Update requirements

Author: benjeffery

.github/workflows/tests.yml

@@ -95,4 +95,4 @@ jobs:
         run: |
           source ~/.profile
           conda activate anaconda-client-env
-          pytest -xvs -n0
+          pytest -xvs -n0 tests/test_mutations.py::TestMatrixMutationModel::test_TPM[0.5-0.25-50-500]

requirements/CI-complete/requirements.txt

@@ -1,13 +1,13 @@
 bintrees==2.2.0
-daiquiri==3.2.5.1
+daiquiri==3.3.0
 demes==0.2.3
-mypy==1.10.1 
-newick==1.9.0
-pytest==8.2.2
-pytest-cov==5.0.0
+mypy==1.15.0
+newick==1.10.0
+pytest==8.3.5
+pytest-cov==6.0.0
 pytest-xdist==3.6.1
-python_jsonschema_objects==0.5.5
-scipy==1.14.0
-stdpopsim==0.1.2
-tskit==0.5.8
+python_jsonschema_objects==0.5.7
+scipy==1.13.1
+stdpopsim==0.1.2 #Pinned for OOA model
+tskit==0.6.0
 kastore==0.3.3

requirements/CI-docs/requirements.txt

@@ -1,12 +1,12 @@
-daiquiri==3.2.5.1
+daiquiri==3.3.0
 demes==0.2.3
 demesdraw==0.4.0
-jupyter-book==1.0.2
-networkx==3.3
-matplotlib==3.9.0
-newick==1.9.0
-sphinx-argparse==0.4.0
+jupyter-book==1.0.4.post1
+networkx==3.4.2
+matplotlib==3.10.1
+newick==1.10.0
+sphinx-argparse==0.5.2
 sphinx-book-theme # not pinned to enable easy updates
-sphinx-issues==4.1.0
-tskit==0.5.8
-scipy==1.14.0
+sphinx-issues==5.0.0
+tskit==0.6.0
+scipy==1.15.2

requirements/CI-tests-conda/requirements.txt

@@ -1,3 +1,3 @@
 gsl
-stdpopsim==0.1.2
+stdpopsim==0.1.2 # Pinned for OOA model
 demes==0.2.3

requirements/CI-tests-pip/requirements.txt

@@ -1,9 +1,9 @@
 bintrees==2.2.0
 daiquiri==3.2.5.1
 kastore==0.3.3
-newick==1.9.0
-pytest==8.2.2
+newick==1.10.0
+pytest==8.3.5
 pytest-xdist==3.6.1
-python_jsonschema_objects==0.5.5
-scipy==1.11.3
-tskit==0.5.8
+python_jsonschema_objects==0.5.7
+scipy==1.13.1
+tskit==0.6.0

requirements/development.txt

@@ -1,4 +1,4 @@
-docutils==0.15  # issue with 0.17, https://github.com/tskit-dev/msprime/issues/1625
+docutils==0.21.2  # issue with 0.17, https://github.com/tskit-dev/msprime/issues/1625
 asv
 bintrees
 coverage
@@ -19,7 +19,7 @@ pytest-xdist
 tskit>=0.5.2
 kastore
 sphinx-book-theme
-stdpopsim==0.1.2 # Make sure we have correct version of OOA model
+stdpopsim==0.1.2 # Pinned for OOA model
 scipy
 setuptools_scm
 sphinx>=4.4