From 59535f859ded445e110c985a3503cb88ff004fad Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 12:38:53 +0200 Subject: [PATCH 01/13] doc package build --- .readthedocs.yaml | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 5f09aba..24a3579 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,19 +5,23 @@ version: 2 # Set the OS, Python version, and other tools you might need +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the version of Python and other tools you might need build: - os: ubuntu-24.04 - tools: - python: "3.12" + os: ubuntu-22.04 + tools: {python: "3.10"} + jobs: + post_install: + - pip install poetry>=1.4.0 + - poetry config virtualenvs.create false + - poetry install --with docs -# Build documentation in the "docs/" directory with Sphinx +# Build documentation in the docs/ directory with Sphinx sphinx: - configuration: docs/conf.py - -# Optionally, but recommended, -# declare the Python requirements required to build your documentation -# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html -# python: -# install: -# - requirements: docs/requirements.txt - + configuration: docs/source/conf.py + fail_on_warning: false \ No newline at end of file From e219ef3116cea8dabe4449b837c7d34a7b85433e Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 13:01:03 +0200 Subject: [PATCH 02/13] switch .rst docs --- README.md | 52 ---------------------------------------------------- 1 file changed, 52 deletions(-) delete mode 100644 README.md diff --git a/README.md b/README.md deleted file mode 100644 index 982367a..0000000 --- a/README.md +++ /dev/null @@ -1,52 +0,0 @@ -# contsub -Image-Plane continuum subtraction for FITS cubes - -## Installation -### PyPI (stable; recommended) -```bash -pip install contsub - -``` -### Latest (in development) -```bash -pip install git+https://github.com/laduma-dev/contsub.git -``` - - - -## Documentation -```bash -Usage: imcontsub [OPTIONS] File - -Options: - --version Show the version and exit. - --order int,int,... Order of spline. If given as a list of size - N, then N iterations will be perfomed. - --segments float,float,... Width of spline segments in km/s. If given - as a list, then it must have same sixe as - --order. - --output-prefix str Name of ouput image - --mask-image File Mask image - --sigma-clip float,float,... Sigma clip for each iteration. Only required - if mask-image is not given. - --fit-model str Fit function to model the continuum. ** Only - the spline is available in this version **. - --cont-fit-tol float Minimum perentage of valid spectrum data - points required to do a fit. Spectra below - this tolerance will be set to NaN. Leaving - this unset may result in poor or NaN spectra - in the output cubes - --overwrite / --no-overwrite Overwrite output image if it already exists - --stokes-index int ### NOT IMPLEMENTED. Stokes index 0 is - assumed ### Index of stokes channel (zero- - based) to use. - --stokes-axis / --no-stokes-axis - ### DEPRECATED #### Set this flag if the - input image has a stokes dimension. (Default - is True). - --ra-chunks int Chunking along RA-axis. If set to zero, no - Chunking is perfomed. - --nworkers int Number of workers (one per CPU) - --help Show this message and exit. - -``` From 1b7b227d42a1b5d84885acc87e9a02c2156e7294 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 13:02:49 +0200 Subject: [PATCH 03/13] add new readme --- README.rst | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 README.rst diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..5e6c483 --- /dev/null +++ b/README.rst @@ -0,0 +1,22 @@ +Contsub +======= + +Image and uv-plane continuum subtraction tools for spectral line data. + +Installation +------------ + +PyPI (stable; recommended) +^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. code-block:: bash + + pip install contsub + +Latest (in development) +^^^^^^^^^^^^^^^^^^^^^^^ + +.. code-block:: bash + + pip install git+https://github.com/laduma-dev/contsub.git + From d676fea5034fda2b40e2930ee0e6d911456ae316 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 13:03:36 +0200 Subject: [PATCH 04/13] add new readme --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4858810..47c91b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ version = "1.0.2" description = "Radio astronomy data continuum subtraction tools" authors = ["Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo"] license = "MIT" -readme = "README.md" +readme = "README.rst" [build-system] requires = ["poetry-core"] From b4ad96ed9e0bec085dd533af56857663d3b72d8e Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 13:15:53 +0200 Subject: [PATCH 05/13] modernise sphinxs deps --- poetry.lock | 218 +++++++++++++++++++++++++++++++++++-------------- pyproject.toml | 9 +- 2 files changed, 160 insertions(+), 67 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5ed6ad5..d681a34 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "alabaster" 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"f46bf4d94de9794df9cf3366ed067b0627c131d2f6be22900df9a44372b4fe5b" diff --git a/pyproject.toml b/pyproject.toml index 47c91b0..1b16afb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,13 +28,14 @@ jupyter = "*" [tool.poetry.group.tests] optional = true [tool.poetry.group.tests.dependencies] -pytest = "^7.1.3" +pytest = "8.4.1" flake8 = "*" [tool.poetry.group.docs] optional = true [tool.poetry.group.docs.dependencies] -Sphinx = "^5.3.0" -sphinx-copybutton = "^0.5.0" -furo = "^2022.9.15" +Sphinx = "^8.1" +sphinx-copybutton = "*" +furo = "*" +sphinx-rtd-theme = "*" From 2e54f03546154ffe4bfbba325ff4c1990f143e97 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 13:32:45 +0200 Subject: [PATCH 06/13] remove placholder module name --- docs/source/conf.py | 40 ++++++++++++++++++++++++++++++++-------- docs/source/index.rst | 2 +- 2 files changed, 33 insertions(+), 9 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 45134ca..ae9cafe 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -6,27 +6,51 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +import contsub +from datetime import date + project = 'contsub' -copyright = '2025, Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo' author = 'Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo' release = '1.0.2' +copyright = f'{date.today().year}, {author}' + +release = contsub.__version__ +version = contsub.__version__ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = [ - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", - "sphinx_rtd_theme", -] templates_path = ['_templates'] exclude_patterns = [] -language = 'Python' +language = 'en' # -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -html_theme = 'alabaster' +html_theme = 'furo' html_static_path = ['_static'] + + +needs_sphinx = "8.1" + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = [ + "sphinx_copybutton", + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.doctest", + "sphinx.ext.intersphinx", + "sphinx.ext.extlinks", +] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = ".rst" + +# The master toctree document. +master_doc = "index" diff --git a/docs/source/index.rst b/docs/source/index.rst index 1f34ed7..d338952 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -12,7 +12,7 @@ Welcome to contsub's documentation! -.. automodule:: your_module +.. automodule:: contsub :members: From 5d43aee4493a9dae28946e8c46c75c3a1a034235 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 14:50:37 +0200 Subject: [PATCH 07/13] untrack poetry lock file --- .readthedocs.yaml | 3 +- poetry.lock | 3624 --------------------------------------------- 2 files changed, 2 insertions(+), 3625 deletions(-) delete mode 100644 poetry.lock diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 24a3579..5eb3ad2 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -18,7 +18,8 @@ build: jobs: post_install: - 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pip install poetry>=1.4.0 - - poetry config virtualenvs.create true - - poetry config virtualenvs.in-project true - - poetry install --with docs + - pip install -e .[docs] # Build documentation in the docs/ directory with Sphinx sphinx: From 29f194fc8149c2b5f820e4193a3d9dd728c9a345 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 15:21:05 +0200 Subject: [PATCH 10/13] reconfigure build and install --- .readthedocs.yaml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ea4e489..93f27ef 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,19 +8,17 @@ version: 2 # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details -# Required -version: 2 - # Set the version of Python and other tools you might need build: os: ubuntu-22.04 - tools: {python: "3.10"} + tools: + python: "3.10" jobs: + post_create_environment: + - pip install poetry>=1.8.3 post_install: - - pip install poetry>=1.4.0 - - pip install -e .[docs] + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs # Build documentation in the docs/ directory with Sphinx sphinx: - configuration: docs/source/conf.py - fail_on_warning: false \ No newline at end of file + configuration: docs/source/conf.py \ No newline at end of file From a80d918d0296daaf1a430f3f7bc665ce5c23f88d Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 18:53:43 +0200 Subject: [PATCH 11/13] add usage docs --- .readthedocs.yaml | 2 +- contsub/parser/imcontsub.yaml | 2 +- docs/source/conf.py | 1 + docs/source/how-to/installation.rst | 16 ++++++++++++++++ docs/source/index.rst | 7 ++++--- docs/source/reference/reference.rst | 12 ++++++++++++ docs/source/tutorials/tutorials.rst | 5 +++++ pyproject.toml | 1 + 8 files changed, 41 insertions(+), 5 deletions(-) create mode 100644 docs/source/how-to/installation.rst create mode 100644 docs/source/reference/reference.rst create mode 100644 docs/source/tutorials/tutorials.rst diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 93f27ef..056fa7f 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -21,4 +21,4 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: - configuration: docs/source/conf.py \ No newline at end of file + configuration: docs/source/conf.py diff --git a/contsub/parser/imcontsub.yaml b/contsub/parser/imcontsub.yaml index 070e59e..d244fa1 100644 --- a/contsub/parser/imcontsub.yaml +++ b/contsub/parser/imcontsub.yaml @@ -25,7 +25,7 @@ inputs: policies: repeat: "[]" fit-model: - info: Fit function to model the continuum. ** Only the spline is available in this version **. + info: "### NOT IMPLEMENTED ### Fit function to model the continuum." dtype: str choices: - spline diff --git a/docs/source/conf.py b/docs/source/conf.py index 42fd54b..6cee449 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -45,6 +45,7 @@ "sphinx.ext.doctest", "sphinx.ext.intersphinx", "sphinx.ext.extlinks", + "sphinx_click.ext", ] # The suffix(es) of source filenames. diff --git a/docs/source/how-to/installation.rst b/docs/source/how-to/installation.rst new file mode 100644 index 0000000..f9bb772 --- /dev/null +++ b/docs/source/how-to/installation.rst @@ -0,0 +1,16 @@ +.. _installation: + + +Installation +============= +The stable version Simms 3.0 is available on `PyPI `_ and can be installed using: + +.. code-block:: bash + + pip install contsub + +The latest (in development) version can be installed directly from GitHub by using: + +.. code-block:: bash + + pip install git+https://github.com/laduma-dev/contsub.git \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst index d338952..07bfa1e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -10,11 +10,12 @@ Welcome to contsub's documentation! :maxdepth: 2 :caption: Contents: + how-to/installation + how-to/usage + tutorials/tutorials + reference/reference -.. automodule:: contsub - :members: - Indices and tables diff --git a/docs/source/reference/reference.rst b/docs/source/reference/reference.rst new file mode 100644 index 0000000..ae301b1 --- /dev/null +++ b/docs/source/reference/reference.rst @@ -0,0 +1,12 @@ +.. _reference: + +Reference +########### + +Array Telescope Simulation (``telsim``) +======================================== + + + +Sky Simulations (``skysim``) +============================= \ No newline at end of file diff --git a/docs/source/tutorials/tutorials.rst b/docs/source/tutorials/tutorials.rst new file mode 100644 index 0000000..7d4c843 --- /dev/null +++ b/docs/source/tutorials/tutorials.rst @@ -0,0 +1,5 @@ +.. highlight: yml +.. _tutorials: + +Tutorials +############################## \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 1b16afb..1cadac4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,3 +39,4 @@ Sphinx = "^8.1" sphinx-copybutton = "*" furo = "*" sphinx-rtd-theme = "*" +sphinx_click = "6.0.0" From 820b17e7f487b655c321722df332b7ac3b9c480c Mon Sep 17 00:00:00 2001 From: sphemakh Date: Sun, 22 Jun 2025 18:53:59 +0200 Subject: [PATCH 12/13] add usage docs --- docs/source/how-to/usage.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 docs/source/how-to/usage.rst diff --git a/docs/source/how-to/usage.rst b/docs/source/how-to/usage.rst new file mode 100644 index 0000000..9a1723d --- /dev/null +++ b/docs/source/how-to/usage.rst @@ -0,0 +1,12 @@ +.. _usage: + +.. role:: raw-math(raw) + :format: latex html + +Command-line Applications +================================= + +.. click:: contsub.parser.imcontsub:runit + :prog: imcontsub + :nested: full + From 92a13d56efd322b9808988e2734a51914324a5f8 Mon Sep 17 00:00:00 2001 From: sphemakh Date: Mon, 23 Jun 2025 20:23:46 +0200 Subject: [PATCH 13/13] add usage docs --- docs/source/how-to/usage.rst | 34 ++++++++++++++++++++++++++--- docs/source/index.rst | 2 +- docs/source/reference/reference.rst | 9 ++++---- 3 files changed, 37 insertions(+), 8 deletions(-) diff --git a/docs/source/how-to/usage.rst b/docs/source/how-to/usage.rst index 9a1723d..c913ada 100644 --- a/docs/source/how-to/usage.rst +++ b/docs/source/how-to/usage.rst @@ -6,7 +6,35 @@ Command-line Applications ================================= -.. click:: contsub.parser.imcontsub:runit - :prog: imcontsub - :nested: full +:command:`imcontsub` +--------------------- +The image-plane application :command:`imcontsub` is used to perform continuum subtraction on spectral line data cubes. It can handle large data cubes efficiently by processing them in chunks. The chunking is done along the RA-axis, i.e, the data cube is split into smaller sub-cubes that are processed in parallel. + + +A key advantage of image-plane continuum subtraction is that it allows for robust on-the-fly thresholding due to the high signal-to-noise ratio compared to the uv-plane. This is particularly useful on for data cubes unknown line emission, which, if not accounted for, can lead to significant errors in the continuum subtraction process. This on-the-fly thresholding can be enabled by setting the ``--sigma-clip`` parameter. + +.. code-block:: bash + + imcontsub --output-prefix output_prefix \ + --sigma-clip 5 \ + --order 3 \ + --segments 250 \ + --ra-chunks 64 \ + --nworkers 8 \ + input_fits_cube.fits + +However, if the line emission is known, a binary mask can be provided to the ``--mask-image`` option. In this case, the ``--sigma-clip`` parameter will be ignored (if set.) + +:command:`imcontsub` also allows the user to specify multiple ``--sigma-clip``, ``--order`` and ``--segments`` parameters. This allows the user to do the continuum subtraction in multiple iterations, each time using a different set of parameters. The advantage of this is that the user can start with a large ``--sigma-clip`` and wide ``--segments`` values to remove the most significant line emission, and then gradually decrease both to remove smaller line emission features. When using this mode, the ``--segments`` and ``--order`` must have the same length. Here's an example + +.. code-block:: bash + + imcontsub --output-prefix output_prefix \ + --sigma-clip 5 5 3 \ + --order 3 2 2 \ + --segments 400 300 250 \ + --ra-chunks 64 \ + --nworkers 8 \ + input_fits_cube.fits + diff --git a/docs/source/index.rst b/docs/source/index.rst index 07bfa1e..752d360 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -12,8 +12,8 @@ Welcome to contsub's documentation! how-to/installation how-to/usage - tutorials/tutorials reference/reference + tutorials/tutorials diff --git a/docs/source/reference/reference.rst b/docs/source/reference/reference.rst index ae301b1..6dcb850 100644 --- a/docs/source/reference/reference.rst +++ b/docs/source/reference/reference.rst @@ -2,11 +2,12 @@ Reference ########### +.. role:: raw-math(raw) + :format: latex html -Array Telescope Simulation (``telsim``) -======================================== +.. click:: contsub.parser.imcontsub:runit + :prog: imcontsub + :nested: full -Sky Simulations (``skysim``) -============================= \ No newline at end of file