Upgrade to latest tskit

.github/workflows/build.yml

@@ -41,13 +41,17 @@ jobs:
         # We need to remove R to pull in a version that's compatible with CRAN, weirdly.
         sudo apt-get update
         sudo apt-get remove r-base-core
-        sudo apt-get install r-cran-reticulate r-cran-pbdzmq r-cran-uuid r-cran-ape
-        sudo R -e 'install.packages("IRkernel")'
+        sudo apt-get install r-cran-pbdzmq r-cran-uuid r-cran-ape
+        # Numpy 2 needs a newer reticulate version than ubuntu-24.04 + r-cran-reticulate
+        sudo R -e 'install.packages(c("reticulate", "IRkernel"))'
         R -e 'IRkernel::installspec()'
 
     # Build the book
     - name: Build the book
-      run: ./build.sh
+      run: |
+        # Ensure R (reticulate) uses the python version with the new installed packages
+        export RETICULATE_PYTHON=$(which python)
+        ./build.sh
 
     - name: Copy files for users to run tutorials
       run: |

requirements-CI.txt

@@ -1,17 +1,17 @@
-git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3
+git+https://github.com/tskit-dev/tsconvert@4ed3c0f9bbbb79c7c394b352c58f5386cfef2b90
 demes==0.2.3
 demesdraw==0.4.0
 jupyter-book==1.0.2
 jupyter-cache==0.6.1
 msprime==1.3.2
 networkx==3.3
-numpy==1.26.4
-pandas==2.2.2
+numpy==2.2.6
+pandas==2.3.3
 pygraphviz==1.13
-scikit-allel==1.3.8
+scikit-allel==1.3.13
 stdpopsim==0.3.0
 tqdm==4.66.3
-tskit==0.5.8
-tskit_arg_visualizer==0.0.1
+tskit==1.0.0
+tskit_arg_visualizer==0.1.1
 tszip==0.2.4
 jsonschema==4.18.6 # Pinned due to 4.19 "AttributeError module jsonschema has no attribute _validators"

requirements.txt

@@ -1,15 +1,15 @@
-git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3
+git+https://github.com/tskit-dev/tsconvert@4ed3c0f9bbbb79c7c394b352c58f5386cfef2b90
 demes
 demesdraw
-jupyter-book>=0.12.0
+jupyter-book >= 0.12.0, < 2.0
 jupyter-cache
 msprime>=1.0
 networkx
 pandas
 pygraphviz
-scikit-allel
+scikit-allel>=1.3.9
 stdpopsim>=0.3
 tqdm
-tskit>=0.5.4
-tskit_arg_visualizer
+tskit>=1.0.0
+tskit_arg_visualizer>=0.1.1
 tszip