Update README.md, remove unnecessary files and sent env variable for openbabel within processligand

Author: ThomasDesc

CMakeLists.txt

@@ -1,20 +1,25 @@
 # CMakeLists.txt
 
 cmake_minimum_required(VERSION 3.15)
-project(processligand_builder C)
+project(processligand_builder C CXX)
 
 include(FetchContent)
 
+set(BUILD_STATIC_EXECUTABLE ON CACHE BOOL "Build static executable" FORCE)
+set(CMAKE_BUILD_TYPE Release)
+
 FetchContent_Declare(
   processligand_repo
   GIT_REPOSITORY https://github.com/NRGlab/Process_Ligand.git
   GIT_TAG        cmake
 )
 
-set(CMAKE_BUILD_TYPE Release)
-set(BUILD_STATIC_EXECUTABLE ON)
+FetchContent_GetProperties(processligand_repo)
+if(NOT processligand_repo_POPULATED)
+  FetchContent_Populate(processligand_repo)
+endif()
 
-FetchContent_MakeAvailable(processligand_repo)
+add_subdirectory(${processligand_repo_SOURCE_DIR} ${processligand_repo_BINARY_DIR})
 
 set(PROCESSLIGAND_EXECUTABLE $<TARGET_FILE:ProcessLigand>)
 
@@ -23,7 +28,7 @@ install(PROGRAMS ${PROCESSLIGAND_EXECUTABLE}
 )
 
 install(FILES
-    ${CMAKE_CURRENT_SOURCE_DIR}/processligandpy/__init__.py
-    ${CMAKE_CURRENT_SOURCE_DIR}/processligandpy/processligand_wrapper.py
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/processligandpy/__init__.py
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/processligandpy/processligand_wrapper.py
     DESTINATION ${CMAKE_INSTALL_PREFIX}
 )

README.md

@@ -9,15 +9,19 @@ A Python package designed to prepare arguments and run `ProcessLigand`.
 ```
 from processligandpy import run_processligand
 
-result = run_processligand(f='path/to/target_or_ligand')
+# For a ligand
+result_ligand = run_processligand(file_path='path/to/target_or_ligand')
+
+# For a target:
+# result_target = run_processligand(file_path='path/to/target_or_ligand', target=True)
 
 # Using arguments:
-# result = run_processligand(f='path/to/target_or_ligand', target=True, atom_index=1)
+# result = run_processligand(file_path='path/to/target_or_ligand', atom_index=1)
 
-# Optional:
-output = result.stdout
-error = result.stderr
-returncode = result.returncode
+# Expanding the result:
+output = result_ligand.stdout
+error = result_ligand.stderr
+returncode = result_ligand.returncode
 ```
 
 ---
@@ -26,9 +30,9 @@ returncode = result.returncode
 
 ### Required Argument
 
-| Arg | Description                                        |
-|:----|:---------------------------------------------------|
-| `f` | Input file (not listed in the provided dictionary) |
+| Arg         | Description                                        |
+|:------------|:---------------------------------------------------|
+| `file_path` | Input file (not listed in the provided dictionary) |
 
 ### Optional Arguments
 

processligandpy/__init__.py

@@ -33,6 +33,7 @@ wheel.install-dir = "processligandpy"
 wheel.py-api = "py3"
 metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
 cmake.build-type = "Release"
+wheel.exclude = ["obabel", "roundtrip", "**/lib", "**/include", "**/share/man"]
 
 [tool.setuptools.packages.find]
 include = ["processligandpypy","processligandpypy.*"]

pyproject.toml

@@ -0,0 +1,18 @@
+import os
+import sys
+
+if 'BABEL_DATADIR' not in os.environ:
+    try:
+        import importlib.resources
+        data_dir = os.path.join(str(importlib.resources.files('processligandpy')), 'share', 'openbabel', '3.1.1')
+        if not os.path.isdir(data_dir):
+            data_dir = os.path.join(str(importlib.resources.files('processligandpy')), 'bin', 'data')
+    except (ImportError, AttributeError):
+        import pkg_resources
+        data_dir = os.path.join(str(pkg_resources.resource_filename('processligandpy', '')), 'share', 'openbabel',
+                                '3.1.1')
+        if not os.path.isdir(data_dir):
+            data_dir = os.path.join(str(pkg_resources.resource_filename('processligandpy', '')), 'bin', 'data')
+    os.environ['BABEL_DATADIR'] = data_dir
+
+from .processligand_wrapper import run_processligand