From 4417005e2cb0f8b198df53271aef87bb35bc52f3 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@gmail.com>
Date: Tue, 17 May 2022 20:31:43 +0100
Subject: [PATCH] PKG Add msprime and deps including libgsl (#2548)

msprime is a widely used genetic simulation tool.
---
 docs/project/changelog.md        |  3 ++-
 packages/demes/meta.yaml         | 18 ++++++++++++++++++
 packages/libgsl/meta.yaml        | 12 ++++++++++++
 packages/msprime/meta.yaml       | 29 +++++++++++++++++++++++++++++
 packages/msprime/test_msprime.py | 18 ++++++++++++++++++
 packages/newick/meta.yaml        | 14 ++++++++++++++
 packages/ruamel/meta.yaml        | 16 ++++++++++++++++
 7 files changed, 109 insertions(+), 1 deletion(-)
 create mode 100644 packages/demes/meta.yaml
 create mode 100644 packages/libgsl/meta.yaml
 create mode 100644 packages/msprime/meta.yaml
 create mode 100644 packages/msprime/test_msprime.py
 create mode 100644 packages/newick/meta.yaml
 create mode 100644 packages/ruamel/meta.yaml

diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index aa40269c9..20c29b22e 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -111,7 +111,8 @@ substitutions:
 
 - New packages: opencv-python v4.5.5.64 {pr}`2305`, ffmpeg {pr}`2305`, libwebp {pr}`2305`,
   h5py, pkgconfig and libhdf5 {pr}`2411`, bitarray {pr}`2459`, gsw {pr}`2511`, cftime {pr}`2504`,
-  svgwrite, jsonschema, tskit {pr}`2506`, xarray {pr}`2538`
+  svgwrite, jsonschema, tskit {pr}`2506`, xarray {pr}`2538`, demes, libgsl, newick,
+  ruamel, msprime {pr}`4138`.
 
 ## Version 0.20.0
 
diff --git a/packages/demes/meta.yaml b/packages/demes/meta.yaml
new file mode 100644
index 000000000..55a8907ae
--- /dev/null
+++ b/packages/demes/meta.yaml
@@ -0,0 +1,18 @@
+package:
+  name: demes
+  version: 0.2.2
+source:
+  url: https://files.pythonhosted.org/packages/2f/e4/86796d77ea453aa96f1ce758b461cdf738177f441a18c832cc9f29848903/demes-0.2.2-py3-none-any.whl
+  sha256: 54f0110e9f1b5167347fb4793f0b1d297a58dfe3857f5e5287762aa50dea6036
+requirements:
+  run:
+    - attrs
+    - ruamel
+test:
+  imports:
+    - demes
+about:
+  home: https://github.com/popsim-consortium/demes-python
+  PyPI: https://pypi.org/project/demes
+  summary: tools for describing demographic models
+  license: ISC
diff --git a/packages/libgsl/meta.yaml b/packages/libgsl/meta.yaml
new file mode 100644
index 000000000..38121f9b6
--- /dev/null
+++ b/packages/libgsl/meta.yaml
@@ -0,0 +1,12 @@
+package:
+  name: libgsl
+  version: "2.7"
+source:
+  sha256: efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b
+  url: https://ftp.gnu.org/gnu/gsl/gsl-2.7.tar.gz
+build:
+  library: true
+  script: |
+    emconfigure ./configure \
+        CFLAGS="-fPIC"
+    emmake make -j ${PYODIDE_JOBS:-3}
diff --git a/packages/msprime/meta.yaml b/packages/msprime/meta.yaml
new file mode 100644
index 000000000..7c830964f
--- /dev/null
+++ b/packages/msprime/meta.yaml
@@ -0,0 +1,29 @@
+package:
+  name: msprime
+  version: 1.1.1
+source:
+  url: https://files.pythonhosted.org/packages/30/ac/22b9d2dc6e3233cc35e613b714d52cf87e4af00064a53d226824401629cb/msprime-1.1.1.tar.gz
+  sha256: e840bed2ba37ae572b234f0b55af006dc408881593f184304481ee6058ea6f30
+build:
+  cflags: |
+    -I$(PYODIDE_ROOT)/packages/libgsl/build/libgsl-2.7
+  ldflags: |
+    -L$(PYODIDE_ROOT)/packages/libgsl/build/libgsl-2.7/.libs
+    -L$(PYODIDE_ROOT)/packages/libgsl/build/libgsl-2.7/cblas/.libs
+requirements:
+  run:
+    - numpy
+    - newick
+    - tskit
+    - demes
+    - libgsl
+test:
+  imports:
+    - msprime
+about:
+  home: https://tskit.dev/msprime
+  PyPI: https://pypi.org/project/msprime
+  summary:
+    Simulate genealogical trees and genomic sequence data using population
+    genetic models
+  license: GNU GPLv3+
diff --git a/packages/msprime/test_msprime.py b/packages/msprime/test_msprime.py
new file mode 100644
index 000000000..a18779d33
--- /dev/null
+++ b/packages/msprime/test_msprime.py
@@ -0,0 +1,18 @@
+from pyodide_test_runner import run_in_pyodide
+
+
+@run_in_pyodide(
+    packages=[
+        "msprime",
+    ]
+)
+def test_msprime():
+    import msprime
+    import tskit
+
+    # basic test
+    ts = msprime.sim_ancestry(10, random_seed=42)
+    ts.dump("/tmp/msprime.trees")
+    ts = tskit.load("/tmp/msprime.trees")
+    ts2 = msprime.sim_ancestry(10, random_seed=42)
+    ts.tables.assert_equals(ts2.tables, ignore_provenance=True)
diff --git a/packages/newick/meta.yaml b/packages/newick/meta.yaml
new file mode 100644
index 000000000..27985dc5b
--- /dev/null
+++ b/packages/newick/meta.yaml
@@ -0,0 +1,14 @@
+package:
+  name: newick
+  version: 1.3.2
+source:
+  url: https://files.pythonhosted.org/packages/95/11/4db3f40c604b6cb1a574cbf06f66e217af03835385cca1605530d58cacc7/newick-1.3.2-py2.py3-none-any.whl
+  sha256: 6fced6f48b045225ccc4ee4cdbfe78c42b538274f1b866c6add349cf02752fdd
+test:
+  imports:
+    - newick
+about:
+  home: https://github.com/dlce-eva/python-newick
+  PyPI: https://pypi.org/project/newick
+  summary: A python module to read and write the Newick format
+  license: Apache 2
diff --git a/packages/ruamel/meta.yaml b/packages/ruamel/meta.yaml
new file mode 100644
index 000000000..a7b9fb0b3
--- /dev/null
+++ b/packages/ruamel/meta.yaml
@@ -0,0 +1,16 @@
+package:
+  name: ruamel
+  version: 0.17.21
+source:
+  url: https://files.pythonhosted.org/packages/9e/cb/938214ac358fbef7058343b3765c79a1b7ed0c366f7f992ce7ff38335652/ruamel.yaml-0.17.21-py3-none-any.whl
+  sha256: 742b35d3d665023981bd6d16b3d24248ce5df75fdb4e2924e93a05c1f8b61ca7
+test:
+  imports:
+    - ruamel
+about:
+  home: https://sourceforge.net/p/ruamel-yaml/code/ci/default/tree
+  PyPI: https://pypi.org/project/ruamel.yaml
+  summary:
+    ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation
+    of comments, seq/map flow style, and map key order
+  license: MIT license