pythonradex 1.0.2__tar.gz → 1.0.8__tar.gz

pythonradex-1.0.8/.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,32 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out the repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch hatch-vcs
+
+    - name: Build the package
+      run: hatch build
+
+    - name: Publish to PyPI
+      env:
+        HATCH_INDEX_USER: ${{ secrets.PYPI_USERNAME }}
+        HATCH_INDEX_AUTH: ${{ secrets.PYPI_PASSWORD }}
+      run: hatch publish

pythonradex-1.0.8/.github/workflows/run_tests.yml

@@ -0,0 +1,49 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    #branches is necessary to avoid running this when new tags are pushed 
+    branches:
+      - '**'  # Matches all branches
+    paths:
+      - 'src/**'
+      - 'tests/**'
+  pull_request:
+    paths:
+      - 'src/**'
+      - 'tests/**'
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10","3.11","3.12","3.13"]
+        os: [ubuntu-latest,windows-latest,macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install -e .
+    - name: Lint with flake8
+      shell: bash
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 tests src --count --select=E9,F63,F7,F82 --show-source --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests/

{pythonradex-1.0.2 → pythonradex-1.0.8}/.gitignore

@@ -114,6 +114,7 @@ manual_tests_and_benchmarks/molpop-cep_benchmark/Gianni_models/*.out
 manual_tests_and_benchmarks/molpop-cep_benchmark/molpop
 manual_tests_and_benchmarks/molpop-cep_benchmark/molpop-cep-master
 manual_tests_and_benchmarks/benchmarking_vs_RADEX_and_LIME/*.fits
+manual_tests_and_benchmarks/performance_tests/radex_test_preformance.inp
 manual_tests_and_benchmarks/performance_tests/radex_test_performance.out
 documents
 **/radex.out

{pythonradex-1.0.2 → pythonradex-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonradex
-Version: 1.0.2
+Version: 1.0.8
 Summary: 1D non-LTE radiative transfer
 Project-URL: Documentation, https://pythonradex.readthedocs.io/en/latest/
 Project-URL: Issues, https://github.com/gica3618/pythonradex/issues

pythonradex-1.0.8/docs/citation.rst

@@ -0,0 +1,3 @@
+Citation
+===================
+A paper describing ``pythonradex`` will be published shortly. In the mean time, please just cite the gihub repository (https://github.com/gica3618/pythonradex) in your paper.

{pythonradex-1.0.2 → pythonradex-1.0.8}/docs/index.rst

@@ -8,7 +8,7 @@ Welcome to the ``pyhonradex`` documentation!
 
 ``pythonradex`` solves the radiative transfer for a uniform medium in non-LTE with an escape probability formalism. The code can be used to quickly estimate the emission from an astrophysical gas given input parameters such as the kinetic temperature, the column density and the density of the collision partners.
 
-``pythonradex`` is a python re-implementation of the RADEX code [vanderTak07]_. It is generally faster than RADEX (when calculating a grid of models) and provides additional functionality that is not included in RADEX (treatment of overlapping lines, treatment of internal dust continuum, output of spectra,...).
+``pythonradex`` is a python re-implementation of the RADEX code [vanderTak07]_. Depending on the setup, it can be faster than RADEX when calculating a grid of models. It also provides additional functionality that is not included in RADEX (treatment of overlapping lines, treatment of internal dust continuum, output of spectra,...).
 
 ``pyhonradex`` also provides a convenient method to read files from the LAMDA_ database.
 

pythonradex-1.0.8/docs/installation.rst

@@ -0,0 +1,16 @@
+Installation
+=================
+
+``pythonradex`` requires python version >=3.10. ``pythonradex`` is available on `PyPi <https://pypi.org/project/pythonradex/>`_. It can be installed with the ``pip`` command as follows:
+
+.. code-block:: bash
+
+    pip install pythonradex
+
+``pythonradex`` is also available on `anaconda <https://anaconda.org/conda-forge/pythonradex>`_. Use the following command to install it with conda:
+
+.. code-block:: bash
+
+    conda install conda-forge::pythonradex
+
+If you have any trouble installing, please raise an issue `here <https://github.com/gica3618/pythonradex/issues>`_. The ``pythonradex`` code is publicly available on `github <https://github.com/gica3618/pythonradex>`_.

{pythonradex-1.0.2 → pythonradex-1.0.8}/manual_tests_and_benchmarks/performance_tests/radex_vs_pythonradex_performance.py

@@ -34,13 +34,13 @@ radex_executable = '../../tests/Radex/bin/radex_static_sphere'
 # geometry = 'LVG slab'
 # radex_executable = '../../tests/Radex/bin/radex_LVG_slab'
 
-# data_filename = 'co.dat'
-# colliders = ['para-H2','ortho-H2']
+data_filename = 'co.dat'
+colliders = ['para-H2','ortho-H2']
 # log_N_limits = 13+4,18+4
 # Tmin,Tmax = 20,250
 #narrow range where RADEX does not throw warnings:
-# log_N_limits = 16+4,16.3+4
-# Tmin,Tmax = 50,51
+log_N_limits = 16+4,16.3+4
+Tmin,Tmax = 50,51
 
 # data_filename = 'hco+.dat'
 # colliders = ['H2',]
@@ -52,10 +52,10 @@ radex_executable = '../../tests/Radex/bin/radex_static_sphere'
 # log_N_limits = 10+4,12+4
 # Tmin,Tmax = 60,250
 
-data_filename = 'c.dat'
-colliders = ['para-H2','ortho-H2']
-log_N_limits = 12+4,18+4
-Tmin,Tmax = 60,250
+# data_filename = 'c.dat'
+# colliders = ['para-H2','ortho-H2']
+# log_N_limits = 12+4,18+4
+# Tmin,Tmax = 60,250
 
 
 # #ATTENTION: if no H2 is given, RADEX just puts 1e5 cm-3 by default! WTF!

{pythonradex-1.0.2 → pythonradex-1.0.8}/pyproject.toml

@@ -1,11 +1,9 @@
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling","hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
 name = "pythonradex"
-# be careful, PyPi will return "400 bad request" error if you delete your project on PyPi and then try to publish again with a previously published version!
-version = "1.0.2"
 description = '1D non-LTE radiative transfer'
 readme = "README.txt"
 requires-python = ">=3.10"
@@ -23,6 +21,10 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dependencies = ['scipy>=1.14','numpy>=2.0','numba>=0.61.0']
+dynamic = ["version"]
+
+[tool.hatch.version]
+source = "vcs"
 
 [project.urls]
 Documentation = "https://pythonradex.readthedocs.io/en/latest/"

{pythonradex-1.0.2 → pythonradex-1.0.8}/src/pythonradex/atomic_transition.py

@@ -309,7 +309,7 @@ class EmissionLine(RadiativeTransition):
             
 class CollisionalTransition(Transition):
 
-    '''Represent the collisional transition between two energy levels
+    '''Represents the collisional transition between two energy levels
     
     Attributes:
         up (pythonradex.atomic_transition.Level): the upper level of the transition
@@ -348,4 +348,4 @@ class CollisionalTransition(Transition):
         K21 = np.interp(Tkin,self.Tkin_data,self.K21_data)
         K12 = compute_K12(K21=K21,g_up=self.up.g,g_low=self.low.g,Delta_E=self.Delta_E,
                           Tkin=Tkin)
-        return [K12,K21]
+        return [K12,K21]

pythonradex-1.0.2/docs/citation.rst

@@ -1,3 +0,0 @@
-Citation
-===================
-If you use ``pythonradex`` in your research, please cite XXXXXXXXXXXXXXXXXXXXXXXXXXX

pythonradex-1.0.2/docs/installation.rst

@@ -1,10 +0,0 @@
-Installation
-=================
-
-``pythonradex`` requires python version >=3.10. ``pythonradex`` is available on `PyPi <https://pypi.org/project/pythonradex/>`_. It can be installed with the ``pip`` command as follows:
-
-* ``pip install pythonradex``
-
-If you have any trouble installing, please raise an issue `here <https://github.com/gica3618/pythonradex/issues>`_.
-
-The ``pythonradex`` code is publicly available on `github <https://github.com/gica3618/pythonradex>`_.

pythonradex-1.0.2/manual_tests_and_benchmarks/performance_tests/radex_test_preformance.inp

@@ -1,13 +0,0 @@
-c.dat
-radex_test_performance.out
-0 0
-250.0
-2
-p-H2
-100000.0
-o-H2
-100000.0
-2.73
-1e+18
-1.0
-0