scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/gen/_print_config.py

@@ -17,7 +17,6 @@ Example:
     python _print_config.py PATH.TITAN.MAT
 """
 
-
 import sys
 import os
 import argparse
@@ -26,7 +25,6 @@ import sys
 
 
 def print_config(key):
-
     CONFIG = scitex.io.load_configs()
 
     if key is None:
@@ -38,7 +36,6 @@ def print_config(key):
         keys = key.split(".")
         value = CONFIG
         for k in keys:
-
             if isinstance(value, (dict, scitex.gen.utils._DotDict.DotDict)):
                 value = value.get(k)
 

scitex/gen/_src.py

@@ -4,6 +4,7 @@
 # File: /ssh:sp:/home/ywatanabe/proj/SciTeX-Code/src/scitex/gen/_src.py
 # ----------------------------------------
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -36,9 +37,7 @@ def src(obj):
         # scitex.gen.less(source_code)
 
         # Open a subprocess to use `less` for displaying the source code
-        process = subprocess.Popen(
-            ["less"], stdin=subprocess.PIPE, encoding="utf8"
-        )
+        process = subprocess.Popen(["less"], stdin=subprocess.PIPE, encoding="utf8")
         process.communicate(input=source_code)
         if process.returncode != 0:
             print(f"Process exited with return code {process.returncode}")

scitex/gen/_title_case.py

@@ -8,7 +8,6 @@
 This script does XYZ.
 """
 
-
 """
 Imports
 """
@@ -81,7 +80,9 @@ def main():
 
 
 if __name__ == "__main__":
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
+        sys, plt, verbose=False
+    )
     main()
     scitex.session.close(CONFIG, verbose=False, notify=False)
 

scitex/gen/_to_even.py

@@ -33,7 +33,7 @@ def to_even(n):
     -2
     """
     import math
-    
+
     # Handle integers directly to avoid float conversion issues with large numbers
     # Note: bool is a subclass of int, so we need to exclude it
     if isinstance(n, int) and not isinstance(n, bool):
@@ -41,7 +41,7 @@ def to_even(n):
             return int(n)  # Ensure we return int, not bool
         else:
             return int(n - 1)  # Ensure we return int, not bool
-    
+
     # Handle special float values
     if isinstance(n, float):
         if math.isnan(n):
@@ -50,9 +50,9 @@ def to_even(n):
             raise OverflowError("Cannot convert infinity to even")
         # Python can actually convert sys.float_info.max to int, so we don't need this check
         # Only infinity truly can't be converted
-    
+
     # Try to handle custom objects with __int__ (but not float types)
-    if hasattr(n, '__int__') and not isinstance(n, (float, bool)):
+    if hasattr(n, "__int__") and not isinstance(n, (float, bool)):
         try:
             n_int = int(n)
             if n_int % 2 == 0:
@@ -61,20 +61,20 @@ def to_even(n):
                 return int(n_int - 1)
         except:
             pass
-    
+
     # Check for string type explicitly - raise TypeError
     if isinstance(n, str):
         raise TypeError(f"must be real number, not {type(n).__name__}")
-    
+
     # Convert to float for all other cases
     try:
         n_float = float(n)
     except (TypeError, ValueError):
         raise TypeError(f"must be real number, not {type(n).__name__}")
-    
+
     # Use floor for float values
     floored = int(math.floor(n_float))
-    
+
     # If odd, subtract 1 to get the next lower even number
     if floored % 2 != 0:
         return int(floored - 1)  # Ensure we return int, not bool

scitex/gen/_transpose.py

@@ -31,7 +31,7 @@ def transpose(arr_like, src_dims, tgt_dims):
     AssertionError
         If source and target dimensions don't contain the same elements.
     """
-    assert set(src_dims) == set(
-        tgt_dims
-    ), "Source and target dimensions must contain the same elements"
+    assert set(src_dims) == set(tgt_dims), (
+        "Source and target dimensions must contain the same elements"
+    )
     return arr_like.transpose(*[np.where(src_dims == dim)[0][0] for dim in tgt_dims])

scitex/gen/misc.py

@@ -216,7 +216,6 @@ def is_later_or_equal(package, tgt_version, format="MAJOR.MINOR.PATCH"):
         return False
 
     if imp_major == tgt_major:
-
         ## Minor
         if imp_minor > tgt_minor:
             return True
@@ -225,7 +224,6 @@ def is_later_or_equal(package, tgt_version, format="MAJOR.MINOR.PATCH"):
             return False
 
         if imp_minor == tgt_minor:
-
             ## Patch
             if imp_patch > tgt_patch:
                 return True
@@ -264,7 +262,6 @@ def _copy_a_file(src, dst, allow_overwrite=False):
         print(f"\n/dev/null was not copied.\n")
 
     else:
-
         if dst.endswith("/"):
             _, src_fname, src_ext = scitex.path.split(src)
             # src_fname = src + src_ext

scitex/gists/_SigMacro_processFigure_S.py

@@ -1,6 +1,6 @@
 def sigmacro_process_figure_s():
     """Print a macro for SigmaPlot (v12.0) to format a panel.
-    
+
     Please refer to the 'Automating Routine Tasks' section of the official documentation.
     """
     print(
@@ -123,6 +123,6 @@ def SigMacro_processFigure_S():
     warnings.warn(
         "SigMacro_processFigure_S is deprecated, use sigmacro_process_figure_s() instead",
         DeprecationWarning,
-        stacklevel=2
+        stacklevel=2,
     )
     return sigmacro_process_figure_s()

scitex/gists/_SigMacro_toBlue.py

@@ -1,6 +1,6 @@
 def sigmacro_to_blue():
     """Print a macro for SigmaPlot (v12.0) that changes the color and style of the selected object.
-    
+
     Please refer to the 'Automating Routine Tasks' section of the official documentation.
     """
     print(
@@ -167,6 +167,6 @@ def SigMacro_toBlue():
     warnings.warn(
         "SigMacro_toBlue is deprecated, use sigmacro_to_blue() instead",
         DeprecationWarning,
-        stacklevel=2
+        stacklevel=2,
     )
     return sigmacro_to_blue()

scitex/gists/__init__.py

@@ -1,7 +1,10 @@
 #!/usr/bin/env python3
 """Scitex gists module."""
 
-from ._SigMacro_processFigure_S import SigMacro_processFigure_S, sigmacro_process_figure_s
+from ._SigMacro_processFigure_S import (
+    SigMacro_processFigure_S,
+    sigmacro_process_figure_s,
+)
 from ._SigMacro_toBlue import SigMacro_toBlue, sigmacro_to_blue
 
 __all__ = [

scitex/git/_branch.py

@@ -66,13 +66,13 @@ def git_branch_rename(repo_path: Path, new_name: str, verbose: bool = True) -> b
 
     with _in_directory(repo_path):
         result = sh(
-            ["git", "branch", "-M", new_name],
-            verbose=verbose,
-            return_as="dict"
+            ["git", "branch", "-M", new_name], verbose=verbose, return_as="dict"
         )
 
         if not result["success"]:
-            error_msg = result['stderr'].strip() if result['stderr'] else "Unknown error"
+            error_msg = (
+                result["stderr"].strip() if result["stderr"] else "Unknown error"
+            )
             logger.error(f"Failed to rename branch in {repo_path}: {error_msg}")
             return False
 
@@ -81,7 +81,9 @@ def git_branch_rename(repo_path: Path, new_name: str, verbose: bool = True) -> b
         return True
 
 
-def git_checkout_new_branch(repo_path: Path, branch_name: str, verbose: bool = True) -> bool:
+def git_checkout_new_branch(
+    repo_path: Path, branch_name: str, verbose: bool = True
+) -> bool:
     """
     Create and checkout a new branch.
 
@@ -123,14 +125,16 @@ def git_checkout_new_branch(repo_path: Path, branch_name: str, verbose: bool = T
 
     with _in_directory(repo_path):
         result = sh(
-            ["git", "checkout", "-b", branch_name],
-            verbose=verbose,
-            return_as="dict"
+            ["git", "checkout", "-b", branch_name], verbose=verbose, return_as="dict"
         )
 
         if not result["success"]:
-            error_msg = result['stderr'].strip() if result['stderr'] else "Unknown error"
-            logger.error(f"Failed to create branch {branch_name} in {repo_path}: {error_msg}")
+            error_msg = (
+                result["stderr"].strip() if result["stderr"] else "Unknown error"
+            )
+            logger.error(
+                f"Failed to create branch {branch_name} in {repo_path}: {error_msg}"
+            )
             return False
 
         if verbose:
@@ -142,7 +146,9 @@ def main(args):
     if args.action == "rename":
         success = git_branch_rename(args.repo_path, args.branch_name, args.verbose)
     elif args.action == "checkout":
-        success = git_checkout_new_branch(args.repo_path, args.branch_name, args.verbose)
+        success = git_checkout_new_branch(
+            args.repo_path, args.branch_name, args.verbose
+        )
     else:
         return EXIT_FAILURE
     return EXIT_SUCCESS if success else EXIT_FAILURE
@@ -151,6 +157,7 @@ def main(args):
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser()
     parser.add_argument("--repo-path", type=Path, required=True)
     parser.add_argument("--action", choices=["rename", "checkout"], required=True)
@@ -162,6 +169,7 @@ def parse_args():
 def run_session():
     """Initialize scitex framework, run main function, and cleanup."""
     from ._session import run_with_session
+
     run_with_session(parse_args, main)
 
 

scitex/git/_clone.py

@@ -14,7 +14,13 @@ from ._constants import EXIT_SUCCESS, EXIT_FAILURE
 logger = getLogger(__name__)
 
 
-def clone_repo(url: str, target_path: Path, branch: str = None, tag: str = None, verbose: bool = True) -> bool:
+def clone_repo(
+    url: str,
+    target_path: Path,
+    branch: str = None,
+    tag: str = None,
+    verbose: bool = True,
+) -> bool:
     """
     Safely clone a git repository.
 
@@ -47,7 +53,9 @@ def clone_repo(url: str, target_path: Path, branch: str = None, tag: str = None,
 
     # Validate mutual exclusivity
     if branch and tag:
-        raise ValueError("Cannot specify both 'branch' and 'tag' parameters. They are mutually exclusive.")
+        raise ValueError(
+            "Cannot specify both 'branch' and 'tag' parameters. They are mutually exclusive."
+        )
 
     if not _validate_git_url(url):
         logger.error(f"Invalid git URL: {url}")
@@ -63,11 +71,7 @@ def clone_repo(url: str, target_path: Path, branch: str = None, tag: str = None,
         ref_info = f" (tag: {tag})"
     cmd.extend([url, str(target_path)])
 
-    result = sh(
-        cmd,
-        verbose=verbose,
-        return_as="dict"
-    )
+    result = sh(cmd, verbose=verbose, return_as="dict")
 
     if not result["success"]:
         logger.error(f"Failed to clone repository: {result['stderr']}")
@@ -101,11 +105,7 @@ def git_init(repo_path: Path, verbose: bool = True) -> bool:
         return False
 
     with _in_directory(repo_path):
-        result = sh(
-            ["git", "init", "-b", "main"],
-            verbose=verbose,
-            return_as="dict"
-        )
+        result = sh(["git", "init", "-b", "main"], verbose=verbose, return_as="dict")
 
         if not result["success"]:
             logger.warning(f"Failed to initialize git repository: {result['stderr']}")
@@ -121,7 +121,9 @@ def main(args):
         if not args.url:
             logger.error("URL required for clone action")
             return EXIT_FAILURE
-        success = clone_repo(args.url, args.path, branch=args.branch, tag=args.tag, verbose=args.verbose)
+        success = clone_repo(
+            args.url, args.path, branch=args.branch, tag=args.tag, verbose=args.verbose
+        )
         return EXIT_SUCCESS if success else EXIT_FAILURE
     elif args.action == "init":
         success = git_init(args.path, args.verbose)
@@ -131,12 +133,17 @@ def main(args):
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser()
     parser.add_argument("--action", choices=["clone", "init"], required=True)
     parser.add_argument("--url", help="Repository URL for cloning")
     parser.add_argument("--path", type=Path, required=True)
-    parser.add_argument("--branch", help="Branch to clone (mutually exclusive with --tag)")
-    parser.add_argument("--tag", help="Tag/release to clone (mutually exclusive with --branch)")
+    parser.add_argument(
+        "--branch", help="Branch to clone (mutually exclusive with --tag)"
+    )
+    parser.add_argument(
+        "--tag", help="Tag/release to clone (mutually exclusive with --branch)"
+    )
     parser.add_argument("--verbose", action="store_true")
     return parser.parse_args()
 
@@ -144,6 +151,7 @@ def parse_args():
 def run_session():
     """Initialize scitex framework, run main function, and cleanup."""
     from ._session import run_with_session
+
     run_with_session(parse_args, main)
 
 

scitex/git/_commit.py

@@ -59,14 +59,12 @@ def git_add_all(repo_path: Path, verbose: bool = True) -> bool:
         return False
 
     with _in_directory(repo_path):
-        result = sh(
-            ["git", "add", "."],
-            verbose=verbose,
-            return_as="dict"
-        )
+        result = sh(["git", "add", "."], verbose=verbose, return_as="dict")
 
         if not result["success"]:
-            error_msg = result['stderr'].strip() if result['stderr'] else "Unknown error"
+            error_msg = (
+                result["stderr"].strip() if result["stderr"] else "Unknown error"
+            )
             logger.error(f"Failed to add files to {repo_path}: {error_msg}")
             return False
 
@@ -115,14 +113,12 @@ def git_commit(repo_path: Path, message: str, verbose: bool = True) -> bool:
         return False
 
     with _in_directory(repo_path):
-        result = sh(
-            ["git", "commit", "-m", message],
-            verbose=verbose,
-            return_as="dict"
-        )
+        result = sh(["git", "commit", "-m", message], verbose=verbose, return_as="dict")
 
         if not result["success"]:
-            error_msg = result['stderr'].strip() if result['stderr'] else "Unknown error"
+            error_msg = (
+                result["stderr"].strip() if result["stderr"] else "Unknown error"
+            )
             logger.error(f"Failed to commit in {repo_path}: {error_msg}")
             return False
 
@@ -146,6 +142,7 @@ def main(args):
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser()
     parser.add_argument("--repo-path", type=Path, required=True)
     parser.add_argument("--action", choices=["add", "commit"], required=True)
@@ -157,6 +154,7 @@ def parse_args():
 def run_session():
     """Initialize scitex framework, run main function, and cleanup."""
     from ._session import run_with_session
+
     run_with_session(parse_args, main)
 
 

scitex/git/_init.py

@@ -29,9 +29,7 @@ def find_parent_git(project_dir: Path) -> Optional[Path]:
         Path to parent git root, or None if not found
     """
     try:
-        repo_parent = Repo(
-            project_dir.parent, search_parent_directories=True
-        )
+        repo_parent = Repo(project_dir.parent, search_parent_directories=True)
         return Path(repo_parent.git_dir).parent
     except InvalidGitRepositoryError:
         return None
@@ -58,19 +56,16 @@ def remove_child_git(project_dir: Path) -> bool:
 
     try:
         import shutil
+
         logger.info(f"Removing child .git to use parent repository...")
         shutil.rmtree(child_git)
         logger.success(f"Removed child .git from {project_dir}")
         return True
     except PermissionError as e:
-        logger.error(
-            f"Permission denied removing .git from {project_dir}: {e}"
-        )
+        logger.error(f"Permission denied removing .git from {project_dir}: {e}")
         return False
     except Exception as e:
-        logger.error(
-            f"Failed to remove child .git from {project_dir}: {e}"
-        )
+        logger.error(f"Failed to remove child .git from {project_dir}: {e}")
         return False
 
 
@@ -89,46 +84,34 @@ def create_child_git(project_dir: Path) -> Optional[Path]:
     try:
         try:
             repo = Repo(project_dir)
-            logger.info(
-                f"Project is already a git repository at {project_dir}"
-            )
+            logger.info(f"Project is already a git repository at {project_dir}")
             # Validate project structure even if repo already exists
             from scitex.writer._validate_tree_structures import validate_tree_structures
+
             validate_tree_structures(project_dir)
             return project_dir
         except InvalidGitRepositoryError:
-            logger.info(
-                f"Initializing new git repository at {project_dir}"
-            )
+            logger.info(f"Initializing new git repository at {project_dir}")
             repo = Repo.init(project_dir)
 
         repo.index.add(["."])
         repo.index.commit("Initial commit from scitex template")
 
-        logger.success(
-            f"Git repository initialized at {project_dir}"
-        )
+        logger.success(f"Git repository initialized at {project_dir}")
         return project_dir
     except PermissionError as e:
-        logger.error(
-            f"Permission denied creating git repository at {project_dir}: {e}"
-        )
+        logger.error(f"Permission denied creating git repository at {project_dir}: {e}")
         return None
     except OSError as e:
-        logger.error(
-            f"IO error creating git repository at {project_dir}: {e}"
-        )
+        logger.error(f"IO error creating git repository at {project_dir}: {e}")
         return None
     except Exception as e:
-        logger.error(
-            f"Failed to create child git repository at {project_dir}: {e}"
-        )
+        logger.error(f"Failed to create child git repository at {project_dir}: {e}")
         return None
 
 
 def init_git_repo(
-    project_dir: Path,
-    git_strategy: Optional[str] = "child"
+    project_dir: Path, git_strategy: Optional[str] = "child"
 ) -> Optional[Path]:
     """
     Initialize or detect git repository based on git_strategy.
@@ -149,9 +132,7 @@ def init_git_repo(
         return None
 
     if git_strategy == "parent":
-        logger.info(
-            "Using 'parent' git strategy, searching for parent repository..."
-        )
+        logger.info("Using 'parent' git strategy, searching for parent repository...")
         parent_git = find_parent_git(project_dir)
 
         if parent_git:
@@ -166,15 +147,11 @@ def init_git_repo(
         return create_child_git(project_dir)
 
     if git_strategy == "child":
-        logger.info(
-            "Using 'child' git strategy, creating isolated repository..."
-        )
+        logger.info("Using 'child' git strategy, creating isolated repository...")
         return create_child_git(project_dir)
 
     if git_strategy == "origin":
-        logger.info(
-            "Using 'origin' git strategy, template git history preserved..."
-        )
+        logger.info("Using 'origin' git strategy, template git history preserved...")
         try:
             repo = Repo(project_dir)
             logger.info(f"Found git repository at {project_dir}")

scitex/git/_remote.py

@@ -16,7 +16,9 @@ from ._constants import EXIT_SUCCESS, EXIT_FAILURE
 logger = getLogger(__name__)
 
 
-def get_remote_url(repo_path: Path, remote_name: str = "origin", verbose: bool = False) -> Optional[str]:
+def get_remote_url(
+    repo_path: Path, remote_name: str = "origin", verbose: bool = False
+) -> Optional[str]:
     """
     Get remote URL for a git repository.
 
@@ -47,7 +49,7 @@ def get_remote_url(repo_path: Path, remote_name: str = "origin", verbose: bool =
         result = sh(
             ["git", "config", "--get", f"remote.{remote_name}.url"],
             verbose=verbose,
-            return_as="dict"
+            return_as="dict",
         )
         if result["success"]:
             return result["stdout"].strip()
@@ -111,7 +113,9 @@ def _normalize_git_url(url: str) -> str:
     return url
 
 
-def is_cloned_from(repo_path: Path, expected_url: str, remote_name: str = "origin") -> bool:
+def is_cloned_from(
+    repo_path: Path, expected_url: str, remote_name: str = "origin"
+) -> bool:
     """
     Check if directory is a git repository cloned from specific URL.
     Handles both HTTPS and SSH URL formats.
@@ -157,6 +161,7 @@ def main(args):
 def parse_args():
     """Parse command line arguments."""
     import argparse
+
     parser = argparse.ArgumentParser()
     parser.add_argument("--action", choices=["get-url", "check-origin"], required=True)
     parser.add_argument("--repo-path", type=Path, required=True)
@@ -169,6 +174,7 @@ def parse_args():
 def run_session():
     """Initialize scitex framework, run main function, and cleanup."""
     from ._session import run_with_session
+
     run_with_session(parse_args, main)
 
 

scitex/git/_result.py

@@ -26,6 +26,7 @@ class GitResult:
     stderr : Optional[str]
         Standard error from git command
     """
+
     success: bool
     error: Optional[str] = None
     stdout: Optional[str] = None
@@ -42,6 +43,7 @@ class CommitResult(GitResult):
     commit_hash : Optional[str]
         Hash of created commit if successful
     """
+
     commit_hash: Optional[str] = None
 
 
@@ -55,6 +57,7 @@ class BranchResult(GitResult):
     branch_name : Optional[str]
         Name of created or renamed branch if successful
     """
+
     branch_name: Optional[str] = None
 
 

scitex/git/_retry.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = "./src/scitex/git/retry.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -81,11 +82,7 @@ def git_retry(
             stderr = (
                 e.stderr
                 if isinstance(e.stderr, str)
-                else (
-                    e.stderr.decode("utf-8", errors="ignore")
-                    if e.stderr
-                    else ""
-                )
+                else (e.stderr.decode("utf-8", errors="ignore") if e.stderr else "")
             )
 
             if "index.lock" in stderr and attempt < max_retries - 1:

scitex/git/_types.py

@@ -46,6 +46,7 @@ class GitResult:
     ...     print(f"Error: {result.message}")
     ...     print(f"Details: {result.stderr}")
     """
+
     success: bool
     message: Optional[str] = None
     stdout: Optional[str] = None
@@ -73,6 +74,7 @@ class CommitResult(GitResult):
     >>> if result.success:
     ...     print(f"Created commit {result.commit_hash}")
     """
+
     commit_hash: Optional[str] = None
 
 
@@ -96,6 +98,7 @@ class CloneResult(GitResult):
     >>> if result.success:
     ...     print(f"Cloned to {result.repo_path}")
     """
+
     repo_path: Optional[str] = None
 
 
@@ -119,6 +122,7 @@ class BranchResult(GitResult):
     >>> if result.success:
     ...     print(f"Branch: {result.branch_name}")
     """
+
     branch_name: Optional[str] = None