MAINT: upgrade anaconda=2025.06 and python=3.13

[mmcky]

This PR upgrades

• ananconda=2025.06
• python=3.13
• quantecon-book-theme=0.9.2 (fixes for modal issues)

and associated compatible build infrastructure.

Tasks

• migrate to use lychee for link checking
• migrate figure to image in exercises
• merge the np.sum -> @ updates
• [interpolation] Package is outdated and cannot install #223
• [match_transport] upgrades required for compatibility with numpy>=2 #225
• [amss2, amss3] lecture needs to be updated for compat with numpy>=2 #224

[mmcky]

• fix execution incompatibilities with anaconda=2025.06 and numpy>=2.0

amss.err.log
amss2.err.log
amss3.err.log
match_transport.err.log

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[mmcky]

@kp992 this is currently blocked by amss and the interpolations package.

There are some suggestions in #223

We were thinking of Step 1 removing our dependency on interpolations then Step 2 look at converting this lecture to JAX. @HumphreyYang and I gave copilot a go in #244 if those ideas are helpful. Also please liaise with @HumphreyYang through #236 for the jax translation but I think Step 1 would be good to do first.

[kp992]

Thanks @mmcky. I will look into it.

[HumphreyYang]

Many thanks @mmcky and @kp992,

There is a drop-in replacement for the interpolation in #228.

We can move it into one of script in the static Python file.

This produces the same figures.

Here is a copy of the replacement if that is helpful:

@njit
def get_grid_nodes(grid):
    """
    Get the actual grid points from a grid tuple.
    """
    x_min, x_max, x_num = grid
    return np.linspace(x_min, x_max, x_num)

@njit
def linear_interp_1d_scalar(x_min, x_max, x_num, y_values, x_val):
    """Helper function for scalar interpolation"""
    x_nodes = np.linspace(x_min, x_max, x_num)

    # Extrapolation with linear extension
    if x_val <= x_nodes[0]:
        # Linear extrapolation using first two points
        if x_num >= 2:
            slope = (y_values[1] - y_values[0]) / (x_nodes[1] - x_nodes[0])
            return y_values[0] + slope * (x_val - x_nodes[0])
        else:
            return y_values[0]

    if x_val >= x_nodes[-1]:
        # Linear extrapolation using last two points
        if x_num >= 2:
            slope = (y_values[-1] - y_values[-2]) / (x_nodes[-1] - x_nodes[-2])
            return y_values[-1] + slope * (x_val - x_nodes[-1])
        else:
            return y_values[-1]

    # Binary search for the right interval
    left = 0
    right = x_num - 1
    while right - left > 1:
        mid = (left + right) // 2
        if x_nodes[mid] <= x_val:
            left = mid
        else:
            right = mid

    # Linear interpolation
    x_left = x_nodes[left]
    x_right = x_nodes[right]
    y_left = y_values[left]
    y_right = y_values[right]

    weight = (x_val - x_left) / (x_right - x_left)
    return y_left * (1 - weight) + y_right * weight

@njit
def linear_interp_1d(x_grid, y_values, x_query):
    """
    Perform 1D linear interpolation.
    """
    x_min, x_max, x_num = x_grid
    return linear_interp_1d_scalar(x_min, x_max, x_num, y_values, x_query[0])

[kp992]

Thanks @HumphreyYang for sharing this. Should we add this in the quantecon package? This is because we can reuse the same snippets across all the series?

[HumphreyYang]

Thanks @HumphreyYang for sharing this. Should we add this in the quantecon package? This is because we can reuse the same snippets across all the series?

I think for now we can put it into the script that is used across the lecture since we are going to rewrite things in JAX later.

[HumphreyYang]

Hi @mmcky, I will use this PR to test the workaround now.

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[mmcky]

@HumphreyYang nice work!

The preview is looking pretty good. Are you happy for me to merge this?

[mmcky]

@HumphreyYang it is interesting that the modal issue is still a problem in this preview build. So this isn't going to directly solve the problem.

[HumphreyYang]

@HumphreyYang nice work!

The preview is looking pretty good. Are you happy for me to merge this?

Sounds great! I will commence stage 2 when migrating it to JAX since JAX result looks a bit different.

@HumphreyYang it is interesting that the modal issue is still a problem in this preview build.

Could you please let me know which model issue you are referring to?

[mmcky]

@HumphreyYang nice work!
The preview is looking pretty good. Are you happy for me to merge this?

Sounds great! I will commence stage 2 when migrating it to JAX since JAX result looks a bit different.

@HumphreyYang it is interesting that the modal issue is still a problem in this preview build.

Could you please let me know which model issue you are referring to?

Thanks @HumphreyYang a modal is an html object that shows as a window. The colab button should show a modal :-)

[kp992]

Thanks @HumphreyYang and @mmcky for taking it forward. I missed the track of this PR somehow while working on the other JAX lectures.

[HumphreyYang]

Thanks @HumphreyYang a modal is an html object that shows as a window. The colab button should show a modal :-)

Ah roger that. I thought the namedtuple model has some problem : )

[mmcky]

@HumphreyYang, @kp992 has submitted a patch to fix the modal issue on the theme. Are you happy if we merge this as we will need the later version of sphinx unless we want to back port the fix to an earlier version of quantecon-book-theme but that is a lot of work. I'd prefer to merge this if we can.

[HumphreyYang]

Hi @mmcky, please feel free to merge when you are ready!

[mmcky]

• test Update index.js to fix reference error quantecon-book-theme#311

if works then,

• get Update index.js to fix reference error quantecon-book-theme#311 merged (update the CI)
• release new version of quantecon-book-theme
• update this PR to use new version
• merge PR to update software.

[mmcky]

thanks @kp992 and @HumphreyYang -- once I get the green tick of approval I will merge this.