update pinnings of demes, demesdraw, and msprime to demes~=0.2.0

* API and test fixes * add test of two sources for a pulse * pin numpy to < 1.21.(for numba)
molpopgen · Dec 10, 2021 · d74161f · d74161f
1 parent c063db5
commit d74161f
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diff --git a/doc/misc/changelog.md b/doc/misc/changelog.md
@@ -9,6 +9,8 @@ Dependencies:
 
 * Clean up pinning of `demes` and `demesdraw`.
   PR {pr}`869` 
+* Update to `demes` ~=0.2.0.
+  PR {pr}`873`
 
 ## 0.17.0a3
 

diff --git a/doc/requirements.in b/doc/requirements.in
@@ -1,6 +1,7 @@
 jupyter-book
 matplotlib
 msprime>=1.0.1
+numpy<1.21.0
 pandas
 sphinx-issues
-demesdraw==0.1.4
+demesdraw~=0.2.0
diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
+# This file is autogenerated by pip-compile with python 3.9
 # To update, run:
 #
 #    pip-compile
@@ -8,13 +8,14 @@ alabaster==0.7.12
     # via sphinx
 anyio==3.4.0
     # via jupyter-server
-argon2-cffi==21.1.0
+argon2-cffi==21.2.0
     # via
     #   jupyter-server
     #   notebook
+argon2-cffi-bindings==21.2.0
+    # via argon2-cffi
 attrs==21.2.0
     # via
-    #   -c ../requirements.in
     #   demes
     #   jsonschema
     #   jupyter-cache
@@ -33,8 +34,8 @@ bleach==4.1.0
 certifi==2021.10.8
     # via requests
 cffi==1.15.0
-    # via argon2-cffi
-charset-normalizer==2.0.8
+    # via argon2-cffi-bindings
+charset-normalizer==2.0.9
     # via requests
 click==7.1.2
     # via
@@ -51,12 +52,11 @@ decorator==5.1.0
     # via ipython
 defusedxml==0.7.1
     # via nbconvert
-demes==0.1.2
+demes==0.2.1
     # via
-    #   -c ../requirements.in
     #   demesdraw
     #   msprime
-demesdraw==0.1.4
+demesdraw==0.2.0
     # via -r requirements.in
 docutils==0.16
     # via
@@ -74,7 +74,7 @@ entrypoints==0.3
     # via
     #   jupyter-client
     #   nbconvert
-fonttools==4.28.2
+fonttools==4.28.3
     # via matplotlib
 gitdb==4.0.9
     # via gitpython
@@ -90,13 +90,11 @@ imagesize==1.3.0
     # via sphinx
 importlib-metadata==4.8.2
     # via myst-nb
-importlib-resources==5.4.0
-    # via sphinx-jupyterbook-latex
-ipykernel==6.5.1
+ipykernel==6.6.0
     # via
     #   ipywidgets
     #   notebook
-ipython==7.29.0
+ipython==7.30.1
     # via
     #   ipykernel
     #   ipywidgets
@@ -144,7 +142,7 @@ jupyter-core==4.9.1
     #   nbconvert
     #   nbformat
     #   notebook
-jupyter-server==1.12.0
+jupyter-server==1.13.0
     # via
     #   jupyter-server-mathjax
     #   nbdime
@@ -185,10 +183,8 @@ mdit-py-plugins==0.2.8
     #   myst-parser
 mistune==0.8.4
     # via nbconvert
-msprime==1.0.3
-    # via
-    #   -c ../requirements.in
-    #   -r requirements.in
+msprime==1.0.4
+    # via -r requirements.in
 myst-nb==0.13.1
     # via jupyter-book
 myst-parser==0.15.2
@@ -217,7 +213,7 @@ nbformat==5.1.3
     #   nbconvert
     #   nbdime
     #   notebook
-nest-asyncio==1.5.1
+nest-asyncio==1.5.4
     # via
     #   jupyter-client
     #   nbclient
@@ -228,7 +224,7 @@ notebook==6.4.6
     # via widgetsnbextension
 numpy==1.20.3
     # via
-    #   -c ../requirements.in
+    #   -r requirements.in
     #   demesdraw
     #   matplotlib
     #   msprime
@@ -245,7 +241,7 @@ pandas==1.3.4
     # via -r requirements.in
 pandocfilters==1.5.0
     # via nbconvert
-parso==0.8.2
+parso==0.8.3
     # via jedi
 pexpect==4.8.0
     # via ipython
@@ -257,7 +253,7 @@ prometheus-client==0.12.0
     # via
     #   jupyter-server
     #   notebook
-prompt-toolkit==3.0.22
+prompt-toolkit==3.0.24
     # via ipython
 ptyprocess==0.7.0
     # via
@@ -318,17 +314,13 @@ ruamel.yaml==0.17.17
 ruamel.yaml.clib==0.2.6
     # via ruamel.yaml
 scipy==1.7.3
-    # via
-    #   -c ../requirements.in
-    #   demesdraw
+    # via demesdraw
 send2trash==1.8.0
     # via
     #   jupyter-server
     #   notebook
 setuptools-scm==6.3.2
-    # via
-    #   -c ../requirements.in
-    #   matplotlib
+    # via matplotlib
 six==1.16.0
     # via
     #   bleach
@@ -344,7 +336,7 @@ snowballstemmer==2.2.0
     # via sphinx
 soupsieve==2.3.1
     # via beautifulsoup4
-sphinx==4.3.0
+sphinx==4.3.1
     # via
     #   jupyter-book
     #   jupyter-sphinx
@@ -434,10 +426,8 @@ traitlets==5.1.1
     #   nbformat
     #   notebook
 tskit==0.3.7
-    # via
-    #   -c ../requirements.in
-    #   msprime
-typing-extensions==4.0.0
+    # via msprime
+typing-extensions==4.0.1
     # via gitpython
 uc-micro-py==1.0.1
     # via linkify-it-py
@@ -447,16 +437,14 @@ wcwidth==0.2.5
     # via prompt-toolkit
 webencodings==0.5.1
     # via bleach
-websocket-client==1.2.1
+websocket-client==1.2.3
     # via jupyter-server
 wheel==0.37.0
     # via sphinx-togglebutton
 widgetsnbextension==3.5.2
     # via ipywidgets
 zipp==3.6.0
-    # via
-    #   importlib-metadata
-    #   importlib-resources
+    # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools
diff --git a/fwdpy11/_functions/import_demes.py b/fwdpy11/_functions/import_demes.py
@@ -10,13 +10,18 @@
 
 from .. import class_decorators
 from .._demography import exponential_growth_rate
-from ..demographic_models import (DemographicModelCitation,
-                                  DemographicModelDetails)
-from ..discrete_demography import (DiscreteDemography, MassMigration,
-                                   MigrationMatrix, SetDemeSize,
-                                   SetExponentialGrowth, SetMigrationRates,
-                                   SetSelfingRate, copy_individuals,
-                                   move_individuals)
+from ..demographic_models import DemographicModelCitation, DemographicModelDetails
+from ..discrete_demography import (
+    DiscreteDemography,
+    MassMigration,
+    MigrationMatrix,
+    SetDemeSize,
+    SetExponentialGrowth,
+    SetMigrationRates,
+    SetSelfingRate,
+    copy_individuals,
+    move_individuals,
+)
 
 
 # TODO: need type hints for dg
@@ -614,24 +619,25 @@ def _process_pulses(
 ) -> None:
     for p in dg.pulses:
         when = burnin_generation + int(model_times.model_start_time - p.time - 1)
-        events.migration_rate_changes.append(
-            _MigrationRateChange(
-                when=when,
-                source=idmap[p.source],
-                destination=idmap[p.dest],
-                rate_change=p.proportion,
-                from_deme_graph=False,
+        for source, proportion in zip(p.sources, p.proportions):
+            events.migration_rate_changes.append(
+                _MigrationRateChange(
+                    when=when,
+                    source=idmap[source],
+                    destination=idmap[p.dest],
+                    rate_change=proportion,
+                    from_deme_graph=False,
+                )
             )
-        )
-        events.migration_rate_changes.append(
-            _MigrationRateChange(
-                when=when + 1,
-                source=idmap[p.source],
-                destination=idmap[p.dest],
-                rate_change=-p.proportion,
-                from_deme_graph=False,
+            events.migration_rate_changes.append(
+                _MigrationRateChange(
+                    when=when + 1,
+                    source=idmap[source],
+                    destination=idmap[p.dest],
+                    rate_change=-proportion,
+                    from_deme_graph=False,
+                )
             )
-        )
 
 
 def _process_admixtures(

diff --git a/requirements.in b/requirements.in
@@ -2,12 +2,12 @@
 # with requirements.in and doc/requirements.in
 # and may require regenerating the .txt files.
 pybind11[global]
-numpy
+numpy<1.21.0
 sparse
 scipy
 attrs
 black
-demes==0.1.2
+demes~=0.2.0
 
 #below are for building package
 #and running tests

diff --git a/requirements.txt b/requirements.txt
@@ -11,15 +11,15 @@ attrs==21.2.0
     #   flake8-bugbear
     #   jsonschema
     #   pytest
-black==21.11b1
+black==21.12b0
     # via
     #   -r requirements.in
     #   blacken-docs
 blacken-docs==1.12.0
     # via -r requirements.in
 click==8.0.3
     # via black
-demes==0.1.2
+demes==0.2.1
     # via
     #   -r requirements.in
     #   msprime
@@ -29,7 +29,7 @@ flake8==4.0.1
     # via
     #   -r requirements.in
     #   flake8-bugbear
-flake8-bugbear==21.9.2
+flake8-bugbear==21.11.29
     # via -r requirements.in
 iniconfig==1.1.1
     # via pytest
@@ -39,7 +39,7 @@ llvmlite==0.37.0
     # via numba
 mccabe==0.6.1
     # via flake8
-msprime==1.0.3
+msprime==1.0.4
     # via -r requirements.in
 mypy-extensions==0.4.3
     # via black
@@ -90,8 +90,6 @@ pytest-forked==1.3.0
     # via pytest-xdist
 pytest-xdist==2.4.0
     # via -r requirements.in
-regex==2021.11.10
-    # via black
 ruamel.yaml==0.17.17
     # via demes
 ruamel.yaml.clib==0.2.6
@@ -116,7 +114,7 @@ tskit==0.3.7
     # via
     #   -r requirements.in
     #   msprime
-typing-extensions==4.0.0
+typing-extensions==4.0.1
     # via black
 
 # The following packages are considered to be unsafe in a requirements file:

diff --git a/requirements/conda_minimal_deps.txt b/requirements/conda_minimal_deps.txt
@@ -12,4 +12,4 @@ autoconf
 automake
 pytest
 pytest-xdist
-demes
+demes==0.2.0
diff --git a/setup.cfg b/setup.cfg
@@ -26,7 +26,7 @@ install_requires =
     numpy
     sparse
     tskit >= 0.3.6
-    demes == 0.1.2
+    demes ~= 0.2.0
 setup_requires =
     setuptools
     setuptools_scm