paths" of log-probabilities and compute the evidence
+    for each using trapezoidal integration.
+
+    The evidence is then the mean of those ``num`` integrations, while the error is
+    their standard deviation.
+    """
+    integrals = np.zeros(shape=num)
+    for i in range(num):
+        rand_idx = RNG.choice(log_probs.shape[1], size=log_probs.shape[0])
+        drawn_accuracy = log_probs[np.arange(log_probs.shape[0]), rand_idx].copy()
+        integrals[i] = trapezoid(y=drawn_accuracy, x=temp_schedule)
+    return np.mean(integrals), np.std(integrals)
+
+def compute_ti_results(
+    settings: EvidenceCLI,
+    temp_schedule: np.ndarray,
+    metrics: dict,
+    ndim: int,
+    h5_file: Path,
+) -> tuple[np.ndarray, np.ndarray]:
+    """Compute the results in case of a thermodynamic integration run."""
+    num_temps = len(temp_schedule)
+
+    if num_temps != len(h5_file["ti"]):
+        raise RuntimeError(
+            f"Parameters suggest temp schedule of length {num_temps}, "
+            f"but stored are {len(h5_file['ti'])}",
+        )
+
+    nwalker = ndim * settings.sampling.walkers_per_dim
+    nsteps = settings.sampling.num_steps
+    ti_log_probs = np.zeros(shape=(num_temps, nsteps * nwalker))
+
+    for i, run in enumerate(h5_file["ti"]):
+        reader = emcee.backends.HDFBackend(settings.sampling.storage_file, name=f"ti/{run}", read_only=True)
+        ti_log_probs[i] = reader.get_blobs(flat=True)['log_prob']
+
+    evidence, evidence_std = compute_evidence(temp_schedule, ti_log_probs)
+    metrics["evidence"] = evidence
+    metrics["evidence_std"] = evidence_std
+
+    return temp_schedule, ti_log_probs
+
+
+class EvidenceCLI(BaseCLI):
+    """Compute model evidence from thermodynamic integration samples."""
+
+    data: DataConfig
+    sampling: SamplingConfig
+    schedule: ScheduleConfig = Field(
+        description="Configuration for generating inverse temperature schedule."
+    )
+    plots: Path = Field(
+        default="./plots",
+        description="Directory for storing plots.",
+    )
+    metrics: Path = Field(
+        default="./metrics.json",
+        description="Path to metrics file.",
+    )
+
+
+    def cli_cmd(self) -> None:
+        """Start the evidence computation process."""
+
+        data = self.data.load()
+
+        metrics = {}
+
+        # temperature schedule: use direct list or generate
+        if self.schedule.values is not None:
+            temp_schedule = np.array(self.schedule.values)
+            logger.info(f"Using direct temperature values: {temp_schedule}")
+        else:
+            func = SCHEDULES[self.schedule.method]
+            temp_schedule = func(self.schedule.num, self.schedule.power)
+            logger.info(f"Generated {self.schedule.method} schedule: {temp_schedule}")
+        
+
+        with h5py.File(self.sampling.storage_file, mode='r') as h5_file:
+            # Get ndim from the HDF5 backend
+            backend = emcee.backends.HDFBackend(self.sampling.storage_file, read_only=True, name=self.sampling.dataset)
+            ndim = backend.shape[1]
+            logger.info(f"Inferred {ndim} parameters from stored samples")
+            
+            # if TI has been performed, compute the evidence
+            if "ti" in h5_file:
+                temp_schedule, ti_log_probs = compute_ti_results(
+                    settings=self,
+                    temp_schedule=temp_schedule,
+                    metrics=metrics,
+                    ndim=ndim,
+                    h5_file=h5_file,
+                )
+
+                logger.info(
+                    "Computed results of thermodynamic integration with "
+                    f"{len(temp_schedule)} steps",
+                )
+
+                # store inverse temperatures and log-probs in CSV file
+                self.plots.parent.mkdir(parents=True, exist_ok=True)
+
+                beta_vs_accuracy = pd.DataFrame(
+                    np.array(
+                        [
+                            temp_schedule,
+                            np.mean(ti_log_probs, axis=1),
+                            np.std(ti_log_probs, axis=1),
+                        ],
+                    ).T,
+                    columns=["β", "accuracy", "std"],
+                )
+                beta_vs_accuracy.to_csv(self.plots, index=False)
+                logger.info(f"Plotted β vs accuracy at {self.plots}")
+            
+            # use blobs, because also for TI, this is the unscaled log-prob
+            final_log_probs = backend.get_blobs()['log_prob']
+            logger.info(f"Opened samples from emcee backend from {self.sampling.storage_file}")
+
+            # store metrics in JSON file
+            self.metrics.parent.mkdir(parents=True, exist_ok=True)
+            self.metrics.touch(exist_ok=True)
+
+            metrics["BIC"] = comp_bic(
+                log_probs=final_log_probs,
+                num_params=ndim,
+                num_data=len(data),
+            )
+            metrics["max_llh"] = np.max(final_log_probs)
+            metrics["mean_llh"] = np.mean(final_log_probs)
+
+            with open(self.metrics, mode="w", encoding="utf-8") as metrics_file:
+                json.dump(metrics, metrics_file)
+            
+            logger.info(f"Wrote out metrics to {self.metrics}")
+
+if __name__ == "__main__":
+    main = assemble_main(settings_cls=EvidenceCLI, prog_name="compute evidence")
+    main()
+
+
diff --git a/src/lyscripts/sample.py b/src/lyscripts/sample.py
index 083b16d..1fe7096 100644
--- a/src/lyscripts/sample.py
+++ b/src/lyscripts/sample.py
@@ -342,7 +342,7 @@ def init_sampler(settings: SampleCLI, ndim: int, pool: Any) -> emcee.EnsembleSam
         moves=[(emcee.moves.DEMove(), 0.8), (emcee.moves.DESnookerMove(), 0.2)],
         backend=backend,
         pool=pool,
-        blobs_dtype=[("inverse_temp", np.float64)],
+        blobs_dtype=[("log_prob", np.float64)],
         parameter_names=list(MODEL.get_named_params().keys()),
     )
 

From b76802269d6cdf3444d6fa43fba47683506d4dc5 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 31 Jul 2025 09:36:16 +0200
Subject: [PATCH 05/22] build: fix lydata to commit ID for now

---
 pyproject.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 705fa9e..ef1ae69 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,8 +50,8 @@ dependencies = [
     "pydantic",
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
-    "lydata >= 0.4.0",
     "loguru",
+    "lydata",
 ]
 dynamic = ["version"]
 
@@ -193,8 +193,8 @@ ignore_tags = ""
 topo_order = false
 # sort the commits inside sections by oldest/newest order
 sort_commits = "oldest"
-
-[tool.uv.sources]
-lydata = { path = "../lydata-package", editable = true }
 # limit the number of commits included in the changelog.
 # limit_commits = 42
+
+[tool.uv.sources]
+lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "d4658b71161ea80f014cf817e2beaa470f9a38c1" }

From 59352069b62633b87de9b3694a686b625d912f7a Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 31 Jul 2025 09:42:09 +0200
Subject: [PATCH 06/22] build: bump lydata package

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ef1ae69..0606775 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -197,4 +197,4 @@ sort_commits = "oldest"
 # limit_commits = 42
 
 [tool.uv.sources]
-lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "d4658b71161ea80f014cf817e2beaa470f9a38c1" }
+lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "374b25647fbe52ffb1e5583218bd06fbf8f3d403" }

From b72d2fe74ba4ecccfdfa8b98724b4501ff1a9145 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 31 Jul 2025 14:06:18 +0200
Subject: [PATCH 07/22] fix: change "info" to "core" for midlvl lydata col

---
 pyproject.toml                       | 2 +-
 src/lyscripts/compute/prevalences.py | 2 +-
 src/lyscripts/data/lyproxify.py      | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0606775..fd04f29 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -197,4 +197,4 @@ sort_commits = "oldest"
 # limit_commits = 42
 
 [tool.uv.sources]
-lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "374b25647fbe52ffb1e5583218bd06fbf8f3d403" }
+lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "2a1b20cc318931b86e2c82c05b674a2cec094dac" }
diff --git a/src/lyscripts/compute/prevalences.py b/src/lyscripts/compute/prevalences.py
index f48ea0a..89b84c9 100644
--- a/src/lyscripts/compute/prevalences.py
+++ b/src/lyscripts/compute/prevalences.py
@@ -141,7 +141,7 @@ def observe_prevalence(
     QueryPortion(match=np.int64(7), total=np.int64(79))
     """
     mapping = mapping or DataConfig.model_fields["mapping"].default_factory()
-    key = ("tumor", "1", "t_stage") if is_old(data) else ("tumor", "info", "t_stage")
+    key = ("tumor", "1", "t_stage") if is_old(data) else ("tumor", "core", "t_stage")
     data[key] = data.ly.t_stage.map(mapping)
 
     has_t_stage = C("t_stage").isin(scenario_config.t_stages)
diff --git a/src/lyscripts/data/lyproxify.py b/src/lyscripts/data/lyproxify.py
index 3b14a63..d810824 100644
--- a/src/lyscripts/data/lyproxify.py
+++ b/src/lyscripts/data/lyproxify.py
@@ -226,7 +226,7 @@ def transform_to_lyprox(
     .. code-block:: python
 
         column_map = {
-            ("patient", "info", "age"): {
+            ("patient", "core", "age"): {
                 "func": compute_age_from_raw,
                 "kwargs": {"randomize": False},
                 "columns": ["birthday", "date of diagnosis"]
@@ -237,7 +237,7 @@ def transform_to_lyprox(
     values of the columns ``"birthday"`` and ``"date of diagnosis"`` as positional
     arguments, and the keyword argument ``"randomize"`` is set to ``False``. The
     function then returns the patient's age, which is subsequently stored in the column
-    ``("patient", "info", "age")``.
+    ``("patient", "core", "age")``.
 
     Note that the ``column_map`` dictionary must have either a ``"default"`` key or
     ``"func"`` along with ``"columns"`` and ``"kwargs"``, depending on the function

From 305e3b0bc8a91cfe783f1903f57a71a11c79067e Mon Sep 17 00:00:00 2001
From: noemibuehrer <nritzmann@student.ethz.ch>
Date: Tue, 5 Aug 2025 08:28:37 +0200
Subject: [PATCH 08/22] docs: update documentation for `integrate` and
 `evidence` commands

---
 src/lyscripts/compute/evidence.py | 12 ++++++++++--
 src/lyscripts/integrate.py        | 20 ++++++++++++++++++--
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/src/lyscripts/compute/evidence.py b/src/lyscripts/compute/evidence.py
index 8959d46..53aa885 100644
--- a/src/lyscripts/compute/evidence.py
+++ b/src/lyscripts/compute/evidence.py
@@ -1,4 +1,7 @@
-"""Given samples drawn during thermodynamic integration, compute the model log evidence."""
+"""Given the samples drawn during thermodynamic integration and their
+respective log likelihoods, compute the model log evidence and 
+the Bayesian Information Criterion.
+"""
 
 from __future__ import annotations
 import numpy as np
@@ -112,7 +115,12 @@ class EvidenceCLI(BaseCLI):
 
 
     def cli_cmd(self) -> None:
-        """Start the evidence computation process."""
+        """Start the ``evidence`` subcommand.
+        Given the MCMC samples from thermodynamic integration provided by the ``sampling``
+        argument and the corresponding inverse temperature schedule, specified in the
+        ``schedule`` argument, the model evidence is computed using the functions
+        ``compute_ti_results`` and ``compute_evidence``. Further the BIC is evaluated.
+        """
 
         data = self.data.load()
 
diff --git a/src/lyscripts/integrate.py b/src/lyscripts/integrate.py
index d54a9d6..926e547 100644
--- a/src/lyscripts/integrate.py
+++ b/src/lyscripts/integrate.py
@@ -1,5 +1,10 @@
 """
 Perform thermodynamic integration to evaluate the model evidence.
+
+Using the functions provided by the `sample` module, this script implements
+thermodynamic integration (TI) in order to compute the model evidence.
+This is done by sampling the model parameters at different inverse temperatures
+following a specified schedule.
 """
 
 from __future__ import annotations
@@ -42,7 +47,7 @@ def init_ti_sampler(
     inv_temp: float, 
     pool: Any    
 ) -> emcee.EnsembleSampler:
-    """Initialize the ``emcee.EnsembleSampler``with the given ``settings''."""
+    """Initialize the ``emcee.EnsembleSampler`` for TI with the given ``settings''."""
     nwalkers = ndim * settings.sampling.walkers_per_dim
     backend = get_hdf5_backend(
                     file_path=settings.sampling.storage_file,
@@ -88,7 +93,18 @@ class IntegrateCLI(BaseCLI):
 
 
     def cli_cmd(self) -> None:
-        """Start the thermodynamic integration process."""
+        """Start the ``integrate`` subcommand.
+        
+        The model construction and setup is done analogously to the 
+        ``sample`` command. Afterwards, an :py:class:`emcee.EnsembleSampler` 
+        is initialized (see :py:func:`init_sampler`) and :py:func:`run_sampling`, 
+        implemented in the ``sample``module, is executed twice for each TI step:
+        once for the burn-in phase and once for the actual sampling phase. 
+        Thereby, the log likelihood is scaled by the respective inverse 
+        temperature of that step. All necessary settings for the sampling 
+        are passed by the ``sampling``argument, except for the inverse 
+        temperatures, which are provided by the ``schedule`` argument.
+        """
         # as recommended in https://emcee.readthedocs.io/en/stable/tutorials/parallel/#
         os.environ["OMP_NUM_THREADS"] = "1"
 

From 74551fed623356bc26f59e5cad9a532e5756da2e Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Tue, 5 Aug 2025 17:59:41 +0200
Subject: [PATCH 09/22] build: fix tmp new lydata package version

---
 pyproject.toml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index fd04f29..5fd868d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ dependencies = [
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
     "loguru",
-    "lydata",
+    "lydata @ git+https://github.com/lycosystem/lydata-package@116a70b433c6fd5947a6656619aa8a1d3dba58a2",
 ]
 dynamic = ["version"]
 
@@ -191,10 +191,7 @@ skip_tags = "v0.1.0-beta.1"
 ignore_tags = ""
 # sort the tags topologically
 topo_order = false
-# sort the commits inside sections by oldest/newest order
-sort_commits = "oldest"
 # limit the number of commits included in the changelog.
 # limit_commits = 42
-
-[tool.uv.sources]
-lydata = { git = "https://github.com/lycosystem/lydata-package", rev = "2a1b20cc318931b86e2c82c05b674a2cec094dac" }
+# sort the commits inside sections by oldest/newest order
+sort_commits = "oldest"

From 5f1d089a3a9d6e8a716200d01f63315f38690df9 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 6 Aug 2025 17:20:05 +0200
Subject: [PATCH 10/22] build: pin fixed lydata again

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5fd868d..5659c16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ dependencies = [
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
     "loguru",
-    "lydata @ git+https://github.com/lycosystem/lydata-package@116a70b433c6fd5947a6656619aa8a1d3dba58a2",
+    "lydata @ git+https://github.com/lycosystem/lydata-package@eb99daf6cd65d93879cfa3552923f25c0a9c29bf",
 ]
 dynamic = ["version"]
 

From e2311bdc842345617a54b0e8c811d22e8d7b3d81 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 13 Aug 2025 10:15:06 +0200
Subject: [PATCH 11/22] change: centralize inv temp schedule generation

---
 src/lyscripts/compute/evidence.py | 81 +++++++++++++-------------
 src/lyscripts/configs.py          | 91 ++++++++++++++++++++++-------
 src/lyscripts/integrate.py        | 95 ++++++++++++++-----------------
 src/lyscripts/schedule.py         | 58 +------------------
 4 files changed, 158 insertions(+), 167 deletions(-)

diff --git a/src/lyscripts/compute/evidence.py b/src/lyscripts/compute/evidence.py
index 53aa885..1cd51e2 100644
--- a/src/lyscripts/compute/evidence.py
+++ b/src/lyscripts/compute/evidence.py
@@ -1,18 +1,21 @@
-"""Given the samples drawn during thermodynamic integration and their
-respective log likelihoods, compute the model log evidence and 
-the Bayesian Information Criterion.
+"""Compute the model evidence from MCMC samples.
+
+Given the samples drawn during thermodynamic integration and their respective log
+likelihoods, compute the model log evidence and the Bayesian Information Criterion.
 """
 
 from __future__ import annotations
-import numpy as np
+
 import json
+from pathlib import Path
+
+import emcee
+import h5py
+import numpy as np
 import pandas as pd
 from loguru import logger
 from pydantic import Field
-
-import h5py
-import emcee
-from pathlib import Path
+from scipy.integrate import trapezoid
 
 from lyscripts.cli import assemble_main
 from lyscripts.configs import (
@@ -21,12 +24,10 @@
     SamplingConfig,
     ScheduleConfig,
 )
-from lyscripts.schedule import SCHEDULES
-
-from scipy.integrate import trapezoid
 
 RNG = np.random.default_rng()
 
+
 def comp_bic(log_probs: np.ndarray, num_params: int, num_data: int) -> float:
     r"""Compute the negative one half of the Bayesian Information Criterion (BIC).
 
@@ -65,6 +66,7 @@ def compute_evidence(
         integrals[i] = trapezoid(y=drawn_accuracy, x=temp_schedule)
     return np.mean(integrals), np.std(integrals)
 
+
 def compute_ti_results(
     settings: EvidenceCLI,
     temp_schedule: np.ndarray,
@@ -86,8 +88,12 @@ def compute_ti_results(
     ti_log_probs = np.zeros(shape=(num_temps, nsteps * nwalker))
 
     for i, run in enumerate(h5_file["ti"]):
-        reader = emcee.backends.HDFBackend(settings.sampling.storage_file, name=f"ti/{run}", read_only=True)
-        ti_log_probs[i] = reader.get_blobs(flat=True)['log_prob']
+        reader = emcee.backends.HDFBackend(
+            settings.sampling.storage_file,
+            name=f"ti/{run}",
+            read_only=True,
+        )
+        ti_log_probs[i] = reader.get_blobs(flat=True)["log_prob"]
 
     evidence, evidence_std = compute_evidence(temp_schedule, ti_log_probs)
     metrics["evidence"] = evidence
@@ -102,7 +108,7 @@ class EvidenceCLI(BaseCLI):
     data: DataConfig
     sampling: SamplingConfig
     schedule: ScheduleConfig = Field(
-        description="Configuration for generating inverse temperature schedule."
+        description="Configuration for generating inverse temperature schedule.",
     )
     plots: Path = Field(
         default="./plots",
@@ -113,35 +119,31 @@ class EvidenceCLI(BaseCLI):
         description="Path to metrics file.",
     )
 
-
     def cli_cmd(self) -> None:
         """Start the ``evidence`` subcommand.
-        Given the MCMC samples from thermodynamic integration provided by the ``sampling``
-        argument and the corresponding inverse temperature schedule, specified in the
-        ``schedule`` argument, the model evidence is computed using the functions
-        ``compute_ti_results`` and ``compute_evidence``. Further the BIC is evaluated.
-        """
 
+        Given the MCMC samples from thermodynamic integration provided by the
+        ``sampling`` argument and the corresponding inverse temperature schedule,
+        specified in the ``schedule`` argument, the model evidence is computed using
+        the functions :py:func:`compute_ti_results` and :py:func`compute_evidence`.
+        Further the BIC is evaluated.
+        """
         data = self.data.load()
 
         metrics = {}
 
-        # temperature schedule: use direct list or generate
-        if self.schedule.values is not None:
-            temp_schedule = np.array(self.schedule.values)
-            logger.info(f"Using direct temperature values: {temp_schedule}")
-        else:
-            func = SCHEDULES[self.schedule.method]
-            temp_schedule = func(self.schedule.num, self.schedule.power)
-            logger.info(f"Generated {self.schedule.method} schedule: {temp_schedule}")
-        
-
-        with h5py.File(self.sampling.storage_file, mode='r') as h5_file:
+        temp_schedule = self.schedule.get_schedule()
+
+        with h5py.File(self.sampling.storage_file, mode="r") as h5_file:
             # Get ndim from the HDF5 backend
-            backend = emcee.backends.HDFBackend(self.sampling.storage_file, read_only=True, name=self.sampling.dataset)
+            backend = emcee.backends.HDFBackend(
+                self.sampling.storage_file,
+                read_only=True,
+                name=self.sampling.dataset,
+            )
             ndim = backend.shape[1]
             logger.info(f"Inferred {ndim} parameters from stored samples")
-            
+
             # if TI has been performed, compute the evidence
             if "ti" in h5_file:
                 temp_schedule, ti_log_probs = compute_ti_results(
@@ -172,10 +174,12 @@ def cli_cmd(self) -> None:
                 )
                 beta_vs_accuracy.to_csv(self.plots, index=False)
                 logger.info(f"Plotted β vs accuracy at {self.plots}")
-            
+
             # use blobs, because also for TI, this is the unscaled log-prob
-            final_log_probs = backend.get_blobs()['log_prob']
-            logger.info(f"Opened samples from emcee backend from {self.sampling.storage_file}")
+            final_log_probs = backend.get_blobs()["log_prob"]
+            logger.info(
+                f"Opened samples from emcee backend from {self.sampling.storage_file}",
+            )
 
             # store metrics in JSON file
             self.metrics.parent.mkdir(parents=True, exist_ok=True)
@@ -191,11 +195,10 @@ def cli_cmd(self) -> None:
 
             with open(self.metrics, mode="w", encoding="utf-8") as metrics_file:
                 json.dump(metrics, metrics_file)
-            
+
             logger.info(f"Wrote out metrics to {self.metrics}")
 
+
 if __name__ == "__main__":
     main = assemble_main(settings_cls=EvidenceCLI, prog_name="compute evidence")
     main()
-
-
diff --git a/src/lyscripts/configs.py b/src/lyscripts/configs.py
index ed9ffb5..ebae236 100644
--- a/src/lyscripts/configs.py
+++ b/src/lyscripts/configs.py
@@ -18,7 +18,7 @@
 from collections.abc import Callable, Sequence
 from copy import deepcopy
 from pathlib import Path
-from typing import Annotated, Any, Literal, Optional
+from typing import Annotated, Any, Literal
 
 import numpy as np
 import pandas as pd
@@ -436,7 +436,7 @@ class SamplingConfig(BaseModel):
         default=None,
         description=(
             "Number of burn-in steps to take. If None, burn-in runs until convergence."
-        )
+        ),
     )
     num_steps: int | None = Field(
         default=100,
@@ -466,28 +466,75 @@ def load(self, thin: int = 1) -> np.ndarray:
             thin=thin,
         )
 
+
+def geometric_schedule(num: int, *_a) -> np.ndarray:
+    """Create a geometric sequence of ``num`` numbers from 0 to 1."""
+    log_seq = np.logspace(0.0, 1.0, num)
+    shifted_seq = log_seq - 1.0
+    return shifted_seq / 9.0
+
+
+def linear_schedule(num: int, *_a) -> np.ndarray:
+    """Create a linear sequence of ``num`` numbers from 0 to 1.
+
+    Equivalent to the :py:func:`power_schedule` with ``power=1``.
+    """
+    return np.linspace(0.0, 1.0, num)
+
+
+def power_schedule(num: int, power: float, *_a) -> np.ndarray:
+    """Create a power sequence of ``num`` numbers from 0 to 1.
+
+    This is essentially a :py:func:`linear_schedule` of ``num`` numbers from 0 to 1,
+    but each number is raised to the power of ``power``.
+    """
+    lin_seq = np.linspace(0.0, 1.0, num)
+    return lin_seq**power
+
+
+SCHEDULES = {
+    "geometric": geometric_schedule,
+    "linear": linear_schedule,
+    "power": power_schedule,
+}
+
+
 class ScheduleConfig(BaseModel):
-        """Configuration for generating a schedule of inverse temperatures."""
+    """Configuration for generating a schedule of inverse temperatures."""
+
+    method: Literal["geometric", "linear", "power"] = Field(
+        default="power",
+        description="Method to generate the inverse temperature schedule.",
+    )
+    num: int = Field(
+        default=32,
+        description="Number of inverse temperatures in the schedule.",
+    )
+    power: float = Field(
+        default=4.0,
+        description="If a power schedule is chosen, use this as power.",
+    )
+    values: list[float] | None = Field(
+        default=None,
+        description=(
+            "List of inverse temperatures to use instead of generating a schedule. "
+            "If a list is provided, the other parameters are ignored."
+        ),
+    )
+
+    def get_schedule(self) -> np.ndarray:
+        """Get the inverse temperature schedule as a numpy array."""
+        if self.values is not None:
+            logger.debug("Using provided inverse temperature values.")
+            schedule = np.array(self.values)
+        else:
+            logger.debug(f"Generating inverse temperature schedule with {self.method}.")
+            func = SCHEDULES[self.method]
+            schedule = func(self.num, self.power)
+
+        logger.info(f"Generated inverse temperature schedule: {schedule}")
+        return schedule
 
-        method: Literal["geometric", "linear", "power"] = Field(
-            default="power",
-            description="Method to generate the inverse temperature schedule.",
-        )
-        num: int = Field(
-            default=32,
-            description="Number of inverse temperatures in the schedule.",
-        )
-        power: float = Field(
-            default=4.0,
-            description="If a power schedule is chosen, use this as power.",
-        )
-        values: list[float] | None = Field(
-            default=None,
-            description=(
-                "List of inverse temperatures to use instead of generating a schedule. "
-                "If a list is provided, the other parameters are ignored."
-            ),
-        )
 
 def map_to_optional_bool(value: Any) -> Any:
     """Try to convert the options in the `PatternType` to a boolean value."""
diff --git a/src/lyscripts/integrate.py b/src/lyscripts/integrate.py
index 926e547..c213116 100644
--- a/src/lyscripts/integrate.py
+++ b/src/lyscripts/integrate.py
@@ -1,5 +1,4 @@
-"""
-Perform thermodynamic integration to evaluate the model evidence.
+"""Perform thermodynamic integration to evaluate the model evidence.
 
 Using the functions provided by the `sample` module, this script implements
 thermodynamic integration (TI) in order to compute the model evidence.
@@ -11,17 +10,16 @@
 
 import os
 from typing import Any
-from loguru import logger
 
 import emcee
-import numpy as np
 import h5py
-
-from lyscripts.cli import assemble_main
-from pydantic import Field
-
+import numpy as np
+from loguru import logger
 from lydata.utils import ModalityConfig
+from pydantic import Field
 
+import lyscripts.sample as sample_module  # Import the module to set its global MODEL
+from lyscripts.cli import assemble_main
 from lyscripts.configs import (
     BaseCLI,
     DataConfig,
@@ -30,31 +28,28 @@
     ModelConfig,
     SamplingConfig,
     ScheduleConfig,
-    construct_model,
     add_distributions,
     add_modalities,
+    construct_model,
 )
-
-import lyscripts.sample as sample_module  # Import the module to set its global MODEL
-from lyscripts.schedule import SCHEDULES
-
 from lyscripts.utils import get_hdf5_backend
 
+
 def init_ti_sampler(
-    settings: IntegrateCLI, 
-    temp_idx: int, 
-    ndim: int, 
-    inv_temp: float, 
-    pool: Any    
+    settings: IntegrateCLI,
+    temp_idx: int,
+    ndim: int,
+    inv_temp: float,
+    pool: Any,
 ) -> emcee.EnsembleSampler:
     """Initialize the ``emcee.EnsembleSampler`` for TI with the given ``settings''."""
     nwalkers = ndim * settings.sampling.walkers_per_dim
     backend = get_hdf5_backend(
-                    file_path=settings.sampling.storage_file,
-                    dataset=f"ti/{temp_idx+1:0>2d}",
-                    nwalkers=nwalkers,
-                    ndim=ndim,
-                )
+        file_path=settings.sampling.storage_file,
+        dataset=f"ti/{temp_idx + 1:0>2d}",
+        nwalkers=nwalkers,
+        ndim=ndim,
+    )
     return emcee.EnsembleSampler(
         nwalkers=nwalkers,
         ndim=ndim,
@@ -67,6 +62,7 @@ def init_ti_sampler(
         parameter_names=list(MODEL.get_named_params().keys()),
     )
 
+
 class IntegrateCLI(BaseCLI):
     """Perform thermodynamic integration to compute the model evidence."""
 
@@ -88,21 +84,20 @@ class IntegrateCLI(BaseCLI):
     data: DataConfig
     sampling: SamplingConfig
     schedule: ScheduleConfig = Field(
-        description="Configuration for generating inverse temperature schedule."
+        description="Configuration for generating inverse temperature schedule.",
     )
 
-
     def cli_cmd(self) -> None:
         """Start the ``integrate`` subcommand.
-        
-        The model construction and setup is done analogously to the 
-        ``sample`` command. Afterwards, an :py:class:`emcee.EnsembleSampler` 
-        is initialized (see :py:func:`init_sampler`) and :py:func:`run_sampling`, 
+
+        The model construction and setup is done analogously to the
+        ``sample`` command. Afterwards, an :py:class:`emcee.EnsembleSampler`
+        is initialized (see :py:func:`init_sampler`) and :py:func:`run_sampling`,
         implemented in the ``sample``module, is executed twice for each TI step:
-        once for the burn-in phase and once for the actual sampling phase. 
-        Thereby, the log likelihood is scaled by the respective inverse 
-        temperature of that step. All necessary settings for the sampling 
-        are passed by the ``sampling``argument, except for the inverse 
+        once for the burn-in phase and once for the actual sampling phase.
+        Thereby, the log likelihood is scaled by the respective inverse
+        temperature of that step. All necessary settings for the sampling
+        are passed by the ``sampling``argument, except for the inverse
         temperatures, which are provided by the ``schedule`` argument.
         """
         # as recommended in https://emcee.readthedocs.io/en/stable/tutorials/parallel/#
@@ -110,41 +105,34 @@ def cli_cmd(self) -> None:
 
         logger.debug(self.model_dump_json(indent=2))
 
-        # ugly, but necessary for pickling  
+        # ugly, but necessary for pickling
         global MODEL
         MODEL = construct_model(self.model, self.graph)
         MODEL = add_distributions(MODEL, self.distributions)
         MODEL = add_modalities(MODEL, self.modalities)
         MODEL.load_patient_data(**self.data.get_load_kwargs())
         ndim = MODEL.get_num_dims()
-        
+
         # set MODEL in the sample module's namespace so log_prob_fn can access it
         sample_module.MODEL = MODEL
 
-        # temperature schedule: use direct list or generate
-        if self.schedule.values is not None:
-            temp_schedule = np.array(self.schedule.values)
-            logger.info(f"Using direct temperature values: {temp_schedule}")
-        else:
-            func = SCHEDULES[self.schedule.method]
-            temp_schedule = func(self.schedule.num, self.schedule.power)
-            logger.info(f"Generated {self.schedule.method} schedule: {temp_schedule}")
-        
+        schedule = self.schedule.get_schedule()
+
         # emcee does not support numpy's new random number generator yet.
-        np.random.seed(self.sampling.seed) # noqa: NPY002
+        np.random.seed(self.sampling.seed)  # noqa: NPY002
 
         with sample_module.get_pool(self.sampling.cores) as pool:
-            for idx, inv_temp in enumerate(temp_schedule):
+            for idx, inv_temp in enumerate(schedule):
                 sampler = init_ti_sampler(
                     settings=self,
                     temp_idx=idx,
                     ndim=ndim,
                     inv_temp=inv_temp,
-                    pool=pool
+                    pool=pool,
                 )
 
                 sample_module.run_sampling(
-                    description=f"Burn-in phase: TI step {idx+1}/{len(temp_schedule)}",
+                    description=f"Burn-in phase: TI step {idx + 1}/{len(schedule)}",
                     sampler=sampler,
                     num_steps=self.sampling.burnin_steps,
                     check_interval=self.sampling.check_interval,
@@ -154,7 +142,7 @@ def cli_cmd(self) -> None:
                 )
 
                 sample_module.run_sampling(
-                    description=f"Sampling phase: TI step {idx+1}/{len(temp_schedule)}",
+                    description=f"Sampling phase: TI step {idx + 1}/{len(schedule)}",
                     sampler=sampler,
                     num_steps=self.sampling.num_steps,
                     reset_backend=True,
@@ -163,8 +151,13 @@ def cli_cmd(self) -> None:
                 )
             # copy last sampling round over to a group in the HDF5 file called "mcmc"
             with h5py.File(self.sampling.storage_file, mode="r+") as h5_file:
-                h5_file.copy(f"ti/{len(temp_schedule):0>2d}", h5_file, name=self.sampling.dataset)
+                h5_file.copy(
+                    f"ti/{len(schedule):0>2d}",
+                    h5_file,
+                    name=self.sampling.dataset,
+                )
+
 
 if __name__ == "__main__":
     main = assemble_main(settings_cls=IntegrateCLI, prog_name="integrate")
-    main()
\ No newline at end of file
+    main()
diff --git a/src/lyscripts/schedule.py b/src/lyscripts/schedule.py
index 16b367f..99fa334 100644
--- a/src/lyscripts/schedule.py
+++ b/src/lyscripts/schedule.py
@@ -10,72 +10,20 @@
 :math:`\beta_i^k` where :math:`k` could e.g. be 5.
 """
 
-from typing import Literal
-
-import numpy as np
 from loguru import logger
-from pydantic import Field
 
 from lyscripts.cli import assemble_main
-from lyscripts.configs import BaseCLI
-
-
-def geometric_schedule(num: int, *_a) -> np.ndarray:
-    """Create a geometric sequence of ``num`` numbers from 0 to 1."""
-    log_seq = np.logspace(0.0, 1.0, num)
-    shifted_seq = log_seq - 1.0
-    return shifted_seq / 9.0
-
-
-def linear_schedule(num: int, *_a) -> np.ndarray:
-    """Create a linear sequence of ``num`` numbers from 0 to 1.
-
-    Equivalent to the :py:func:`power_schedule` with ``power=1``.
-    """
-    return np.linspace(0.0, 1.0, num)
-
+from lyscripts.configs import BaseCLI, ScheduleConfig
 
-def power_schedule(num: int, power: float, *_a) -> np.ndarray:
-    """Create a power sequence of ``num`` numbers from 0 to 1.
 
-    This is essentially a :py:func:`linear_schedule` of ``num`` numbers from 0 to 1,
-    but each number is raised to the power of ``power``.
-    """
-    lin_seq = np.linspace(0.0, 1.0, num)
-    return lin_seq**power
-
-
-SCHEDULES = {
-    "geometric": geometric_schedule,
-    "linear": linear_schedule,
-    "power": power_schedule,
-}
-
-
-class ScheduleCLI(BaseCLI):
+class ScheduleCLI(ScheduleConfig, BaseCLI):
     """Generate an inverse temperature schedule for thermodynamic integration."""
 
-    method: Literal["geometric", "linear", "power"] = Field(
-        default="geometric",
-        description="Choose the method to distribute the inverse temperatures.",
-    )
-    num: int = Field(
-        default=32,
-        description="Number of inverse temperatures in the schedule.",
-    )
-    power: float = Field(
-        default=4,
-        description="If a power schedule is chosen, use this as power.",
-    )
-
     def cli_cmd(self) -> None:
         """Start the ``schedule`` command."""
         logger.debug(self.model_dump_json(indent=2))
 
-        func = SCHEDULES[self.method]
-        schedule = func(self.num, self.power)
-
-        for inv_temp in schedule:
+        for inv_temp in self.get_schedule():
             # print is necessary to allow piping the output
             print(inv_temp)  # noqa: T201
 

From 663bd69c54dfd050cabad5ea3acdd071a389bf4a Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 13 Aug 2025 12:13:55 +0200
Subject: [PATCH 12/22] change: store selected loglevel globally

---
 src/lyscripts/cli.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/lyscripts/cli.py b/src/lyscripts/cli.py
index 26870c7..c1baae2 100644
--- a/src/lyscripts/cli.py
+++ b/src/lyscripts/cli.py
@@ -17,6 +17,8 @@
 from rich.logging import RichHandler
 from rich_argparse import ArgumentDefaultsRichHelpFormatter
 
+_current_log_level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "INFO"
+
 
 def assemble_main(
     settings_cls: type[BaseSettings],
@@ -80,11 +82,12 @@ def configure_logging(
     """
     logger.enable("lyscripts")
     logger.enable("lydata")
-    log_level = somewhat_safely_get_loglevel(argv=argv)
+    global _current_log_level
+    _current_log_level = somewhat_safely_get_loglevel(argv=argv)
     logger.remove()
     handler = RichHandler(console=console)
     logger.add(
         sink=handler,
-        level=log_level,
+        level=_current_log_level,
         format="<lvl>{message}</>",
     )

From ef6f51bf7e7cf920dd5db7c7cf72303d913e60ed Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 13 Aug 2025 13:54:07 +0200
Subject: [PATCH 13/22] feat: add collector utility/command

---
 pyproject.toml                          |  11 +-
 src/lyscripts/__init__.py               |   2 +-
 src/lyscripts/data/__init__.py          |   2 +
 src/lyscripts/data/collect/__init__.py  | 163 ++++++++++++++++++++++++
 src/lyscripts/data/collect/collector.js | 150 ++++++++++++++++++++++
 src/lyscripts/data/collect/index.html   |  26 ++++
 6 files changed, 352 insertions(+), 2 deletions(-)
 create mode 100644 src/lyscripts/data/collect/__init__.py
 create mode 100644 src/lyscripts/data/collect/collector.js
 create mode 100644 src/lyscripts/data/collect/index.html

diff --git a/pyproject.toml b/pyproject.toml
index 5659c16..69ba6a6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ dependencies = [
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
     "loguru",
-    "lydata @ git+https://github.com/lycosystem/lydata-package@eb99daf6cd65d93879cfa3552923f25c0a9c29bf",
+    "lydata @ git+https://github.com/lycosystem/lydata-package@79c5d4996b37a833afca457629d8d854acc05a33",
 ]
 dynamic = ["version"]
 
@@ -81,9 +81,18 @@ dev = [
 [project.scripts]
 lyscripts = "lyscripts:main"
 
+[tool.setuptools]
+include-package-data = true
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools.package-data]
+"lyscripts" = [
+    "src/lyscripts/data/collect/collector.js",
+    "src/lyscripts/data/collect/index.html",
+]
+
 [tool.setuptools_scm]
 write_to = "src/lyscripts/_version.py"
 local_scheme = "no-local-version"
diff --git a/src/lyscripts/__init__.py b/src/lyscripts/__init__.py
index 6727547..e9dbcb1 100644
--- a/src/lyscripts/__init__.py
+++ b/src/lyscripts/__init__.py
@@ -17,7 +17,7 @@
     CliSubCommand,
 )
 
-from lyscripts import compute, data, sample, schedule, integrate  # noqa: F401
+from lyscripts import compute, data, integrate, sample, schedule  # noqa: F401
 from lyscripts._version import version
 from lyscripts.cli import assemble_main, configure_logging
 from lyscripts.utils import console
diff --git a/src/lyscripts/data/__init__.py b/src/lyscripts/data/__init__.py
index c9863ec..eb86dbd 100644
--- a/src/lyscripts/data/__init__.py
+++ b/src/lyscripts/data/__init__.py
@@ -17,6 +17,7 @@
 from pydantic_settings import BaseSettings, CliApp, CliSubCommand
 
 from lyscripts.data import (  # noqa: F401
+    collect,
     enhance,
     fetch,
     generate,
@@ -32,6 +33,7 @@
 class DataCLI(BaseSettings):
     """Work with lymphatic progression data through this CLI."""
 
+    collect: CliSubCommand[collect.CollectorCLI]
     lyproxify: CliSubCommand[lyproxify.LyproxifyCLI]
     join: CliSubCommand[join.JoinCLI]
     split: CliSubCommand[split.SplitCLI]
diff --git a/src/lyscripts/data/collect/__init__.py b/src/lyscripts/data/collect/__init__.py
new file mode 100644
index 0000000..44e1f19
--- /dev/null
+++ b/src/lyscripts/data/collect/__init__.py
@@ -0,0 +1,163 @@
+"""Submodule to collect data interactively using a simple web interface.
+
+With the simply command
+
+.. code-block:: bash
+
+    lyscripts data collect
+
+One can start a very basic web server that serves an interactive UI at
+``http://localhost:8000/``. There, one can enter patient, tumor, and lymphatic
+involvement data one by one. When completed, the "submit" button will parse, validate,
+and convert the data to serve a downloadable CSV file.
+
+This resulting CSV file is in the correct format to be used in `LyProX`_ and for
+inference using our `lymph-model`_ library.
+
+.. _LyProX: https://lyprox.org
+.. _lymph-model: https://lymph-model.readthedocs.io
+"""
+
+import inspect
+import io
+import logging
+from pathlib import Path
+from typing import Any
+
+import lydata
+import lydata.validator
+import pandas as pd
+from fastapi import FastAPI, HTTPException
+from fastapi.responses import StreamingResponse
+from loguru import logger
+from pydantic import Field, RootModel
+from starlette.responses import FileResponse, HTMLResponse
+
+from lyscripts.cli import _current_log_level
+from lyscripts.configs import BaseCLI
+
+app = FastAPI(
+    title="lyDATA Collector",
+    description=(
+        "A simple web interface to collect data for the lyDATA datasets. "
+        "This is a prototype and not intended for production use."
+    ),
+    version=lydata.__version__,
+)
+
+BASE_DIR = Path(__file__).parent
+modalities = lydata.schema.get_default_modalities()
+RecordModel = lydata.schema.create_full_record_model(modalities, title="Record")
+ROOT_MODEL = RootModel[list[RecordModel]]
+
+
+@app.get("/")
+def serve_index() -> HTMLResponse:
+    """Serve the index.html file."""
+    with open(BASE_DIR / "index.html") as file:
+        content = file.read()
+    return HTMLResponse(content=content)
+
+
+@app.get("/schema")
+def serve_schema() -> dict[str, Any]:
+    """Serve the JSON schema for the patient and tumor records."""
+    return ROOT_MODEL.model_json_schema()
+
+
+@app.get("/collector.js")
+def serve_collector_js() -> FileResponse:
+    """Serve the collector.js file."""
+    return FileResponse(BASE_DIR / "collector.js")
+
+
+@app.post("/submit")
+async def process(data: RootModel) -> StreamingResponse:
+    """Convert the submitted data to a DataFrame."""
+    logger.info(f"Received data: {data.root}")
+
+    if len(data.root) == 0:
+        logger.warning("No records provided in the data.")
+        raise HTTPException(
+            status_code=400,
+            detail="No records provided in the data.",
+        )
+
+    flattened_records = []
+
+    for record in data.root:
+        flattened_record = lydata.validator.flatten(record)
+        logger.debug(f"Flattened record: {flattened_record}")
+        flattened_records.append(flattened_record)
+
+    df = pd.DataFrame(flattened_records)
+    df.columns = pd.MultiIndex.from_tuples(flattened_record.keys())
+    logger.info(df.patient.core.head())
+
+    buffer = io.StringIO()
+    df.to_csv(buffer, index=False)
+    buffer.seek(0)
+    logger.success("Data prepared for download")
+    return StreamingResponse(
+        buffer,
+        media_type="text/csv",
+        headers={"Content-Disposition": "attachment; filename=lydata_records.csv"},
+    )
+
+
+class InterceptHandler(logging.Handler):
+    """Intercept logging messages and redirect them to Loguru."""
+
+    def emit(self, record: logging.LogRecord) -> None:
+        """Intercept the log record and redirect it to Loguru."""
+        # Get corresponding Loguru level if it exists.
+        try:
+            level: str | int = logger.level(record.levelname).name
+        except ValueError:
+            level = record.levelno
+
+        # Find caller from where originated the logged message.
+        frame, depth = inspect.currentframe(), 0
+        while frame:
+            filename = frame.f_code.co_filename
+            is_logging = filename == logging.__file__
+            is_frozen = "importlib" in filename and "_bootstrap" in filename
+            if depth > 0 and not (is_logging or is_frozen):
+                break
+            frame = frame.f_back
+            depth += 1
+
+        logger.opt(depth=depth, exception=record.exc_info).log(
+            level,
+            record.getMessage(),
+        )
+
+
+class CollectorCLI(BaseCLI):
+    """Command-line interface for the lyDATA collector."""
+
+    hostname: str = Field(
+        default="localhost",
+        description="Hostname to run the FastAPI app on.",
+    )
+    port: int = Field(
+        default=8000,
+        description="Port to run the FastAPI app on.",
+    )
+
+    def cli_cmd(self) -> None:
+        """Run the FastAPI app."""
+        logger.debug(self.model_dump_json(indent=2))
+        import uvicorn
+
+        # Intercept standard logging and redirect it to Loguru
+        logging.basicConfig(handlers=[InterceptHandler()], level=0, force=True)
+        logger.enable("lydata")
+
+        uvicorn.run(
+            app,
+            host=self.hostname,
+            port=self.port,
+            log_level=_current_log_level.lower(),
+            log_config=None,
+        )
diff --git a/src/lyscripts/data/collect/collector.js b/src/lyscripts/data/collect/collector.js
new file mode 100644
index 0000000..d5e4a59
--- /dev/null
+++ b/src/lyscripts/data/collect/collector.js
@@ -0,0 +1,150 @@
+/**
+ * Client-side helper functions for collecting user input through JSONEditor,
+ * validating it against a fetched JSON Schema, submitting the validated data
+ * to the backend, and presenting a downloadable CSV returned by the server.
+ *
+ * NOTE: Functionality is intentionally unchanged; only readability and
+ * documentation have been improved.
+ */
+
+/**
+ * Ensure an alert element (used to display validation errors) exists.
+ * Creates and appends it if missing.
+ *
+ * @returns {HTMLDivElement} The existing or newly created alert element.
+ */
+function ensureAlertExists() {
+  let alertElement = document.querySelector('.alert');
+  if (!alertElement) {
+    alertElement = document.createElement('div');
+  }
+  alertElement.className = 'alert alert-danger';
+  const editorHolder = document.getElementById('editor_holder');
+  editorHolder.appendChild(alertElement);
+  return alertElement;
+}
+
+/**
+ * Remove an existing validation alert if present.
+ */
+function ensureAlertRemoved() {
+  const existingAlert = document.querySelector('.alert');
+  if (existingAlert) {
+    console.log('Clearing existing alert');
+    existingAlert.remove();
+  }
+}
+
+/**
+ * Remove an existing download button (if it exists) to avoid duplicates.
+ */
+function ensureDownloadButtonRemoved() {
+  const existingButton = document.getElementById('download_link');
+  if (existingButton) {
+    console.log('Clearing existing download button');
+    existingButton.remove();
+  }
+}
+
+/**
+ * Create (or replace) a download button for a CSV blob returned by the server.
+ *
+ * @param {Blob} blob - The CSV data blob to make downloadable.
+ */
+function createDownloadButton(blob) {
+  ensureDownloadButtonRemoved();
+
+  const url = window.URL.createObjectURL(blob);
+  const downloadLink = document.createElement('a');
+  downloadLink.id = 'download_link';
+  downloadLink.href = url;
+  downloadLink.textContent = 'Download CSV';
+  downloadLink.className = 'btn btn-success';
+  downloadLink.download = 'lydata_records.csv';
+
+  document.getElementById('editor_holder').appendChild(downloadLink);
+  console.log('Download button created:', downloadLink);
+}
+
+/**
+ * Send validated editor data to the backend for processing. Expects a CSV blob
+ * in response which is then exposed via a generated download button.
+ *
+ * @param {JSONEditor} editor - The JSONEditor instance from which to read data.
+ */
+async function sendEditorData(editor) {
+  const data = editor.getValue();
+  console.log('Sending data:', data);
+
+  try {
+    const response = await fetch('/submit', {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify(data)
+    });
+
+    if (!response.ok) {
+      // Try to parse error details from JSON, fallback to text
+      let errorMsg = 'Unknown error';
+      try {
+        const err = await response.json();
+        errorMsg = err.detail || err.message || errorMsg;
+      } catch {
+        errorMsg = await response.text();
+      }
+      throw new Error(errorMsg);
+    }
+
+    const blob = await response.blob();
+    console.log('Received processed data as blob:', blob);
+    createDownloadButton(blob);
+  } catch (error) {
+    ensureDownloadButtonRemoved();
+    console.error('Error submitting data:', error);
+    const alert = ensureAlertExists();
+    alert.textContent = 'Error submitting data: ' + error.message;
+    alert.classList.add('alert-danger');
+  }
+}
+
+/**
+ * Validate the editor content. If there are validation errors they are
+ * displayed in an alert; otherwise the data is submitted to the backend.
+ *
+ * @param {JSONEditor} editor - The JSONEditor instance to validate & submit.
+ */
+function processEditor(editor) {
+  const errors = editor.validate();
+
+  if (errors.length) {
+    console.error('Validation errors:', errors);
+    const alert = ensureAlertExists();
+    alert.textContent = 'Validation errors: ' + errors.map(e => e.message).join(', ');
+  } else {
+    console.log('Data successfully validated');
+    ensureAlertRemoved();
+    sendEditorData(editor);
+  }
+}
+
+// Fetch the JSON Schema to initialize the editor
+fetch('/schema')
+  .then(response => response.json())
+  .then(schema => {
+    const element = document.getElementById('editor_holder');
+    const options = {
+      disable_edit_json: true,
+      theme: 'bootstrap5',
+      iconlib: 'bootstrap',
+      object_layout: 'grid',
+      schema: schema
+  };
+  const editor = new JSONEditor(element, options);
+
+    // Bind the submit button to validation + submission flow
+    document.getElementById('submit').addEventListener('click', () => {
+      console.log('Submit button clicked');
+      processEditor(editor);
+    });
+  })
+  .catch(error => console.error('Error loading schema:', error));
diff --git a/src/lyscripts/data/collect/index.html b/src/lyscripts/data/collect/index.html
new file mode 100644
index 0000000..931dacf
--- /dev/null
+++ b/src/lyscripts/data/collect/index.html
@@ -0,0 +1,26 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+  <meta charset="utf-8" />
+  <title>Basic JSON Editor Example</title>
+
+  <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet"
+    integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.13.1/font/bootstrap-icons.min.css">
+
+  <script src="https://cdn.jsdelivr.net/npm/@json-editor/json-editor@latest/dist/jsoneditor.min.js"></script>
+</head>
+
+<body>
+  <main class="container">
+    <h1>LyDATA Collector</h1>
+
+    <div id='editor_holder'></div>
+    <button class="btn btn-primary" id='submit'>Submit (console.log)</button>
+
+    <script src="/collector.js"></script>
+  </main>
+</body>
+
+</html>

From 0bc2a64801acecab04a9711151e3cbd6654a1268 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Wed, 13 Aug 2025 15:02:00 +0200
Subject: [PATCH 14/22] docs: improve collect description

---
 README.md                              |  6 ++-
 docs/source/data/collect.rst           | 13 ++++++
 docs/source/data/init.rst              |  1 +
 docs/source/index.rst                  |  2 +-
 src/lyscripts/cli.py                   | 30 +++++++++++++
 src/lyscripts/data/__init__.py         |  6 +++
 src/lyscripts/data/collect/__init__.py | 61 ++++++++++----------------
 7 files changed, 80 insertions(+), 39 deletions(-)
 create mode 100644 docs/source/data/collect.rst

diff --git a/README.md b/README.md
index 9621e28..e64323b 100644
--- a/README.md
+++ b/README.md
@@ -41,7 +41,11 @@ Simply run
 lyscripts --help
 ```
 
-in your terminal and let the output guide you through the functions of the program.
+in your terminal to display the help text for the main command. It will list all subcommands that are avialable, which you can then also call with `lyscripts <subcommand> --help` to get more information on its use and the available arguments.
+
+For example, one subcommand is `lyscripts data collect`, which will launch a small web server that allows a user to enter patient records on lymphatic involvement in head and neck cancer one row at a time and construct a standardized CSV file from it.
+
+<!--- ### --->
 
 You can also refer to the [documentation] for a written-down version of all these help texts and even more context on how and why to use the provided commands.
 
diff --git a/docs/source/data/collect.rst b/docs/source/data/collect.rst
new file mode 100644
index 0000000..8c8b08b
--- /dev/null
+++ b/docs/source/data/collect.rst
@@ -0,0 +1,13 @@
+.. currentmodule:: lyscripts.data.collect
+
+Collect lyDATA Tables Interactively
+===================================
+
+.. automodule:: lyscripts.data.collect
+    :members:
+    :show-inheritance:
+
+Command Help
+------------
+
+.. program-output:: lyscripts data collect --help
diff --git a/docs/source/data/init.rst b/docs/source/data/init.rst
index e53ee60..014bb85 100644
--- a/docs/source/data/init.rst
+++ b/docs/source/data/init.rst
@@ -19,6 +19,7 @@ Submodules
 .. toctree::
     :maxdepth: 1
 
+    collect
     lyproxify
     join
     split
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 1f36252..647e4e1 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -8,7 +8,7 @@ Introduction
 
 
 .. include:: ../../README.md
-    :end-line: 30
+    :end-before: <!--- ### --->
     :parser: myst_parser.sphinx_
 
 
diff --git a/src/lyscripts/cli.py b/src/lyscripts/cli.py
index c1baae2..b6448d0 100644
--- a/src/lyscripts/cli.py
+++ b/src/lyscripts/cli.py
@@ -8,6 +8,8 @@
 .. _loguru: https://loguru.readthedocs.io/en/stable
 """
 
+import inspect
+import logging
 from collections.abc import Callable
 from typing import Literal
 
@@ -91,3 +93,31 @@ def configure_logging(
         level=_current_log_level,
         format="<lvl>{message}</>",
     )
+
+
+class InterceptHandler(logging.Handler):
+    """Intercept logging messages and redirect them to Loguru."""
+
+    def emit(self, record: logging.LogRecord) -> None:
+        """Intercept the log record and redirect it to Loguru."""
+        # Get corresponding Loguru level if it exists.
+        try:
+            level: str | int = logger.level(record.levelname).name
+        except ValueError:
+            level = record.levelno
+
+        # Find caller from where originated the logged message.
+        frame, depth = inspect.currentframe(), 0
+        while frame:
+            filename = frame.f_code.co_filename
+            is_logging = filename == logging.__file__
+            is_frozen = "importlib" in filename and "_bootstrap" in filename
+            if depth > 0 and not (is_logging or is_frozen):
+                break
+            frame = frame.f_back
+            depth += 1
+
+        logger.opt(depth=depth, exception=record.exc_info).log(
+            level,
+            record.getMessage(),
+        )
diff --git a/src/lyscripts/data/__init__.py b/src/lyscripts/data/__init__.py
index eb86dbd..29ffe69 100644
--- a/src/lyscripts/data/__init__.py
+++ b/src/lyscripts/data/__init__.py
@@ -7,6 +7,12 @@
 the installed datasets provided by the `lydata`_ package and directly from the
 associated `GitHub repository`_.
 
+Another cool feature is the built-in mini web application that allows collecting nodal
+involvement data interactively and in the same standardized format as we have published
+in the past, both on `LyProX`_ and in our `GitHub repository`_. It can be launched by
+running `lyscripts data collect` in the terminal. See the docs for the
+:py:mod:`lyscripts.data.collect` submodule on more information.
+
 .. _Make: https://www.gnu.org/software/make/
 .. _DVC: https://dvc.org
 .. _LyProX: https://lyprox.org
diff --git a/src/lyscripts/data/collect/__init__.py b/src/lyscripts/data/collect/__init__.py
index 44e1f19..cd681c8 100644
--- a/src/lyscripts/data/collect/__init__.py
+++ b/src/lyscripts/data/collect/__init__.py
@@ -1,6 +1,6 @@
 """Submodule to collect data interactively using a simple web interface.
 
-With the simply command
+With the simple command
 
 .. code-block:: bash
 
@@ -11,14 +11,13 @@
 involvement data one by one. When completed, the "submit" button will parse, validate,
 and convert the data to serve a downloadable CSV file.
 
-This resulting CSV file is in the correct format to be used in `LyProX`_ and for
+The resulting CSV file is in the correct format to be used in `LyProX`_ and for
 inference using our `lymph-model`_ library.
 
 .. _LyProX: https://lyprox.org
 .. _lymph-model: https://lymph-model.readthedocs.io
 """
 
-import inspect
 import io
 import logging
 from pathlib import Path
@@ -33,7 +32,7 @@
 from pydantic import Field, RootModel
 from starlette.responses import FileResponse, HTMLResponse
 
-from lyscripts.cli import _current_log_level
+from lyscripts.cli import InterceptHandler, _current_log_level
 from lyscripts.configs import BaseCLI
 
 app = FastAPI(
@@ -52,8 +51,8 @@
 
 
 @app.get("/")
-def serve_index() -> HTMLResponse:
-    """Serve the index.html file."""
+def serve_index_html() -> HTMLResponse:
+    """Serve the ``index.html`` file at the URL's root."""
     with open(BASE_DIR / "index.html") as file:
         content = file.read()
     return HTMLResponse(content=content)
@@ -67,13 +66,29 @@ def serve_schema() -> dict[str, Any]:
 
 @app.get("/collector.js")
 def serve_collector_js() -> FileResponse:
-    """Serve the collector.js file."""
+    """Serve the ``collector.js`` file under ``"http://{host}:{port}/collector.js"``.
+
+    This frontend JavaScript file loads the `JSON-Editor`_ library and initializes it
+    using the schema returned by the :py:func:`serve_schema` function.
+
+    .. _JSON-Editor: https://github.com/json-editor/json-editor/
+    """
     return FileResponse(BASE_DIR / "collector.js")
 
 
 @app.post("/submit")
 async def process(data: RootModel) -> StreamingResponse:
-    """Convert the submitted data to a DataFrame."""
+    """Process the submitted data to a DataFrame.
+
+    `FastAPI`_ will automatically parse the received JSON data into the list of
+    instances of he pydantic type defined by the
+    :py:func:`lydata.schema.create_full_record_model` function.
+
+    From this list, we create a pandas DataFrame and return it as a downloadable CSV
+    file.
+
+    .. _FastAPI: https://fastapi.tiangolo.com/
+    """
     logger.info(f"Received data: {data.root}")
 
     if len(data.root) == 0:
@@ -105,36 +120,8 @@ async def process(data: RootModel) -> StreamingResponse:
     )
 
 
-class InterceptHandler(logging.Handler):
-    """Intercept logging messages and redirect them to Loguru."""
-
-    def emit(self, record: logging.LogRecord) -> None:
-        """Intercept the log record and redirect it to Loguru."""
-        # Get corresponding Loguru level if it exists.
-        try:
-            level: str | int = logger.level(record.levelname).name
-        except ValueError:
-            level = record.levelno
-
-        # Find caller from where originated the logged message.
-        frame, depth = inspect.currentframe(), 0
-        while frame:
-            filename = frame.f_code.co_filename
-            is_logging = filename == logging.__file__
-            is_frozen = "importlib" in filename and "_bootstrap" in filename
-            if depth > 0 and not (is_logging or is_frozen):
-                break
-            frame = frame.f_back
-            depth += 1
-
-        logger.opt(depth=depth, exception=record.exc_info).log(
-            level,
-            record.getMessage(),
-        )
-
-
 class CollectorCLI(BaseCLI):
-    """Command-line interface for the lyDATA collector."""
+    """Serve a FastAPI web app for collecting involvement patterns as CSV files."""
 
     hostname: str = Field(
         default="localhost",

From 1bb0cbfa515250138ca23f779458d7b70950915a Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Fri, 15 Aug 2025 11:33:46 +0200
Subject: [PATCH 15/22] chore: add CITATION.cff

---
 CITATION.cff | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100755 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100755
index 0000000..70404a2
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,25 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: lyscripts
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Roman
+    family-names: Ludwig
+    orcid: 'https://orcid.org/0000-0001-9434-328X'
+    affiliation: University Hospital Zurich
+repository-code: 'https://github.com/lycosystem/lyscripts'
+url: 'https://lyscripts.readthedocs.io'
+abstract: >-
+  Scripts for reproducible research on lymphatic tumor
+  progression in head and neck cancer.
+keywords:
+  - cancer
+  - metastasis
+  - lymphatic system
+  - head and neck
+license: MIT

From 73e60688bd7d12b66fbccb4132377b23a06f734f Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Mon, 18 Aug 2025 13:48:29 +0200
Subject: [PATCH 16/22] build: add uvicorn, fastapi to deps

---
 pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 69ba6a6..112ecf2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,6 +51,8 @@ dependencies = [
     "pydantic-settings >= 2.7.0, != 2.9.1, != 2.9.0",
     "numpydantic",
     "loguru",
+    "fastapi",
+    "uvicorn",
     "lydata @ git+https://github.com/lycosystem/lydata-package@79c5d4996b37a833afca457629d8d854acc05a33",
 ]
 dynamic = ["version"]

From fbff10240ab7e7fced48bea4880c13a133b7a252 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Mon, 18 Aug 2025 13:48:42 +0200
Subject: [PATCH 17/22] change: disable properties in collector

---
 src/lyscripts/data/collect/collector.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/lyscripts/data/collect/collector.js b/src/lyscripts/data/collect/collector.js
index d5e4a59..3d8d5d9 100644
--- a/src/lyscripts/data/collect/collector.js
+++ b/src/lyscripts/data/collect/collector.js
@@ -137,6 +137,7 @@ fetch('/schema')
       theme: 'bootstrap5',
       iconlib: 'bootstrap',
       object_layout: 'grid',
+      disable_properties: true,
       schema: schema
   };
   const editor = new JSONEditor(element, options);

From 4d49a9f6db3e3017826968755267e2d21c608866 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Tue, 26 Aug 2025 11:17:01 +0200
Subject: [PATCH 18/22] fix: use fixed lydata `.enhance()` method

---
 pyproject.toml                         | 2 +-
 src/lyscripts/data/collect/__init__.py | 2 +-
 src/lyscripts/data/enhance.py          | 5 +----
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 112ecf2..af6b90d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ dependencies = [
     "loguru",
     "fastapi",
     "uvicorn",
-    "lydata @ git+https://github.com/lycosystem/lydata-package@79c5d4996b37a833afca457629d8d854acc05a33",
+    "lydata @ git+https://github.com/lycosystem/lydata-package@8469a26bea1d275b7ced43fbe3a269c8b30b60f4",
 ]
 dynamic = ["version"]
 
diff --git a/src/lyscripts/data/collect/__init__.py b/src/lyscripts/data/collect/__init__.py
index cd681c8..425c728 100644
--- a/src/lyscripts/data/collect/__init__.py
+++ b/src/lyscripts/data/collect/__init__.py
@@ -46,7 +46,7 @@
 
 BASE_DIR = Path(__file__).parent
 modalities = lydata.schema.get_default_modalities()
-RecordModel = lydata.schema.create_full_record_model(modalities, title="Record")
+RecordModel = lydata.schema.create_full_record_model(modalities, model_name="Record")
 ROOT_MODEL = RootModel[list[RecordModel]]
 
 
diff --git a/src/lyscripts/data/enhance.py b/src/lyscripts/data/enhance.py
index a8a795a..87b1e23 100644
--- a/src/lyscripts/data/enhance.py
+++ b/src/lyscripts/data/enhance.py
@@ -40,12 +40,9 @@ def cli_cmd(self) -> None:
         logger.debug(self.model_dump_json(indent=2))
 
         data: LyDataFrame = self.input.load()
-        data[self.method] = data.ly.combine(
+        data = data.ly.enhance(
             modalities=self.modalities,
             method=self.method,
-        )
-        data[self.method] = data.ly.augment(
-            modality=self.method,
             subdivisions=self.lnl_subdivisions,
         )
         save_table_to_csv(file_path=self.output_file, table=data)

From 7cddc7a9964e5848cfec8952845b3cf38b6510c5 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Tue, 26 Aug 2025 12:06:33 +0200
Subject: [PATCH 19/22] test: update tests for new lydata

---
 tests/compute/prevalences_test.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/compute/prevalences_test.py b/tests/compute/prevalences_test.py
index 471b78d..3fe2151 100644
--- a/tests/compute/prevalences_test.py
+++ b/tests/compute/prevalences_test.py
@@ -2,7 +2,7 @@
 
 import pandas as pd
 import pytest
-from lydata import infer_and_combine_levels, load_datasets
+from lydata import load_datasets
 
 from lyscripts.compute.prevalences import observe_prevalence
 from lyscripts.configs import DiagnosisConfig, ScenarioConfig
@@ -24,7 +24,7 @@ def scenario_config() -> ScenarioConfig:
 def data() -> pd.DataFrame:
     """Load one of the lyDATA datasets."""
     data = next(load_datasets(year=2021, institution="usz"))
-    return infer_and_combine_levels(data)
+    return data.ly.enhance()
 
 
 def test_observe_prevalence(
@@ -37,5 +37,5 @@ def test_observe_prevalence(
         scenario_config=scenario_config,
     )
 
-    assert portion.match == 67
+    assert portion.match == 66
     assert portion.total == 150

From 255af68809ea9af8691d05ccc9ba6e105f77e3be Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 4 Sep 2025 11:28:53 +0200
Subject: [PATCH 20/22] build: require at least lydata 0.4.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index af6b90d..1f095be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ dependencies = [
     "loguru",
     "fastapi",
     "uvicorn",
-    "lydata @ git+https://github.com/lycosystem/lydata-package@8469a26bea1d275b7ced43fbe3a269c8b30b60f4",
+    "lydata >= 0.4.0",
 ]
 dynamic = ["version"]
 

From e4f38fa791cc0b981e60e53ab18b84982ba98f46 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 4 Sep 2025 11:34:40 +0200
Subject: [PATCH 21/22] chore: update changelog

---
 CHANGELOG.md | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cfdd3f0..4b0fcda 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,44 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.0.0] - 2025-09-04
+
+### Bug Fixes
+
+- Change `info` to `core` for mid-level lydata columns
+- Use bug-fixed lydata `.ly.enhance()` method.
+
+### Documentation
+
+- Update documentation for `integrate` and `evidence` commands.
+- Improve `data collect` description.
+
+### Features
+
+- Add `integrate` command for thermodynamic integration. Thanks [@noemibuehrer]!
+- Add command spawning websever for interactive data collection.
+
+### Miscellaneous Tasks
+
+- Add missing links to changelog.
+- Add CITATION.cff.
+
+### Testing
+
+- Update tests for new lydata.
+
+### Build
+
+- Add uvicorn, fastapi to deps.
+- Require at least lydata 0.4.0.
+
+### Change
+
+- Make compatible with new lyDATA version.
+- Centralize inverse temperature schedule generation.
+- Store selected log-level globally.
+- Disable properties in collector.
+
 ## [1.0.0rc3] - 2025-07-22
 
 ### Documentation
@@ -871,6 +909,7 @@ returns `None` instead. Fixes [#11]
 ## [0.5.3] - 2022-08-22
 
 <!-- markdownlint-disable-file MD024 -->
+[1.0.0]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc3...1.0.0
 [1.0.0rc3]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc2...1.0.0rc3
 [1.0.0rc2]: https://github.com/lycosystem/lyscripts/compare/1.0.0rc1...1.0.0rc2
 [1.0.0rc1]: https://github.com/lycosystem/lyscripts/compare/1.0.0.a7...1.0.0rc1
@@ -938,3 +977,4 @@ returns `None` instead. Fixes [#11]
 [`rich`]: https://rich.readthedocs.io/en/latest/
 [`rich_argparse`]: https://github.com/hamdanal/rich_argparse
 [LyProX]: https://lyprox.org
+[@noemibuehrer]: https://github.com/noemibuehrer

From 8e3f0324547073422eebe6ef5a0faebe640e0897 Mon Sep 17 00:00:00 2001
From: Roman Ludwig <48687784+rmnldwg@users.noreply.github.com>
Date: Thu, 4 Sep 2025 11:38:38 +0200
Subject: [PATCH 22/22] change: update JSON schema for YAML files

---
 schemas/ly.json         | 103 +++++++++++++++++++++++++++++++++++++---
 src/lyscripts/schema.py |   1 +
 2 files changed, 98 insertions(+), 6 deletions(-)

diff --git a/schemas/ly.json b/schemas/ly.json
index 6bb3ca1..561127c 100644
--- a/schemas/ly.json
+++ b/schemas/ly.json
@@ -308,18 +308,46 @@
           "type": "string"
         },
         "repo_name": {
+          "anyOf": [
+            {
+              "minLength": 1,
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
           "default": "lycosystem/lydata",
           "description": "GitHub `repository/owner`.",
-          "minLength": 1,
-          "title": "Repo Name",
-          "type": "string"
+          "title": "Repo Name"
         },
         "ref": {
+          "anyOf": [
+            {
+              "minLength": 1,
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
           "default": "main",
           "description": "Branch/tag/commit of the repo.",
-          "minLength": 1,
-          "title": "Ref",
-          "type": "string"
+          "title": "Ref"
+        },
+        "local_dataset_dir": {
+          "anyOf": [
+            {
+              "format": "directory-path",
+              "type": "string"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "Path to directory containing all the dataset subdirectories. So, e.g. if `path_on_disk` is `~/datasets` and the dataset is `2023-clb-multisite`, then the CSV file is expected to be at `~/datasets/2023-clb-multisite/data.csv`.",
+          "title": "Local Dataset Dir"
         }
       },
       "required": [
@@ -501,6 +529,19 @@
           "title": "Relative Thresh",
           "type": "number"
         },
+        "burnin_steps": {
+          "anyOf": [
+            {
+              "type": "integer"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "Number of burn-in steps to take. If None, burn-in runs until convergence.",
+          "title": "Burnin Steps"
+        },
         "num_steps": {
           "anyOf": [
             {
@@ -623,6 +664,52 @@
       ],
       "title": "ScenarioConfig",
       "type": "object"
+    },
+    "ScheduleConfig": {
+      "description": "Configuration for generating a schedule of inverse temperatures.",
+      "properties": {
+        "method": {
+          "default": "power",
+          "description": "Method to generate the inverse temperature schedule.",
+          "enum": [
+            "geometric",
+            "linear",
+            "power"
+          ],
+          "title": "Method",
+          "type": "string"
+        },
+        "num": {
+          "default": 32,
+          "description": "Number of inverse temperatures in the schedule.",
+          "title": "Num",
+          "type": "integer"
+        },
+        "power": {
+          "default": 4.0,
+          "description": "If a power schedule is chosen, use this as power.",
+          "title": "Power",
+          "type": "number"
+        },
+        "values": {
+          "anyOf": [
+            {
+              "items": {
+                "type": "number"
+              },
+              "type": "array"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "default": null,
+          "description": "List of inverse temperatures to use instead of generating a schedule. If a list is provided, the other parameters are ignored.",
+          "title": "Values"
+        }
+      },
+      "title": "ScheduleConfig",
+      "type": "object"
     }
   },
   "description": "Settings for generating a JSON schema for lyscripts configuration files.",
@@ -685,6 +772,10 @@
       },
       "title": "Scenarios",
       "type": "array"
+    },
+    "schedule": {
+      "$ref": "#/$defs/ScheduleConfig",
+      "default": null
     }
   },
   "required": [
diff --git a/src/lyscripts/schema.py b/src/lyscripts/schema.py
index cab7c68..7470af3 100644
--- a/src/lyscripts/schema.py
+++ b/src/lyscripts/schema.py
@@ -53,6 +53,7 @@ class SchemaSettings(BaseModel):
     model: configs.ModelConfig = None
     sampling: configs.SamplingConfig = None
     scenarios: list[configs.ScenarioConfig] = []
+    schedule: configs.ScheduleConfig = None
 
 
 def main() -> None: