addressing doctests failure (numpy-2.0)

.github/workflows/tests.yml

@@ -69,9 +69,20 @@ jobs:
         run: 'python -c "import geopandas; geopandas.show_versions();"'
         if: contains(matrix.environment-file, 'DEV')
 
-      - name: run tests
-        run: pytest giddy --cov giddy -v -n auto -r a --doctest-modules --color yes --cov-report term-missing --cov-report xml
-
+      - name: run pytest
+        run: pytest giddy -r a -v -n auto --cov giddy --cov-report xml --color yes --cov-append --cov-report term-missing
+
+      - name: run docstring tests
+        if: contains(matrix.environment-file, '311-DEV') && contains(matrix.os, 'ubuntu')
+        run: |
+          pytest \
+          -v \
+          -r a \
+          -n auto \
+          --color yes \
+          --cov giddy --cov-report xml --cov-append \
+          --doctest-only --doctest-continue-on-failure giddy
+
       - name: codecov
         uses: codecov/codecov-action@v3
         with:

ci/311-DEV.yaml

@@ -8,6 +8,10 @@ dependencies:
   - pip
   - quantecon>=0.4.7
   - scipy>=1.3.0
+  - esda>=2.1.1
+  - libpysal>=4.0.1
+  - mapclassify>=2.1.1
+  - splot
   # testing
   - codecov
   - ipywidgets
@@ -16,3 +20,10 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
+  - pytest-doctestplus
+  # docs (this env only)
+  - nbsphinx
+  - numpydoc
+  - sphinx>=1.4.3
+  - sphinxcontrib-bibtex
+  - sphinx_bootstrap_theme

ci/311.yaml

@@ -17,9 +17,3 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
-  # docs (this env only)
-  - nbsphinx
-  - numpydoc
-  - sphinx>=1.4.3
-  - sphinxcontrib-bibtex
-  - sphinx_bootstrap_theme

giddy/markov.py

@@ -1119,7 +1119,7 @@ def chi2(T1, T2):
            [  1.,  92., 815.,  51.],
            [  1.,   0.,  60., 903.]])
     >>> chi2(T1,T2)
-    (23.39728441473295, 0.005363116704861337, 9)
+    (np.float64(23.39728441473295), np.float64(0.005363116704861337), np.int64(9))
 
     Notes
     -----
@@ -1468,20 +1468,20 @@ def spillover(self, quadrant=1, neighbors_on=False):
         >>> lm_random = LISA_Markov(pci, w, permutations=99)
         >>> r = lm_random.spillover()
         >>> (r['components'][:, 12] > 0).sum()
-        17
+        np.int64(17)
         >>> (r['components'][:, 13]>0).sum()
-        23
+        np.int64(23)
         >>> (r['spill_over'][:,12]>0).sum()
-        6
+        np.int64(6)
 
         Including neighbors of core neighbors
         >>> rn = lm_random.spillover(neighbors_on=True)
         >>> (rn['components'][:, 12] > 0).sum()
-        26
+        np.int64(26)
         >>> (rn["components"][:, 13] > 0).sum()
-        34
+        np.int64(34)
         >>> (rn["spill_over"][:, 12] > 0).sum()
-        8
+        np.int64(8)
 
         """
         n, k = self.q.shape
@@ -2081,7 +2081,7 @@ def sojourn_time(p, summary=True):
 
     >>> p = np.array([[.5, .25, .25], [.5, 0, .5],[ 0, 0, 0]])
     >>> sojourn_time(p)
-    Sojourn times are infinite for absorbing states! In this Markov Chain, states [2] are absorbing states.
+    Sojourn times are infinite for absorbing states! In this Markov Chain, states [np.int64(2)] are absorbing states.
     array([ 2.,  1., inf])
     """  # noqa E501
 

giddy/rank.py

@@ -469,10 +469,10 @@ class Tau_Local:
             0.48387097,  0.93548387,  0.61290323,  0.74193548,  0.41935484,
             0.61290323,  0.61290323])
     >>> tau_local.tau
-    0.6612903225806451
+    np.float64(0.6612903225806451)
     >>> tau_classic = Tau(r[:,0],r[:,1])
     >>> tau_classic.tau
-    0.6612903225806451
+    np.float64(0.6612903225806451)
 
     """
 
@@ -586,10 +586,10 @@ class Tau_Local_Neighbor:
     array([-1,  1,  1,  1,  1,  1,  1, -1,  1,  1,  1,  1,  1,  1,  1,  1,  1,
             1,  1, -1, -1, -1,  1,  1,  1,  1,  1,  1,  1,  1,  1, -1])
     >>> (res.tau_ln * res.tau_ln_weights).sum() #global spatial tau
-    0.39682539682539675
+    np.float64(0.39682539682539675)
     >>> res1 = SpatialTau(r[:,0],r[:,1],w,permutations=999)
     >>> res1.tau_spatial
-    0.3968253968253968
+    np.float64(0.3968253968253968)
 
     """