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sphinx/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 0e918c43ff610a6f90209f51808e2ed6
+config: d382fc15a30caa93103124f98690e435
 tags: 645f666f9bcd5a90fca523b33c5a78b7

sphinx/_build/html/_sources/caracalREADME.rst.txt

@@ -0,0 +1,130 @@
+Installation & Run
+==================
+
+Usage and publication policy
+-------------------------------
+
+When using CARACal please be aware of and adhere to the `CARACal publication policy <https://docs.google.com/document/d/e/2PACX-1vTqZoKhdewnWvxvEI4C9DxI-IHP1FTCoC5Iqz_MqlX63q8UnnpcqoZvVf-sSfqACu8sA_nufkXICUH6/pub>`_.
+
+Requirements
+------------
+* `Python <https://www.python.org>`_ 3.8 or higher.
+* Container technology of your choice. It can be one of the following:
+    * `Docker <https://www.docker.com>`_
+    * `Podman <https://podman.io/>`_
+    * `Singularity <https://github.com/sylabs/singularity>`_ 3.5 - 3.9 (nearly all functionality available for > 2.6.0-dist, see `here <https://github.com/caracal-pipeline/caracal/issues/1154>`_ for further information) 
+        * `Apptainer <https://apptainer.org>`_ does not support all CARACal functionalities (at the moment).
+
+============
+Installation
+============
+
+We strongly recommend and describe an installation using a `Python3` virtual environment. Only try outside a virtual environment if you know what you are doing. Any name as ``${name}`` occurring in the description below can be chosen arbitrarily. If it symbolises directories or files, those directories or files should exist and the user should have **write** access.
+
+There are three (3) available methods to install the `caracal` pipeline: 
+
+1. Manual
+---------
+
+Choose the name of the virtual environment `${caracal-venv}`. Then:
+
+..  code-block:: bash
+
+    $ python3 -m venv ${caracal-venv}
+
+OR, if the command above does not work
+
+..  code-block:: bash
+
+    virtualenv -p python3 ${caracal-venv}
+    source ${caracal-venv}/bin/activate
+    pip install -U pip setuptools wheel
+
+For a CARACal stable release run:
+
+..  code-block:: bash
+
+    pip install -U caracal
+
+CARACal has a few optional dependencies (*scipy, astropy, regions, astroquery*) which are not installed by default. But to get full functionality, you can install them by running:
+
+..  code-block:: bash
+
+    pip install -U caracal[all]
+
+And CARACal developer version which is not recommended for users:
+
+..  code-block:: bash
+
+    pip install -U 'caracal[all] @ git+https://github.com/caracal-pipeline/caracal.git@master'
+
+
+
+*Ignore any error messages concerning `pyregion`.*
+
+2. `caratekit.sh` script
+----------------------
+
+Download the installation script `caratekit.sh <https://github.com/caracal-pipeline/caracal/blob/master/caratekit.sh>`_ . Choose the parent directory ``${workspace}`` and the name of the CARACal directory ``${caracal_dir}``. Any name as ``${name}`` occurring in the description below can be chosen arbitrarily. If it symbolises directories or files, those directories or files should exist and the user should have write acccess.
+
+If using `Docker <https://www.docker.com>`_:
+
+..  code-block:: bash
+
+    caratekit.sh -ws ${workspace} -cr -di -ct ${caracal_dir} -rp install -f -kh
+
+
+If using `Singularity <https://github.com/sylabs/singularity>`_:
+
+..  code-block:: bash
+
+    caratekit.sh -ws ${workspace} -cr -si -ct ${caracal_testdir} -rp install -f -kh
+
+
+3. Poetry (For developers)
+---------
+
+Installation from source using `poetry`. First, install poetry:
+
+..  code-block:: bash
+
+    pip install poetry
+
+
+In the working directory where source is checked out run `poetry install` or to include all optional dependencies:
+
+..  code-block:: bash
+
+    poetry install --extras all
+
+=========================================
+Installation on (ILIFU) slurm environment
+=========================================
+
+The installation of CARACal on ilifu has been tried and tested on the Ubuntu 20.0 operating system, although, it should also work on other OS versions. On the login node, follow these instructions:
+
+..  code-block:: bash
+
+    cd /path/to/working/area
+    module add python/3.9.4
+    python3 -m venv <venv-name>
+    source <venv-name>/bin/activate
+    pip install -U pip setuptools wheel
+    git clone https://github.com/caracal-pipeline/caracal.git
+    pip install -U -e caracal
+    deactivate
+
+where ``/path/to/working/area`` is the actual path to the directory where you wish to install CARACal.
+In principle, this can also be done in the Slurm environment of ILIFU by submitting an *sbatch* script.
+Please amend your `pip install` command with `[all]` option when needed in accordance with the instructions above.
+Install the latest release with:
+
+..  code-block:: bash
+
+    pip install -U caracal
+
+
+NB: The stimela singularity images needed for CARACal are stored in this location: ``/software/astro/caracal/``
+where you can access the latest version of the images, for example, ``/software/astro/caracal/STIMELA_IMAGES_1.7.0``. 
+
+=======

sphinx/_build/html/_sources/manual/workers/crosscal/index.rst.txt

@@ -142,6 +142,12 @@ Carry out Cross calibration of the data (delay, bandpass and gain calibration).
 
     Fraction of system RAM that can be used when using Crystalball to predict calibrator visibilities in the model column. Used when setting automatically the chunk size.
 
+  **meerkat_crystalball_ncpu**
+
+    *int*, *optional*, *default = 0*
+
+    Explicitly set the number of worker threads. Default is 0, meaning it uses all threads.
+
   **meerkat_crystalball_num_sources**
 
     *int*, *optional*, *default = 0*

sphinx/_build/html/_sources/manual/workers/line/index.rst.txt

@@ -620,7 +620,7 @@ Process visibilities for spectral line work and create line cubes and images.
 
     *int*, *optional*, *default = 2*
 
-    Maximum number of WSClean + SoFiA iterations. The initial cleaning is done with WSClean automasking or with a user-provided clean mask. Subsequent iterations use a SoFiA clean mask. A value of 1 means that WSClean is only executed once and SoFiA is not used.
+    Maximum number of WSClean + SoFiA iterations. The initial cleaning is done with WSClean automasking or with a user-provided clean mask. Subsequent iterations use a SoFiA clean mask. A value of 1 means that WSClean is only executed once and SoFiA is not used. The value of this parameter must be >= 1. Values < 1 will be ignored, and a value of 1 will be used instead.
 
   **wscl_sofia_converge**
 

sphinx/_build/html/_sources/manual/workers/selfcal/index.rst.txt

@@ -314,6 +314,18 @@ Perform self-calibration on the data.
 
 
 
+.. _selfcal_img_channelrange:
+
+--------------------------------------------------
+**img_channelrange**
+--------------------------------------------------
+
+  *list* *of int*, *optional*, *default = -1*
+
+  Only image the given channel range. Indices specify channel indices, end index is exclusive. .e.g. 0, 1023. Default '-1' means all channels.
+
+
+
 .. _selfcal_img_joinchans:
 
 --------------------------------------------------
@@ -636,6 +648,24 @@ Perform self-calibration on the data.
 
     Maximum number of time/freq data-chunks to load into memory simultaneously. If set to 0, then as many data-chunks as possible will be loaded.
 
+  **out_derotate**
+
+    *bool*, *optional*, *default = False*
+
+    Explicitly enables or disables derotation of output visibilities. Default (None) is to use the –model-pa-rotate and –model-feed-rotate settings.
+
+  **model_pa_rotate**
+
+    *bool*, *optional*, *default = False*
+
+    Apply parallactic angle rotation to model visibilities. Enable this for alt-azmounts, unless your model visibilities are already rotated.
+
+  **model_feed_rotate**
+
+    *str*, *optional*, *default = ' '*
+
+    Apply a feed angle rotation to the model visibilities. Use 'auto' to read angles from FEED subtable, or give an explicit value in degrees.
+
   **ragavi_plot**
 
     Use ragavi to plot diagnostic plots for self-calibration.
@@ -900,7 +930,7 @@ Perform self-calibration on the data.
 
     *list* *of str*, *optional*, *default = CORR_DATA*
 
-    Data to output after calibration. Options are 'CORR_DATA', 'CORR_RES' or 'CORRECTED_DATA', where CORR_DATA and CORRECTED_DATA are synonyms.
+    Data to output after calibration. Options are 'PA_DATA', 'CORR_RES', 'CORR_DATA' or 'CORRECTED_DATA', where CORR_DATA and CORRECTED_DATA are synonyms. Note that for 'PA_DATA' only parallactic angle corrections will be applied to the data to produce 'CORRECTED_DATA' column.
 
   **gain_matrix_type**
 

sphinx/_build/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
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+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}