Merge pull request #94 from GalSim-developers/fb/sphinx_doc

Sphinx documentation
GalSim-developers · Dec 4, 2024 · 373eb17 · 373eb17
2 parents bf28672 + 6c7d4f1
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diff --git a/.gitignore b/.gitignore
@@ -69,7 +69,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+#docs/_build/
 
 # PyBuilder
 .pybuilder/

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,3 @@
+Changes from v0.0.0 to v0.9.0
+=========================
+Made repo public.
diff --git a/README.rst b/README.rst
@@ -35,7 +35,18 @@ Attribution for software and data used by particular routines in this library is
 Installation
 ==================
 
-Please view the `installation instructions <INSTALL.rst>`_ for details on how to install GalSim-Euclid-Like.
+The source code for GalSim-Euclid-Like has not been published to pypi. To install from source code::
+
+    git clone [email protected]:GalSim-developers/GalSim-Euclid-Like.git
+
+and install by running::
+
+    conda create -n euclidlike python=3.10
+    cd GalSim-Euclid-Like
+    conda activate euclidlike
+    pip install .
+
+Please view the `Installation Instructions` (in INSTALL.rst) for further details on how to install GalSim-Euclid-Like.
 
 Downloading relevant data
 ==================                                                                              
@@ -57,7 +68,7 @@ Feel free to `open a GitHub issue <https://github.com/GalSim-developers/GalSim-E
 Attribution
 ==================                                   
 
-This software is open source and may be used according to the terms of its `license <LICENSE>`_.
+This software is open source and may be used according to the terms of its `license <https://github.com/GalSim-developers/GalSim-Euclid-Like/blob/main/LICENSE>`_.
 
 When using this software, please provide the URL to the repository in the resulting paper or note.  Once there is a Zenodo DOI or journal article, this README will be updated and we will ask those using the code in their research to cite the relevant journal article.
 
diff --git a/VERSION b/VERSION
@@ -0,0 +1 @@
+0.9.0
diff --git a/config/README.md b/config/README.md
diff --git a/config/README.rst b/config/README.rst
@@ -0,0 +1,49 @@
+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
+   [...]
+
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# 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)
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/euclidlike.doctree b/docs/_build/doctrees/euclidlike.doctree
diff --git a/docs/_build/doctrees/euclidlike_imsim.doctree b/docs/_build/doctrees/euclidlike_imsim.doctree
diff --git a/docs/_build/doctrees/examples.doctree b/docs/_build/doctrees/examples.doctree
diff --git a/docs/_build/doctrees/history.doctree b/docs/_build/doctrees/history.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/install.doctree b/docs/_build/doctrees/install.doctree
diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
diff --git a/docs/_build/doctrees/overview.doctree b/docs/_build/doctrees/overview.doctree
diff --git a/docs/_build/doctrees/scripts.doctree b/docs/_build/doctrees/scripts.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -0,0 +1,4 @@
+# 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: 4eb1993e7d6d79d4c633c84663c8829c
+tags: 645f666f9bcd5a90fca523b33c5a78b7