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Sphinx documentation #94

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Sphinx documentation #94

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da6b419
Initial skeleton for Sphinx docs
Nov 6, 2024
251394f
Changed file structure
Nov 6, 2024
1133d67
Remove docs/_build from .gitignore
FedericoBerlfein Nov 6, 2024
6454870
Fix missing _build directory
Nov 6, 2024
7e9b74b
Updated structure
Nov 8, 2024
f0621d7
Fixed broken links, updated theme
Nov 14, 2024
d1509d4
Made parameters in docstring consistent
Nov 14, 2024
6578ca4
Small changes to headings for euclidlike_imsim
Nov 14, 2024
c64a29c
Small change to main README
Nov 14, 2024
b87de69
Small changes to versioning, install instructions, API name
Nov 27, 2024
eb0ca64
Fix bug with reading version
Nov 27, 2024
cde4f87
Missing os import
Nov 27, 2024
6c7d4f1
Fix broken link, broken bold font
Dec 4, 2024
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2 changes: 1 addition & 1 deletion .gitignore
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Expand Up @@ -69,7 +69,7 @@ instance/
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# Sphinx documentation
docs/_build/
#docs/_build/

# PyBuilder
.pybuilder/
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Changes from v0.0.0 to v0.0.1
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Not a comment to you specifically.
We should discuss this at some point. But I think it would be more appropriate to use v0.1.0 or even v1.0.0.
We should chat about that as a group.

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Change 0.9.0

=========================
Made repo public.
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Config imsim
============

``was.yaml``: *euclidlike_imsim example* config file.
You will want to update the following entries:

- ``input.obseq_data.file_name``: path to the observing sequence. Link to ``euclidlike/data/euclid_obseq.fits``
- ``input.sky_catalog.file_name``: path to the skyCatalog to use
- ``output.dir``: path to the output directory for the simulated images
- ``output.truth.dir``: path to the output directory for the true catalogs

To run the code:

.. code-block:: bash

galsim was.yaml

You might want to specify some config entries on the command line, like:

.. code-block:: bash

galsim was.yaml input.obseq_data.visit=33690 image.CCD=1


Config SLURM
============

``slurm_runner.sh`` contains the SLURM configuration to run "large scale" simulations.
You will want to update the following lines:

- ``#!/bin/zsh``: depending on the shell you are using, you might want to change it to: ``#!/bin/bash``
- ``#SBATCH --output=/path/to/slurm-%A-%a.out``: SLURM stdout file
- ``#SBATCH --error=/path/to/slurm-%A-%a.err``: SLURM stderr file
- ``source activate [env_name]``: conda environment to use
- ``file_list='/path/to/run_list.txt'``: file containing the pointings to simulate (see note below)

The ``run_list.txt`` is a 2-column file with the pointing and the ``CCD_ID`` to simulate. It should look like:

.. code-block:: text

33688 0
33688 1
33688 2
[...]
33688 35
33689 0
33689 1
[...]

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# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build

# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

.PHONY: help Makefile

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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# Sphinx build info version 1
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 11d168bc3ba21763cf541d100b9a19c3
tags: 645f666f9bcd5a90fca523b33c5a78b7
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<!DOCTYPE html>

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<h1>Source code for euclidlike_imsim.bandpass</h1><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">euclidlike</span>
<span class="kn">from</span> <span class="nn">galsim.config</span> <span class="kn">import</span> <span class="n">BandpassBuilder</span><span class="p">,</span> <span class="n">RegisterBandpassType</span><span class="p">,</span> <span class="n">GetAllParams</span>


<div class="viewcode-block" id="EuclidlikeBandpassBuilder">
<a class="viewcode-back" href="../../euclidlike_imsim.html#euclidlike_imsim.bandpass.EuclidlikeBandpassBuilder">[docs]</a>
<span class="k">class</span> <span class="nc">EuclidlikeBandpassBuilder</span><span class="p">(</span><span class="n">BandpassBuilder</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;A class for loading a Bandpass from a file</span>

<span class="sd"> FileBandpass expected the following parameter:</span>

<span class="sd"> name (str) The name of the Euclid filter to get. (required)</span>
<span class="sd"> &quot;&quot;&quot;</span>
<div class="viewcode-block" id="EuclidlikeBandpassBuilder.buildBandpass">
<a class="viewcode-back" href="../../euclidlike_imsim.html#euclidlike_imsim.bandpass.EuclidlikeBandpassBuilder.buildBandpass">[docs]</a>
<span class="k">def</span> <span class="nf">buildBandpass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">config</span><span class="p">,</span> <span class="n">base</span><span class="p">,</span> <span class="n">logger</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Build the Bandpass based on the specifications in the config dict.</span>

<span class="sd"> Parameters:</span>
<span class="sd"> config: The configuration dict for the bandpass type.</span>
<span class="sd"> base: The base configuration dict.</span>
<span class="sd"> logger: If provided, a logger for logging debug statements.</span>

<span class="sd"> Returns:</span>
<span class="sd"> the constructed Bandpass object.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">req</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">}</span>
<span class="n">kwargs</span><span class="p">,</span> <span class="n">safe</span> <span class="o">=</span> <span class="n">GetAllParams</span><span class="p">(</span><span class="n">config</span><span class="p">,</span> <span class="n">base</span><span class="p">,</span> <span class="n">req</span><span class="o">=</span><span class="n">req</span><span class="p">)</span>

<span class="n">name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
<span class="c1"># Hard set the limit due to PSF definition</span>
<span class="n">bandpass</span> <span class="o">=</span> <span class="n">euclidlike</span><span class="o">.</span><span class="n">getBandpasses</span><span class="p">()[</span><span class="n">name</span><span class="p">]</span>

<span class="k">return</span> <span class="n">bandpass</span><span class="p">,</span> <span class="n">safe</span></div>
</div>



<span class="n">RegisterBandpassType</span><span class="p">(</span><span class="s1">&#39;EuclidlikeBandpass&#39;</span><span class="p">,</span> <span class="n">EuclidlikeBandpassBuilder</span><span class="p">())</span>
<span class="n">RegisterBandpassType</span><span class="p">(</span><span class="s1">&#39;EuclidlikeBandpassTrimmed&#39;</span><span class="p">,</span> <span class="n">EuclidlikeBandpassBuilder</span><span class="p">())</span>
</pre></div>

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