Add CLI scripts to pyproject with script for auto-updating pyproject.…

…toml

pyproject.toml

@@ -1,43 +1,42 @@
 [build-system]
-requires = ["setuptools"]
+requires = [ "setuptools",]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "maize-biosimspace"
 description = "Custom maize nodes and subgraphs"
 version = "0.1.0"
-authors = [{name = "Finlay CLark"}]
-maintainers = [{name = "Finlay Clark", email = "[email protected]"}]
 requires-python = ">=3.10"
-dependencies = [
-    "maize>=0.6.0",
-    "rdkit>=2022.9.5",
-    "pandas>=2.0.0",
-    "biosimspace"
-]
+dependencies = [ "maize>=0.6.0", "rdkit>=2022.9.5", "pandas>=2.0.0", "biosimspace",]
+[[project.authors]]
+name = "Finlay CLark"
 
+[[project.maintainers]]
+name = "Finlay Clark"
+email = "[email protected]"
 
 [project.scripts]
-bss_system_prep_free = "maize.graphs.exs.biosimspace.system_preparation:system_preparation_free"
-bss_system_prep_bound = "maize.graphs.exs.biosimspace.system_preparation:system_preparation_bound"
-
-# Not quite sure why this is required (rather than listing the packages explicitly),
-# but without this will only install using --editable, see also:
-# https://stackoverflow.com/questions/43430852/import-only-works-when-module-installed-using-editable-pip-flag
-[tool.setuptools.packages.find]
-include = ["maize*"]
-
-[tool.pytest.ini_options]
-config = "test-config.toml"
-log_cli = true
-log_cli_level = "DEBUG"
-addopts = ["-vv"]
-python_files = ["*.py"]
-python_classes = ["TestSuite*"]
-testpaths = [
-    "maize/steps",
-    "tests",
-]
+bss_system_prep_free = "maize.graphs.exs.biosimspace.system_preparation:system_prep_free_exposed"
+bss_system_prep_bound = "maize.graphs.exs.biosimspace.system_preparation:system_prep_bound_exposed"
+bss_abfe_no_prep = "maize.graphs.exs.biosimspace.abfe:abfe_no_prep_exposed"
+bss_abfe_with_prep = "maize.graphs.exs.biosimspace.abfe:abfe_with_prep_exposed"
+bss_parameterise = "maize.steps.exs.biosimspace.parameterise:parameterise_exposed"
+bss_solvate = "maize.steps.exs.biosimspace.solvate:solvate_exposed"
+bss_minimise_gromacs = "maize.steps.exs.biosimspace.minimise:minimise_gromacs_exposed"
+bss_minimise_pmemd_cuda = "maize.steps.exs.biosimspace.minimise:minimise_pmemd_cuda_exposed"
+bss_minimise_pmemd = "maize.steps.exs.biosimspace.minimise:minimise_pmemd_exposed"
+bss_minimise_sander = "maize.steps.exs.biosimspace.minimise:minimise_sander_exposed"
+bss_minimise_somd = "maize.steps.exs.biosimspace.minimise:minimise_somd_exposed"
+bss_equilibrate_gromacs = "maize.steps.exs.biosimspace.equilibrate:equilibrate_gromacs_exposed"
+bss_equilibrate_pmemd_cuda = "maize.steps.exs.biosimspace.equilibrate:equilibrate_pmemd_cuda_exposed"
+bss_equilibrate_pmemd = "maize.steps.exs.biosimspace.equilibrate:equilibrate_pmemd_exposed"
+bss_equilibrate_sander = "maize.steps.exs.biosimspace.equilibrate:equilibrate_sander_exposed"
+bss_equilibrate_somd = "maize.steps.exs.biosimspace.equilibrate:equilibrate_somd_exposed"
+bss_production_gromacs = "maize.steps.exs.biosimspace.production:production_gromacs_exposed"
+bss_production_pmemd_cuda = "maize.steps.exs.biosimspace.production:production_pmemd_cuda_exposed"
+bss_production_pmemd = "maize.steps.exs.biosimspace.production:production_pmemd_exposed"
+bss_production_sander = "maize.steps.exs.biosimspace.production:production_sander_exposed"
+bss_production_somd = "maize.steps.exs.biosimspace.production:production_somd_exposed"
 
 [tool.mypy]
 follow_imports = "silent"
@@ -51,3 +50,15 @@ line-length = 100
 
 [tool.ruff]
 line-length = 100
+
+[tool.pytest.ini_options]
+config = "test-config.toml"
+log_cli = true
+log_cli_level = "DEBUG"
+addopts = [ "-vv",]
+python_files = [ "*.py",]
+python_classes = [ "TestSuite*",]
+testpaths = [ "maize/steps", "tests",]
+
+[tool.setuptools.packages.find]
+include = [ "maize*",]

update_pyproject.py

@@ -0,0 +1,58 @@
+"""
+Script to automatically update pyproject.toml with auto-generated
+command-line functions in the project.scripts section.
+"""
+
+import os
+from setuptools import setup, find_packages
+import toml
+
+CLI_MODULES = [
+    # Steps
+    "maize.steps.exs.biosimspace.parameterise",
+    "maize.steps.exs.biosimspace.solvate",
+    "maize.steps.exs.biosimspace.minimise",
+    "maize.steps.exs.biosimspace.equilibrate",
+    "maize.steps.exs.biosimspace.production",
+    # Graphs
+    "maize.graphs.exs.biosimspace.system_preparation",
+    "maize.graphs.exs.biosimspace.abfe",
+]
+
+def get_cli_functions(cli_modules: list[str]) -> dict[str, str]:
+    """Get a dictionary of command-line functions and their entry points."""
+
+    cli_functions = {}
+    for module_name_full in cli_modules:
+        # Find all functions called "exposed" in the module
+        module_name_short = module_name_full.split('.')[-1]
+        module = __import__(module_name_full, fromlist=[module_name_short])
+        for name in dir(module):
+            if name.endswith("_exposed"):
+                cli_name = f"bss_{name.replace('_exposed', '')}"
+                cli_functions[cli_name] = f"{module_name_full}:{name}"
+
+    return cli_functions
+
+
+def update_pyproject_toml(cli_modules: list[str]) -> None:
+    """Update pyproject.toml with auto-generated command-line functions."""
+
+    pyproject_path = 'pyproject.toml'
+    if os.path.exists(pyproject_path):
+        pyproject_data = toml.load(pyproject_path)
+    else:
+        pyproject_data = {}
+
+    # Define the command-line functions and their entry points
+    cli_functions = get_cli_functions(cli_modules)
+
+    # Update the pyproject.toml data in the project.scripts section
+    pyproject_data.setdefault('project', {}).setdefault('scripts', {}).update(cli_functions)
+
+    # Write the updated data back to pyproject.toml
+    with open(pyproject_path, 'w') as toml_file:
+        toml.dump(pyproject_data, toml_file)
+
+if __name__ == "__main__":
+    update_pyproject_toml(CLI_MODULES)