release-related tweaks

virgesmith · Sep 16, 2020 · 979c7ab · 979c7ab
1 parent 13dca11
commit 979c7ab
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Showing 23 changed files with 21 additions and 53 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,4 @@
 include VERSION
 include LICENCE
 include README.md
+include test/*.csv
diff --git a/README.md b/README.md
@@ -4,6 +4,8 @@
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/neworder)](https://pypi.org/project/neworder/)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/neworder)](https://pypi.org/project/neworder/)
 
+[![DOI](https://zenodo.org/badge/111997710.svg)](https://zenodo.org/badge/latestdoi/111997710)
+
 [![Build Status](https://travis-ci.org/virgesmith/neworder.png?branch=master)](https://travis-ci.org/virgesmith/neworder) 
 [![Build status](https://ci.appveyor.com/api/projects/status/oycn4is2insoiun7?svg=true)](https://ci.appveyor.com/project/virgesmith/neworder)
 [![License](https://img.shields.io/github/license/mashape/apistatus.svg)](https://opensource.org/licenses/MIT)

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.0.5
+0.0.6
diff --git a/docs/citing.md b/docs/citing.md
@@ -4,11 +4,11 @@ BibTex:
 
 ```bibtex
 @software{neworder,
-   doi = { TODO... },
-   author = {Andrew P. Smith},
+   doi = {10.5281/zenodo.4031822},
+   author = {Andrew P Smith},
    year = {2020},
-   version = {1.0.0},
+   version = {0.0.6},
    url = {https://neworder.readthedocs.io/},
-   title = {neworder: A dynamic microsimulation module for python}
+   title = {neworder: Dynamic microsimulation in python}
 }
 ```
diff --git a/scripts/package.sh b/scripts/package.sh
@@ -5,6 +5,6 @@ version=$(cat VERSION)
 # package as source dist
 python setup.py sdist 
 # upload
-twine upload --repository-url https://test.pypi.org/legacy/ dist/neworder-$version.tar.gz
-#twine upload --repository-url https://upload.pypi.org/legacy/ dist/neworder-$version*
+#twine upload --repository-url https://test.pypi.org/legacy/ dist/neworder-$version.tar.gz
+twine upload --repository-url https://upload.pypi.org/legacy/ dist/neworder-$version*
 
diff --git a/setup.py b/setup.py
@@ -124,18 +124,18 @@ def build_extensions(self):
   version=version(),
   author='Andrew P Smith',
   author_email='a.p.smith@leeds.ac.uk',
-  url='https://github.com/virgesmith/neworder',
+  url='https://neworder.readthedocs.io',
   description='A dynamic microsimulation framework',
   long_description = readme(),
   long_description_content_type="text/markdown",
   ext_modules=ext_modules,
   setup_requires=['pybind11>=2.5.0', 'pytest-runner'],
   tests_require=['pytest'],    
   cmdclass={'build_ext': BuildExt},
-  classifiers=(
+  classifiers=[
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
-  ),    
+  ],    
   zip_safe=False,
 )
diff --git a/tests/benchmark.py → test/benchmark.py b/tests/benchmark.py → test/benchmark.py
@@ -8,7 +8,7 @@
 no.verbose()
 
 # define some global variables describing where the starting population and the parameters of the dynamics come from
-INITIAL_POPULATION = "./tests/ssm_hh_E09000001_OA11_2011.csv"
+INITIAL_POPULATION = "./ssm_hh_E09000001_OA11_2011.csv"
 
 t = np.array([
   [0.9,  0.05, 0.05, 0.,   0.,   0.  ],

diff --git a/tests/correlated.py → test/correlated.py b/tests/correlated.py → test/correlated.py
diff --git a/tests/df.csv → test/df.csv b/tests/df.csv → test/df.csv
diff --git a/tests/ssm_E09000001_MSOA11_ppp_2011.csv → test/df2.csv b/tests/ssm_E09000001_MSOA11_ppp_2011.csv → test/df2.csv
diff --git a/tests/mc.py → test/mc.py b/tests/mc.py → test/mc.py
diff --git a/tests/module.py → test/module.py b/tests/module.py → test/module.py
@@ -84,13 +84,13 @@ def test():
   # # DataFrame ops
 
   # modify df passing column
-  df = pd.read_csv("../../tests/df.csv")
+  df = pd.read_csv("../../test/df.csv")
 
   # modify df passing directly
   no.df.testfunc(model, df, "DC2101EW_C_ETHPUK11")
   t.check(np.array_equal(df["DC2101EW_C_ETHPUK11"].values, np.zeros(len(df)) + 3))
 
-  df = pd.read_csv("../../tests/df.csv")
+  df = pd.read_csv("../../test/df.csv")
   cats = np.array(range(4))
   transitions = np.identity(len(cats)) * 0 + 0.25
   #no.log(transitions)

diff --git a/tests/mpi.py → test/mpi.py b/tests/mpi.py → test/mpi.py
@@ -41,7 +41,7 @@ def test():
     neworder.log("MPI: 0 sent {}={} 1 recd {}={}".format(type(x), x, type(y), y))
     t.check(np.array_equal(x,y))
 
-  df = pd.read_csv("../../tests/ssm_E09000001_MSOA11_ppp_2011.csv")
+  df = pd.read_csv("../../test/df2.csv")
   if neworder.mpi.rank() == 0:
     neworder.log("sending (as csv) df len %d rows from 0" % len(df))
     neworder.mpi.send_csv(df, 1)

diff --git a/tests/op.py → test/op.py b/tests/op.py → test/op.py
diff --git a/tests/test.py → test/test.py b/tests/test.py → test/test.py
diff --git a/tests/test_df.py → test/test_df.py b/tests/test_df.py → test/test_df.py
@@ -10,7 +10,7 @@
 
 def test_errors():
 
-  df = pd.read_csv("./tests/df.csv")
+  df = pd.read_csv("./test/df.csv")
 
   # base model for MC engine
   model = no.Model(no.Timeline.null(), no.MonteCarlo.deterministic_identical_stream)
@@ -83,7 +83,7 @@ def test_basic():
 
 def test():
 
-  df = pd.read_csv("./tests/df.csv")
+  df = pd.read_csv("./test/df.csv")
 
   # base model for MC engine
   model = no.Model(no.Timeline.null(), no.MonteCarlo.deterministic_identical_stream)
@@ -113,38 +113,3 @@ def test():
   assert np.array_equal(np.sort(df["DC2101EW_C_ETHPUK11"].unique()), np.array([0, 3]))
 
 
-# def todo():
-
-#   # define some global variables describing where the starting population and the parameters of the dynamics come from
-#   initial_population = "examples/households/data/ssm_hh_E09000001_OA11_2011.csv"
-
-#   hh = pd.read_csv(initial_population)
-
-#   print(hh.columns.values)
-#   c = hh.LC4408_C_AHTHUK11.unique()
-#   print(c)
-#   t = np.identity(len(c))
-
-#   # [ 3  5  1  2 -1  4]
-#   t = np.array([[0.9,  0.05, 0.05, 0.0,  0.0,  0.0],
-#                 [0.05, 0.9,  0.04, 0.01, 0.0,  0.0],
-#                 [0.0,  0.05, 0.9,  0.05, 0.0,  0.0],
-#                 [0.0,  0.0,  0.05, 0.9,  0.05, 0.0],
-#                 [0.1,  0.1,  0.1,  0.1,  0.5,  0.1],
-#                 [0.0,  0.0,  0.00, 0.0,  0.2,  0.8]])
-
-#   #print(t[1]) # horz
-#   #print(t[:,1]) # vert
-#   tc = np.cumsum(t, axis=1)
-#   # TODO timing...
-#   u = np.random.sample(len(hh))
-#   for i in range(len(hh)):
-#     current = hh.loc[i, "LC4408_C_AHTHUK11"]
-#     hh.loc[i, "LC4408_C_AHTHUK11"] = sample(u[i], tc[current], c)
-
-#   print(hh.LC4408_C_AHTHUK11.head())
-
-#   tc = np.cumsum(t, axis=1)
-
-#   print(np.cumsum(t[1]))
-#   #print()
diff --git a/tests/test_mc.py → test/test_mc.py b/tests/test_mc.py → test/test_mc.py
diff --git a/tests/test_model.py → test/test_model.py b/tests/test_model.py → test/test_model.py
diff --git a/tests/test_module.py → test/test_module.py b/tests/test_module.py → test/test_module.py
diff --git a/tests/test_mpi.py → test/test_mpi.py b/tests/test_mpi.py → test/test_mpi.py
@@ -40,7 +40,7 @@ def test_arrays():
       y = comm.recv(source=0)
       assert np.array_equal(x,y)
 
-    df = pd.read_csv("./tests/ssm_E09000001_MSOA11_ppp_2011.csv")
+    df = pd.read_csv("./test/df2.csv")
     if no.mpi.rank() == 0:
       comm.send(df, dest=1)
     if no.mpi.rank() == 1:

diff --git a/tests/test_timeline.py → test/test_timeline.py b/tests/test_timeline.py → test/test_timeline.py
diff --git a/tests/test_wrapper.py → test/test_wrapper.py b/tests/test_wrapper.py → test/test_wrapper.py
diff --git a/tests/trans.py → test/trans.py b/tests/trans.py → test/trans.py
@@ -14,7 +14,7 @@ def test():
 
   t = test_.Test()
 
-  df = pd.read_csv("../../tests/df.csv")
+  df = pd.read_csv("../../test/df.csv")
 
   # base model for MC engine
   model = no.Model(no.Timeline.null(), no.MonteCarlo.deterministic_identical_stream)