terra-st 0.0.0__tar.gz

terra_st-0.0.0/.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

terra_st-0.0.0/.editorconfig

@@ -0,0 +1,18 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

terra_st-0.0.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,89 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        anndata             0.8.0rc2.dev27+ge524389
+        session_info        1.0.0
+        -----
+        asttokens           NA
+        awkward             1.8.0
+        backcall            0.2.0
+        cython_runtime      NA
+        dateutil            2.8.2
+        debugpy             1.6.0
+        decorator           5.1.1
+        entrypoints         0.4
+        executing           0.8.3
+        h5py                3.7.0
+        ipykernel           6.15.0
+        jedi                0.18.1
+        mpl_toolkits        NA
+        natsort             8.1.0
+        numpy               1.22.4
+        packaging           21.3
+        pandas              1.4.2
+        parso               0.8.3
+        pexpect             4.8.0
+        pickleshare         0.7.5
+        pkg_resources       NA
+        prompt_toolkit      3.0.29
+        psutil              5.9.1
+        ptyprocess          0.7.0
+        pure_eval           0.2.2
+        pydev_ipython       NA
+        pydevconsole        NA
+        pydevd              2.8.0
+        pydevd_file_utils   NA
+        pydevd_plugins      NA
+        pydevd_tracing      NA
+        pygments            2.12.0
+        pytz                2022.1
+        scipy               1.8.1
+        setuptools          62.5.0
+        setuptools_scm      NA
+        six                 1.16.0
+        stack_data          0.3.0
+        tornado             6.1
+        traitlets           5.3.0
+        wcwidth             0.2.5
+        zmq                 23.1.0
+        -----
+        IPython             8.4.0
+        jupyter_client      7.3.4
+        jupyter_core        4.10.0
+        -----
+        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+        -----
+        Session information updated at 2022-07-07 17:55

terra_st-0.0.0/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

terra_st-0.0.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for cookiecutter-scverse-instance
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

terra_st-0.0.0/.github/workflows/build.yaml

@@ -0,0 +1,29 @@
+name: Check Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

terra_st-0.0.0/.github/workflows/release.yaml

@@ -0,0 +1,29 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/{{ cookiecutter.package_name }}
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

terra_st-0.0.0/.github/workflows/test.yaml

@@ -0,0 +1,67 @@
+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+          - os: ubuntu-latest
+            python: "3.11"
+          - os: ubuntu-latest
+            python: "3.11"
+            pip-flags: "--pre"
+            name: PRE-RELEASE DEPENDENCIES
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes
+      - name: Report coverage
+        run: |
+          coverage report
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

terra_st-0.0.0/.gitignore

@@ -0,0 +1,33 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.mypy_cache/
+.ruff_cache/
+
+# Distribution / packaging
+/build/
+/dist/
+/*.egg-info/
+
+# Tests and coverage
+/.pytest_cache/
+/.cache/
+/data/
+
+# docs
+/docs/generated/
+/docs/_build/
+
+# IDEs
+/.idea/
+/.vscode/
+
+logs/
+wandb/
+.ipynb_checkpoints
+artifacts/

terra_st-0.0.0/.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

terra_st-0.0.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+sphinx:
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: true
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

terra_st-0.0.0/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [Unreleased]
+
+### Added
+
+-   Basic tool, preprocessing and plotting functions

terra_st-0.0.0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Lotfollahi-lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

terra_st-0.0.0/PKG-INFO

@@ -0,0 +1,146 @@
+Metadata-Version: 2.4
+Name: terra-st
+Version: 0.0.0
+Summary: Spatial transcriptomics foundation model
+Project-URL: Documentation, https://terra.readthedocs.io/
+Project-URL: Source, https://github.com/Lotfollahi-lab/terra
+Project-URL: Home-page, https://github.com/Lotfollahi-lab/terra
+Author: Sebastian Birk, Mohammad Vali Sanian
+Maintainer-email: Sebastian Birk <sebastian.birk@helmholtz-munich.de>, Mohammad Vali Sanian <mohammad.sanian@helsinki.fi>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Lotfollahi-lab
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: anndata
+Requires-Dist: datasets
+Requires-Dist: ipykernel
+Requires-Dist: jupyterlab
+Requires-Dist: leidenalg
+Requires-Dist: peft
+Requires-Dist: pyensembl
+Requires-Dist: scib-metrics
+Requires-Dist: scikit-misc
+Requires-Dist: session-info
+Requires-Dist: squidpy
+Requires-Dist: torch
+Requires-Dist: transformers
+Requires-Dist: wandb
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: twine>=4.0.2; extra == 'dev'
+Provides-Extra: doc
+Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
+Requires-Dist: ipykernel; extra == 'doc'
+Requires-Dist: ipython; extra == 'doc'
+Requires-Dist: myst-nb; extra == 'doc'
+Requires-Dist: pandas; extra == 'doc'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'doc'
+Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Requires-Dist: sphinx>=4; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
+Requires-Dist: sphinxext-opengraph; extra == 'doc'
+Provides-Extra: eval
+Requires-Dist: cellphonedb; extra == 'eval'
+Requires-Dist: omnipath; extra == 'eval'
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# TERRA
+
+## Installation
+
+To install the project and its dependencies, run:
+
+```shell
+pip install -e .
+```
+
+## Repository Structure
+1. **`main.py`**  
+   The main entry point for the project, which supports running training and evaluation sweeps. It includes command-line arguments for customization and handles multi-GPU setups.
+
+2. **`configs/$DATASET.yaml`**  
+   Configuration file that defines the dataset specific hyperparameters and settings used during the training process, such as model architecture, data handling, and optimization settings (```$DATASET``` is the name of the dataset, e.g. ```merfish_300k```).
+
+3. **`src/terra/models/gene_transformer.py`**  
+   Contains the model definition for the gene transformer, implementing the core architecture that will be trained and evaluated.
+
+4. **`src/terra/train.py`**  
+   Handles the training process in a distributed setting. This script contains the logic for executing the training loop and logging results.
+
+5. **`src/terra/infer.py`**  
+   Manages the evaluation process. It evaluates the trained model on the specified tasks and logs the performance metrics.
+
+6. **`src/terra/utils/config.py`**  
+   Includes helper functions to setup the model and batch size params.
+
+7. **`src/terra/utils/embedding.py`**  
+   Provides utility functions for handling and loading embeddings required by the model during training and inference.
+
+8. **`src/terra/utils/evaluation.py`**  
+   Includes helper functions to streamline the evaluation process, such as metrics calculations and data preparation.
+
+9. **`src/terra/datasets/cell_neighborhood_dataset.py`**
+   Includes helper functions to create torch datasets for data loading.
+
+10. **`tests`**  
+   Includes test cases for different functionalities.
+
+## Usage
+
+### Training
+
+To start training with a single GPU, use the following command:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0
+```
+where ```$DATASET``` is the name of the dataset, e.g. ```merfish_300k```.
+
+To start training with multiple GPUs, use the following command:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0 cuda:1
+```
+
+To perform a sweep during training, use:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0 --do_sweep
+```
+
+For multi-node training, first configure the required settings in your job_config file. 
+Then, execute the following command:
+
+```shell
+bsub_mn_mg_yaml configs/job/hst_corpus_70m_test.yaml
+```

terra_st-0.0.0/README.md

@@ -0,0 +1,70 @@
+# TERRA
+
+## Installation
+
+To install the project and its dependencies, run:
+
+```shell
+pip install -e .
+```
+
+## Repository Structure
+1. **`main.py`**  
+   The main entry point for the project, which supports running training and evaluation sweeps. It includes command-line arguments for customization and handles multi-GPU setups.
+
+2. **`configs/$DATASET.yaml`**  
+   Configuration file that defines the dataset specific hyperparameters and settings used during the training process, such as model architecture, data handling, and optimization settings (```$DATASET``` is the name of the dataset, e.g. ```merfish_300k```).
+
+3. **`src/terra/models/gene_transformer.py`**  
+   Contains the model definition for the gene transformer, implementing the core architecture that will be trained and evaluated.
+
+4. **`src/terra/train.py`**  
+   Handles the training process in a distributed setting. This script contains the logic for executing the training loop and logging results.
+
+5. **`src/terra/infer.py`**  
+   Manages the evaluation process. It evaluates the trained model on the specified tasks and logs the performance metrics.
+
+6. **`src/terra/utils/config.py`**  
+   Includes helper functions to setup the model and batch size params.
+
+7. **`src/terra/utils/embedding.py`**  
+   Provides utility functions for handling and loading embeddings required by the model during training and inference.
+
+8. **`src/terra/utils/evaluation.py`**  
+   Includes helper functions to streamline the evaluation process, such as metrics calculations and data preparation.
+
+9. **`src/terra/datasets/cell_neighborhood_dataset.py`**
+   Includes helper functions to create torch datasets for data loading.
+
+10. **`tests`**  
+   Includes test cases for different functionalities.
+
+## Usage
+
+### Training
+
+To start training with a single GPU, use the following command:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0
+```
+where ```$DATASET``` is the name of the dataset, e.g. ```merfish_300k```.
+
+To start training with multiple GPUs, use the following command:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0 cuda:1
+```
+
+To perform a sweep during training, use:
+
+```shell
+python -m pdb main.py --fname configs/$DATASET.yaml --devices cuda:0 --do_sweep
+```
+
+For multi-node training, first configure the required settings in your job_config file. 
+Then, execute the following command:
+
+```shell
+bsub_mn_mg_yaml configs/job/hst_corpus_70m_test.yaml
+```

terra_st-0.0.0/configs/job/chl59-8b_1p/chl59-8b_1p.yaml

@@ -0,0 +1,30 @@
+# All keys in this YAML file must be in capital letters since
+# they will be treated as environmental variables.
+
+job_requirement:
+  LSB_DEFAULT_USERGROUP: team361  # The user group to be used for scheduling the job.
+  QUEUE: "training-parallel" # "gpu-lotfollahi", "gpu-lotfollahi-train"  # The job queue to be used for scheduling the job.
+  NUM_NODES: 1  # Number of compute nodes required for the job.
+  NUM_GPUS_NODE: 1  # Number of GPUs per node.
+  NUM_PROCESSES_NODE: 16  # Number of processes per node.
+  MEM_NODE: 64  # Memory allocated per node (in GB).
+  
+infiniband:
+  NCCL_IB_DISABLE: 1  # 1: Disable InfiniBand, 0: Enable InfiniBand
+
+environment:
+  ENV_PATH: "/nfs/users/nfs_s/sb75/.venvs/terra"  # Path to the environment to be activated.
+
+artifact:
+  ARTIFACT_LOCATION: "/nfs/team361/sb75/terra-reproducibility/artifacts/chl59-8b_1p"  # Path to store the artifacts.
+  WAREHOUSE_PATH: "/nfs/team361/sb75/terra-reproducibility/artifacts/chl59-8b_1p"  # Path to store the artifacts.
+  OUTPUT_DIR: "/nfs/team361/sb75/terra-reproducibility/artifacts/chl59-8b_1p"  # Path to store the artifacts.
+  LOG_DIR: "/nfs/team361/sb75/terra-reproducibility/artifacts/chl59-8b_1p"
+  EXPERIMENT_NAME: "terra_chl59-8b_1p"  # Name of the experiment.
+  RUN_NAME: "run4"  # Name of the run.
+
+runner_script:
+  RUNNER_SCRIPT: "/nfs/team361/sb75/terra/src/app/training/train_model_lsf_mpirun_sanger.sh"  # Path to the runner script.
+  TRAINING_SCRIPT_PATH: "/nfs/team361/sb75/terra/src/app/training/main.py"  # Path to the training script.
+  BACKEND: "nccl"  # Backend for distributed training.
+  CONFIG_FILE: "/nfs/team361/sb75/terra/configs/model/chl59-8b_1p/chl59-8b_1p.yaml"