MAINT: upgrade anaconda=2025.06 and python=3.13 (#215)

* MAINT: upgrade anaconda=2025.06 and python=3.13

* add back in sphinx-proof

* migrate to lychee for linkchecking

* fix figure to image in exercise

* fix align option

* tmp: disable build cahce

* update match_transport for numpy2

* convert np.asfarray -> np.assarray( , dtype=float)

* update amss to remove dependency  on interpolation

* TST: fix on quantecon-book-theme

* update quantecon-book-theme=0.9.2

* restore build cache:

---------

Co-authored-by: Humphrey Yang <u6474961@anu.edu.au>
Co-authored-by: Humphrey Yang <39026988+HumphreyYang@users.noreply.github.com>

Author: mmcky

.github/workflows/cache.yml

@@ -15,7 +15,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install latex dependencies

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install latex dependencies

.github/workflows/execution.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
       - name: Checkout
         uses: actions/checkout@v5
@@ -53,7 +53,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["macos-latest"]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
     steps:
       - name: Checkout
         uses: actions/checkout@v5
@@ -85,7 +85,7 @@ jobs:
   #     fail-fast: false
   #     matrix:
   #       os: ["windows-latest"]
-  #       python-version: ["3.11"]
+  #       python-version: ["3.13"]
   #   steps:
   #     - name: Checkout
   #       uses: actions/checkout@v2

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
           auto-update-conda: true
           auto-activate-base: true
           miniconda-version: 'latest'
-          python-version: "3.12"
+          python-version: "3.13"
           environment-file: environment.yml
           activate-environment: quantecon
       - name: Install latex dependencies

.gitignore

@@ -1,2 +1,4 @@
 _build/
-.DS_Store
+.DS_Store
+.ipynb_checkpoints/
+.virtual_documents/

environment.yml

@@ -2,20 +2,18 @@ name: quantecon
 channels:
   - default
 dependencies:
-  - python=3.12
-  - anaconda=2024.10
+  - python=3.13
+  - anaconda=2025.06
   - pip
   - pip:
-    - jupyter-book==1.0.3
-    - quantecon-book-theme==0.7.6
-    - sphinx-tojupyter==0.3.0
+    - jupyter-book==1.0.4post1
+    - quantecon-book-theme==0.9.2
+    - sphinx-tojupyter==0.3.1
     - sphinxext-rediraffe==0.2.7
-    - sphinx-reredirects==0.1.4
     - sphinx-exercise==1.0.1
-    - sphinx-proof==0.2.0
-    - ghp-import==1.1.0
-    - sphinxcontrib-youtube==1.3.0 #Version 1.3.0 is required as quantecon-book-theme is only compatible with sphinx<=5
+    - sphinx-proof==0.2.1
+    - sphinxcontrib-youtube==1.4.1
     - sphinx-togglebutton==0.3.2
-    # Docker Requirements
-    - pytz
+    - sphinx-reredirects==0.1.4
+
 

lectures/_static/lecture_specific/amss/recursive_allocation.py

@@ -1,3 +1,64 @@
+import numpy as np
+from numba import njit, prange
+from quantecon import optimize
+
+@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])
+
 class AMSS:
     # WARNING: THE CODE IS EXTREMELY SENSITIVE TO CHOCIES OF PARAMETERS.
     # DO NOT CHANGE THE PARAMETERS AND EXPECT IT TO WORK
@@ -78,6 +139,10 @@ def simulate(self, s_hist, b_0):
         pref = self.pref
         x_grid, g, β, S = self.x_grid, self.g, self.β, self.S
         σ_v_star, σ_w_star = self.σ_v_star, self.σ_w_star
+        Π = self.Π
+
+        # Extract the grid tuple from the list
+        grid_tuple = x_grid[0] if isinstance(x_grid, list) else x_grid
 
         T = len(s_hist)
         s_0 = s_hist[0]
@@ -111,8 +176,8 @@ def simulate(self, s_hist, b_0):
             T = np.zeros(S)
             for s in range(S):
                 x_arr = np.array([x_])
-                l[s] = eval_linear(x_grid, σ_v_star[s_, :, s], x_arr)
-                T[s] = eval_linear(x_grid, σ_v_star[s_, :, S+s], x_arr)
+                l[s] = linear_interp_1d(grid_tuple, σ_v_star[s_, :, s], x_arr)
+                T[s] = linear_interp_1d(grid_tuple, σ_v_star[s_, :, S+s], x_arr)
 
             c = (1 - l) - g
             u_c = pref.Uc(c, l)
@@ -135,6 +200,8 @@ def simulate(self, s_hist, b_0):
 
 def obj_factory(Π, β, x_grid, g):
     S = len(Π)
+    # Extract the grid tuple from the list
+    grid_tuple = x_grid[0] if isinstance(x_grid, list) else x_grid
 
     @njit
     def obj_V(σ, state, V, pref):
@@ -152,7 +219,7 @@ def obj_V(σ, state, V, pref):
         V_next = np.zeros(S)
 
         for s in range(S):
-            V_next[s] = eval_linear(x_grid, V[s], np.array([x[s]]))
+            V_next[s] = linear_interp_1d(grid_tuple, V[s], np.array([x[s]]))
 
         out = Π[s_] @ (pref.U(c, l) + β * V_next)
 
@@ -167,7 +234,7 @@ def obj_W(σ, state, V, pref):
         c = (1 - l) - g[s_]
         x = -pref.Uc(c, l) * (c - T - b_0) + pref.Ul(c, l) * (1 - l)
 
-        V_next = eval_linear(x_grid, V[s_], np.array([x]))
+        V_next = linear_interp_1d(grid_tuple, V[s_], np.array([x]))
 
         out = pref.U(c, l) + β * V_next
 
@@ -178,9 +245,11 @@ def obj_W(σ, state, V, pref):
 
 def bellman_operator_factory(Π, β, x_grid, g, bounds_v):
     obj_V, obj_W = obj_factory(Π, β, x_grid, g)
-    n = x_grid[0][2]
+    # Extract the grid tuple from the list
+    grid_tuple = x_grid[0] if isinstance(x_grid, list) else x_grid
+    n = grid_tuple[2]
     S = len(Π)
-    x_nodes = nodes(x_grid)
+    x_nodes = get_grid_nodes(grid_tuple)
 
     @njit(parallel=True)
     def T_v(V, V_new, σ_star, pref):
@@ -209,4 +278,4 @@ def T_w(W, σ_star, V, b_0, pref):
             W[s_] = res.fun
             σ_star[s_] = res.x
 
-    return T_v, T_w
+    return T_v, T_w

lectures/_static/lecture_specific/amss2/recursive_allocation.py

@@ -230,7 +230,7 @@ def objf(z):
         def objf_prime(x):
 
             epsilon = 1e-7
-            x0 = np.asfarray(x)
+            x0 = np.asarray(x, dtype=float)
             f0 = np.atleast_1d(objf(x0))
             jac = np.zeros([len(x0), len(f0)])
             dx = np.zeros(len(x0))

lectures/amss.md

@@ -27,7 +27,6 @@ In addition to what's in Anaconda, this lecture will need the following librarie
 tags: [hide-output]
 ---
 !pip install --upgrade quantecon
-!pip install interpolation
 ```
 
 ## Overview
@@ -38,12 +37,80 @@ Let's start with following imports:
 import numpy as np
 import matplotlib.pyplot as plt
 from scipy.optimize import root
-from interpolation.splines import eval_linear, UCGrid, nodes
 from quantecon import optimize, MarkovChain
 from numba import njit, prange, float64
 from numba.experimental import jitclass
 ```
 
+Now let's define numba-compatible interpolation functions for this lecture.
+
+We will soon use the following interpolation functions to interpolate the value function and the policy functions
+
+```{code-cell} ipython
+:tags: [collapse-40]
+
+@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])
+```
+
+Let's start with following imports:
+
 In {doc}`an earlier lecture <opt_tax_recur>`, we described a model of
 optimal taxation with state-contingent debt due to
 Robert E. Lucas, Jr.,  and Nancy Stokey  {cite}`LucasStokey1983`.
@@ -774,7 +841,7 @@ x_min = -1.5555
 x_max = 17.339
 x_num = 300
 
-x_grid = UCGrid((x_min, x_max, x_num))
+x_grid = [(x_min, x_max, x_num)]
 
 crra_pref = CRRAutility(β=β, σ=σ, γ=γ)
 
@@ -788,7 +855,7 @@ amss_model = AMSS(crra_pref, β, Π, g, x_grid, bounds_v)
 ```{code-cell} python3
 # WARNING: DO NOT EXPECT THE CODE TO WORK IF YOU CHANGE PARAMETERS
 V = np.zeros((len(Π), x_num))
-V[:] = -nodes(x_grid).T ** 2
+V[:] = -get_grid_nodes(x_grid[0]) ** 2
 
 σ_v_star = np.ones((S, x_num, S * 2))
 σ_v_star[:, :, :S] = 0.0
@@ -914,14 +981,14 @@ x_min = -3.4107
 x_max = 3.709
 x_num = 300
 
-x_grid = UCGrid((x_min, x_max, x_num))
+x_grid = [(x_min, x_max, x_num)]
 log_pref = LogUtility(β=β, ψ=ψ)
 
 S = len(Π)
 bounds_v = np.vstack([np.zeros(2 * S), np.hstack([1 - g, np.ones(S)]) ]).T
 
 V = np.zeros((len(Π), x_num))
-V[:] = -(nodes(x_grid).T + x_max) ** 2 / 14
+V[:] = -(get_grid_nodes(x_grid[0]) + x_max) ** 2 / 14
 
 σ_v_star = 1 - np.full((S, x_num, S * 2), 0.55)
 
@@ -1026,4 +1093,4 @@ lump-sum transfers to the private sector.
 problem, there exists another realization $\tilde s^t$ with
 the same history up until the previous period, i.e., $\tilde s^{t-1}=
 s^{t-1}$, but where the multiplier on constraint {eq}`AMSS_46` takes  a positive value, so
-$\gamma_t(\tilde s^t)>0$.
+$\gamma_t(\tilde s^t)>0$.