update range of support Python versions (#1347)

Author: molpopgen

.github/workflows/black.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ "3.12" ]
+        python: [ "3.13" ]
         os:  [ ubuntu-22.04 ]
     defaults:
       run:

.github/workflows/macos_CI.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ "3.11", "3.12" ]
+        python: [ "3.12", "3.13" ]
         os:  [ macos-14, macos-13 ]
         rust: [1.62.1]
     defaults:

.github/workflows/ubuntu.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.9, "3.10", "3.11", "3.12" ]
+        python: [ "3.10", "3.11", "3.12", "3.13" ]
         os:  [ ubuntu-22.04 ]
         compiler: [gcc, clang14]
         rust: [1.62.1]

.github/workflows/wheels.yml

@@ -107,7 +107,7 @@ jobs:
     needs: ['build_sdist']
     strategy:
       matrix:
-        python: [3.9, "3.10", "3.11", "3.12"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
@@ -144,7 +144,7 @@ jobs:
     needs: ['manylinux2_28']
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11", "3.12"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
@@ -172,7 +172,7 @@ jobs:
     needs: ['macos-wheels']
     strategy:
       matrix:
-        python: ["3.11", "3.12"]
+        python: ["3.12", "3.13"]
         os: [macos-14, macos-13]
     steps:
       - name: Cancel Previous Runs

doc/long_vignettes/tskitconvert_vignette.md

@@ -159,9 +159,14 @@ We can pass the `params` object on when exporting the data to `tskit`:
 ```{code-cell} python
 ts = pop.dump_tables_to_tskit(model_params=params)
 def rebuild_params(md):
+    import copy
+    import inspect
     import fwdpy11
+    md = copy.deepcopy(md)
     for i in dir(fwdpy11):
-        exec(f"from fwdpy11 import {i}")
+        if md.find(i) > 0:
+            if inspect.isclass(eval(f"fwdpy11.{i}")):
+                md = md.replace(i, "fwdpy11." + i)
     recovered_params = fwdpy11.ModelParams(**eval(md)) 
     return recovered_params
 recovered_params = rebuild_params(ts.metadata["model_params"])

pyproject.toml

@@ -30,7 +30,7 @@ dependencies = [
     "demes ~= 0.2.2",
     "Deprecated",
 ]
-requires-python = ">=3.9, <3.13"
+requires-python = ">=3.10, <3.14"
 
 [project.scripts]
 fwdpy11 = "fwdpy11.__main__:main"
@@ -59,7 +59,7 @@ test-requires = "pytest msprime hypothesis"
 build-frontend = "build"
 
 [tool.cibuildwheel.macos]
-build = "cp3{11,12}-*"
+build = "cp3{12,13}-*"
 before-all = "./deployment/macos_wheels/install_gsl.sh"
 
 [tool.cibuildwheel.linux]

tests/test_metadata_roundtrips_via_simulation.py

@@ -201,11 +201,16 @@ def test_metadata_roundtrip_single_deme_sim_with_parameters(rng, pdict, pop, inc
     provenance = json.loads(ts.provenance(0).record)
 
     def rebuild_pdict(provenance):
+        import copy
         import fwdpy11
+        import inspect
 
+        params = copy.deepcopy(provenance["parameters"]["params_dict"])
         for i in dir(fwdpy11):
-            exec(f"from fwdpy11 import {i}")
-        params_dict = eval(provenance["parameters"]["params_dict"])
+            if params.find(i) > 0:
+                if inspect.isclass(eval(f"fwdpy11.{i}")):
+                    params = params.replace(i, "fwdpy11." + i)
+        params_dict = eval(params)
         return params_dict
 
     params_dict = rebuild_pdict(provenance)

tests/test_tskit_metadata.py

@@ -16,8 +16,9 @@
 # You should have received a copy of the GNU General Public License
 # along with fwdpy11.  If not, see <http://www.gnu.org/licenses/>.
 #
+import copy
+import inspect
 
-import demes
 import fwdpy11
 import pytest
 import tskit
@@ -62,10 +63,12 @@ def test_single_model_params(pop, pdict1):
     ts = pop.dump_tables_to_tskit(model_params=mp)
 
     # reconstruct
+    params = copy.deepcopy(ts.metadata["model_params"])
     for i in dir(fwdpy11):
-        exec(f"from fwdpy11 import {i}")
+        if inspect.isclass(eval(f"fwdpy11.{i}")):
+            params = params.replace(i, "fwdpy11." + i)
 
-    mp_rebuilt = fwdpy11.ModelParams(**eval(ts.metadata["model_params"]))
+    mp_rebuilt = fwdpy11.ModelParams(**eval(params))
 
     assert mp == mp_rebuilt