flekspy 0.3.2__tar.gz → 0.3.4__tar.gz

{flekspy-0.3.2 → flekspy-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: flekspy
-Version: 0.3.2
+Version: 0.3.4
 Summary: Python utilities for processing FLEKS data
 Author-email: Yuxi Chen <yuxichen@umich.edu>, Hongyang Zhou <hyzhou@umich.edu>
 License-File: LICENSE.md

{flekspy-0.3.2 → flekspy-0.3.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "flekspy"
-version = "0.3.2"
+version = "0.3.4"
 description = "Python utilities for processing FLEKS data"
 authors = [
     {name = "Yuxi Chen", email = "yuxichen@umich.edu"},

{flekspy-0.3.2 → flekspy-0.3.4}/src/flekspy/idl/idl.py

@@ -212,14 +212,14 @@ class IDLData(object):
         with open(saveName, "w") as f:
             f.write(self.unit + "\n")
             f.write(
-                "{:d}\t{:e}\t{:d}\t{:d}\t{:d}\n".format(
+                "{0:d}\t{1:e}\t{2:d}\t{3:d}\t{4:d}\n".format(
                     self.iter, self.time, self.ndim, self.nparam, self.nvar
                 )
             )
-            [f.write("{:d}\t".format(i)) for i in self.grid]
+            [f.write("{0:d}\t".format(i)) for i in self.grid]
             f.write("\n")
             if self.nparam > 0:
-                [f.write("{:e}\t".format(i)) for i in self.para]
+                [f.write("{0:e}\t".format(i)) for i in self.para]
                 f.write("\n")
             [f.write(i + " ") for i in self.variables]
             f.write("\n")
@@ -231,7 +231,7 @@ class IDLData(object):
                 for jj in range(nj):
                     for ii in range(ni):
                         [
-                            f.write("{:e}\t".format(i))
+                            f.write("{0:e}\t".format(i))
                             for i in self.data.array[:, ii, jj, kk]
                         ]
                         f.write("\n")
@@ -424,30 +424,30 @@ class IDLData(object):
     def read_binary_instance(self, infile):
         self.get_file_head(infile)
         nrow = self.ndim + self.nvar
-        self.data.array = np.zeros((nrow, self.npoints), dtype=np.float32)
 
-        # Get the grid points...
+        if self.pformat == "f":
+            dtype = np.float32
+        else:
+            dtype = np.float64
+
+        self.data.array = np.empty((nrow, self.npoints), dtype=dtype)
+        dtype_str = f"{self.end_char}{self.pformat}"
+
+        # Get the grid points
         (old_len, record_len) = struct.unpack(self.end_char + "2l", infile.read(8))
-        for i in range(0, self.ndim):
-            # Read the data into a temporary grid
-            tempgrid = np.array(
-                struct.unpack(
-                    "{0}{1}{2}".format(self.end_char, self.npoints, self.pformat),
-                    infile.read(int(record_len // self.ndim)),
-                )
-            )
-            self.data.array[i, :] = tempgrid
+        buffer = infile.read(record_len)
+        grid_data = np.frombuffer(
+            buffer, dtype=dtype_str, count=self.npoints * self.ndim
+        )
+        self.data.array[0 : self.ndim, :] = grid_data.reshape((self.ndim, self.npoints))
 
         # Get the actual data and sort
         for i in range(self.ndim, self.nvar + self.ndim):
             (old_len, record_len) = struct.unpack(self.end_char + "2l", infile.read(8))
-            tmp = np.array(
-                struct.unpack(
-                    "{0}{1}{2}".format(self.end_char, self.npoints, self.pformat),
-                    infile.read(record_len),
-                )
+            buffer = infile.read(record_len)
+            self.data.array[i, :] = np.frombuffer(
+                buffer, dtype=dtype_str, count=self.npoints
             )
-            self.data.array[i, :] = tmp
         # Consume the last record length
         infile.read(4)
 

{flekspy-0.3.2 → flekspy-0.3.4}/src/flekspy/util/data_container.py

@@ -119,19 +119,27 @@ class DataContainer(object):
             expression (str): Python codes to be executed
             Example: expression = "np.log({rhos0}+{rhos1})"
         """
+        import re
 
-        if expression.find("{") < 0:
+        if "{" not in expression:
             return self.get_variable(expression, unit)
 
-        exp1 = expression.replace("{", "self.get_variable('")
+        # A dictionary to store the variables for eval.
+        eval_context = {"np": np}
 
-        exp2 = exp1.replace("}", "',unit)")
-        exp2 = r"result=" + exp2
+        def repl(match):
+            var_name = match.group(1)
+            # Add the variable to the context for eval.
+            # Use a name that is valid for a python identifier.
+            eval_context[var_name] = self.get_variable(var_name, unit)
+            return var_name
 
-        print(exp2)
-        exec(exp2)
+        # Replace `{var}` with `var` and populate `eval_context`.
+        expression_for_eval = re.sub(r"\{(.*?)\}", repl, expression)
 
-        return locals()["result"]
+        # Evaluate the expression in the prepared context.
+        # We provide an empty `__builtins__` to restrict access to other built-in functions for security.
+        return eval(expression_for_eval, {"__builtins__": {}}, eval_context)
 
     def add_variable(self, name, val):
         r"""
@@ -161,6 +169,7 @@ class DataContainer(object):
         Return: YTArray
         """
 
+        ytarr = None
         if var in self.data.keys():
             varUnit = get_unit(var, unit)
             ytarr = self.data[var]
@@ -202,6 +211,9 @@ class DataContainer(object):
                     varUnit = "dimensionless"
                     ytarr = yt.YTArray(ytarr, varUnit)
 
+        if ytarr is None:
+            raise KeyError(f"Variable '{var}' not found in dataset.")
+
         return ytarr if str(ytarr.units) == "dimensionless" else ytarr.in_units(varUnit)
 
 
@@ -323,8 +335,8 @@ class DataContainer2D(DataContainer):
         nlevels: int = 200,
         cmap: str = "turbo",
         figsize=(10, 6),
-        f = None,
-        axes = None,
+        f=None,
+        axes=None,
         pcolor=False,
         logscale=False,
         addgrid=False,

{flekspy-0.3.2 → flekspy-0.3.4}/src/flekspy/util/utilities.py

@@ -152,7 +152,7 @@ def download_testfile(url: str, target_path="."):
         target_dir.mkdir(parents=True, exist_ok=True)
 
         with tarfile.open(temp_file, "r:gz") as tar:
-            tar.extractall(target_dir)
+            tar.extractall(target_dir, filter="data")
 
     except requests.exceptions.RequestException as e:
         print(f"Error downloading file: {e}")