Merge pull request #26 from asemposki/slalit

updates to code

Author: sudhanvalalit

src/slmemulator/EOS_Codes/MSEOS.py

@@ -340,7 +340,7 @@ def main(self, Ls, Lv, zeta, xi, out_file=None):
         xf = (10.0, 10.0, 2e-3, 2e-3)
         ls = (zeta, xi)
         paths = get_paths()
-        eos_data_dir = paths["eos_data_dir"]
+        eos_data_dir = paths["package_eos_data_dir"]
 
         mft_path = eos_data_dir / "MFT_ns6p.dat"
         lowden = np.loadtxt(mft_path)

src/slmemulator/EOS_Codes/Quarkyonia.py

@@ -54,7 +54,7 @@ def generate_quarkyonia_eos(lamInput, kappa, output_filepath):
     kArray = np.linspace(kfmin, kfmax, 400)
     # set paths
     paths = get_paths()
-    eos_data_dir = paths["eos_data_dir"]
+    eos_data_dir = paths["package_eos_data_dir"]
     output_filepath = Path(output_filepath)
     output_filepath.parent.mkdir(parents=True, exist_ok=True)
     # Initialize arrays

src/slmemulator/__init__.py

@@ -1,22 +1,22 @@
+# __init__.py for automatic discovery
 import os
 import sys
-# from .recombination import *
-# from .SLM import *
-# from .TOV_class import TOV
-# from .plotData import *
-# from .config import get_paths
-# from .cleanData import *
-# from .pSLM import *
-# from .EOS_Codes import Quarkyonia, MSEOS
+
+# Import everything from the listed sub-modules:
+from .recombination import * # This will expose every function/class from recombination.py
+from .SLM import *
+from .TOV_class import *
+from .plotData import *
+from .config import * # This will expose get_paths (and anything else)
+from .cleanData import * # This will expose clean_directory (and anything else)
+from .pSLM import *
+from .EOS_Codes import * # This will expose MSEOS (and anything else)
+
+# This line is not needed if you use from .EOS_Codes import *
 # from .EOS_Codes.Quarkyonia import generate_quarkyonia_eos
 
-# from . import *
-# Add base directory (project root) to sys path
-# If __file__ is /project_root/src/slmemulator/__init__.py,
-# then this correctly calculates /project_root/
+# [Rest of your config and path code...]
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 if BASE_DIR not in sys.path:
     sys.path.insert(0, BASE_DIR)
-
-# Versioning (good practice)
-__version__ = "0.1.0"
+__version__ = "0.1.0"

src/slmemulator/config.py

@@ -16,7 +16,7 @@
 DEFAULT_PLOTS_SUBDIR_NAME = "Plots"
 DEFAULT_RESULTS_SUBDIR_NAME = "Results"
 DEFAULT_TOV_DATA_SUBDIR_NAME = "TOV_data"
-DEFAULT_TEST_DATA_SUBDIR_NAME = "testData"
+DEFAULT_TEST_DATA_SUBDIR_NAME = "testData" # This is the base for test/QEOS/pSLM
 DEFAULT_TRAIN_DATA_SUBDIR_NAME = "trainData"
 DEFAULT_DOCS_SUBDIR_NAME = "docs"
 DEFAULT_TESTS_SUBDIR_NAME = "tests"
@@ -28,231 +28,168 @@
 
 # Default subdirectory name for Parametric SLM results/plots
 DEFAULT_PSLM_SUBDIR_NAME = "pSLM"
-# NEW: Default subdirectory name for non-Parametric SLM results/plots
+# Default subdirectory name for non-Parametric SLM results/plots
 DEFAULT_SLM_SUBDIR_NAME = "SLM"
 
 
 def get_paths(
     output_base_dir: Path = None,
-    use_mseos: bool = True,
+    eos_name: str = "MSEOS",
     is_parametric_run: bool = True,
-    include_slm_paths: bool = True,  # New parameter to control SLM specific paths
+    include_slm_paths: bool = True,
 ) -> dict:
     """
     Returns a dictionary of resolved paths for data input/output and other project directories.
-    Prioritizes explicit arguments for output_base_dir, then sensible defaults.
-    Conditionally sets 'current' EOS/TOV/results paths based on the use_mseos flag.
+    All 'current' paths are dynamically set based on the provided 'eos_name'.
 
     Args:
-        output_base_dir (Path, optional): The base directory for all generated outputs
-                                         and user-managed data. If None, defaults to
-                                         the overall PROJECT_ROOT.
-        use_mseos (bool): If True, 'current' paths will point to MSEOS-related directories.
-                          If False, 'current' paths will point to QEOS-related directories.
-                          Defaults to True.
-        is_parametric_run (bool): If True, indicates a parametric run, affecting result/plot
-                                  subdirectories. Defaults to True.
-        include_slm_paths (bool): If True, SLM-specific results and plots directories
-                                  will be included. If False, these paths are omitted.
-                                  Defaults to True.
+        output_base_dir (Path, optional): The base directory for all generated outputs.
+        eos_name (str): The name of the Equation of State (e.g., "MSEOS", "QEOS", "APR").
+                        This name is used to create specific subdirectories. Defaults to "MSEOS".
+        is_parametric_run (bool): If True, affects result/plot/test subdirectories (pSLM vs SLM).
+        include_slm_paths (bool): If True, SLM-specific results, plots, and test directories are included.
 
     Returns:
         dict: A dictionary containing all relevant path configurations.
     """
-    # The overall project root, constant regardless of output_base_dir
     project_root = PROJECT_ROOT
-
-    # The base directory for all generated outputs and user-managed data.
-    # If output_base_dir is provided, use it. Otherwise, use the overall project_root.
     output_data_base = output_base_dir or project_root
-
-    # The source directory, always relative to the overall project_root
     src_dir = project_root / DEFAULT_SRC_SUBDIR_NAME
+    
+    # Define extensions to strip
+    EXTENSIONS_TO_STRIP = [".txt", ".dat", ".table"]
+    
+    # Strip extensions and convert to uppercase for directory naming
+    clean_eos_name = eos_name
+    for ext in EXTENSIONS_TO_STRIP:
+        if clean_eos_name.lower().endswith(ext):
+            clean_eos_name = clean_eos_name[:-len(ext)]
+            break # Stop after stripping the first matching extension
+            
+    # --- Dynamic EOS-specific folder name, ensuring it's uppercase for directories ---
+    EOS_FOLDER_NAME = clean_eos_name.upper()
+    
+    # --- Define SLM subdirectory based on run type (SLM or pSLM) ---
+    SLM_SUBDIR = DEFAULT_PSLM_SUBDIR_NAME if is_parametric_run else DEFAULT_SLM_SUBDIR_NAME
 
     paths = {
         "project_root": project_root,
         "src_dir": src_dir,
-        # Internal package resources (read-only, typically part of the installed package)
-        # Assumes the package is named 'slmemulator' for pkg_resources.
+        # Internal package resources (read-only)
         "package_eos_codes_dir": pkg_resources.files("slmemulator").joinpath(
             DEFAULT_EOS_CODES_SUBDIR_NAME
         ),
         "package_eos_data_dir": pkg_resources.files("slmemulator").joinpath(
             DEFAULT_EOS_DATA_SUBDIR_NAME
         ),
-        # Directories for generated outputs and user-managed data, relative to output_data_base.
-        # These are the directories your application will typically write to.
+        # General output directories
         "plots_dir": output_data_base / DEFAULT_PLOTS_SUBDIR_NAME,
         "results_dir": output_data_base / DEFAULT_RESULTS_SUBDIR_NAME,
         "docs_dir": output_data_base / DEFAULT_DOCS_SUBDIR_NAME,
         "tests_dir": output_data_base / DEFAULT_TESTS_SUBDIR_NAME,
         "tutorials_dir": output_data_base / DEFAULT_TUTORIALS_SUBDIR_NAME,
-        # User-managed/project-level EOS and TOV data (can be inputs or outputs)
+        
+        # User-managed/project-level EOS and TOV data
         "user_eos_data_dir": output_data_base / DEFAULT_EOS_DATA_SUBDIR_NAME,
-        "user_tov_data_dir": output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME,
         "test_data_dir": output_data_base / DEFAULT_TEST_DATA_SUBDIR_NAME,
         "train_path": output_data_base / DEFAULT_TRAIN_DATA_SUBDIR_NAME,
-        # Generated EOS files (e.g., from MSEOS.py/Quarkyonia.py)
         "generated_eos_files_dir": output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME,
-        # Specific paths for QEOS and MSEOS generated files within generated_eos_files_dir
-        "qeos_path_specific": (output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME)
-        / "QEOS",
-        "mseos_path_specific": (output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME)
-        / "MSEOS",
-        # Specific TOV data paths within user_tov_data_dir
-        "qeos_tov_path_specific": (output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME)
-        / "QEOS",
-        "mseos_tov_path_specific": (output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME)
-        / "MSEOS",
-        # Removed DMD-related output directories from here. They will be user-defined.
+        
+        # Current Dynamic EOS/TOV/Generated paths
+        "current_eos_input_dir": (
+            output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME
+        ) / EOS_FOLDER_NAME,
+        "current_tov_data_dir": (
+            output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME
+        ) / EOS_FOLDER_NAME,
+        
+        # Kept old names for minimal compatibility changes
+        "qeos_path_specific": (output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME) / "QEOS",
+        "mseos_path_specific": (output_data_base / DEFAULT_EOS_FILES_SUBDIR_NAME) / "MSEOS",
+        "qeos_tov_path_specific": (output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME) / "QEOS",
+        "mseos_tov_path_specific": (output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME) / "MSEOS",
+        "user_tov_data_dir": output_data_base / DEFAULT_TOV_DATA_SUBDIR_NAME,
     }
 
-    # Conditionally add SLM-specific result/plot subdirectories
+    # Conditionally add SLM-specific result/plot/test subdirectories
     if include_slm_paths:
-        # General SLM specific result/plot subdirectories (non-parametric)
-        paths["slm_res_mseos_specific"] = (
-            output_data_base
-            / DEFAULT_RESULTS_SUBDIR_NAME
-            / "MSEOS"
-            / DEFAULT_SLM_SUBDIR_NAME
-        )
-        paths["slm_res_qeos_specific"] = (
-            output_data_base
-            / DEFAULT_RESULTS_SUBDIR_NAME
-            / "QEOS"
-            / DEFAULT_SLM_SUBDIR_NAME
-        )
-        paths["slm_plots_mseos_specific"] = (
-            output_data_base
-            / DEFAULT_PLOTS_SUBDIR_NAME
-            / "MSEOS"
-            / DEFAULT_SLM_SUBDIR_NAME
-        )
-        paths["slm_plots_qeos_specific"] = (
-            output_data_base
-            / DEFAULT_PLOTS_SUBDIR_NAME
-            / "QEOS"
-            / DEFAULT_SLM_SUBDIR_NAME
-        )
-
-        # Parametric SLM specific result/plot subdirectories
-        paths["slm_res_mseos_parametric_specific"] = (
+        
+        # Define the dynamic current SLM results and plots paths
+        paths["current_slm_results_dir"] = (
             output_data_base
             / DEFAULT_RESULTS_SUBDIR_NAME
-            / "MSEOS"
-            / DEFAULT_PSLM_SUBDIR_NAME
+            / EOS_FOLDER_NAME
+            / SLM_SUBDIR
         )
-        paths["slm_res_qeos_parametric_specific"] = (
-            output_data_base
-            / DEFAULT_RESULTS_SUBDIR_NAME
-            / "QEOS"
-            / DEFAULT_PSLM_SUBDIR_NAME
-        )
-        paths["slm_plots_mseos_parametric_specific"] = (
+        paths["current_slm_plots_dir"] = (
             output_data_base
             / DEFAULT_PLOTS_SUBDIR_NAME
-            / "MSEOS"
-            / DEFAULT_PSLM_SUBDIR_NAME
+            / EOS_FOLDER_NAME
+            / SLM_SUBDIR
         )
-        paths["slm_plots_qeos_parametric_specific"] = (
-            output_data_base
-            / DEFAULT_PLOTS_SUBDIR_NAME
-            / "QEOS"
-            / DEFAULT_PSLM_SUBDIR_NAME
-        )
-
-    # Conditionally set the "current" paths based on the use_mseos flag AND `is_parametric_run`
-    # These 'current' paths also depend on whether SLM paths are included.
-    if use_mseos:
-        paths["current_eos_input_dir"] = paths["mseos_path_specific"]
-        paths["current_tov_data_dir"] = paths["mseos_tov_path_specific"]
-        if include_slm_paths:  # Only set if SLM paths are desired
-            if is_parametric_run:
-                paths["current_slm_results_dir"] = paths[
-                    "slm_res_mseos_parametric_specific"
-                ]
-                paths["current_slm_plots_dir"] = paths[
-                    "slm_plots_mseos_parametric_specific"
-                ]
-            else:  # Non-parametric SLM run for MSEOS
-                paths["current_slm_results_dir"] = paths["slm_res_mseos_specific"]
-                paths["current_slm_plots_dir"] = paths["slm_plots_mseos_specific"]
-    else:  # QEOS
-        paths["current_eos_input_dir"] = paths["qeos_path_specific"]
-        paths["current_tov_data_dir"] = paths["qeos_tov_path_specific"]
-        if include_slm_paths:  # Only set if SLM paths are desired
-            if is_parametric_run:
-                paths["current_slm_results_dir"] = paths[
-                    "slm_res_qeos_parametric_specific"
-                ]
-                paths["current_slm_plots_dir"] = paths[
-                    "slm_plots_qeos_parametric_specific"
-                ]
-            else:  # Non-parametric SLM run for QEOS
-                paths["current_slm_results_dir"] = paths["slm_res_qeos_specific"]
-                paths["current_slm_plots_dir"] = paths["slm_plots_qeos_specific"]
 
-    # Ensure all paths are Path objects, handling cases where a key might not be set
-    # if include_slm_paths is False and a 'current_slm_...' path was attempted to be accessed.
+        # --- NEW PATH: Dynamic SLM Test Data Path ---
+        if is_parametric_run:
+            # Only create the /pSLM folder for tests if it's a parametric run
+            paths["current_slm_tests_dir"] = (
+                output_data_base
+                / DEFAULT_TEST_DATA_SUBDIR_NAME
+                / EOS_FOLDER_NAME
+                / DEFAULT_PSLM_SUBDIR_NAME  # Always use 'pSLM' for parametric tests
+            )
+        else:
+            # If not parametric, use the base testData/EOS_NAME folder
+            paths["current_slm_tests_dir"] = (
+                output_data_base
+                / DEFAULT_TEST_DATA_SUBDIR_NAME
+                / EOS_FOLDER_NAME
+            )
+    
+    # Ensure all paths are Path objects and filter out any None/non-Path values
     final_paths = {}
     for k, v in paths.items():
         if isinstance(v, Path):
             final_paths[k] = v
+        elif include_slm_paths and k.startswith("current_slm_") and k in paths:
+             final_paths[k] = paths[k]
 
     return final_paths
 
 
 def create_necessary_dirs(paths: dict, additional_dirs: list[Path] = None):
     """
     Creates directories for specified output and user-managed data paths if they do not already exist.
-    This function focuses on creating directories that the application will write to.
-
-    Args:
-        paths (dict): A dictionary of Path objects, typically obtained from get_paths().
-        additional_dirs (list[Path], optional): A list of additional Path objects
-                                                to create (e.g., user-input directories).
-                                                Defaults to None.
     """
+    
     # Define a list of keys corresponding to directories that should be created.
-    # These are typically output directories or user-managed data directories.
-    # This list should be exhaustive for all directories you intend your application to write to.
-    # Note: 'current_*' paths are included as they are the effective targets for writing.
     output_directory_keys = [
         "plots_dir",
         "results_dir",
-        "docs_dir",  # If generated docs/reports go here
-        "tests_dir",  # If test reports/output go here
-        "tutorials_dir",  # If generated tutorial output goes here
+        "docs_dir",
+        "tests_dir",
+        "tutorials_dir",
         "user_eos_data_dir",
         "user_tov_data_dir",
         "test_data_dir",
         "train_path",
         "generated_eos_files_dir",
-        "qeos_path_specific",
-        "mseos_path_specific",
-        "qeos_tov_path_specific",
-        "mseos_tov_path_specific",
-        # SLM specific paths (will only be present in 'paths' if include_slm_paths was True)
-        "slm_res_mseos_specific",
-        "slm_res_qeos_specific",
-        "slm_plots_mseos_specific",
-        "slm_plots_qeos_specific",
-        "slm_res_mseos_parametric_specific",
-        "slm_res_qeos_parametric_specific",
-        "slm_plots_mseos_parametric_specific",
-        "slm_plots_qeos_parametric_specific",
-        # The 'current' paths are the effective targets, so ensure they are also created
+        
+        # The 'current' paths are the effective targets, so ensure they are created
         "current_eos_input_dir",
         "current_tov_data_dir",
         "current_slm_results_dir",
         "current_slm_plots_dir",
-        # Removed "dmd_output_base_dir", "foo_files_dir", "dmd_input_dir" from here.
-        # They will be passed dynamically via 'additional_dirs'.
+        "current_slm_tests_dir", # <-- ADDED NEW PATH
+        
+        # Kept for backward compatibility
+        "qeos_path_specific",
+        "mseos_path_specific",
+        "qeos_tov_path_specific",
+        "mseos_tov_path_specific",
     ]
 
     unique_dirs_to_create = set()
     for key in output_directory_keys:
-        # Only add to the set if the key exists in 'paths' and its value is a Path object
         if key in paths and isinstance(paths[key], Path):
             unique_dirs_to_create.add(paths[key])
 
@@ -268,4 +205,4 @@ def create_necessary_dirs(paths: dict, additional_dirs: list[Path] = None):
                 path.mkdir(parents=True, exist_ok=True)
                 print(f"Created directory: {path}")
             except OSError as e:
-                print(f"Error creating directory {path}: {e}")
+                print(f"Error creating directory {path}: {e}")