[fix] Hotfix the bug that numojo crashes on mojopkg (#227) Numojo 0.6.1

This pull request includes several changes to the `mojoproject.toml`
file and the `numojo` package, focusing on improving the build process,
testing, and formatting functionalities. Additionally, there are updates
to the handling of print options in the `numojo` package.

### Improvements to build and testing process:
*
[`mojoproject.toml`](diffhunk://#diff-1b0ef62120bccf4c05a76e60e13fe686f33eb92d5897b3f05e0c3f8d737fc5c0L19-R27):
Updated the `package` task to include copying the package to the tests
folder and modified the `test` task to test the built package.
*
[`mojoproject.toml`](diffhunk://#diff-1b0ef62120bccf4c05a76e60e13fe686f33eb92d5897b3f05e0c3f8d737fc5c0L43-R44):
Simplified the `final` task to run format and test commands, and updated
the `f` alias to run the `final` task.

### Dependency updates:
*
[`mojoproject.toml`](diffhunk://#diff-1b0ef62120bccf4c05a76e60e13fe686f33eb92d5897b3f05e0c3f8d737fc5c0L53-R53):
Updated the `max` dependency version to `25.1.1`.

### Codebase simplification:
* `numojo/__init__.mojo`, `numojo/core/complex/complex_ndarray.mojo`,
`numojo/routines/io/__init__.mojo`: Removed the unused `printoptions`
import.
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*
[`numojo/routines/io/formatting.mojo`](diffhunk://#diff-ebe0524c71023004d26ae3e618bbaabd5177b5261be63254bf3d483f16af991aL23-R23):
Replaced `GLOBAL_PRINT_OPTIONS` with a local `default_print_options`
instance in several functions and methods, and added new parameters to
the `format_floating_scientific` and `format_floating_precision`
functions for better control over formatting behavior.
[[1]](diffhunk://#diff-ebe0524c71023004d26ae3e618bbaabd5177b5261be63254bf3d483f16af991aL23-R23)
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---------

Co-authored-by: MadAlex1997 <[email protected]>

Author: forfudan

.gitignore

@@ -27,7 +27,7 @@ magic.lock
 
 # Miscellaneous files
 mojo
-/numojo.mojopkg
+numojo.mojopkg
 /bench.mojo
 /test*.mojo
 /test*.ipynb

mojoproject.toml

@@ -16,15 +16,15 @@ license = "Apache-2.0"
 readme = "README.MD"
 
 [tasks]
-# compile the package
-package = "magic run mojo package numojo"
+# compile the package and copy it to the tests folder
+package = "magic run mojo package numojo && cp numojo.mojopkg tests/"
 p = "clear && magic run package"
 
 # format the package
-format = "magic run mojo format ./ && magic run mojo format docs/readthedocs/docs.py"
+format = "magic run mojo format ./"
 
-# test whether tests pass and the package can be built
-test = "magic run mojo test tests -I ./ -I ./tests/ && magic run package"
+# test whether tests pass on the built package
+test = "magic run package && magic run mojo test tests -I ./tests/"
 t = "clear && magic run test"
 
 # run individual tests to avoid overheat
@@ -40,8 +40,8 @@ test_statistics = "magic run mojo test tests/routines/test_statistics.mojo -I ./
 test_sorting = "magic run mojo test tests/routines/test_sorting.mojo -I ./ -I ./tests/"
 
 # run all final checks before a commit
-final = "magic run test && magic run format && magic run package"
-f = "clear && magic run test && magic run format && magic run package"
+final = "magic run format && magic run test"
+f = "clear && magic run final"
 
 # Automatically Generate doc pages
 doc_pages = "mojo doc numojo/ -o docs.json"
@@ -50,7 +50,7 @@ doc_pages = "mojo doc numojo/ -o docs.json"
 release = "clear && magic run final && magic run doc_pages"
 
 [dependencies]
-max = "=25.1"
+max = "=25.1.1"
 python = ">=3.11"
 numpy = ">=1.19"
 scipy = ">=1.14"

numojo/__init__.mojo

@@ -62,7 +62,7 @@ from numojo.routines.io import (
     loadtxt,
     savetxt,
 )
-from numojo.routines.io import printoptions, set_printoptions
+from numojo.routines.io import set_printoptions
 
 from numojo.routines import linalg
 from numojo.routines.linalg.misc import diagonal
@@ -181,7 +181,7 @@ from numojo.routines.creation import (
 )
 
 from numojo.routines import indexing
-from numojo.routines.indexing import where, compress
+from numojo.routines.indexing import where, compress, take_along_axis
 
 from numojo.routines.functional import apply_along_axis
 

numojo/core/complex/complex_ndarray.mojo

@@ -34,7 +34,6 @@ from numojo.routines.io.formatting import (
     format_floating_scientific,
     format_value,
     PrintOptions,
-    printoptions,
     GLOBAL_PRINT_OPTIONS,
 )
 import numojo.routines.linalg as linalg

numojo/routines/indexing.mojo

@@ -232,3 +232,126 @@ fn compress[
 
     else:
         return compress(condition, ravel(a), axis=0)
+
+
+fn take_along_axis[
+    dtype: DType, //,
+](
+    arr: NDArray[dtype], indices: NDArray[DType.index], axis: Int = 0
+) raises -> NDArray[dtype]:
+    """
+    Takes values from the input array along the given axis based on indices.
+
+    Raises:
+        Error: If the axis is out of bounds for the given array.
+        Error: If the ndim of arr and indices are not the same.
+        Error: If the shape of indices does not match the shape of the
+            input array except along the given axis.
+
+    Parameters:
+        dtype: DType of the input array.
+
+    Args:
+        arr: The source array.
+        indices: The indices array.
+        axis: The axis along which to take values. Default is 0.
+
+    Returns:
+        An array with the same shape as indices with values taken from the
+            input array along the given axis.
+
+    Examples:
+
+    ```console
+    > var a = nm.arange[i8](12).reshape(Shape(3, 4))
+    > print(a)
+    [[ 0  1  2  3]
+     [ 4  5  6  7]
+     [ 8  9 10 11]]
+    > ind = nm.array[intp]("[[0, 1, 2, 0], [1, 0, 2, 1]]")
+    > print(ind)
+    [[0 1 2 0]
+     [1 0 2 1]]
+    > print(nm.indexing.take_along_axis(a, ind, axis=0))
+    [[ 0  5 10  3]
+     [ 4  1 10  7]]
+    ```
+    .
+    """
+    var normalized_axis = axis
+    if normalized_axis < 0:
+        normalized_axis = arr.ndim + normalized_axis
+    if (normalized_axis >= arr.ndim) or (normalized_axis < 0):
+        raise Error(
+            String(
+                "\nError in `take_along_axis`: Axis {} is out of bound for"
+                " array with {} dimensions"
+            ).format(axis, arr.ndim)
+        )
+
+    # Check if the ndim of arr and indices are same
+    if arr.ndim != indices.ndim:
+        raise Error(
+            String(
+                "\nError in `take_along_axis`: The ndim of arr and indices must"
+                " be same. Got {} and {}.".format(arr.ndim, indices.ndim)
+            )
+        )
+
+    # broadcast indices to the shape of arr if necessary
+    # When broadcasting, the shape of indices must match the shape of arr
+    # except along the axis
+
+    var broadcasted_indices = indices
+
+    if arr.shape != indices.shape:
+        var arr_shape_new = arr.shape
+        arr_shape_new[normalized_axis] = indices.shape[normalized_axis]
+
+        try:
+            broadcasted_indices = numojo.broadcast_to(indices, arr_shape_new)
+        except e:
+            raise Error(
+                String(
+                    "\nError in `take_along_axis`: Shape of indices must match"
+                    " shape of array except along the given axis. "
+                    + String(e)
+                )
+            )
+
+    # Create output array with same shape as broadcasted_indices
+    var result = NDArray[dtype](Shape(broadcasted_indices.shape))
+
+    var arr_iterator = arr.iter_along_axis(normalized_axis)
+    var indices_iterator = broadcasted_indices.iter_along_axis(normalized_axis)
+    var length_of_iterator = result.size // result.shape[normalized_axis]
+
+    if normalized_axis == arr.ndim - 1:
+        # If axis is the last axis, the data is contiguous.
+        for i in range(length_of_iterator):
+            var arr_slice = arr_iterator.ith(i)
+            var indices_slice = indices_iterator.ith(i)
+            var arr_slice_after_applying_indices = arr_slice[indices_slice]
+            memcpy(
+                result._buf.ptr + i * result.shape[normalized_axis],
+                arr_slice_after_applying_indices._buf.ptr,
+                result.shape[normalized_axis],
+            )
+    else:
+        # If axis is not the last axis, the data is not contiguous.
+        for i in range(length_of_iterator):
+            var indices_slice_offsets: NDArray[DType.index]
+            var indices_slice: NDArray[DType.index]
+            indices_slice_offsets, indices_slice = (
+                indices_iterator.ith_with_offsets(i)
+            )
+            var arr_slice = arr_iterator.ith(i)
+            var arr_slice_after_applying_indices = arr_slice[indices_slice]
+            for j in range(arr_slice_after_applying_indices.size):
+                (
+                    result._buf.ptr + Int(indices_slice_offsets[j])
+                ).init_pointee_copy(
+                    arr_slice_after_applying_indices._buf.ptr[j]
+                )
+
+    return result

numojo/routines/io/__init__.mojo

@@ -6,7 +6,5 @@ from .files import (
 from .formatting import (
     format_floating_scientific,
     PrintOptions,
-    printoptions,
-    GLOBAL_PRINT_OPTIONS,
     set_printoptions,
 )

numojo/routines/io/formatting.mojo

@@ -20,25 +20,7 @@ alias DEFAULT_FORMATTED_WIDTH = 8
 alias DEFAULT_EXPONENT_THRESHOLD = 4
 alias DEFAULT_SUPPRESS_SCIENTIFIC = False
 
-var GLOBAL_PRINT_OPTIONS: PrintOptions = PrintOptions(
-    precision=DEFAULT_PRECISION,
-    suppress_small=DEFAULT_SUPPRESS_SMALL,
-    separator=DEFAULT_SEPARATOR,
-    padding=DEFAULT_PADDING,
-    threshold=DEFAULT_THRESHOLD,
-    line_width=DEFAULT_LINE_WIDTH,
-    edge_items=DEFAULT_EDGE_ITEMS,
-    sign=DEFAULT_SIGN,
-    float_format=DEFAULT_FLOAT_FORMAT,
-    complex_format=DEFAULT_COMPLEX_FORMAT,
-    nan_string=DEFAULT_NAN_STRING,
-    inf_string=DEFAULT_INF_STRING,
-    formatted_width=DEFAULT_FORMATTED_WIDTH,
-    exponent_threshold=DEFAULT_EXPONENT_THRESHOLD,
-    suppress_scientific=DEFAULT_SUPPRESS_SCIENTIFIC,
-)
-
-alias printoptions = PrintOptions
+alias GLOBAL_PRINT_OPTIONS = PrintOptions()
 
 
 @value
@@ -146,7 +128,8 @@ struct PrintOptions:
         self.suppress_scientific = suppress_scientific
 
     fn __enter__(mut self) -> Self:
-        GLOBAL_PRINT_OPTIONS.set_options(
+        var default_print_options = PrintOptions()
+        default_print_options.set_options(
             precision=self.precision,
             suppress_small=self.suppress_small,
             separator=self.separator,
@@ -163,10 +146,11 @@ struct PrintOptions:
             exponent_threshold=self.exponent_threshold,
             suppress_scientific=self.suppress_scientific,
         )
-        return GLOBAL_PRINT_OPTIONS
+        return default_print_options
 
     fn __exit__(mut self):
-        GLOBAL_PRINT_OPTIONS.set_options(
+        var default_print_options = PrintOptions()
+        default_print_options.set_options(
             precision=DEFAULT_PRECISION,
             suppress_small=DEFAULT_SUPPRESS_SMALL,
             separator=DEFAULT_SEPARATOR,
@@ -192,7 +176,8 @@ fn set_printoptions(
     padding: String = DEFAULT_PADDING,
     edge_items: Int = DEFAULT_EDGE_ITEMS,
 ):
-    GLOBAL_PRINT_OPTIONS.set_options(
+    var default_print_options = PrintOptions()
+    default_print_options.set_options(
         precision,
         suppress_small,
         separator,
@@ -204,7 +189,14 @@ fn set_printoptions(
 # FIXME: fix the problem where precision > number of digits in the mantissa results in a not so exact value.
 fn format_floating_scientific[
     dtype: DType = DType.float64
-](x: Scalar[dtype], precision: Int = 10, sign: Bool = False) raises -> String:
+](
+    x: Scalar[dtype],
+    precision: Int = 10,
+    sign: Bool = False,
+    suppress_scientific: Bool = False,
+    exponent_threshold: Int = 4,
+    formatted_width: Int = 8,
+) raises -> String:
     """
     Format a float in scientific notation.
 
@@ -218,6 +210,11 @@ fn format_floating_scientific[
         x: The float to format.
         precision: The number of decimal places to include in the mantissa.
         sign: Whether to include the sign of the float in the result. Defaults to False.
+        suppress_scientific: Whether to suppress scientific notation for small numbers.
+            Defaults to False.
+        exponent_threshold: The threshold for suppressing scientific notation.
+            Defaults to 4.
+        formatted_width: The width of the formatted string. Defaults to 8.
 
     Returns:
         A string representation of the float in scientific notation.
@@ -235,10 +232,6 @@ fn format_floating_scientific[
         raise Error("Precision must be a non-negative integer.")
 
     try:
-        var suppress_scientific = GLOBAL_PRINT_OPTIONS.suppress_scientific
-        var exponent_threshold = GLOBAL_PRINT_OPTIONS.exponent_threshold
-        var formatted_width = GLOBAL_PRINT_OPTIONS.formatted_width
-
         if x == 0:
             if sign:
                 var result: String = "+0." + "0" * precision + "e+00"
@@ -290,7 +283,12 @@ fn format_floating_scientific[
 
 fn format_floating_precision[
     dtype: DType
-](value: Scalar[dtype], precision: Int, sign: Bool = False) raises -> String:
+](
+    value: Scalar[dtype],
+    precision: Int,
+    sign: Bool = False,
+    suppress_small: Bool = False,
+) raises -> String:
     """
     Format a floating-point value to the specified precision.
 
@@ -299,6 +297,7 @@ fn format_floating_precision[
         precision: The number of decimal places to include.
         sign: Whether to include the sign of the float in the result.
             Defaults to False.
+        suppress_small: Whether to suppress small numbers. Defaults to False.
 
     Returns:
         The formatted value as a string.
@@ -316,7 +315,6 @@ fn format_floating_precision[
     if precision < 0:
         raise Error("Precision must be a non-negative integer.")
 
-    var suppress_small = GLOBAL_PRINT_OPTIONS.suppress_small
     if suppress_small and abs(value) < 1e-10:
         var result: String = String("0.")
         for _ in range(precision):
@@ -349,12 +347,19 @@ fn format_floating_precision[
 
 fn format_floating_precision[
     cdtype: CDType, dtype: DType
-](value: ComplexSIMD[cdtype, dtype=dtype]) raises -> String:
+](
+    value: ComplexSIMD[cdtype, dtype=dtype],
+    precision: Int = 4,
+    sign: Bool = False,
+) raises -> String:
     """
     Format a complex floating-point value to the specified precision.
 
     Args:
         value: The complex value to format.
+        precision: The number of decimal places to include.
+        sign: Whether to include the sign of the float in the result.
+            Defaults to False.
 
     Returns:
         The formatted value as a string.
@@ -363,9 +368,6 @@ fn format_floating_precision[
         Error: If the complex value cannot be formatted.
     """
     try:
-        var precision = GLOBAL_PRINT_OPTIONS.precision
-        var sign = GLOBAL_PRINT_OPTIONS.sign
-
         return (
             "("
             + format_floating_precision(value.re, precision, sign)