From a59c716e824d950777490009a8191e57801a2f4f Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Thu, 11 Jul 2024 10:38:33 +0100 Subject: [PATCH 1/2] Update requirements for numpy 2 This won't work until scikit-allel is numpy 2.0 compatible. See https://github.com/cggh/scikit-allel/issues/415 --- _config.yml | 4 ++-- args.md | 2 +- counting_topologies.md | 2 +- requirements-CI.txt | 16 ++++++++-------- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/_config.yml b/_config.yml index cc6c4f3a..86592f87 100644 --- a/_config.yml +++ b/_config.yml @@ -35,12 +35,12 @@ sphinx: config: html_theme: sphinx_book_theme html_theme_options: - pygment_dark_style: monokai + pygments_dark_style: monokai todo_include_todos: true intersphinx_mapping: py: ["https://docs.python.org/3", null] tskit: ["https://tskit.dev/tskit/docs/stable", null] - tszip: ["https://tszip.readthedocs.io/en/stable/", null] + tszip: ["https://tskit.dev/tszip/docs/latest/", null] msprime: ["https://tskit.dev/msprime/docs/stable", null] pyslim: ["https://tskit.dev/pyslim/docs/stable", null] numpy: ["https://numpy.org/doc/stable/", null] diff --git a/args.md b/args.md index df812930..f8f209b5 100644 --- a/args.md +++ b/args.md @@ -312,7 +312,7 @@ difference between some classical ARG formulations, and the ARG formulation used in `tskit`. Classically, nodes in an ARG are taken to represent _events_ (specifically, "common ancestor", "recombination", and "sampling" events), and genomic regions of inheritance are encoded by storing a specific breakpoint location on -each recombination node. In contrast, [nodes](tskit:sec_data_model_definitions_node) in a `tskit` +each recombination node. In contrast, {ref}`nodes` in a `tskit` ARG correspond to _genomes_. More crucially, inherited regions are defined by intervals stored on *edges* (via the {attr}`~Edge.left` and {attr}`~Edge.right` properties), rather than on nodes. Here, for example, is the edge table from our ARG: diff --git a/counting_topologies.md b/counting_topologies.md index 76d1ac90..be5bf255 100644 --- a/counting_topologies.md +++ b/counting_topologies.md @@ -51,7 +51,7 @@ def create_notebook_data(): This tutorial is intended to be a gentle introduction to the combinatorial treatment of tree topologies in `tskit`. For a more formal introduction, see the {ref}`sec_combinatorics` section of the -[official `tskit` documentation](tskit:sec_introduction). +official `tskit` {ref}`documentation`. The *topology* of a single tree is the term used to describe the branching pattern, regardless of the lengths of the branches. For example, both trees below have the diff --git a/requirements-CI.txt b/requirements-CI.txt index 2915baf5..db1e68c0 100644 --- a/requirements-CI.txt +++ b/requirements-CI.txt @@ -1,16 +1,16 @@ git+https://github.com/tskit-dev/tsconvert@e99c837e4e26ccbf4f480a4c48626338eeff7dc3 demes==0.2.3 demesdraw==0.4.0 -jupyter-book==0.15.1 +jupyter-book==1.0.2 jupyter-cache==0.6.1 -msprime==1.2.0 -networkx==3.1 -pandas==2.1.1 -pygraphviz==1.10 -scikit-allel==1.3.7 +msprime==1.3.2 +networkx==3.3 +pandas==2.2.2 +pygraphviz==1.13 +scikit-allel==1.3.8 stdpopsim==0.2.0 tqdm==4.66.3 -tskit==0.5.5 +tskit==0.5.8 tskit_arg_visualizer==0.0.1 -tszip==0.2.2 +tszip==0.2.4 jsonschema==4.18.6 # Pinned due to 4.19 "AttributeError module jsonschema has no attribute _validators" From f30a66ffcbf4c6d67025f55099f3b8b5faea2eca Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Wed, 24 Jul 2024 21:25:57 +0100 Subject: [PATCH 2/2] Pin numpy to < 2 --- requirements-CI.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-CI.txt b/requirements-CI.txt index db1e68c0..24fdd65e 100644 --- a/requirements-CI.txt +++ b/requirements-CI.txt @@ -5,6 +5,7 @@ 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 pygraphviz==1.13 scikit-allel==1.3.8