Update for numpy 1.24

4 files changed, 107 insertions, 22 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 9613e50462e9..d3ee6701843d 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = python-astrodendro
 	pkgdesc = Python package for computation of astronomical dendrograms
 	pkgver = 0.2.0
-	pkgrel = 2
+	pkgrel = 3
 	url = https://dendrograms.readthedocs.io
 	arch = any
 	license = MIT
@@ -13,14 +13,16 @@ pkgbase = python-astrodendro
 	makedepends = python-aplpy
 	source = https://files.pythonhosted.org/packages/source/a/astrodendro/astrodendro-0.2.0.tar.gz
 	source = fix-collection-py3.10.patch
+	source = fix-compability-to-numpy-1.24.patch
 	source = new-doc-building.patch
 	md5sums = 6f4155b1d4a4b2d9cb9ae154f88c5710
-	md5sums = 1b5d8b8c5d0387a09b15c02fc1b40714
+	md5sums = 85f81c440ce6d9f38fe0f3dd3166c911
+	md5sums = 11ee36f5a91348ae6843da182d54299f
 	md5sums = 2bd96deeaa18ae57c196246b74ee8030
 
 pkgname = python-astrodendro
 	depends = python
-	depends = python-numpy>=1.4.1
+	depends = python-numpy>=1.24
 	depends = python-astropy>=0.2.0
 	depends = python-h5py>=0.2.0
 	optdepends = python-matplotlib: For plotting
diff --git a/PKGBUILD b/PKGBUILD
index 63f0d2132774..93368204a4af 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -3,7 +3,7 @@ pkgbase=python-astrodendro
 _pyname=${pkgbase#python-}
 pkgname=("python-${_pyname}" "python-${_pyname}-doc")
 pkgver=0.2.0
-pkgrel=2
+pkgrel=3
 pkgdesc="Python package for computation of astronomical dendrograms"
 arch=('any')
 url="https://dendrograms.readthedocs.io"
@@ -19,15 +19,18 @@ checkdepends=('python-pytest'
               'python-h5py') # 'python-astropy' 'python-matplotlib'
 source=("https://files.pythonhosted.org/packages/source/${_pyname:0:1}/${_pyname}/${_pyname}-${pkgver}.tar.gz"
         'fix-collection-py3.10.patch'
+        'fix-compability-to-numpy-1.24.patch'
         'new-doc-building.patch')
 md5sums=('6f4155b1d4a4b2d9cb9ae154f88c5710'
-         '1b5d8b8c5d0387a09b15c02fc1b40714'
+         '85f81c440ce6d9f38fe0f3dd3166c911'
+         '11ee36f5a91348ae6843da182d54299f'
          '2bd96deeaa18ae57c196246b74ee8030')
 
 prepare() {
     cd ${srcdir}/${_pyname}-${pkgver}
 
     patch -Np1 -i "${srcdir}/fix-collection-py3.10.patch"
+    patch -Np1 -i "${srcdir}/fix-compability-to-numpy-1.24.patch"
     patch -Np1 -i "${srcdir}/new-doc-building.patch"
 }
 
@@ -37,19 +40,18 @@ build() {
 #   python -m build --wheel --no-isolation
 
     msg "Building Docs"
-    cd ${srcdir}/${_pyname}-${pkgver}/docs
-##   python setup.py build_sphinx
-    PYTHONPATH="../build/lib" make html
+#   python setup.py build_sphinx
+    PYTHONPATH="../build/lib" make -C docs html
 }
 
 check() {
     cd ${srcdir}/${_pyname}-${pkgver}
 
-    pytest || warning "Tests failed"
+    pytest || warning "Tests failed" # -vv --color=yes
 }
 
 package_python-astrodendro() {
-    depends=('python' 'python-numpy>=1.4.1' 'python-astropy>=0.2.0' 'python-h5py>=0.2.0')
+    depends=('python' 'python-numpy>=1.24' 'python-astropy>=0.2.0' 'python-h5py>=0.2.0')
     optdepends=('python-matplotlib: For plotting'
                 'python-pytest: For testing'
                 'python-mock: For testing'
diff --git a/fix-collection-py3.10.patch b/fix-collection-py3.10.patch
index ac3a3738dab9..31d260b36f40 100644
--- a/fix-collection-py3.10.patch
+++ b/fix-collection-py3.10.patch
@@ -1,23 +1,23 @@
---- a/astrodendro/dendrogram.py	2016-09-29 17:23:53.000000000 +0800
-+++ b/astrodendro/dendrogram.py	2022-08-22 16:14:19.114340172 +0800
+Description: Add try-except clause for importing Iterable pre/post Python 3.9.
+Origin: https://github.com/dendrograms/astrodendro/commit/3fde58f1e06bf7f966ed52712d1bf8929282be41.patch
+Author: nbrunett <nate.brunetti@gmail.com>
+Date: Tue, 15 Feb 2022 13:55:09 -0500
+Last-Update: 2022-04-10
+
+
+--- a/astrodendro/dendrogram.py
++++ b/astrodendro/dendrogram.py
 @@ -5,7 +5,12 @@
  # - An ancestor is the largest structure that a structure is part of
  
  import numpy as np
 -from collections import Iterable
 +try:
-+    # Python > 3.9
-+    from collections.abc import Iterable
-+except ImportError:
 +    # Python <= 3.9
 +    from collections import Iterable
++except ImportError:
++    # Python > 3.9
++    from collections.abc import Iterable
  import copy
  import warnings
  
-@@ -847,4 +852,4 @@
-     # To make the structure.level property fast, we ensure all the structures in the
-     # trunk have their level cached as "0"
-     for structure in dendrogram.trunk:
--        structure._level = 0  # See the definition of level() in structure.py
-\ No newline at end of file
-+        structure._level = 0  # See the definition of level() in structure.py
diff --git a/fix-compability-to-numpy-1.24.patch b/fix-compability-to-numpy-1.24.patch
new file mode 100644
index 000000000000..ce4b34908494
--- /dev/null
+++ b/fix-compability-to-numpy-1.24.patch
@@ -0,0 +1,81 @@
+--- a/astrodendro/analysis.py	2016-09-29 17:23:53.000000000 +0800
++++ b/astrodendro/analysis.py	2023-02-05 13:09:03.929960758 +0800
+@@ -77,7 +77,7 @@
+             Location of each element of values. The i-th array in the tuple
+             describes the ith positional dimension
+         """
+-        self.values = values.astype(np.float)
++        self.values = values.astype(float)
+         self.indices = indices
+ 
+     @memoize
+@@ -126,13 +126,13 @@
+             The variance (or co-variance matrix) of the data along the
+             specified direction(s).
+         """
+-        w = np.atleast_2d(direction).astype(np.float)
++        w = np.atleast_2d(direction).astype(float)
+         for row in w:
+             row /= np.linalg.norm(row)
+ 
+         result = np.dot(np.dot(w, self.mom2()), w.T)
+         if result.size == 1:
+-            result = np.asscalar(result)
++            result = result.item()
+         return result
+ 
+     @memoize
+--- a/astrodendro/dendrogram.py	2023-02-05 13:10:42.786010635 +0800
++++ b/astrodendro/dendrogram.py	2023-02-05 13:07:48.077121718 +0800
+@@ -27,7 +27,7 @@
+ # utility dict to offsets of adjacent pixel list
+ _offsets = dict((ndim, np.concatenate((
+                 np.identity(ndim),
+-                np.identity(ndim) * -1)).astype(np.int))
++                np.identity(ndim) * -1)).astype(int))
+                 for ndim in range(1, 8))
+ 
+ # the formula above generalizes this special case
+@@ -655,11 +655,11 @@
+         #    index[offset[pi] : offset[pi] + npix[pi]]
+         # and including subtrees is
+         #    index[offset[pi] : offset[pi] + npix_subtree[pi]]
+-        offset = np.zeros(idx_ct.size, dtype=np.int)
++        offset = np.zeros(idx_ct.size, dtype=int)
+         npix = offset * 0
+         npix_subtree = offset * 0
+ 
+-        index = -np.ones(sz, dtype=np.int)
++        index = -np.ones(sz, dtype=int)
+         order = dendrogram.all_structures
+ 
+         pos = 0
+@@ -852,4 +852,4 @@
+     # To make the structure.level property fast, we ensure all the structures in the
+     # trunk have their level cached as "0"
+     for structure in dendrogram.trunk:
+-        structure._level = 0  # See the definition of level() in structure.py
+\ 文件尾没有换行符
++        structure._level = 0  # See the definition of level() in structure.py
+--- a/astrodendro/pruning.py	2016-09-29 17:23:53.000000000 +0800
++++ b/astrodendro/pruning.py	2023-02-05 13:07:48.077121718 +0800
+@@ -40,7 +40,7 @@
+     else:  # mode == 'wrap'
+         indices = [i % d for i, d in zip(indices, dims)]
+ 
+-    result = np.zeros(len(multi_index[0]), dtype=np.int)
++    result = np.zeros(len(multi_index[0]), dtype=int)
+     offset = 1
+     for i, d in list(zip(indices, dims))[::-1]:
+         result += (i * offset).ravel()
+--- a/astrodendro/tests/test_compute.py	2016-09-29 17:23:53.000000000 +0800
++++ b/astrodendro/tests/test_compute.py	2023-02-05 13:07:48.080455029 +0800
+@@ -110,7 +110,7 @@
+         assert len(d.leaves) == 55

+ 

+         # Now check every pixel in the data cube (this takes a while).

+-        st_map = -np.ones(self.data.shape, dtype=np.int)

++        st_map = -np.ones(self.data.shape, dtype=int)

+         for st in d.all_structures:

+             st_map[st.indices(subtree=False)] = st.idx

+