[1.0.8] - 2022-10-6

### Added
- forced molecule name in Loader with *molecule* keyword
### Changed
- increased loading performance for Dace data
### Fixed
- ascii conversion for strings in ExoMol data

CHANGELOG.md

@@ -7,6 +7,14 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [1.0.8] - 2022-10-6
+### Added
+- forced molecule name in Loader with *molecule* keyword
+### Changed
+- increased loading performance for Dace data
+### Fixed
+- ascii conversion for strings in ExoMol data
+
 ## [1.0.5] - 2021-05-11
 ### Added
 - support for DACE opacities original data
@@ -24,6 +32,7 @@ First RAPOC release
 
 
 [Unreleased]: https://github.com/ExObsSim/Rapoc
+[1.0.8]: https://github.com/ExObsSim/Rapoc-public/compare/v1.0.5...v1.0.8
 [1.0.5]: https://github.com/ExObsSim/Rapoc-public/compare/v1.0.4...v1.0.5
 [1.0.4]: https://github.com/ExObsSim/Rapoc-public/compare/v1.0.0...v1.0.4
 [1.0.0]: https://github.com/ExObsSim/Rapoc-public/releases/tag/v1.0.0

README.md

@@ -1,4 +1,6 @@
 [![PyPI version](https://badge.fury.io/py/rapoc.svg)](https://badge.fury.io/py/rapoc)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/ExObsSim/Rapoc-public?color=gree&label=GitHub%20release)
+[![Downloads](https://pepy.tech/badge/rapoc)](https://pepy.tech/project/rapoc)
 [![Documentation Status](https://readthedocs.org/projects/rapoc-public/badge/?version=latest)](https://rapoc-public.readthedocs.io/en/latest/?badge=latest)
 ![GitHub](https://img.shields.io/github/license/ExObsSim/Rapoc-public)
 

docs/source/requirements.txt

@@ -143,4 +143,6 @@ webencodings==0.5.1
 Werkzeug==1.0.1
 wrapt==1.12.1
 xlrd==1.2.0
-xlwt==1.3.0
+xlwt==1.3.0
+nbsphinx
+sphinx_rtd_theme

docs/source/user_guide.rst

@@ -67,6 +67,16 @@ After this, two classes can be produced, one for Rosseland and the other for Pla
         ross = Rosseland(input_data=input_file)
         plan = Planck(input_data=input_file)
 
+Identifying the molecule
+++++++++++++++++++++++++++
+Normally, the molecule name is automatically extracted from the input data.
+However, if the molecule name is not present in the input data, it can be manually set using the `molecule` keyword argument:
+
+    .. code-block:: python
+
+        ross = Rosseland(input_data=input_file, molecule='H2O')
+        plan = Planck(input_data=input_file, molecule='H2O')
+
 Calculating the mean opacities
 ------------------------------
 

rapoc/__about__.py

@@ -1,33 +1,48 @@
 import os.path
 
+from datetime import date
+
 __all__ = [
+    '__pkg_name__',
     "__title__",
     "__summary__",
     "__url__",
-    "__commit__",
     "__author__",
     "__email__",
     "__license__",
     "__copyright__",
+    "__branch__",
+    "__commit__",
+    "__base_dir__"
 ]
 
 try:
-    base_dir = os.path.dirname(os.path.abspath(__file__))
+    base_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 except NameError:
     base_dir = None
 
-__title__ = "rapoc"
-__summary__ = "Rosseland And Planck Opacity Converter"
-__url__ = "https://github.com/ExObsSim/Rapoc-public"
-
-if base_dir is not None and os.path.exists(os.path.join(base_dir, ".commit")):
-    with open(os.path.join(base_dir, ".commit")) as fp:
-        __commit__ = fp.read().strip()
+__base_dir__ = base_dir
+__branch__ = None
+if base_dir is not None and os.path.exists(os.path.join(base_dir, ".git")):
+    git_folder = os.path.join(base_dir, ".git")
+    with open(os.path.join(git_folder, "HEAD")) as fp:
+        ref = fp.read().strip()
+    ref_dir = ref[5:]
+    __branch__ = ref[16:]
+    try:
+        with open(os.path.join(git_folder, ref_dir)) as fp:
+            __commit__ = fp.read().strip()
+    except FileNotFoundError:
+        __commit__ = None
 else:
     __commit__ = None
 
+__pkg_name__ = "rapoc"
+__title__ = "RAPOC"
+__summary__ = "Rosseland And Planck Opacity Converter"
+__url__ = "https://github.com/ExObsSim/Rapoc-public"
 __author__ = "Lorenzo V. Mugnai, Darius Modirrousta-Galian"
 __email__ = "lorenzo.mugnai@uniroma1.it"
 
 __license__ = "BSD-3-Clause"
-__copyright__ = "2020 %s" % __author__
+__copyright__ = '2020-{:d}, {}'.format(date.today().year, __author__)

rapoc/__init__.py

@@ -6,7 +6,10 @@
     __license__,
     __summary__,
     __title__,
+    __pkg_name__,
     __url__,
+    __branch__,
+    __base_dir__
 )
 from .__version__ import __version__
 
@@ -18,8 +21,11 @@
     "__license__",
     "__summary__",
     "__title__",
+    "__pkg_name__",
     "__url__",
     "__version__",
+    "__branch__",
+    "__base_dir__"
 ]
 
 from . import models

rapoc/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.5'
+__version__ = '1.0.8'

rapoc/loaders/exoMolFileLoader.py

@@ -32,7 +32,7 @@ def _close(self, opened_file):
         opened_file.close()
 
     def _read_molecule_name(self, opened_file):
-        return opened_file['mol_name'][()][0]
+        return opened_file['mol_name'][()][0].decode('ascii')
 
     def _get_mol_mass(self, mol):
         from molmass import Formula

rapoc/loaders/loader.py

@@ -7,18 +7,21 @@ class FileLoader:
 
     '''
 
-    def __init__(self, filename):
+    def __init__(self, filename, molecule=None):
         '''
         Parameters
         ----------
         filename: str
             data file name
+        molecule: str
+            forced molecule name
         '''
         self.filename = filename
+        self._forced_molname = molecule
 
     def read_content(self):
         '''
-        Reads the file content and returns the needed valued for the opacity models.
+        Reads the file content and returns the needed values for the opacity models.
 
         Returns
         -------
@@ -36,7 +39,10 @@ def read_content(self):
             data opacities grid in si units
         '''
         opened_file = self._open()
-        mol = self._read_molecule_name(opened_file)
+        if self._forced_molname is not None:
+            mol = self._forced_molname
+        else:
+            mol = self._read_molecule_name(opened_file)
         mol_mass = self._get_mol_mass(mol)
         pressure_grid = self._read_pressure_grid(opened_file)
         temperature_grid = self._read_temperature_grid(opened_file)

tests/test_loader.py

@@ -43,6 +43,12 @@ def test_wavenumber_grid(self):
     def test_opacity(self):
         self.assertEqual(self.opacity.unit, u.m ** 2 / u.kg)
 
+class ExoMolLoaderMolNameTest(unittest.TestCase):
+    loaded = ExoMolFileLoader(filename=exomol_file, molecule='H3O')
+    mol, mol_mass, pressure_grid, temperature_grid, wavenumber_grid, opacity, force_t = loaded.read_content()
+
+    def test_mol(self):
+        self.assertEqual(self.mol, 'H3O')
 
 class DaceLoaderTest(unittest.TestCase):
     loaded = DACEFileLoader(filename=dace_file)