PKG Add msprime and deps including libgsl (#2548)

msprime is a widely used genetic simulation tool.

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
 

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

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}

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+

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)

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

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