From c6cc034d5ecf60652edaed44699037287d31ae62 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Fri, 13 Jan 2023 14:01:17 -0500
Subject: [PATCH 01/12] Remove py3.7 add 3.10 and 3.11

---
 .github/workflows/documentation.yml     | 2 +-
 .github/workflows/functional_test.yml   | 2 +-
 .github/workflows/functional_test_2.yml | 2 +-
 .github/workflows/pylint.yml            | 2 +-
 .github/workflows/release.yml           | 2 +-
 environment.yml                         | 2 +-
 pyproject.toml                          | 5 ++---
 7 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 2d1c20ed..1ccdb95c 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -23,7 +23,7 @@ jobs:
         environment-file: ./environment.yml
         environment-name: ocsmesh-env
         extra-specs: |
-          python=3.9
+          python=3.*
     - name: Install dependencies
       shell: bash -l {0}
       run: |
diff --git a/.github/workflows/functional_test.yml b/.github/workflows/functional_test.yml
index b4095c63..bd962646 100644
--- a/.github/workflows/functional_test.yml
+++ b/.github/workflows/functional_test.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.7', '3.8', '3.9' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
 
     steps:
     - uses: actions/checkout@v2
diff --git a/.github/workflows/functional_test_2.yml b/.github/workflows/functional_test_2.yml
index 1039f8ba..cbf88dae 100644
--- a/.github/workflows/functional_test_2.yml
+++ b/.github/workflows/functional_test_2.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
 
     steps:
     - name: Checkout 
diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
index 744654eb..ace1b048 100644
--- a/.github/workflows/pylint.yml
+++ b/.github/workflows/pylint.yml
@@ -15,7 +15,7 @@ jobs:
         environment-file: ./environment.yml
         environment-name: ocsmesh-env
         extra-specs: |
-          python=3.9
+          python=3.*
     - name: Install dependencies
       shell: bash -l {0}
       run: |
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9d69a172..541b1b2a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.7', '3.8', '3.9' ]
+        python-version: [ ''3.8', '3.9', '3.10', '3.11' ]
     steps:
       - name: checkout repository
         uses: actions/checkout@v2
diff --git a/environment.yml b/environment.yml
index 1ef5fb06..74860649 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: ocsmesh
 channels:
   - conda-forge
 dependencies:
-  - python
+  - python>=3.8, <4
   - gdal
   - geos
   - proj
diff --git a/pyproject.toml b/pyproject.toml
index d5382878..577a687d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,13 +19,12 @@ maintainers = [
 description = "Package to generate computational unstructured meshes from planetary modeling."
 license = {file = "LICENSE"}
 readme = "README.md"
-requires-python = '>=3.7, <3.10'
+requires-python = '>=3.8, <4'
 dependencies = [
     "colored-traceback", "fiona", "geoalchemy2", "geopandas",
     "jigsawpy", "matplotlib", "netCDF4", "numba",
     "numpy>=1.21", # introduce npt.NDArray
-    "pyarrow", "pygeos", "pyproj>=3.0", "rasterio", "requests",
-    "scipy<1.8",   # dropping python 3.7
+    "pyarrow", "pygeos", "pyproj>=3.0", "rasterio", "requests", "scipy",
     "shapely>=1.8, <2", "tqdm", "typing_extensions", "utm",
     ]
 dynamic = ["version"]

From ff9d46bd195c455e3d9757017478250c3ee4175b Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Fri, 13 Jan 2023 14:06:02 -0500
Subject: [PATCH 02/12] Fix typo

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 541b1b2a..04f10404 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ ''3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
     steps:
       - name: checkout repository
         uses: actions/checkout@v2

From 9c95c6f79a7ad841410bc85477271157ff4c683c Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Fri, 13 Jan 2023 14:35:43 -0500
Subject: [PATCH 03/12] Remove py3.11, add 3.*

---
 .github/workflows/functional_test.yml   | 2 +-
 .github/workflows/functional_test_2.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/functional_test.yml b/.github/workflows/functional_test.yml
index bd962646..5f313937 100644
--- a/.github/workflows/functional_test.yml
+++ b/.github/workflows/functional_test.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.*' ]
 
     steps:
     - uses: actions/checkout@v2
diff --git a/.github/workflows/functional_test_2.yml b/.github/workflows/functional_test_2.yml
index cbf88dae..d0a6e676 100644
--- a/.github/workflows/functional_test_2.yml
+++ b/.github/workflows/functional_test_2.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.8', '3.9', '3.10', '3.*' ]
 
     steps:
     - name: Checkout 

From f1b2e040a221adfed111b3ea7789135a38245ebf Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Fri, 13 Jan 2023 14:46:35 -0500
Subject: [PATCH 04/12] Remove py3.* due to numba issue with 3.11

---
 .github/workflows/functional_test.yml   | 2 +-
 .github/workflows/functional_test_2.yml | 2 +-
 .github/workflows/release.yml           | 2 +-
 environment.yml                         | 2 +-
 pyproject.toml                          | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/functional_test.yml b/.github/workflows/functional_test.yml
index 5f313937..d11890d3 100644
--- a/.github/workflows/functional_test.yml
+++ b/.github/workflows/functional_test.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.*' ]
+        python-version: [ '3.8', '3.9', '3.10' ]
 
     steps:
     - uses: actions/checkout@v2
diff --git a/.github/workflows/functional_test_2.yml b/.github/workflows/functional_test_2.yml
index d0a6e676..b2862755 100644
--- a/.github/workflows/functional_test_2.yml
+++ b/.github/workflows/functional_test_2.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.*' ]
+        python-version: [ '3.8', '3.9', '3.10' ]
 
     steps:
     - name: Checkout 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 04f10404..57749ff2 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.10' ]
     steps:
       - name: checkout repository
         uses: actions/checkout@v2
diff --git a/environment.yml b/environment.yml
index 74860649..581e3112 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: ocsmesh
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8, <4
+  - python>=3.8, <3.11 # 3.11 not supported by numba
   - gdal
   - geos
   - proj
diff --git a/pyproject.toml b/pyproject.toml
index 577a687d..f817bd04 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ maintainers = [
 description = "Package to generate computational unstructured meshes from planetary modeling."
 license = {file = "LICENSE"}
 readme = "README.md"
-requires-python = '>=3.8, <4'
+requires-python = '>=3.8, <3.11' # 3.11 no supported by numba
 dependencies = [
     "colored-traceback", "fiona", "geoalchemy2", "geopandas",
     "jigsawpy", "matplotlib", "netCDF4", "numba",

From 75dca81a3230df4f13e6603dd2352452ef3c63f9 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Fri, 13 Jan 2023 15:21:52 -0500
Subject: [PATCH 05/12] Update conda dependencies

---
 environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index 581e3112..261a3d87 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,9 +15,9 @@ dependencies:
   - pygeos
   - geopandas
   - utm
-  - scipy<1.8
+  - scipy
   - numba
-  - numpy>=1.21,<1.23 # numpy.typing, scipy 1.7.x support
+  - numpy>=1.21 # numpy.typing
   - matplotlib
   - requests
   - tqdm

From 4e76d4b9c824869a3dadec9e5077bc979a3d8afe Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 10:38:06 -0500
Subject: [PATCH 06/12] Fix interpolation issue with contiguouness of
 constructor grid

---
 ocsmesh/mesh/mesh.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ocsmesh/mesh/mesh.py b/ocsmesh/mesh/mesh.py
index 7905160b..ea8e2e96 100644
--- a/ocsmesh/mesh/mesh.py
+++ b/ocsmesh/mesh/mesh.py
@@ -2078,7 +2078,7 @@ def _mesh_interpolate_worker(
         if method == 'spline':
             f = RectBivariateSpline(
                 xi,
-                np.flip(yi),
+                np.ascontiguousarray(np.flip(yi)),
                 np.flipud(zi).T,
                 kx=3, ky=3, s=0,
                 # bbox=[min(x), max(x), min(y), max(y)]  # ??
@@ -2089,7 +2089,7 @@ def _mesh_interpolate_worker(
             # Inspired by StackOverflow 35807321
             if np.any(zi.mask):
                 m_interp = RegularGridInterpolator(
-                    (xi, np.flip(yi)),
+                    (xi, np.ascontiguousarray(np.flip(yi))),
                     np.flipud(zi.mask).T.astype(bool),
                     method=method
                 )
@@ -2097,7 +2097,7 @@ def _mesh_interpolate_worker(
                 interp_mask = m_interp(coords[_idxs]) > 0
 
             f = RegularGridInterpolator(
-                (xi, np.flip(yi)),
+                (xi, np.ascontiguousarray(np.flip(yi))),
                 np.flipud(zi).T,
                 method=method
             )

From 0129f1022345efe62c4c51552e0b20f0d6903c84 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 10:39:15 -0500
Subject: [PATCH 07/12] Fix shapely version to be below 2

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 261a3d87..a0c2d3a0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - netcdf4
   - udunits2
   - pyproj
-  - shapely>=1.8
+  - shapely>=1.8, <2
   - rasterio
   - fiona
   - pygeos

From 541646b96d9f585d04c326c9d2554f6fb0383353 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 10:58:25 -0500
Subject: [PATCH 08/12] Fix issue due to jigsawpy dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index f817bd04..0e92c4db 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ dependencies = [
     "colored-traceback", "fiona", "geoalchemy2", "geopandas",
     "jigsawpy", "matplotlib", "netCDF4", "numba",
     "numpy>=1.21", # introduce npt.NDArray
+    "packagin", # required by jigsawpy
     "pyarrow", "pygeos", "pyproj>=3.0", "rasterio", "requests", "scipy",
     "shapely>=1.8, <2", "tqdm", "typing_extensions", "utm",
     ]

From c8aa0515124fac73cc30701d5f2feecb9df68d83 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 13:06:16 -0500
Subject: [PATCH 09/12] Fix typo!

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0e92c4db..cdc0f7fa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
     "colored-traceback", "fiona", "geoalchemy2", "geopandas",
     "jigsawpy", "matplotlib", "netCDF4", "numba",
     "numpy>=1.21", # introduce npt.NDArray
-    "packagin", # required by jigsawpy
+    "packaging", # required by jigsawpy
     "pyarrow", "pygeos", "pyproj>=3.0", "rasterio", "requests", "scipy",
     "shapely>=1.8, <2", "tqdm", "typing_extensions", "utm",
     ]

From 5583052ccf1f954bb887ac0ddc6ba69d79464a17 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 13:32:25 -0500
Subject: [PATCH 10/12] Attempt 2 to fix jigsaw dependency!

---
 .github/workflows/functional_test.yml   | 1 +
 .github/workflows/functional_test_2.yml | 1 +
 pyproject.toml                          | 1 -
 3 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/functional_test.yml b/.github/workflows/functional_test.yml
index d11890d3..064f967a 100644
--- a/.github/workflows/functional_test.yml
+++ b/.github/workflows/functional_test.yml
@@ -28,6 +28,7 @@ jobs:
     - name: Install other dependencies
       shell: bash -l {0}
       run: |
+        pip install packaging # jigsaw dependency in its setup.py
         python ./setup.py install_jigsaw
         pip install .
 
diff --git a/.github/workflows/functional_test_2.yml b/.github/workflows/functional_test_2.yml
index b2862755..324cbdbb 100644
--- a/.github/workflows/functional_test_2.yml
+++ b/.github/workflows/functional_test_2.yml
@@ -31,6 +31,7 @@ jobs:
     - name: Install packages
       shell: bash -l {0}
       run: |
+        pip install packaging # jigsaw dependency in its setup.py
         python ./setup.py install_jigsaw
         pip install .
 
diff --git a/pyproject.toml b/pyproject.toml
index cdc0f7fa..f817bd04 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,6 @@ dependencies = [
     "colored-traceback", "fiona", "geoalchemy2", "geopandas",
     "jigsawpy", "matplotlib", "netCDF4", "numba",
     "numpy>=1.21", # introduce npt.NDArray
-    "packaging", # required by jigsawpy
     "pyarrow", "pygeos", "pyproj>=3.0", "rasterio", "requests", "scipy",
     "shapely>=1.8, <2", "tqdm", "typing_extensions", "utm",
     ]

From 50ac831f892fbb09613912a417f90dfbd5afb7c7 Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 16:57:20 -0500
Subject: [PATCH 11/12] Update test since jigsaw size enforcement has changed

---
 tests/api/hfun.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/api/hfun.py b/tests/api/hfun.py
index 98030d7f..9f81f28f 100755
--- a/tests/api/hfun.py
+++ b/tests/api/hfun.py
@@ -565,7 +565,7 @@ def _check_applied_refinement(self, msh_t, refine_gdf, target_size):
         rest_msh_t.size_from_mesh()
         rest_avg = np.mean(rest_msh_t.msh_t().value)
 
-        self.assertTrue(np.isclose(refine_avg, target_size, rtol=1e-1))
+        self.assertTrue(np.isclose(refine_avg, target_size, rtol=3e-1))
         self.assertTrue(rest_avg > target_size * 10)
 
     def _is_refined_by_shape1(self, hfun, target_size):
@@ -576,7 +576,7 @@ def _is_refined_by_shape1(self, hfun, target_size):
         gdf_feature = gpd.GeoDataFrame(
             geometry=[self.shape1], crs=4326
         )
-        gdf_clip = gdf_feature.to_crs(hfun_msh_t.crs).buffer(target_size)
+        gdf_clip = gdf_feature.to_crs(hfun_msh_t.crs).buffer(target_size*1.1)
         self._check_applied_refinement(hfun_msh_t, gdf_clip, target_size)
 
 
@@ -586,7 +586,7 @@ def _is_refined_by_feat1(self, hfun, target_size):
 
         # Nodes close to the feature line must be small
         gdf_feature = gpd.read_file(self.feat1)
-        gdf_clip = gdf_feature.to_crs(hfun_msh_t.crs).buffer(target_size)
+        gdf_clip = gdf_feature.to_crs(hfun_msh_t.crs).buffer(target_size*1.1)
         self._check_applied_refinement(hfun_msh_t, gdf_clip, target_size)
 
     def _is_refined_by_feat2(self, hfun, target_size):

From 3b4b38f4144c2e57706f59f48a719fd2476590cc Mon Sep 17 00:00:00 2001
From: SorooshMani-NOAA <soroosh.mani@noaa.gov>
Date: Tue, 17 Jan 2023 17:21:50 -0500
Subject: [PATCH 12/12] Increase error tolerance for test due to changes in
 Jigsaw

---
 tests/api/hfun.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/api/hfun.py b/tests/api/hfun.py
index 9f81f28f..900c8e4a 100755
--- a/tests/api/hfun.py
+++ b/tests/api/hfun.py
@@ -410,7 +410,7 @@ def test_hfun_coll_cfl_constraint(self):
         # Fast method is much less accurate!
         method_tolerance = {
             'exact': 0.03,
-            'fast': 0.1
+            'fast': 0.2
         }
 
         for method, tol in method_tolerance.items():