Repository: tskit-dev/msprime (language: python)

Issue:
Add tskit version requirement to dev requirements and check setup.cfg requirements.
As found at https://github.com/tskit-dev/msprime/issues/2107#issuecomment-1279720362
Check for valid input in ARG likelihood
This outputs a readable error message when ARGs are requested for trees which aren't binary.

I haven't put in a check for unary nodes because those will legitimately appear on trees due to RE nodes.

Closes #2107 
Check for valid input in ARG likelihood
This outputs a readable error message when ARGs are requested for trees which aren't binary.

I haven't put in a check for unary nodes because those will legitimately appear on trees due to RE nodes.

Closes #2107 


Discussion / hints:

Fix patch:
diff --git a/requirements/CI-complete/requirements.txt b/requirements/CI-complete/requirements.txt
index 076b43cb4..089abe391 100644
--- a/requirements/CI-complete/requirements.txt
+++ b/requirements/CI-complete/requirements.txt
@@ -14,5 +14,5 @@ jsonschema<4.0
 python_jsonschema_objects==0.4.1
 scipy==1.7.3
 stdpopsim==0.1.2
-tskit==0.5.0
+tskit==0.5.3
 kastore==0.3.2
diff --git a/requirements/CI-docs/requirements.txt b/requirements/CI-docs/requirements.txt
index 896d58f5f..4d4b85517 100644
--- a/requirements/CI-docs/requirements.txt
+++ b/requirements/CI-docs/requirements.txt
@@ -7,5 +7,5 @@ matplotlib==3.5.0
 newick==1.3.1
 sphinx-argparse==0.3.1
 sphinx-issues==1.2.0
-tskit==0.4.0
+tskit==0.5.3
 tskit-book-theme==0.3.2
\ No newline at end of file
diff --git a/requirements/development.txt b/requirements/development.txt
index 152b09733..bcc1fbd46 100644
--- a/requirements/development.txt
+++ b/requirements/development.txt
@@ -17,7 +17,7 @@ pre-commit
 pytest
 pytest-cov
 pytest-xdist
-tskit>=0.4.0
+tskit>=0.5.2
 tskit-book-theme
 stdpopsim>=0.1.2 # Make sure we have correct version of OOA model
 scipy
diff --git a/setup.cfg b/setup.cfg
index 3bfba8c1c..c325ad1ee 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,7 +49,7 @@ include_package_data = True
 install_requires =
     numpy
     newick>=1.3.0
-    tskit>=0.4.0
+    tskit>=0.5.2
     demes>=0.2
 
 [options.entry_points]


Test patch:
diff --git a/requirements/CI-tests-conda/requirements.txt b/requirements/CI-tests-conda/requirements.txt
index 9328e3320..8cdad8123 100644
--- a/requirements/CI-tests-conda/requirements.txt
+++ b/requirements/CI-tests-conda/requirements.txt
@@ -3,6 +3,6 @@
 # but demes will pull in the latest so we pin here.
 jsonschema<4.0
 gsl
-tskit==0.5.0
+tskit==0.5.3
 stdpopsim==0.1.2
 demes==0.2.1
diff --git a/requirements/CI-tests-pip/requirements.txt b/requirements/CI-tests-pip/requirements.txt
index 16133e0cc..4cc4ab3e2 100644
--- a/requirements/CI-tests-pip/requirements.txt
+++ b/requirements/CI-tests-pip/requirements.txt
@@ -9,4 +9,4 @@ pytest-xdist==2.4.0
 jsonschema<5.0
 python_jsonschema_objects==0.4.1
 scipy==1.7.3
-tskit==0.5.0
+tskit==0.5.3