Merge branch 'main' into bug_464

.readthedocs.yml

@@ -9,6 +9,7 @@ sphinx:
 python:
   version: 3.7
   install:
+    - requirements: docs/requirements.txt
     - method: pip
       path: .
       extra_requirements:

.zenodo.json

@@ -50,14 +50,19 @@
         },
         {
             "orcid": "0000-0002-4437-0770",
-            "affiliation": "University of Manchester",
+            "affiliation": "University of Oxford, University of Manchester",
             "name": "Ian Harrison"
         },
         {
             "orcid": "0000-0002-5304-9372",
             "affiliation": "University of Portsmouth",
             "name": "Ian Harry"
         },
+        {
+            "orcid": "0000-0001-9994-1115",
+            "affiliation": "University of Geneva",
+            "name": "William G. Hartley"
+        },
         {
             "orcid": "0000-0001-9233-2341",
             "affiliation": "University of Portsmouth",
@@ -103,10 +108,20 @@
             "affiliation": "Institute of Astronomy and Astrophysics Academia Sinica",
             "name": "Keiichi Umetsu"
         },
+        {
+            "orcid": "0000-0001-9841-943X",
+            "affiliation": "University of Portsmouth",
+            "name": "Arthur E. Tolley"
+        },
         {
             "orcid": "0000-0002-7627-8688",
             "affiliation": "University of Portsmouth",
             "name": "Andrew R. Williamson"
+        },
+        {
+            "orcid": "0000-0003-3334-3037",
+            "affiliation": "University of Manchester",
+            "name": "Laura Wolz"
         }
     ],
     "contributors": [

README.rst

@@ -2,7 +2,7 @@
 SkyPy: A package for modelling the Universe
 ===========================================
 
-|Read the Docs| |GitHub| |Codecov|
+|Read the Docs| |GitHub| |Codecov| |Compatibility|
 
 This package contains methods for modelling the Universe, galaxies and the
 Milky Way. SkyPy simulates populations of astronomical objects, generating
@@ -68,7 +68,7 @@ You are welcome to talk about the SkyPy package and code using our
 `Discussions Page`_. For any other questions about the project in general,
 please get in touch with the `SkyPy Co-ordinators`_.
 
- .. _Discussions Page: https://github.com/skypyproject/skypy/discussions 
+ .. _Discussions Page: https://github.com/skypyproject/skypy/discussions
  .. _SkyPy Co-ordinators: mailto:skypy-coordinators@googlegroups.com
 
 Contributing
@@ -95,6 +95,9 @@ in the `Code of Conduct`_.
 .. |GitHub| image:: https://github.com/skypyproject/skypy/workflows/Tests/badge.svg
     :target: https://github.com/skypyproject/skypy/actions
 
+.. |Compatibility| image:: https://github.com/skypyproject/skypy/actions/workflows/compatibility.yaml/badge.svg
+    :target: https://github.com/skypyproject/skypy/actions/workflows/compatibility.yaml
+
 .. |Codecov| image:: https://codecov.io/gh/skypyproject/skypy/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/skypyproject/skypy
 

docs/requirements.txt

@@ -0,0 +1 @@
+setuptools==58.0.0

examples/galaxies/sdss_dered_10deg2.ecsv

@@ -9,15 +9,15 @@
 # - name: magnitude
 #   datatype: float32
 # - name: dered_u
-#   datatype: int
+#   datatype: uint16
 # - name: dered_g
-#   datatype: int
+#   datatype: uint16
 # - name: dered_r
-#   datatype: int
+#   datatype: uint16
 # - name: dered_i
-#   datatype: int
+#   datatype: uint16
 # - name: dered_z
-#   datatype: int
+#   datatype: uint16
 magnitude dered_u dered_g dered_r dered_i dered_z
 15.0 5 6 5 9 9
 15.1 4 5 11 8 17

skypy/galaxies/morphology.py

@@ -251,6 +251,11 @@ def ryden04_ellipticity(mu_gamma, sigma_gamma, mu, sigma, size=None):
     size : int or tuple of ints or None
         Size of the sample. If `None` the size is inferred from the parameters.
 
+    Returns
+    -------
+    ellipticity: (size,) array_like
+        Ellipticities sampled from the Ryden 2004 model.
+
     References
     ----------
     .. [1] Ryden B. S., 2004, ApJ, 601, 214

skypy/pipeline/tests/test_pipeline.py

@@ -8,7 +8,6 @@
 from astropy.utils.data import get_pkg_data_filename
 import networkx
 import numpy as np
-import os
 import pytest
 from skypy.pipeline import Pipeline
 from skypy.pipeline._items import Call, Ref
@@ -21,7 +20,7 @@
     HAS_H5PY = True
 
 
-def test_pipeline():
+def test_pipeline(tmp_path):
 
     # Evaluate and store the default astropy cosmology.
     config = {'test_cosmology': Call(default_cosmology.get)}
@@ -44,7 +43,7 @@ def test_pipeline():
 
     pipeline = Pipeline(config)
     pipeline.execute()
-    output_filename = 'output.fits'
+    output_filename = str(tmp_path / 'output.fits')
     pipeline.write(output_filename)
     assert len(pipeline['test_table']) == size
     assert np.all(pipeline['test_table.column1'] < pipeline['test_table.column2'])
@@ -251,7 +250,7 @@ def value_in_cm(q):
 
 
 @pytest.mark.skipif(not HAS_H5PY, reason='Requires h5py')
-def test_hdf5():
+def test_hdf5(tmp_path):
     size = 100
     string = size*'a'
     config = {'tables': {
@@ -264,8 +263,9 @@ def test_hdf5():
 
     pipeline = Pipeline(config)
     pipeline.execute()
-    pipeline.write('output.hdf5')
-    hdf_table = read_table_hdf5('output.hdf5', 'tables/test_table', character_as_bytes=False)
+    output_filename = str(tmp_path / 'output.hdf5')
+    pipeline.write(output_filename)
+    hdf_table = read_table_hdf5(output_filename, 'tables/test_table', character_as_bytes=False)
     assert np.all(hdf_table == pipeline['test_table'])
 
 
@@ -289,13 +289,3 @@ def test_depends():
     pipeline = Pipeline(config)
     pipeline.execute()
     assert np.all(pipeline['table_1'] == pipeline['table_2'])
-
-
-def teardown_module(module):
-
-    # Remove fits file generated in test_pipeline
-    os.remove('output.fits')
-
-    # Remove hdf5 file generated in test_hdf5
-    if HAS_H5PY:
-        os.remove('output.hdf5')

skypy/pipeline/tests/test_skypy.py

@@ -2,15 +2,14 @@
 from astropy.utils.data import get_pkg_data_filename
 from contextlib import redirect_stdout
 from io import StringIO
-import os
 import pytest
 from skypy import __version__ as skypy_version
 from skypy.pipeline import load_skypy_yaml
 from skypy.pipeline._items import Call
 from skypy.pipeline.scripts import skypy
 
 
-def test_skypy():
+def test_skypy(tmp_path):
 
     # No arguments
     with pytest.raises(SystemExit) as e:
@@ -36,36 +35,39 @@ def test_skypy():
     assert e.value.code == 2
 
     # Process empty config file
-    filename = get_pkg_data_filename('data/empty_config.yml')
-    assert skypy.main([filename, 'empty.fits']) == 0
+    config_filename = get_pkg_data_filename('data/empty_config.yml')
+    output_filename = str(tmp_path / 'empty.fits')
+    assert skypy.main([config_filename, output_filename]) == 0
 
     # Process test config file
-    filename = get_pkg_data_filename('data/test_config.yml')
-    assert skypy.main([filename, 'test.fits']) == 0
+    config_filename = get_pkg_data_filename('data/test_config.yml')
+    output_filename = str(tmp_path / 'test.fits')
+    assert skypy.main([config_filename, output_filename]) == 0
 
     # Invalid file format
+    output_filename = str(tmp_path / 'test.invalid')
     with pytest.raises(SystemExit) as e:
-        skypy.main([filename, 'test.invalid'])
+        skypy.main([config_filename, output_filename])
     assert e.value.code == 2
 
 
-def test_logging(capsys):
+def test_logging(capsys, tmp_path):
 
     # Run skypy with default verbosity and check log is empty
-    filename = get_pkg_data_filename('data/test_config.yml')
-    output_file = 'logging.fits'
-    skypy.main([filename, output_file])
+    config_filename = get_pkg_data_filename('data/test_config.yml')
+    output_filename = str(tmp_path / 'logging.fits')
+    skypy.main([config_filename, output_filename])
     out, err = capsys.readouterr()
     assert(not err)
 
     # Run again with increased verbosity and capture log. Force an exception by
     # not using the "--overwrite" flag when the output file already exists.
     with pytest.raises(SystemExit):
-        skypy.main([filename, output_file, '--verbose'])
+        skypy.main([config_filename, output_filename, '--verbose'])
     out, err = capsys.readouterr()
 
     # Determine all DAG jobs and function calls from config
-    config = load_skypy_yaml(filename)
+    config = load_skypy_yaml(config_filename)
     cosmology = config.pop('cosmology', None)
     tables = config.pop('tables', {})
     config.update({k: v.pop('.init', Call(Table)) for k, v in tables.items()})
@@ -88,21 +90,13 @@ def test_logging(capsys):
         assert("[INFO] skypy.pipeline: Setting cosmology" in err)
 
     # Check writing output file is in the log
-    assert(f"[INFO] skypy: Writing {output_file}" in err)
+    assert(f"[INFO] skypy: Writing {output_filename}" in err)
 
     # Check error for existing output file is in the log
-    assert(f"[ERROR] skypy: File '{output_file}' already exists." in err)
+    assert(f"[ERROR] skypy: File {output_filename!r} already exists." in err)
 
     # Run again with decreased verbosity and check the log is empty
     with pytest.raises(SystemExit):
-        skypy.main([filename, output_file, '-qq'])
+        skypy.main([config_filename, output_filename, '-qq'])
     out, err = capsys.readouterr()
     assert(not err)
-
-
-def teardown_module(module):
-
-    # Remove fits file generated in test_skypy
-    os.remove('empty.fits')
-    os.remove('logging.fits')
-    os.remove('test.fits')

tox.ini

@@ -1,8 +1,8 @@
 [tox]
 envlist =
     py{36,37,38,39}-test{,-all}{,-dev,-latest,-oldest}{,-cov}
-    py{36,37,38,39}-test-numpy{116,117,118,119,120}
-    py{36,37,38,39}-test-scipy{12,13,14,15,16}
+    py{36,37,38,39}-test-numpy{116,117,118,119,120,121}
+    py{36,37,38,39}-test-scipy{12,13,14,15,16,17}
     py{36,37,38,39}-test-astropy{40,41,42}
     build_docs
     linkcheck
@@ -43,11 +43,13 @@ description =
     numpy118: with numpy 1.18.*
     numpy119: with numpy 1.19.*
     numpy120: with numpy 1.20.*
+    numpy121: with numpy 1.21.*
     scipy12: with scipy 1.2.*
     scipy13: with scipy 1.3.*
     scipy14: with scipy 1.4.*
     scipy15: with scipy 1.5.*
     scipy16: with scipy 1.6.*
+    scipy17: with scipy 1.7.*
     astropy40: with astropy 4.0.*
     astropy41: with astropy 4.1.*
     astropy42: with astropy 4.2.*
@@ -60,12 +62,14 @@ deps =
     numpy118: numpy==1.18.*
     numpy119: numpy==1.19.*
     numpy120: numpy==1.20.*
+    numpy121: numpy==1.21.*
 
     scipy12: scipy==1.2.*
     scipy13: scipy==1.3.*
     scipy14: scipy==1.4.*
     scipy15: scipy==1.5.*
     scipy16: scipy==1.6.*
+    scipy17: scipy==1.7.*
 
     astropy40: astropy==4.0.*
     astropy41: astropy==4.1.*
@@ -76,8 +80,8 @@ deps =
     dev: git+https://github.com/astropy/astropy.git#egg=astropy
 
     latest: astropy==4.2.*
-    latest: numpy==1.20.*
-    latest: scipy==1.6.*
+    latest: numpy==1.21.*
+    latest: scipy==1.7.*
 
     oldest: astropy==4.0.*
     oldest: numpy==1.16.*
@@ -88,6 +92,10 @@ extras =
     test
     all: all
 
+# Enable pip to install pre-releases in the dev environment
+pip_pre =
+    dev: True
+
 commands =
     pip freeze
     !cov: pytest --pyargs skypy {toxinidir}/docs {posargs}