pythonradex 1.0.0__tar.gz → 1.0.1__tar.gz

{pythonradex-1.0.0 → pythonradex-1.0.1}/.gitignore

@@ -114,12 +114,8 @@ manual_tests_and_benchmarks/lime/template_model.c
 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
-TODO.txt
-documents
 manual_tests_and_benchmarks/benchmarking_vs_RADEX_and_LIME/*.fits
+manual_tests_and_benchmarks/performance_tests/radex_test_performance.out
+documents
 **/radex.out
 .pytest_cache
-manual_tests_and_benchmarks/performance_tests/radex_test_performance.out
-virtenv_cheatsheet.txt
-pytest_cheatsheet.txt
-testPyPi_instructions.txt

{pythonradex-1.0.0 → pythonradex-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonradex
-Version: 1.0.0
+Version: 1.0.1
 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-1.0.0 → pythonradex-1.0.1}/docs/installation.rst

@@ -1,11 +1,9 @@
 Installation
 =================
 
-``pythonradex`` is compatible with python versions 3.10 to 3.13. ``pythonradex`` can be installed with Pip or Conda:
+``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 XXXXXX
-
-* conda XXXX
+* ``pip install pythonradex``
 
 If you have any trouble installing, please raise an issue `here <https://github.com/gica3618/pythonradex/issues>`_.
 

{pythonradex-1.0.0 → pythonradex-1.0.1}/pyproject.toml

@@ -5,7 +5,7 @@ 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 = "1.0.0"
+version = "1.0.1"
 description = '1D non-LTE radiative transfer'
 readme = "README.txt"
 requires-python = ">=3.10"

{pythonradex-1.0.0 → pythonradex-1.0.1}/tests/test_vs_RADEX.py

@@ -92,8 +92,9 @@ def read_RADEX_output(filepath,molecule):
             'collider_densities':collider_densities,'flux':np.array(flux),
             'tau':np.array(tau),'Tex':np.array(Tex),'level_pop':np.array(level_pop)}
 
-LAMDA_folder = '/home/gianni/science/projects/code/pythonradex/tests/LAMDA_files'
-RADEX_output_folder = '/home/gianni/science/projects/code/pythonradex/tests/RADEX_test_cases'
+here = os.path.dirname(os.path.abspath(__file__))
+LAMDA_folder = os.path.join(here,'LAMDA_files')
+RADEX_output_folder = os.path.join(here,'RADEX_test_cases')
 
 @pytest.mark.filterwarnings("ignore:some lines are overlapping")
 @pytest.mark.filterwarnings("ignore:negative optical depth")

pythonradex-1.0.0/PyPi_publication_cheatsheet.txt

@@ -1,2 +0,0 @@
-see https://www.pyopensci.org/python-package-guide/tutorials/publish-pypi.html
-

pythonradex-1.0.0/virt_env3.10/bin/activate

@@ -1,83 +0,0 @@
-# This file must be used with "source bin/activate" *from bash*
-# you cannot run it directly
-
-
-if [ "${BASH_SOURCE-}" = "$0" ]; then
-    echo "You must source this script: \$ source $0" >&2
-    exit 33
-fi
-
-deactivate () {
-    unset -f pydoc >/dev/null 2>&1 || true
-
-    # reset old environment variables
-    # ! [ -z ${VAR+_} ] returns true if VAR is declared at all
-    if ! [ -z "${_OLD_VIRTUAL_PATH:+_}" ] ; then
-        PATH="$_OLD_VIRTUAL_PATH"
-        export PATH
-        unset _OLD_VIRTUAL_PATH
-    fi
-    if ! [ -z "${_OLD_VIRTUAL_PYTHONHOME+_}" ] ; then
-        PYTHONHOME="$_OLD_VIRTUAL_PYTHONHOME"
-        export PYTHONHOME
-        unset _OLD_VIRTUAL_PYTHONHOME
-    fi
-
-    # The hash command must be called to get it to forget past
-    # commands. Without forgetting past commands the $PATH changes
-    # we made may not be respected
-    hash -r 2>/dev/null
-
-    if ! [ -z "${_OLD_VIRTUAL_PS1+_}" ] ; then
-        PS1="$_OLD_VIRTUAL_PS1"
-        export PS1
-        unset _OLD_VIRTUAL_PS1
-    fi
-
-    unset VIRTUAL_ENV
-    if [ ! "${1-}" = "nondestructive" ] ; then
-    # Self destruct!
-        unset -f deactivate
-    fi
-}
-
-# unset irrelevant variables
-deactivate nondestructive
-
-VIRTUAL_ENV='/home/gianni/science/projects/code/pythonradex/virt_env3.10'
-if ([ "$OSTYPE" = "cygwin" ] || [ "$OSTYPE" = "msys" ]) && $(command -v cygpath &> /dev/null) ; then
-    VIRTUAL_ENV=$(cygpath -u "$VIRTUAL_ENV")
-fi
-export VIRTUAL_ENV
-
-_OLD_VIRTUAL_PATH="$PATH"
-PATH="$VIRTUAL_ENV/bin:$PATH"
-export PATH
-
-# unset PYTHONHOME if set
-if ! [ -z "${PYTHONHOME+_}" ] ; then
-    _OLD_VIRTUAL_PYTHONHOME="$PYTHONHOME"
-    unset PYTHONHOME
-fi
-
-if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
-    _OLD_VIRTUAL_PS1="${PS1-}"
-    if [ "x" != x ] ; then
-        PS1="() ${PS1-}"
-    else
-        PS1="(`basename \"$VIRTUAL_ENV\"`) ${PS1-}"
-    fi
-    export PS1
-fi
-
-# Make sure to unalias pydoc if it's already there
-alias pydoc 2>/dev/null >/dev/null && unalias pydoc || true
-
-pydoc () {
-    python -m pydoc "$@"
-}
-
-# The hash command must be called to get it to forget past
-# commands. Without forgetting past commands the $PATH changes
-# we made may not be respected
-hash -r 2>/dev/null

pythonradex-1.0.0/virt_env3.10/bin/activate.csh

@@ -1,55 +0,0 @@
-# This file must be used with "source bin/activate.csh" *from csh*.
-# You cannot run it directly.
-# Created by Davide Di Blasi <davidedb@gmail.com>.
-
-set newline='\
-'
-
-alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH:q" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT:q" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate && unalias pydoc'
-
-# Unset irrelevant variables.
-deactivate nondestructive
-
-setenv VIRTUAL_ENV '/home/gianni/science/projects/code/pythonradex/virt_env3.10'
-
-set _OLD_VIRTUAL_PATH="$PATH:q"
-setenv PATH "$VIRTUAL_ENV:q/bin:$PATH:q"
-
-
-
-if ('' != "") then
-    set env_name = '() '
-else
-    set env_name = '('"$VIRTUAL_ENV:t:q"') '
-endif
-
-if ( $?VIRTUAL_ENV_DISABLE_PROMPT ) then
-    if ( $VIRTUAL_ENV_DISABLE_PROMPT == "" ) then
-        set do_prompt = "1"
-    else
-        set do_prompt = "0"
-    endif
-else
-    set do_prompt = "1"
-endif
-
-if ( $do_prompt == "1" ) then
-    # Could be in a non-interactive environment,
-    # in which case, $prompt is undefined and we wouldn't
-    # care about the prompt anyway.
-    if ( $?prompt ) then
-        set _OLD_VIRTUAL_PROMPT="$prompt:q"
-        if ( "$prompt:q" =~ *"$newline:q"* ) then
-            :
-        else
-            set prompt = "$env_name:q$prompt:q"
-        endif
-    endif
-endif
-
-unset env_name
-unset do_prompt
-
-alias pydoc python -m pydoc
-
-rehash

pythonradex-1.0.0/virt_env3.10/bin/activate.fish

@@ -1,100 +0,0 @@
-# This file must be used using `source bin/activate.fish` *within a running fish ( http://fishshell.com ) session*.
-# Do not run it directly.
-
-function _bashify_path -d "Converts a fish path to something bash can recognize"
-    set fishy_path $argv
-    set bashy_path $fishy_path[1]
-    for path_part in $fishy_path[2..-1]
-        set bashy_path "$bashy_path:$path_part"
-    end
-    echo $bashy_path
-end
-
-function _fishify_path -d "Converts a bash path to something fish can recognize"
-    echo $argv | tr ':' '\n'
-end
-
-function deactivate -d 'Exit virtualenv mode and return to the normal environment.'
-    # reset old environment variables
-    if test -n "$_OLD_VIRTUAL_PATH"
-        # https://github.com/fish-shell/fish-shell/issues/436 altered PATH handling
-        if test (echo $FISH_VERSION | head -c 1) -lt 3
-            set -gx PATH (_fishify_path "$_OLD_VIRTUAL_PATH")
-        else
-            set -gx PATH $_OLD_VIRTUAL_PATH
-        end
-        set -e _OLD_VIRTUAL_PATH
-    end
-
-    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
-        set -gx PYTHONHOME "$_OLD_VIRTUAL_PYTHONHOME"
-        set -e _OLD_VIRTUAL_PYTHONHOME
-    end
-
-    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
-       and functions -q _old_fish_prompt
-        # Set an empty local `$fish_function_path` to allow the removal of `fish_prompt` using `functions -e`.
-        set -l fish_function_path
-
-        # Erase virtualenv's `fish_prompt` and restore the original.
-        functions -e fish_prompt
-        functions -c _old_fish_prompt fish_prompt
-        functions -e _old_fish_prompt
-        set -e _OLD_FISH_PROMPT_OVERRIDE
-    end
-
-    set -e VIRTUAL_ENV
-
-    if test "$argv[1]" != 'nondestructive'
-        # Self-destruct!
-        functions -e pydoc
-        functions -e deactivate
-        functions -e _bashify_path
-        functions -e _fishify_path
-    end
-end
-
-# Unset irrelevant variables.
-deactivate nondestructive
-
-set -gx VIRTUAL_ENV '/home/gianni/science/projects/code/pythonradex/virt_env3.10'
-
-# https://github.com/fish-shell/fish-shell/issues/436 altered PATH handling
-if test (echo $FISH_VERSION | head -c 1) -lt 3
-   set -gx _OLD_VIRTUAL_PATH (_bashify_path $PATH)
-else
-    set -gx _OLD_VIRTUAL_PATH $PATH
-end
-set -gx PATH "$VIRTUAL_ENV"'/bin' $PATH
-
-# Unset `$PYTHONHOME` if set.
-if set -q PYTHONHOME
-    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
-    set -e PYTHONHOME
-end
-
-function pydoc
-    python -m pydoc $argv
-end
-
-if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
-    # Copy the current `fish_prompt` function as `_old_fish_prompt`.
-    functions -c fish_prompt _old_fish_prompt
-
-    function fish_prompt
-        # Run the user's prompt first; it might depend on (pipe)status.
-        set -l prompt (_old_fish_prompt)
-
-        # Prompt override provided?
-        # If not, just prepend the environment name.
-        if test -n ''
-            printf '(%s) ' ''
-        else
-            printf '(%s) ' (basename "$VIRTUAL_ENV")
-        end
-
-        string join -- \n $prompt # handle multi-line prompts
-    end
-
-    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
-end

pythonradex-1.0.0/virt_env3.10/bin/activate.nu

@@ -1,41 +0,0 @@
-# Setting all environment variables for the venv
-let path-name = (if ((sys).host.name == "Windows") { "Path" } { "PATH" })
-let virtual-env = "/home/gianni/science/projects/code/pythonradex/virt_env3.10"
-let bin = "bin"
-let path-sep = ":"
-
-let old-path = ($nu.path | str collect ($path-sep))
-
-let venv-path = ([$virtual-env $bin] | path join)
-let new-path = ($nu.path | prepend $venv-path | str collect ($path-sep))
-
-# environment variables that will be batched loaded to the virtual env
-let new-env = ([
-    [name, value];
-    [$path-name $new-path]
-    [_OLD_VIRTUAL_PATH $old-path]
-    [VIRTUAL_ENV $virtual-env]
-])
-
-load-env $new-env
-
-# Creating the new prompt for the session
-let virtual_prompt = (if ("" != "") {
-    "() "
-} {
-    (build-string '(' ($virtual-env | path basename) ') ')
-}
-)
-
-# If there is no default prompt, then only the env is printed in the prompt
-let new_prompt = (if ( config | select prompt | empty? ) {
-    ($"build-string '($virtual_prompt)'")
-} {
-    ($"build-string '($virtual_prompt)' (config get prompt | str find-replace "build-string" "")")
-})
-let-env PROMPT_COMMAND = $new_prompt
-
-# We are using alias as the function definitions because only aliases can be
-# removed from the scope
-alias pydoc = python -m pydoc
-alias deactivate = source "/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/deactivate.nu"

pythonradex-1.0.0/virt_env3.10/bin/f2py

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from numpy.f2py.f2py2e import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/numba

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: UTF-8 -*-
-from __future__ import print_function, division, absolute_import
-
-from numba.misc.numba_entry import main
-
-if __name__ == "__main__":
-    main()

pythonradex-1.0.0/virt_env3.10/bin/numpy-config

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from numpy._configtool import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/pip

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pip._internal.cli.main import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/pip-3.10

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pip._internal.cli.main import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/pip3

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pip._internal.cli.main import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/pip3.10

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pip._internal.cli.main import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/py.test

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pytest import console_main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(console_main())

pythonradex-1.0.0/virt_env3.10/bin/pytest

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from pytest import console_main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(console_main())

pythonradex-1.0.0/virt_env3.10/bin/wheel

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from wheel.cli import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/wheel-3.10

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from wheel.cli import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/wheel3

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from wheel.cli import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.10/bin/wheel3.10

@@ -1,8 +0,0 @@
-#!/home/gianni/science/projects/code/pythonradex/virt_env3.10/bin/python
-# -*- coding: utf-8 -*-
-import re
-import sys
-from wheel.cli import main
-if __name__ == '__main__':
-    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
-    sys.exit(main())

pythonradex-1.0.0/virt_env3.12/.gitignore

@@ -1,2 +0,0 @@
-# created by virtualenv automatically
-*