Consolidate scripts and python package

* some functionality from scripts/ would be useful inside the library
* some functionality from the library was replicated in scripts/
-> consolidate, turn separate scripts into entrypoints

* Reduce number of package configuration files

.github/workflows/tests.yml

@@ -23,16 +23,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install --upgrade setuptools wheel
-        pip install -r scripts/requirements.txt
+        cd src/python && pip install -e .
 
     - name: Check with petablint
-      run: ./check_petablint.py
-      working-directory: scripts/
+      run: bmp-petablint
 
     - name: Show overview
-      run: ./overview.py
-      working-directory: scripts/
+      run: bmp-create-overview
 
     - name: Check SBML metadata
-      run: ./check_sbml_metadata.py
-      working-directory: scripts/
+      run: bmp-check-sbml-metadata

src/python/benchmark_models_petab/check_petablint.py

@@ -0,0 +1,23 @@
+from pathlib import Path
+import os
+import sys
+from . import MODELS, get_problem_yaml_path
+
+def main():
+    num_failures = 0
+
+    for petab_problem_id in MODELS:
+        print(petab_problem_id)
+        petab_yaml = get_problem_yaml_path(petab_problem_id)
+        ret = os.system(f"petablint -v {petab_yaml}")
+        print('='*100)  # just for output readability
+
+        if ret:
+            num_failures += 1
+
+    num_passed = len(MODELS) - num_failures
+    print(f'Result: {Path(__file__).stem}')
+    print(f"{num_passed} out of {len(MODELS)} passed.")
+    print(f"{num_failures} out of {len(MODELS)} failed.")
+    # Fail unless all models passed
+    sys.exit(num_failures)

src/python/benchmark_models_petab/check_sbml_metadata.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+
+from pathlib import Path
+import sys
+from .overview import get_reference_uris
+from . import MODELS, get_problem
+
+def main():
+    num_failures = 0
+
+    for petab_problem_id in MODELS:
+        petab_problem = get_problem(petab_problem_id)
+
+        model_id = petab_problem.sbml_model.getId()
+        model_name = petab_problem.sbml_model.getName()
+        reference_uris = get_reference_uris(sbml_model=petab_problem.sbml_model)
+
+        errors = []
+
+        if model_id != petab_problem_id:
+            errors.append(
+                'Please change the model ID to match the problem ID.'
+            )
+
+        if model_name != petab_problem_id:
+            errors.append(
+                'Please change the model name to match the problem ID.'
+            )
+
+        if not reference_uris:
+            errors.append(
+                'Please add relevant references (e.g. the paper) to the model.'
+            )
+
+        errors = ['\t' + error for error in errors]
+
+        print(petab_problem_id)
+        if errors:
+            print('\n'.join(errors))
+            num_failures += 1
+        print('='*100)  # just for output readability
+
+    num_passed = len(MODELS) - num_failures
+    print(f'Result: {Path(__file__).stem}')
+    print(f"{num_passed} out of {len(MODELS)} passed.")
+    print(f"{num_failures} out of {len(MODELS)} failed.")
+    # Fail unless all models passed
+    sys.exit(num_failures)

scripts/overview.py → src/python/benchmark_models_petab/overview.py

@@ -1,16 +1,16 @@
-#!/usr/bin/env python3
 """Print some stats for each benchmark PEtab problem"""
-
-import os
 from typing import Dict, List
+import sys
 
 import libsbml
 import numpy as np
 import pandas as pd
 import petab.v1 as petab
+from pathlib import Path
+from . import get_problem_yaml_path, MODELS, get_problem
+from petab.yaml import load_yaml
 
-from _helpers import petab_yamls, readme_md
-
+readme_md = Path(__file__).resolve().parent.parent / "README.md"
 
 markdown_columns = {
     'conditions': 'Conditions',
@@ -91,8 +91,7 @@ def get_reference_uris(sbml_model: libsbml.Model) -> List[str]:
 
 def get_sbml4humans_urls(petab_problem_id: str) -> List[str]:
     """Get URL to SBML4humans model"""
-    from petab.yaml import load_yaml
-    yaml_file = petab_yamls[petab_problem_id]
+    yaml_file = get_problem_yaml_path(petab_problem_id)
     yaml_dict = load_yaml(yaml_file)
     repo_root = "https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master"
     urls = []
@@ -136,8 +135,8 @@ def get_noise_distributions(observable_df):
 def get_overview_table() -> pd.DataFrame:
     """Get overview table with stats for all benchmark PEtab problems"""
     data = []
-    for petab_problem_id, petab_yaml in petab_yamls.items():
-        petab_problem = petab.Problem.from_yaml(petab_yaml)
+    for petab_problem_id in MODELS:
+        petab_problem = get_problem(petab_problem_id)
         summary = get_summary(petab_problem, petab_problem_id)
         data.append(summary)
     df = pd.DataFrame(data)
@@ -148,7 +147,7 @@ def get_overview_table() -> pd.DataFrame:
 start_overview_table = '\n<!-- START OVERVIEW TABLE -->\n'
 end_overview_table = '\n<!-- END OVERVIEW TABLE -->\n'
 
-def main(
+def create_overview_table(
     markdown: bool = False,
     update_readme: bool = False,
 ):
@@ -188,14 +187,12 @@ def main(
         print(df)
 
 
-if __name__ == '__main__':
-    import sys
-
+def main():
     markdown = False
     update_readme = False
     if '--markdown' in sys.argv:
         markdown = True
     if '--update' in sys.argv:
         markdown = True
         update_readme = True
-    main(markdown=markdown, update_readme=update_readme)
+    create_overview_table(markdown=markdown, update_readme=update_readme)

src/python/build.sh

@@ -24,7 +24,7 @@ mkdir $BUILD_DIR
 # Copy code
 cp -r \
   $CODE_DIR \
-  "setup.cfg" "setup.py" "pyproject.toml" "MANIFEST.in" \
+  "pyproject.toml" "MANIFEST.in" \
   "../../LICENSE" "../../README.md" \
   $BUILD_DIR
 # Remove link

src/python/pyproject.toml

@@ -2,13 +2,51 @@
 requires = [
     "setuptools",
     "wheel",
+    "petab",
 ]
 build-backend = "setuptools.build_meta"
 
+
+[project]
+name = "benchmark_models_petab"
+description = "A collection of models with experimental data in the PEtab format"
+dynamic = ["version"]
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+authors = [
+    { name = "The Benchmark-Models-PEtab maintainers", email = "yannik.schaelte@gmail.com" }
+]
+urls = { "Homepage" = "https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab" }
+dependencies = [
+    "petab>=0.4.0",
+    "numpy",
+    "pandas",
+    "python-libsbml",
+    "tabulate",
+]
+
+[project.optional-dependencies]
+dev = ["flake8"]
+
+[tool.setuptools.dynamic]
+version = {attr = "benchmark_models_petab.__version__"}
+
+[tool.flake8]
+per-file-ignores = { "__init__.py" = ["F401"] }
+
+[project.scripts]
+bmp-petablint = "benchmark_models_petab.check_petablint:main"
+bmp-check-sbml-metadata = "benchmark_models_petab.check_sbml_metadata:main"
+bmp-create-overview = "benchmark_models_petab.overview:main"
+
 [tool.black]
 line-length = 79
 
 [tool.isort]
 profile = "black"
 line_length = 79
 multi_line_output = 3
+
+
+