Merge pull request #846 from chaquo/astropy

Add packages: astropy, pyerfa, photutils

server/pypi/packages/astropy/meta.yaml

@@ -0,0 +1,20 @@
+{% if PY_VER == "3.8" %}
+    {% set numpy_version = "1.19.5" %}
+{% else %}
+    {% set numpy_version = "1.23.3" %}
+{% endif %}
+
+package:
+  name: astropy
+  version: 5.1.1
+
+build:
+  number: 1
+
+requirements:
+  build:
+    - cython 0.29.32
+    - extension-helpers 1.0.0
+    - setuptools-scm 7.1.0
+  host:
+    - numpy {{ numpy_version }}

server/pypi/packages/astropy/patches/chaquopy.patch

@@ -0,0 +1,35 @@
+--- src-original/setup.py	2022-05-24 19:43:02.000000000 +0000
++++ src/setup.py	2023-07-24 14:54:26.328796259 +0000
+@@ -4,6 +4,10 @@
+ # NOTE: The configuration for the package, including the name, version, and
+ # other information are set in the setup.cfg file.
+
++# Chaquopy
++import builtins
++builtins.__NUMPY_SETUP__ = True  # Prevent the compiled parts from being imported.
++
+ import sys
+
+ # First provide helpful messages if contributors try and run legacy commands
+@@ -65,4 +69,7 @@
+ from setuptools import setup  # noqa
+ from extension_helpers import get_extensions  # noqa
+
+-setup(ext_modules=get_extensions())
++# Chaquopy: added `version`, because setuptools_scm isn't finding it automatically for
++# some reason.
++from setuptools_scm import get_version
++setup(ext_modules=get_extensions(), version=get_version())
+--- src-original/astropy/convolution/convolve.py	2022-10-23 08:14:50.000000000 +0000
++++ src/astropy/convolution/convolve.py	2023-07-24 22:01:04.533772774 +0000
+@@ -25,7 +25,9 @@
+         # numpy.distutils is deprecated since numpy 1.23
+         # see https://github.com/astropy/astropy/issues/12865
+         warnings.simplefilter('ignore', DeprecationWarning)
+-        _convolve = load_library("_convolve", LIBRARY_PATH)
++        # Chaquopy: was numpy.ctypeslib.load_library, which requires the file to already
++        # exist (#892).
++        _convolve = ctypes.CDLL(f"{LIBRARY_PATH}/_convolve.so")
+ except Exception:
+     raise ImportError("Convolution C extension is missing. Try re-building astropy.")
+

server/pypi/packages/astropy/test.py

@@ -0,0 +1,12 @@
+import unittest
+
+
+class TestAstropy(unittest.TestCase):
+
+    # https://docs.astropy.org/en/stable/convolution/index.html#getting-started
+    def test_convolution(self):
+        from astropy.convolution import convolve
+        from numpy.testing import assert_allclose
+
+        assert_allclose(convolve([1, 4, 5, 6, 5, 7, 8], [0.2, 0.6, 0.2]),
+                        [1.4, 3.6, 5.0, 5.6, 5.6, 6.8, 6.2])

server/pypi/packages/photutils/meta.yaml

@@ -0,0 +1,17 @@
+{% if PY_VER == "3.8" %}
+    {% set numpy_version = "1.19.5" %}
+{% else %}
+    {% set numpy_version = "1.23.3" %}
+{% endif %}
+
+package:
+  name: photutils
+  version: 1.1.0
+
+requirements:
+  build:
+    - cython 0.29.32
+    - extension-helpers 1.0.0
+    - setuptools-scm 7.1.0
+  host:
+    - numpy {{ numpy_version }}

server/pypi/packages/photutils/patches/chaquopy.patch

@@ -0,0 +1,12 @@
+--- src-original/setup.py     2022-05-24 19:43:02.000000000 +0000
++++ src/setup.py        2023-04-06 16:08:59.631926941 +0000
+@@ -4,5 +4,9 @@
+ # NOTE: The configuration for the package, including the name, version, and
+ # other information are set in the setup.cfg file.
+
++# Chaquopy
++import builtins
++builtins.__NUMPY_SETUP__ = True  # Prevent the compiled parts from being imported.
++
+ import sys
+

server/pypi/packages/photutils/test.py

@@ -0,0 +1,56 @@
+import unittest
+
+
+class TestPhotutils(unittest.TestCase):
+
+    # https://photutils.readthedocs.io/en/stable/getting_started.html
+    def test_basic(self):
+        from astropy.io import fits
+        from astropy.stats import mad_std
+        from io import BytesIO
+        import numpy as np
+        from photutils.aperture import aperture_photometry, CircularAperture
+        from photutils.detection import DAOStarFinder
+
+        # This is equivalent to photutils.datasets.load_star_image.
+        URL = "http://www.astropy.org/astropy-data/photometry/M6707HH.fits"
+        hdu = fits.open(BytesIO(read_url(URL)))[0]
+
+        image = hdu.data[500:700, 500:700].astype(float)
+        image -= np.median(image)
+
+        bkg_sigma = mad_std(image)
+        daofind = DAOStarFinder(fwhm=4.0, threshold=3.0 * bkg_sigma)
+        sources = daofind(image)
+        self.assertEqual(len(sources), 152)
+
+        positions = np.transpose((sources['xcentroid'], sources['ycentroid']))
+        apertures = CircularAperture(positions, r=4.0)
+        phot_table = aperture_photometry(image, apertures)
+
+        phot_table.sort("aperture_sum", reverse=True)
+        brightest = phot_table[0]
+        self.assertEqual(
+            [int(brightest[column].value) for column in ["xcenter", "ycenter"]],
+            [53, 13])  # See image at the bottom of the above link.
+
+
+# Downloading a URL with "Connection: close", as urllib does, causes an intermittent network
+# problem on the emulator (see #5601 and https://issuetracker.google.com/issues/150758736). For
+# small files we could just retry until it succeeds, but for large files a failure is much more
+# likely, and we might have to keep retrying for several minutes. So use the stdlib's low-level
+# HTTP API to make a request with no Connection header.
+def read_url(url):
+    from http.client import HTTPConnection, HTTPSConnection
+    from urllib.parse import urlparse
+
+    parsed = urlparse(url)
+    conn_cls = HTTPSConnection if parsed.scheme == "https" else HTTPConnection
+    conn = conn_cls(parsed.hostname, parsed.port)
+    full_path = parsed.path
+    if parsed.query:
+        full_path += "?" + parsed.query
+    conn.request("GET", full_path)
+    data = conn.getresponse().read()
+    conn.close()
+    return data

server/pypi/packages/pyerfa/meta.yaml

@@ -0,0 +1,15 @@
+{% if PY_VER == "3.8" %}
+    {% set numpy_version = "1.19.5" %}
+{% else %}
+    {% set numpy_version = "1.23.3" %}
+{% endif %}
+
+package:
+  name: pyerfa
+  version: 2.0.0.3
+
+requirements:
+  build:
+    - packaging 23.1
+  host:
+    - numpy {{ numpy_version }}

server/pypi/packages/pyerfa/patches/chaquopy.patch

@@ -0,0 +1,13 @@
+--- src-original/setup.py	2021-11-02 19:17:42.000000000 +0000
++++ src/setup.py	2023-06-03 11:19:23.806406705 +0000
+@@ -26,6 +26,10 @@
+
+     @property
+     def include_dirs(self):
++        # Chaquopy
++        import builtins
++        builtins.__NUMPY_SETUP__ = True  # Prevent the compiled parts from being imported.
++
+         from numpy import get_include
+         return self._include_dirs + [get_include()]
+

server/pypi/packages/pyerfa/test.py

@@ -0,0 +1,13 @@
+import unittest
+
+
+class TestPyerfa(unittest.TestCase):
+
+    # https://pyerfa.readthedocs.io/en/latest/quickstart.html#usage
+    def test_basic(self):
+        import erfa
+        from numpy.testing import assert_allclose
+
+        position, velocity = erfa.plan94(2460000, 0, 1)
+        assert_allclose(position, [0.090837128 , -0.3904139186, -0.2179738913])
+        assert_allclose(velocity, [0.0219234131, 0.0070544853, 0.0014961814])

server/pypi/pkgtest/app/build.gradle

@@ -40,6 +40,7 @@ ext.TEST_PACKAGES = [
     "backports-zoneinfo": ["tzdata"],
     "dlib": ["numpy"],
     "grpcio": ["protobuf"],
+    "photutils": ["scipy"],
     "pycurl": ["certifi"],
     "pyzbar": ["pillow"],
     "qutip": ["setuptools"],
@@ -74,6 +75,7 @@ android {
             pyc {
                 src false  // Include test source code in stack traces.
             }
+            extractPackages "astropy"
         }
 
         ndk {