Fixes for shapely and scipy updates (#174)

* Remove duplicate install of testing dependencies

* Require latest version of model_metadata

* Remove obsolete esmpy requirement

* Don't install components for testing

The subsequent call to `mamba install` updates *shapely* to 2.0,
which breaks the <1.9 requirement from #164.

* import UnitSystem from gimli.units

* remove redundant gimli.units unit tests

* checkout gimli.units raises UdunitsError

* Consolidate requirements in one install step

* Fix typos

* Roll back model_metadata for older models

* Remove shapely version cap

* Convert shapely proxy object to geometries

See https://shapely.readthedocs.io/en/stable/migration.html#other-deprecated-functionality

* Remove scipy version cap

* Mark fail when extrapolating with previous and next methods

See scipy/scipy#16997 (comment)

* Check for AssertionError instead of ValueError

* Revert "Don't install components for testing"

This reverts commit bfb47fc.
The shapely version issue is resolved.

* Limit numpy<2

See #173.

* Set numpy print options to legacy=1.21

Without this setting, the value of legacy=1.25 was being inherited
from Landlab, which isn't allowed in the installed version of numpy<2
(currently 1.26.4).

* Add python=3.11 to tests

* Switch from Mambaforge to Miniforge

* Switch from mamba to conda

* Update versions of packaged actions

* install requirements with pip

* turn off fail-fast

* switch back to conda to install requirements

---------

Co-authored-by: mcflugen <mcflugen@gmail.com>

.github/workflows/black.yml

@@ -15,8 +15,8 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - uses: psf/black@stable
         with:
           options: "--check --verbose --diff"

.github/workflows/docs.yml

@@ -34,21 +34,20 @@ jobs:
             shell: bash -l {0}
 
         steps:
-          - uses: actions/checkout@v2
-          - uses: conda-incubator/setup-miniconda@v2
+          - uses: actions/checkout@v4
+          - uses: conda-incubator/setup-miniconda@v3
             with:
-              miniforge-variant: Mambaforge
               miniforge-version: latest
               python-version: 3.8
 
           - name: Show conda installation info
             run: |
-              mamba info
-              mamba list
+              conda info
+              conda list
     
           - name: Install dependencies
             run: |
-              mamba install --file=requirements.txt --file=requirements-docs.txt gimli.units
+              conda install --file=requirements.txt --file=requirements-docs.txt gimli.units
               pip install -e .
 
           - name: Build documentation

.github/workflows/flake8.yml

@@ -14,9 +14,9 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

.github/workflows/test-notebooks.yml

@@ -27,22 +27,21 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
 
       - name: Show conda installation info
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda list
 
       - name: Install requirements
         run: |
-          mamba install \
+          conda install \
             --file=requirements.txt \
             --file=requirements-testing.txt \
             --file=requirements-notebooks.txt
-          mamba list
+          conda list
 
       - name: Build and install package
         run: |

.github/workflows/test.yml

@@ -18,38 +18,38 @@ jobs:
         shell: bash -l {0}
 
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
 
       - name: Show conda installation info
         run: |
-          mamba info
-          mamba list
+          conda info
+          conda list
 
       - name: Install requirements
         run: |
-          mamba install --file=requirements.txt --file=requirements-testing.txt
-          mamba list
+          conda install --file=requirements.txt --file=requirements-testing.txt
+          conda list
 
-      # - name: Install Windows requirements
-      #   if: matrix.os == 'windows-latest'
-      #   run: |
-      #     mamba install pymt_child pymt_hydrotrend pymt_permamodel
+      - name: Install Windows requirements
+        if: matrix.os == 'windows-latest'
+        run: |
+          conda install pymt_child pymt_hydrotrend pymt_permamodel
 
-      # - name: Install Unix requirements
-      #   if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
-      #   run: |
-      #     mamba install pymt_cem pymt_child pymt_hydrotrend pymt_permamodel
+      - name: Install Unix requirements
+        if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
+        run: |
+          conda install pymt_cem pymt_child pymt_hydrotrend pymt_permamodel
 
       - name: Build and install package
         run: |

pymt/__init__.py

@@ -1,8 +1,11 @@
+import numpy as np
 from gimli.units import UnitSystem
 
 from ._version import __version__
 from .model_collection import ModelCollection
 
+np.set_printoptions(legacy="1.21")
+
 MODELS = ModelCollection()
 
 __all__ = ["__version__", "UnitSystem", "MODELS"]

pymt/grids/map.py

@@ -46,7 +46,7 @@
 
 """
 
-from shapely.geometry import Point, asLineString, asPoint, asPolygon
+from shapely.geometry import Point, LineString, Polygon
 
 from pymt.grids import (
     Rectilinear,
@@ -84,11 +84,11 @@ def __init__(self, *args, **kwargs):
 
             (x, y) = (point_x.take(cell), point_y.take(cell))
             if len(x) > 2:
-                self._polys.append(asPolygon(zip(x, y)))
+                self._polys.append(Polygon(zip(x, y)))
             elif len(x) == 2:
-                self._polys.append(asLineString(zip(x, y)))
+                self._polys.append(LineString(zip(x, y)))
             else:
-                self._polys.append(asPoint(zip(x, y)))
+                self._polys.append(Point(zip(x, y)))
 
     def get_shared_cells(self, point_id):
         """

requirements.txt

@@ -6,9 +6,10 @@ landlab>=2
 matplotlib
 model_metadata<0.8
 netcdf4
+numpy<2  # see #173
 pyyaml
-scipy<1.9  # see #162
-shapely<2  # see #164
+scipy
+shapely
 xarray
 # cfunits
 # esmpy

tests/framework/test_timeinterp.py

@@ -13,7 +13,7 @@ def test_timeinterp():
 
 def test_timeinterp_with_scalars():
     interp = TimeInterpolator(((0.0, 1.0),))
-    with raises(ValueError):
+    with raises(AssertionError):
         assert interp(0.5) == approx(1.5)
     interp.add_data(((1.0, 2.0),))
     assert interp(0.5) == approx(1.5)
@@ -81,6 +81,7 @@ def test_interp_between_points(method):
 
 
 @pytest.mark.parametrize("method", TimeInterpolator.METHODS)
+@pytest.mark.xfail(condition="pytest.param('next')", raises=AssertionError)
 def test_interp_outside_range(method):
     interp = TimeInterpolator(
         ((0.0, 1.0), (1.0, 2.0), (2.0, 3.0), (3.0, 4.0)), method=method
@@ -89,6 +90,7 @@ def test_interp_outside_range(method):
 
 
 @pytest.mark.parametrize("method", TimeInterpolator.METHODS)
+@pytest.mark.xfail(condition="pytest.param('previous')", raises=AssertionError)
 def test_interp_below_range(method):
     interp = TimeInterpolator(
         ((0.0, 4.0), (1.0, 3.0), (2.0, 2.0), (3.0, 1.0)), method=method