Merge pull request #44 from Morisset/devel

1.1.23

docs/CHANGES/1.1.22-1.1.23.txt

@@ -0,0 +1,4 @@
+* Migrate the setup to pyproject.toml. Minimalist version of setup.py is kept. 
+* Remove the version.py file, the version is now in pyproject.toml
+* Move the import ai4neb into a specific config method: pn.config.import_AI4Neb() before using the Machine Learning tools. This avoid annoying message about Tensorflow to appear and speedup the import of pyneb when not using ML facilities.
+* Change the name of the package to pyneb instead of PyNeb (seems to be mandatory soon).

pyneb/__init__.py

@@ -6,7 +6,10 @@
 """
 import sys
 
-from .version import __version__
+#from .version import __version__
+from importlib.metadata import version
+__version__ = version("PyNeb")
+
 from .utils.Config import _Config
 config = _Config()
 log_ = config.log_
@@ -44,7 +47,7 @@
 
 __pyversion__ = sys.version_info[0]
 
-log_.message('Starting PyNeb version %s' % __version__, calling='PyNeb')
+log_.message('Starting PyNeb version %s' % __version__, calling='pyneb')
 
 if sys.version_info[:2] < (2, 6):
     log_.warn('Python version >= 2.6 needed, seems you have {0}'.format(sys.version_info), calling='PyNeb')

pyneb/core/pynebcore.py

@@ -47,8 +47,6 @@
 if config.INSTALLED['ai4neb']:
     from ai4neb import manage_RM
 
-
-
 # Change the profiler to 'cpu', 'mem' or None to profile the execution of Atom.
 profiler = None
 #profiler = 'cpu'
@@ -1685,7 +1683,7 @@ def _getPopulations_ANN(self, tem, den, product=True, NLevels=None):
         Private method to obtain level population using Artificial Neuron Network.
         """
         if not config.INSTALLED['ai4neb']:
-            self.log_.error('_getPopulations_ANN cannot be used in absence of ai4neb package',
+            self.log_.error('_getPopulations_ANN cannot be used if ai4neb is not imported. Try to run pn.config.import_AI4Neb().',
                           calling=self.calling)
             return None
 
@@ -2338,7 +2336,7 @@ def _getTemDen_ANN(self, int_ratio, tem= -1, den= -1, lev_i1= -1, lev_j1= -1, le
                   wave1= -1, wave2= -1, log=True, start_x= -1, end_x= -1, to_eval=None):
 
         if not config.INSTALLED['ai4neb']:
-            self.log_.error('_getTemDen_ANN cannot be used in absence of ai4neb package',
+            self.log_.error('_getTemDen_ANN cannot be used if ai4neb is not imported. Try to run pn.config.import_AI4Neb().',
                           calling=self.calling)
             return None
 

pyneb/utils/Config.py

@@ -100,11 +100,8 @@ def __init__(self):
             self.INSTALLED['cvxopt'] = True
         except:
             self.INSTALLED['cvxopt'] = False   
-        try:
-            from ai4neb import manage_RM
-            self.INSTALLED['ai4neb'] = True
-        except:
-            self.INSTALLED['ai4neb'] = False
+
+        self.INSTALLED['ai4neb'] = False
 
         self.DataFiles = {}
 
@@ -118,6 +115,13 @@ def __init__(self):
         self.vactoair_low_wl = 2000. # UV in vacuum
         self.vactoair_high_wl = 1e30 # no upper limit, IR in air!!!
 
+    def import_AI4Neb(self):
+        try:
+            from ai4neb import manage_RM
+            self.INSTALLED['ai4neb'] = True
+        except:
+            self.INSTALLED['ai4neb'] = False
+
     def set_noExtrapol(self, value):
         self._noExtrapol = bool(value)
 

pyproject.toml

@@ -0,0 +1,48 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyneb"
+version = "1.1.23"
+requires-python = ">= 3.8"
+dependencies = [
+"numpy",
+"matplotlib",
+"scipy",
+"h5py",
+# astropy
+]
+description = "A Python package for nebular analysis"
+authors = [
+    { name = "Christophe Morisset", email = "[email protected]" },
+    { name = "Valentina Luridiana"}
+]
+license = { file = "LICENCE.md" }
+readme = "README.rst"
+keywords = ["nebular", "analysis", "astronomy"]
+
+[project.urls]
+Homepage = "http://www.iac.es/proyecto/PyNeb/"
+Repository = "https://github.com/Morisset/PyNeb_devel"
+Documentation = "http://morisset.github.io/PyNeb_devel/"
+Changelog = "https://github.com/Morisset/PyNeb_devel/tree/master/docs/CHANGES"
+
+[tool.setuptools]
+packages=['pyneb',
+		  'pyneb.core',
+		  'pyneb.plot',
+		  'pyneb.utils',
+		  'pyneb.extinction']
+
+[tool.setuptools.package-data]
+'pyneb'=['atomic_data_fits/*.fits',
+			     'atomic_data_fits/*.hdf5',
+			     'atomic_data_fits/old_fits/*.fits',
+			     'atomic_data/*.dat',
+			     'atomic_data/*.func',
+			     'atomic_data/*.txt',
+			     'atomic_data/levels/*.dat',
+                 'atomic_data/deprecated/*.dat']
+'pyneb.extinction'=['*.txt']
+'pyneb.plot'=['level_diagrams/*.png']

setup.py

@@ -1,41 +1,28 @@
 #!/usr/bin/env python
 
 # Always prefer setuptools over distutils
-from setuptools import setup, find_packages
+from setuptools import setup
 # To use a consistent encoding
-from codecs import open
-from os import path
 
-here = path.abspath(path.dirname(__file__))
-# Get the long description from the README file
-with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
-    long_description = f.read()
+#from pyneb.version import __version__
 
-from pyneb.version import __version__
-
-setup(name='PyNeb', 
-      version=__version__,
-      description='Nebular tools',
-      author='Christophe Morisset, Valentina Luridiana',
-      long_description=long_description,
-      author_email='[email protected]',
-      url='http://www.iac.es/proyecto/PyNeb/',
-      py_modules=['pyneb.test.test_pyneb'],
-      packages=['pyneb',
-		'pyneb.core',
-		'pyneb.plot',
-		'pyneb.utils',
-		'pyneb.extinction'],
-      package_data={'pyneb':['atomic_data_fits/*.fits',
-			     'atomic_data_fits/*.hdf5',
-			     'atomic_data_fits/old_fits/*.fits',
-			     'atomic_data/*.dat',
-			     'atomic_data/*.func',
-			     'atomic_data/*.txt',
-			     'atomic_data/levels/*.dat',
-                 'atomic_data/deprecated/*.dat'],
-                    'pyneb.extinction':['*.txt'],
-                    'pyneb.plot':['level_diagrams/*.png']
-                    }
-     )
+setup()
+#name='PyNeb', 
+#      packages=['pyneb',
+#		'pyneb.core',
+#		'pyneb.plot',
+#		'pyneb.utils',
+#		'pyneb.extinction'],
+#      package_data={'pyneb':['atomic_data_fits/*.fits',
+#			     'atomic_data_fits/*.hdf5',
+#			     'atomic_data_fits/old_fits/*.fits',
+#			     'atomic_data/*.dat',
+#			     'atomic_data/*.func',
+#			     'atomic_data/*.txt',
+#			     'atomic_data/levels/*.dat',
+#                'atomic_data/deprecated/*.dat'],
+#                    'pyneb.extinction':['*.txt'],
+#                    'pyneb.plot':['level_diagrams/*.png']
+#                    }
+#    )
 

updatePyNeb.md

@@ -16,10 +16,10 @@ Pool request to master
 
 Once the devel branch is validated and passed all the tests:
 
-* update the version removing the beta indices
+* update the version in pyproject.toml removing the beta indices
 * Merge it to the master branch
 
-Make a new release tab on the github server
+Make a new release tag on the github server
 ==============================
 
 
@@ -29,9 +29,9 @@ Publish the new version on the pypi server
 * Switch to master branch
 * synchronize with repository: git pull
 * Run the following from the root directory (where dist is) and check the tar file is created in dist:
-    `python setup.py sdist`
+    `python -m build`
 * Run the following to upload the tar file to pypi server. **Update the value of the distribution in {0}:**
-    `twine upload dist/PyNeb-{0}.tar.gz`
+    `twine upload dist/pyneb-{0}*`
 * Check that the new relase is the current one on pypi server: https://pypi.org/project/PyNeb/
 
 Publish the new release on the Google group