From 6ac93abaa6daeb635e861a4da0a44e213e44ffa1 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 10:26:58 +0000 Subject: [PATCH 01/10] #49 Update consts module --- ndradex/consts.py | 10 +++++----- ndradex/grid.py | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ndradex/consts.py b/ndradex/consts.py index e855b24..6ea933f 100644 --- a/ndradex/consts.py +++ b/ndradex/consts.py @@ -5,7 +5,7 @@ "RADEX_VERSION", "LAMDA_ALIASES", "DV", - "ESC", + "GEOM", "N_H2", "N_MOL", "T_BG", @@ -89,8 +89,8 @@ def getval(toml: Path, keys: str, default: T) -> T: DV = getval(NDRADEX_CONFIG, "defaults.dv", 1.0) """Default value for the ``dv`` argument.""" -ESC = getval(NDRADEX_CONFIG, "defaults.esc", "1") -"""Default value for the ``esc`` argument.""" +GEOM = getval(NDRADEX_CONFIG, "defaults.geom", "uni") +"""Default value for the ``geom`` argument.""" N_H2 = getval(NDRADEX_CONFIG, "defaults.n_H2", 1e3) """Default value for the ``n_H2`` argument.""" @@ -107,13 +107,13 @@ def getval(toml: Path, keys: str, default: T) -> T: SQUEEZE = getval(NDRADEX_CONFIG, "defaults.squeeze", True) """Default value for the ``squeeze`` argument.""" -TIMEOUT = getval(NDRADEX_CONFIG, "defaults.timeout", 30) +TIMEOUT = getval(NDRADEX_CONFIG, "defaults.timeout", 30.0) """Default value for the ``timeout`` argument.""" T_BG = getval(NDRADEX_CONFIG, "defaults.T_bg", 2.73) """Default value for the ``T_bg`` argument.""" -T_KIN = getval(NDRADEX_CONFIG, "defaults.T_kin", 100) +T_KIN = getval(NDRADEX_CONFIG, "defaults.T_kin", 100.0) """Default value for the ``T_kin`` argument.""" diff --git a/ndradex/grid.py b/ndradex/grid.py index ae8956f..88c3ee3 100644 --- a/ndradex/grid.py +++ b/ndradex/grid.py @@ -17,7 +17,7 @@ from tqdm import tqdm from .consts import ( DV, - ESC, + GEOM, N_E, N_H, N_H2, @@ -83,7 +83,7 @@ def run( n_Hp=N_HP, T_bg=T_BG, dv=DV, - geom=ESC, + geom=GEOM, *, squeeze=SQUEEZE, progress=PROGRESS, From 884ac852580bd64feaa3566f4bc6a24c85a371be Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 16:49:57 +0000 Subject: [PATCH 02/10] #49 Use CITATION file instead of Zenodo config --- .zenodo.json | 9 --------- CITATION.cff | 15 +++++++++++++++ 2 files changed, 15 insertions(+), 9 deletions(-) delete mode 100644 .zenodo.json create mode 100644 CITATION.cff diff --git a/.zenodo.json b/.zenodo.json deleted file mode 100644 index 71bee5d..0000000 --- a/.zenodo.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "creators": [ - { - "name": "Akio Taniguchi", - "affiliation": "Nagoya University", - "orcid": "0000-0002-9695-6183" - } - ] -} diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..4d95823 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,15 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." + +title: "ndradex" +abstract: "Multidimensional grid RADEX calculator" +version: 0.3.0 +date-released: 2023-05-19 +license: "MIT" +doi: "10.5281/zenodo.3384031" +url: "https://github.com/astropenguin/ndradex" +authors: + - given-names: "Akio" + family-names: "Taniguchi" + affiliation: "Nagoya University" + orcid: "https://orcid.org/0000-0002-9695-6183" From 5145786ed131975c99e89eea58c97e8278aaa341 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 16:50:08 +0000 Subject: [PATCH 03/10] #49 Update year period of license --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index b9fd5b0..5a7bbf7 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2019-2020 Akio Taniguchi +Copyright (c) 2019-2023 Akio Taniguchi Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 6c515150c8e1dcf00b20e2d08c376dcd79466a32 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 16:50:28 +0000 Subject: [PATCH 04/10] #49 Update project description --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0fe55be..5171704 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "ndradex" version = "0.2.2" -description = "Python package for RADEX grid calculation" +description = " Multidimensional grid RADEX calculator" authors = ["Akio Taniguchi "] keywords = ["astronomy", "radio-astronomy", "radex"] license = "MIT" From 737e334a116dae36e8b358f9ffec2fa236aa9f37 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:19:38 +0000 Subject: [PATCH 05/10] #49 Update README --- README.md | 83 +++++++++++++++++++++++++------------------------------ 1 file changed, 37 insertions(+), 46 deletions(-) diff --git a/README.md b/README.md index 4de8022..4130311 100644 --- a/README.md +++ b/README.md @@ -1,31 +1,31 @@ # ndRADEX -[![](https://img.shields.io/pypi/v/ndradex.svg?label=PyPI&style=flat-square)](https://pypi.org/pypi/ndradex/) -[![](https://img.shields.io/pypi/pyversions/ndradex.svg?label=Python&color=yellow&style=flat-square)](https://pypi.org/pypi/ndradex/) -[![Test](https://img.shields.io/github/workflow/status/astropenguin/ndradex/Test?logo=github&label=Test&style=flat-square)](https://github.com/astropenguin/ndradex/actions) -[![License](https://img.shields.io/badge/license-MIT-blue.svg?label=License&style=flat-square)](LICENSE) -[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3384031-blue?style=flat-square)](https://doi.org/10.5281/zenodo.3384031) +[![Release](https://img.shields.io/pypi/v/ndradex?label=Release&color=cornflowerblue&style=flat-square)](https://pypi.org/project/ndradex/) +[![Python](https://img.shields.io/pypi/pyversions/ndradex?label=Python&color=cornflowerblue&style=flat-square)](https://pypi.org/project/ndradex/) +[![Downloads](https://img.shields.io/pypi/dm/ndradex?label=Downloads&color=cornflowerblue&style=flat-square)](https://pepy.tech/project/ndradex) +[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3384031-cornflowerblue?style=flat-square)](https://doi.org/10.5281/zenodo.3384031) +[![Tests](https://img.shields.io/github/actions/workflow/status/astropenguin/ndradex/tests.yml?label=Tests&style=flat-square)](https://github.com/astropenguin/ndradex/actions) -Python package for RADEX grid calculation +Multidimensional grid RADEX calculator -## TL;DR +## Overview -ndRADEX is a Python package which can run [RADEX], non-LTE molecular radiative transfer code, with parameters of multiple values (i.e., RADEX with grid parameters). -The output will be multi-dimensional arrays, which may be useful for parameter search of physical conditions in comparison with observed values. +ndRADEX is a Python package which can run [RADEX], non-LTE molecular radiative transfer code, with multiple grid parameters. +The output will be multidimensional arrays provided by [xarray], which would be useful for parameter search of physical conditions in comparison with observed values. -## Features +### Features - **Grid calculation:** ndRADEX has a simple `run()` function, where all parameters of RADEX can be griddable (i.e., they can be list-like with length of more than one). -- **Builtin RADEX:** ndRADEX provides builtin RADEX binaries in the package, which are automatically downloaded and built during the package installation. This also enables us to do RADEX calculations in the cloud such as [Google Colaboratory](https://colab.research.google.com). +- **Builtin RADEX:** ndRADEX provides builtin RADEX binaries in the package, which are automatically downloaded and built on the first import. This also enables us to do RADEX calculations in the cloud such as [Google Colaboratory](https://colab.research.google.com). - **Multiprocessing:** ndRADEX supports multiprocessing RADEX run by default. At least twice speedup is expected compared to single processing. -- **Handy I/O:** The output of ndRADEX is a [xarray]'s Dataset, a standard multi-dimensional data structure as well as [pandas]. You can handle it in the same manner as NumPy and pandas (i.e., element-wise operation, save/load data, plotting, etc). +- **Handy I/O:** The output of ndRADEX is a [xarray]'s Dataset, a standard multidimensional data structure as well as [pandas]. You can handle it in the same manner as NumPy and pandas (i.e., element-wise operation, save/load data, plotting, etc). -## Requirements +### Requirements -- Python 3.6, 3.7, or 3.8 (tested by the author) +- Python 3.8-3.11 (tested by the author) - gfortran (necessary to build RADEX) -## Installation +### Installation You can install ndRADEX with pip: @@ -33,8 +33,6 @@ You can install ndRADEX with pip: $ pip install ndradex ``` -Please make sure that all requirements are met before the installation. - ## Usages Within Python, import the package like: @@ -43,22 +41,22 @@ Within Python, import the package like: >>> import ndradex ``` -### Single RADEX run +### Single RADEX calculation -The main funtion of ndRADEX is `ndradex.run()`. -For example, to get RADEX results of CO(1-0) with kinetic temperature of 100 K, CO column density of 1e15 cm^-2, and H2 density of 1e3 cm^-3: +The main function of ndRADEX is `ndradex.run()`. +For example, to get RADEX results of CO(1-0) with kinetic temperature of 100.0 K, CO column density of 1e15 cm^-2, and H2 density of 1e3 cm^-3: ```python ->>> ds = ndradex.run('co.dat', '1-0', 100, 1e15, 1e3) +>>> ds = ndradex.run("co.dat", "1-0", 100.0, 1e15, 1e3) ``` -where `'co.dat'` is a name of [LAMDA] datafile and `'1-0'` is a name of transition. +where `"co.dat"` is a name of [LAMDA] datafile and `"1-0"` is a name of transition. The available values are listed in [List of available LAMDA datafiles and transitions](https://github.com/astropenguin/ndradex/wiki/List-of-available-LAMDA-datafiles-and-transitions). -Note that you don't need to any download datafiles: +Note that you do not need to any download datafiles: ndRADEX automatically manage this. In this case, other parameters like line width, background temperature are default values defined in the function. -The geometry of escape probability is uniform (`'uni'`) by default. +The geometry of escape probability is uniform (`"uni"`) by default. You can change these values with custom config (see customizations below). The output is a [xarray]'s Dataset with no dimension: @@ -92,15 +90,15 @@ Data variables: You can access each result value like: ```python ->>> flux = ds['F'].values +>>> flux = ds["F"].values ``` -### Grid RADEX run +### Grid RADEX calculation As a natural extension, you can run grid RADEX calculation like: ```python ->>> ds = ndradex.run('co.dat', ['1-0', '2-1'], T_kin=[100, 200, 300], +>>> ds = ndradex.run("co.dat", ["1-0", "2-1"], T_kin=[100.0, 200.0, 300.0], N_mol=1e15, n_H2=[1e3, 1e4, 1e5, 1e6, 1e7]) ``` @@ -137,23 +135,23 @@ Data variables: For more information, run `help(ndradex.run)` to see the docstrings. -### Save/load results +### Save and load results You can save and load the dataset like: ```python # save results to a netCDF file ->>> ndradex.save_dataset(ds, 'results.nc') +>>> ndradex.save_dataset(ds, "results.nc") # load results from a netCDF file ->>> ds = ndradex.load_dataset('results.nc') +>>> ds = ndradex.load_dataset("results.nc") ``` -## Customizations +## Customization For the first time you import ndRADEX, the custom configuration file is created as `~/.config/ndradex/config.toml`. By editing this, you can customize the following two settings of ndRADEX. -Note that you can change the path of configuration file by setting an environment variable, `NDRADEX_PATH`. +Note that you can change the path of configuration directory by setting an environment variable, `NDRADEX_DIR`. ### Changing default values @@ -162,11 +160,11 @@ As mentioned above, you can change the default values of the `run()` function li ```toml # config.toml -[grid] -T_bg = 10 # change default background temp to 10 K -geom = "lvg" # change default geometry to LVG -timeout = 30 -n_procs = 2 +[defaults] +T_bg = 10.0 # change default background temp to 10.0 K +geom = "lvg" # change default geometry to LVG +timeout = 60.0 +n_procs = 8 ``` You can also change the number of multiprocesses (`n_procs`) and timeout (`timeout`) here. @@ -179,7 +177,7 @@ For convenience, you can define aliases of datafile names like: ```toml # config.toml -[lamda] +[lamda.aliaes] CS = "cs@lique.dat" CO = "~/your/local/co.dat" H13CN = "https://home.strw.leidenuniv.nl/~moldata/datafiles/h13cn@xpol.dat" @@ -189,16 +187,9 @@ As shown in the second and third examples, you can also specify a local file pat After the customization, you can use these aliases in the `run()` function: ```python ->>> ds = ndradex.run('CS', '1-0', ...) # equiv to cs@lique.dat +>>> ds = ndradex.run("CS", "1-0", ...) # equiv to cs@lique.dat ``` -## References - -- [RADEX] -- [LAMDA] -- [xarray] -- [pandas] - [xarray]: http://xarray.pydata.org/en/stable/ [RADEX]: https://home.strw.leidenuniv.nl/~moldata/radex.html [LAMDA]: https://home.strw.leidenuniv.nl/~moldata/ From ac21697823c8551f7975cb90b6fc9e05d0d870cf Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:19:58 +0000 Subject: [PATCH 06/10] #49 Update workflows --- .github/workflows/{pypi.yml => pypi.yaml} | 0 .github/workflows/{test.yml => tests.yaml} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{pypi.yml => pypi.yaml} (100%) rename .github/workflows/{test.yml => tests.yaml} (100%) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yaml similarity index 100% rename from .github/workflows/pypi.yml rename to .github/workflows/pypi.yaml diff --git a/.github/workflows/test.yml b/.github/workflows/tests.yaml similarity index 100% rename from .github/workflows/test.yml rename to .github/workflows/tests.yaml From e50acd1c786deba60b6d2cc3ed45526afd5eb27e Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:20:45 +0000 Subject: [PATCH 07/10] =?UTF-8?q?#49=20Update=20package=20version=20(0.2.2?= =?UTF-8?q?=20=E2=86=92=200.3.0)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ndradex/__init__.py | 2 +- pyproject.toml | 2 +- tests/test_metadata.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ndradex/__init__.py b/ndradex/__init__.py index b2cc9ce..aac3d7b 100644 --- a/ndradex/__init__.py +++ b/ndradex/__init__.py @@ -9,7 +9,7 @@ "save_dataset", "load_dataset", ] -__version__ = "0.2.2" +__version__ = "0.3.0" __author__ = "Akio Taniguchi" diff --git a/pyproject.toml b/pyproject.toml index 5171704..e458bc6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ndradex" -version = "0.2.2" +version = "0.3.0" description = " Multidimensional grid RADEX calculator" authors = ["Akio Taniguchi "] keywords = ["astronomy", "radio-astronomy", "radex"] diff --git a/tests/test_metadata.py b/tests/test_metadata.py index de29810..b59be7b 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -5,7 +5,7 @@ # test functions def test_version(): """Make sure the version is valid.""" - assert ndradex.__version__ == "0.2.2" + assert ndradex.__version__ == "0.3.0" def test_author(): From abf27dc42a82f1233997e2cf84d4adcb0a50bd62 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:28:29 +0000 Subject: [PATCH 08/10] #49 Add docs --- .github/workflows/tests.yaml | 2 + .gitignore | 1 + docs/build | 7 + docs/conf.py | 25 +++ docs/index.md | 11 + poetry.lock | 400 ++++++++++++++++++++++++++++++++++- pyproject.toml | 4 + 7 files changed, 449 insertions(+), 1 deletion(-) create mode 100755 docs/build create mode 100644 docs/conf.py create mode 100644 docs/index.md diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index a909ce5..4f7efdf 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -34,3 +34,5 @@ jobs: run: black --check ndradex tests - name: Test code's execution (pytest) run: pytest -v tests + - name: Test docs' building (Sphinx) + run: docs/build diff --git a/.gitignore b/.gitignore index ad4a1f1..728bca0 100644 --- a/.gitignore +++ b/.gitignore @@ -73,6 +73,7 @@ instance/ .scrapy # Sphinx documentation +docs/_apidoc/ docs/_build/ # PyBuilder diff --git a/docs/build b/docs/build new file mode 100755 index 0000000..5e251e4 --- /dev/null +++ b/docs/build @@ -0,0 +1,7 @@ +#!/bin/bash -eu + +# auto-generate package guide +sphinx-apidoc -efT -o docs/_apidoc ndradex + +# build website +sphinx-build -a docs docs/_build diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..eb67d36 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,25 @@ +# Project information +author = "Akio Taniguchi" +copyright = "2019-2023 Akio Taniguchi" + + +# General configuration +extensions = [ + "myst_parser", + "sphinx.ext.autodoc", + "sphinx.ext.viewcode", + "sphinx.ext.napoleon", + "sphinx.ext.autosummary", +] +templates_path = ["_templates"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + +# Options for HTML output +html_static_path = ["_static"] +html_theme = "pydata_sphinx_theme" +html_theme_options = { + "logo": {"text": "ndRADEX"}, + "github_url": "https://github.com/astropenguin/ndradex/", + "twitter_url": "https://twitter.com/astropengu_in/", +} diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..8559832 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,11 @@ +```{include} ../README.md +``` + +```{toctree} +--- +hidden: +--- + +Home +Package guide <_apidoc/ndradex> +``` diff --git a/poetry.lock b/poetry.lock index 34fd9d4..6492bd2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,32 @@ # 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[tool.poetry.dev-dependencies] black = "^23.3" ipython = "^8.12" +myst-parser = "^1.0" +pydata-sphinx-theme = "^0.13" pytest = "^7.3" +sphinx = "^6.2" [tool.pyright] typeCheckingMode = "basic" From 6f66c689db9ab58a306ffeb537869df8e7e64de8 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:30:24 +0000 Subject: [PATCH 09/10] #49 Update URL of tests budge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4130311..21cf0f7 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ [![Python](https://img.shields.io/pypi/pyversions/ndradex?label=Python&color=cornflowerblue&style=flat-square)](https://pypi.org/project/ndradex/) [![Downloads](https://img.shields.io/pypi/dm/ndradex?label=Downloads&color=cornflowerblue&style=flat-square)](https://pepy.tech/project/ndradex) [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.3384031-cornflowerblue?style=flat-square)](https://doi.org/10.5281/zenodo.3384031) -[![Tests](https://img.shields.io/github/actions/workflow/status/astropenguin/ndradex/tests.yml?label=Tests&style=flat-square)](https://github.com/astropenguin/ndradex/actions) +[![Tests](https://img.shields.io/github/actions/workflow/status/astropenguin/ndradex/tests.yaml?label=Tests&style=flat-square)](https://github.com/astropenguin/ndradex/actions) Multidimensional grid RADEX calculator From 78019d35aad40ec81e493c5c40569c734af192e2 Mon Sep 17 00:00:00 2001 From: Akio Taniguchi Date: Thu, 18 May 2023 17:33:42 +0000 Subject: [PATCH 10/10] #49 Update project keywords --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ba39e09..c895369 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "ndradex" version = "0.3.0" description = " Multidimensional grid RADEX calculator" authors = ["Akio Taniguchi "] -keywords = ["astronomy", "radio-astronomy", "radex"] +keywords = ["astronomy", "radio-astronomy", "radex", "xarray"] license = "MIT" homepage = "https://github.com/astropenguin/ndradex/" documentation = "https://astropenguin.github.io/ndradex/"