Add package: netcdf4

README.githubweather

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+Uploaded meta.yaml file to my repos Mar 22, 2023.

meta.yaml

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+{% set version = "1.6.2" %}
+
+package:
+  name: chaquopy-netcdf4
+  version: {{ version }}
+
+source:
+#  url: https://pypi.org/project/netCDF4/#files/netcdf4-{{ version }}.tar.gz
+#  url: https://pypi.org/project/netCDF4/#files/netCDF4-1.6.2.tar.gz
+#  url:  http://www.unidata.ucar.edu/downloads/netcdf/ftp/netCDF4-1.6.2.tar.gz
+  git_url: https://github.com/Unidata/netcdf4-python.git
+  git_rev: v{{ version }}
+
+build:
+  number: 1
+
+requirements:
+  build:
+    - numpy 1.24.2
+#    - h5py 3.8.0
+#    - hdf5 1.12.2
+    - cftime 1.6.2
+  host:
+    - python

server/pypi/packages/chaquopy-cftime/meta.yaml

@@ -0,0 +1,19 @@
+package:
+  name: cftime
+  version: 1.6.2
+
+build:
+  number: 0
+
+source:
+  git_url: https://github.com/Unidata/cftime.git
+  git_rev: v1.6.2rel
+
+requirements:
+  build:
+    - Cython 0.29.32
+  host:
+    - python
+#    - numpy 1.23.3
+    - numpy 1.25.0
+#    - numpy 1.19.5

server/pypi/packages/chaquopy-cftime/patches/chaquopy.patch

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+--- src-orig/setup.py	2023-05-16 17:26:57.704081052 -0600
++++ src/setup.py	2023-05-16 17:29:08.581181155 -0600
+@@ -2,6 +2,10 @@
+
+ import os
+ import sys
++#Chaquopy
++import builtins
++sys.path.insert(0,os.path.abspath("../requirements"))  # For numpy.distutils
++builtins.__NUMPY_SETUP__ = True # Prevent the rest of NumPY from being imported so that this setup.py can work with what it only needs
+ import numpy
+
+ from setuptools import Command, Extension, setup

server/pypi/packages/chaquopy-netcdf4-python/meta.yaml

@@ -0,0 +1,27 @@
+package:
+#  name: chaquopy-netcdf4-python
+  name: netCDF4
+#  version: 1.6.3
+  version: 1.6.4
+
+build:
+  number: 0
+
+source:
+  git_url: https://github.com/Unidata/netcdf4-python.git
+#  git_rev: v1.6.3rel
+  git_rev: v1.6.4rel
+
+requirements:
+  build:
+    - Cython 0.29.32
+  host:
+    - python
+#    - numpy 1.19.5
+#    - numpy 1.23.3
+    - numpy 1.25.0
+    - chaquopy-hdf5 1.10.2
+#    - hdf5 1.10.2
+#is this needed (6/27/23) ?    - h5py 2.10.0
+#new add below
+    - chaquopy-netcdf4 4.9.2

server/pypi/packages/chaquopy-netcdf4-python/patches/chaquopy.patch

@@ -0,0 +1,59 @@
+--- src-original/setup.py	2023-05-29 14:09:26.624130338 -0600
++++ src/setup.py	2023-05-29 14:09:19.180410341 -0600
+@@ -5,6 +5,11 @@
+ from setuptools import setup, Extension
+ from setuptools.dist import Distribution
+
++# Chaquopy
++import builtins
++sys.path.insert(0, os.path.abspath("../requirements"))  # For numpy.distutils
++builtins.__NUMPY_SETUP__ = True  # Prevent the rest of NumPy from being imported
++
+ open_kwargs = {'encoding': 'utf-8'}
+
+
+@@ -390,8 +395,8 @@
+                     sys.stdout.write('%s found in %s\n' %
+                                     (hdf5_version,HDF5_dir))
+                     break
+-            if HDF5_dir is None:
+-                raise ValueError('did not find HDF5 headers')
++#turn off            if HDF5_dir is None:
++#turn off                raise ValueError('did not find HDF5 headers')
+         else:
+             if HDF5_incdir is None:
+                 HDF5_incdir = os.path.join(HDF5_dir, 'include')
+@@ -487,14 +492,14 @@
+     if netCDF4_incdir is not None: inc_dirs.append(netCDF4_incdir)
+
+     # add szip to link if desired.
+-    if szip_libdir is None and szip_dir is not None:
++    if szip_libdir is None and szip_dir is not None: 
+         szip_libdir = os.path.join(szip_dir, 'lib')
+     if szip_incdir is None and szip_dir is not None:
+         szip_incdir = os.path.join(szip_dir, 'include')
+     if szip_incdir is not None and szip_libdir is not None:
+         libs.append('sz')
+         lib_dirs.append(szip_libdir)
+-        inc_dirs.append(szip_incdir)
++        inc_dirs.append(szip_incdir) 
+     # add hdf4 to link if desired.
+     if hdf4_libdir is None and hdf4_dir is not None:
+         hdf4_libdir = os.path.join(hdf4_dir, 'lib')
+@@ -515,14 +520,14 @@
+         lib_dirs.append(jpeg_libdir)
+         inc_dirs.append(jpeg_incdir)
+     # add curl to link if desired.
+-    if curl_libdir is None and curl_dir is not None:
++    if curl_libdir is None and curl_dir is not None: 
+         curl_libdir = os.path.join(curl_dir, 'lib')
+     if curl_incdir is None and curl_dir is not None:
+         curl_incdir = os.path.join(curl_dir, 'include')
+     if curl_incdir is not None and curl_libdir is not None:
+         libs.append('curl')
+         lib_dirs.append(curl_libdir)
+-        inc_dirs.append(curl_incdir)
++        inc_dirs.append(curl_incdir) 
+
+ if sys.platform == 'win32':
+     runtime_lib_dirs = []

server/pypi/packages/chaquopy-netcdf4/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+set -eu
+
+export LIBS=-lz
+
+# Some internal libraries can't be built with this flag.             
+LDFLAGS=$(echo $LDFLAGS | sed 's/-Wl,--no-undefined//')
+
+./configure --host=$HOST --disable-netcdf4 --disable-dap --disable-byterange
+make -j $CPU_COUNT all
+make install prefix=$PREFIX

server/pypi/packages/chaquopy-netcdf4/meta.yaml

@@ -0,0 +1,28 @@
+{% set version = "4.9.2" %}
+
+package:
+  name: chaquopy-netcdf4
+  version: {{ version }}
+
+source:
+#  wget_url: ftp.unidata.ucar.edu/pub/netcdf/netcdf-{{ version }}
+#  git_rev: v{{ version }}
+  git_url: https://github.com/Unidata/netcdf-c.git
+  git_rev: v{{ version }}
+
+build:
+  number: 1
+
+#requirements:
+#  build:
+#    - numpy 1.24.2
+#    - h5py 3.8.0
+#    - hdf5 1.12.2
+#    - cftime 1.6.2
+#    - zlib 1.2.13
+#  host:
+#    - numpy 1.24.2
+#    - numpy 1.17.4
+#    - h5py 1.24.2
+#    - h5py 2.10.0
+#    - python

server/pypi/packages/h5py/meta.yaml

@@ -1,14 +1,18 @@
 package:
   name: h5py
-  version: 2.10.0
+  version: 3.9.0
 
 build:
   number: 1
 
 requirements:
   build:
-    - cython 0.29.14
+#    - cython 0.29.14
+    - cython 0.29.36
     - pkgconfig 1.3.1
   host:
     - chaquopy-hdf5 1.10.2
-    - numpy 1.17.4
+#    - chaquopy-hdf5 1.14.1
+#    - numpy 1.17.4
+#    - numpy 1.25.0
+    - numpy 1.23.3

server/pypi/packages/h5py/meta.yaml.orig

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+package:
+  name: h5py
+  version: 2.10.0
+
+build:
+  number: 1
+
+requirements:
+  build:
+    - cython 0.29.14
+    - pkgconfig 1.3.1
+  host:
+    - chaquopy-hdf5 1.10.2
+    - numpy 1.17.4

server/pypi/packages/h5py/patches.HOLD/chaquopy.patch

@@ -0,0 +1,84 @@
+diff -ru src-original/setup_build.py src/setup_build.py
+--- src-original/setup_build.py	2018-02-11 15:15:06.000000000 +0000
++++ src/setup_build.py	2018-07-28 20:23:17.575560442 +0000
+@@ -76,7 +76,6 @@
+         This is the point at which custom directories, MPI options, etc.
+         enter the build process.
+         """
+-        import numpy
+         import pkgconfig
+
+         settings = COMPILER_SETTINGS.copy()
+@@ -98,12 +97,8 @@
+             settings['include_dirs'].extend(FALLBACK_PATHS['include_dirs'])
+             settings['library_dirs'].extend(FALLBACK_PATHS['library_dirs'])
+
+-        try:
+-            numpy_includes = numpy.get_include()
+-        except AttributeError:
+-            # if numpy is not installed get the headers from the .egg directory
+-            import numpy.core
+-            numpy_includes = os.path.join(os.path.dirname(numpy.core.__file__), 'include')
++        # Chaquopy
++        numpy_includes = os.path.abspath("../requirements/numpy/core/include")
+
+         settings['include_dirs'] += [numpy_includes]
+         if config.mpi:
+@@ -154,7 +149,6 @@
+         """ Distutils calls this method to run the command """
+
+         from Cython.Build import cythonize
+-        import numpy
+
+         # Provides all of our build options
+         config = self.distribution.get_command_obj('configure')
+@@ -192,7 +186,10 @@
+                     'mpi': bool(config.mpi),
+                     'mpi4py_v2': bool(v2),
+                     'version': tuple(int(x) for x in config.hdf5_version.split('.')),
+-                    'complex256_support': hasattr(numpy, 'complex256')
++
++                    # Chaquopy: was `hasattr(numpy, 'complex256')`: erring on the side of caution.
++                    # TODO: see if there's another way to detect this.
++                    'complex256_support': False
+                 }
+                 s = s.encode('utf-8')
+                 f.write(s)
+diff -ru src-original/setup_configure.py src/setup_configure.py
+--- src-original/setup_configure.py     2018-12-20 04:15:31.000000000 +0000
++++ src/setup_configure.py      2019-03-14 17:58:50.250639920 +0000
+@@ -90,7 +90,7 @@
+                     ('reset', 'r', 'Reset config options') ]
+
+     def initialize_options(self):
+-        self.hdf5 = None
++        self.hdf5 = op.abspath("../requirements/chaquopy")
+         self.hdf5_version = None
+         self.mpi = None
+         self.reset = None
+@@ -203,6 +203,13 @@
+
+     import pkgconfig
+
++    # Chaquopy: added
++    for line in open(op.join(hdf5_dir, "include/H5public.h")):
++        match = re.search(r"HDF5 library version: ([0-9.]+)", line)
++        if match:
++            return match.group(1)
++    raise ValueError("Failed to find version string in header files")
++
+     if sys.platform.startswith('darwin'):
+         regexp = re.compile(r'^libhdf5.dylib')
+     else:
+diff -ru src-original/setup.py src/setup.py
+--- src-original/setup.py	2018-06-05 03:20:51.000000000 +0000
++++ src/setup.py	2018-07-28 20:19:37.761977082 +0000
+@@ -32,7 +32,7 @@
+ # these are required to build h5py
+ # RUN_REQUIRES is included as setup.py test needs RUN_REQUIRES for testing
+ # RUN_REQUIRES can be removed when setup.py test is removed
+-SETUP_REQUIRES = RUN_REQUIRES + [NUMPY_DEP, 'Cython>=0.23', 'pkgconfig']
++SETUP_REQUIRES = []  # Chaquopy: handled by meta.yaml
+
+ # Needed to avoid trying to install numpy/cython on pythons which the latest
+ # versions don't support

server/pypi/packages/numpy/meta.yaml

@@ -1,6 +1,8 @@
 package:
   name: numpy
-  version: 1.23.3
+#  version: 1.23.3
+#  version: 1.25.0rc1
+  version: 1.25.0
 
 build:
   number: 0