done

CITATIONS.rst

@@ -1,20 +1,20 @@
-.. _references:
-
-Citations & References
-======================
-
-The bibtex entries for **PyAutoCTI** and its affiliated software packages can be found
-`here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.bib>`_, with example text for citing **PyAutoCTI**
-in `.tex format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.tex>`_ format here and
-`.md format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.md>`_.
-
-As shown in the examples, we would greatly appreciate it if you mention **PyAutoCTI** by name and include a link to
-our GitHub page!
-
-**PyAutoCTI** is published in the `Journal of Open Source Software <https://joss.theoj.org/papers/10.21105/joss.02825#>`_ and its
-entry in the above .bib file is under the citation key ``pyautocti``.
-
-You should also specify the non-linear search(es) you use in your analysis (e.g. Dynesty, Emcee, PySwarms, etc) in
-the main body of text, and delete as appropriate any packages your analysis did not use. The citations.bib file includes
-the citation key for all of these projects.
-
+.. _references:
+
+Citations & References
+======================
+
+The bibtex entries for **PyAutoCTI** and its affiliated software packages can be found
+`here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.bib>`_, with example text for citing **PyAutoCTI**
+in `.tex format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.tex>`_ format here and
+`.md format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.md>`_.
+
+As shown in the examples, we would greatly appreciate it if you mention **PyAutoCTI** by name and include a link to
+our GitHub page!
+
+**PyAutoCTI** is published in the `Journal of Open Source Software <https://joss.theoj.org/papers/10.21105/joss.02825#>`_ and its
+entry in the above .bib file is under the citation key ``pyautocti``.
+
+You should also specify the non-linear search(es) you use in your analysis (e.g. Dynesty, Emcee, PySwarms, etc) in
+the main body of text, and delete as appropriate any packages your analysis did not use. The citations.bib file includes
+the citation key for all of these projects.
+

MANIFEST.in

@@ -1,19 +1,22 @@
 # MANIFEST.in
 exclude .gitignore
-exclude .coverage
-exclude .travis.yml
-exclude docs
 include README.rst
 include setup.cfg
+include CITATIONS.rst
+include LICENSE
+include requirements.txt
+include optional_requirements.txt
+
 prune .cache
 prune .git
 prune build
 prune dist
-recursive-include autocti/config *
+
 recursive-exclude *.egg-info *
-recursive-include tests *
-include requirements.txt
-recursive-include data *
+
+recursive-include autocti/config *
+
+exclude docs
 
 global-exclude test_autocti
 recursive-exclude test_autocti *

autocti/charge_injection/layout.py

@@ -335,7 +335,7 @@ def injection_total(self) -> int:
 
         injection_range = self.injection_end - self.injection_start
 
-        for injection_total in range(50):
+        for injection_total in range(100):
 
             total_pixels = math.floor(
                 (injection_total + 1) * (self.injection_on)

autocti/charge_injection/ou_sim_ci.py

@@ -1,3 +1,4 @@
+import math
 import numpy as np
 from typing import List, Union
 
@@ -6,7 +7,6 @@
 
 from autocti.instruments.euclid import euclid_util
 
-from autocti.instruments import euclid
 from autoarray.layout import layout_util
 from autoarray.structures.arrays.uniform_2d import Array2D
 
@@ -74,13 +74,35 @@ def quadrant_id_from(iquad: int) -> str:
     elif iquad == 3:
         return "G"
 
+def injection_total_from(
+    injection_start: int,
+    injection_end: int,
+    injection_on: int ,
+    injection_off: int,
+):
+    """
+    The total number of charge injection regions for these electronics settings.
+    """
+
+    injection_range = injection_end - injection_start
+
+    for injection_total in range(100):
+
+        total_pixels = math.floor(
+            (injection_total + 1) * (injection_on)
+            + injection_total * injection_off
+        )
+
+        if total_pixels > injection_range:
+            return injection_total
+
 
 def charge_injection_array_from(
     ccd_id: str,
     quadrant_id: str,
     injection_norm: float,
-    injection_total: int = 5,
-    injection_start: int = 0,
+    injection_start: int = 16,
+    injection_end: int = 2066,
     injection_on: int = 200,
     injection_off: int = 200,
     parallel_size: int = 2086,
@@ -129,6 +151,13 @@ def charge_injection_array_from(
     """
     shape_native = (parallel_size, serial_size)
 
+    injection_total = injection_total_from(
+        injection_start=injection_start,
+        injection_end=injection_end,
+        injection_on=injection_on,
+        injection_off=injection_off,
+    )
+
     """
     Specify the charge injection regions on the CCDPhase, which in this case is 5 equally spaced rectangular blocks.
     

docs/general/citations.rst

@@ -1,20 +1,20 @@
-.. _references:
-
-Citations & References
-======================
-
-The bibtex entries for **PyAutoGalaxy** and its affiliated software packages can be found
-`here <https://github.com/Jammy2211/PyAutoGalaxy/blob/master/files/citations.bib>`_, with example text for citing **PyAutoGalaxy**
-in `.tex format here <https://github.com/Jammy2211/PyAutoGalaxy/blob/master/files/citations.tex>`_ format here and
-`.md format here <https://github.com/Jammy2211/PyAutoGalaxy/blob/master/files/citations.md>`_.
-
-As shown in the examples, we would greatly appreciate it if you mention **PyAutoGalaxy** by name and include a link to
-our GitHub page!
-
-**PyAutoGalaxy** is published in the `Journal of Open Source Software <https://joss.theoj.org/papers/10.21105/joss.02825#>`_ and its
-entry in the above .bib file is under the citation key ``pyautogalaxy``.
-
-You should also specify the non-linear search(es) you use in your analysis (e.g. Dynesty, Emcee, PySwarms, etc) in
-the main body of text, and delete as appropriate any packages your analysis did not use. The citations.bib file includes
-the citation key for all of these projects.
-
+.. _references:
+
+Citations & References
+======================
+
+The bibtex entries for **PyAutoCTI** and its affiliated software packages can be found
+`here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.bib>`_, with example text for citing **PyAutoCTI**
+in `.tex format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.tex>`_ format here and
+`.md format here <https://github.com/Jammy2211/PyAutoCTI/blob/master/files/citations.md>`_.
+
+As shown in the examples, we would greatly appreciate it if you mention **PyAutoCTI** by name and include a link to
+our GitHub page!
+
+**PyAutoCTI** is published in the `Journal of Open Source Software <https://joss.theoj.org/papers/10.21105/joss.02825#>`_ and its
+entry in the above .bib file is under the citation key ``pyautocti``.
+
+You should also specify the non-linear search(es) you use in your analysis (e.g. Dynesty, Emcee, PySwarms, etc) in
+the main body of text, and delete as appropriate any packages your analysis did not use. The citations.bib file includes
+the citation key for all of these projects.
+

docs/general/configs.rst

@@ -1,27 +1,26 @@
-Configs
-=======
-
-**PyAutoLens** uses a number of configuration files that customize the default behaviour of the non-linear searches,
-visualization and other aspects of **PyAutoLens**.
-
-Descriptions of every configuration file and their input parameters are provided in the ``README.rst`` in
-the `config directory of the workspace <https://github.com/Jammy2211/autolens_workspace/tree/release/config>`_
-
-
-Setup
------
-
-By default, **PyAutoLens** looks for the config files in a ``config`` folder in the current working directory, which is
-why we run autolens scripts from the ``autolens_workspace`` directory.
-
-The configuration path can also be set manually in a script using the project **PyAutoConf** and the following
-command (the path to the ``output`` folder where the results of a non-linear search are stored is also set below):
-
-.. code-block:: bash
-
-    from autoconf import conf
-
-    conf.instance.push(
-        config_path="path/to/config",
-        output_path=f"path/to/output"
-    )
+Configs
+=======
+
+**PyAutoCTI** uses a number of configuration files that customize the default behaviour of the non-linear searches,
+visualization and other aspects of **PyAutoCTI**.
+
+Descriptions of every configuration file and their input parameters are provided in the ``README.rst`` in
+the `config directory of the workspace <https://github.com/Jammy2211/autocti_workspace/tree/release/config>`_
+
+Setup
+-----
+
+By default, **PyAutoCTI** looks for the config files in a ``config`` folder in the current working directory, which is
+why we run autocti scripts from the ``autocti_workspace`` directory.
+
+The configuration path can also be set manually in a script using the project **PyAutoConf** and the following
+command (the path to the ``output`` folder where the results of a non-linear search are stored is also set below):
+
+.. code-block:: bash
+
+    from autoconf import conf
+
+    conf.instance.push(
+        config_path="path/to/config",
+        output_path=f"path/to/output"
+    )

docs/general/credits.rst

@@ -1,35 +1,16 @@
-.. _credits:
-
-
-Credits
--------
-
-**Developers**:
-
-`James Nightingale <https://github.com/Jammy2211>`_: Lead developer & PyAutoLens guru.
-
-`Richard Hayes <https://github.com/rhayes777>`_: Lead developer & `PyAutoFit <https://github.com/rhayes777/PyAutoFit>`_ guru.
-
-`Aristeidis Amvrosiadis <https://github.com/Sketos>`_: Interferometer Analysis.
-
-`Amy Etherington <https://github.com/amyetherington>`_ : Magnification, Critical Curves and Caustic Calculations.
-
-Qiuhan He: NFW Profile Lensing Calculations.
-
-`Johnathan Frawley <https://github.com/jonathanfrawley>`_: Profiling, optimization and build server tools.
-
-`Ashley Kelly <https://github.com/AshKelly>`_: Developer of `pyquad <https://github.com/AshKelly/pyquad>`_ for fast deflections computations.
-
-`Xiaoyue Cao <https://github.com/caoxiaoyue>`_: Analytic Ellipitcal Power-Law Deflection Angle Calculations.
-
-`Nan Li <https://github.com/linan7788626>`_: Docker integration & support.
-
-**Code Donors**:
-
-`Andrew Robertson <https://github.com/Andrew-Robertson>`_: Critical curve & caustic calculations.
-
-Mattia Negrello: Visibility models in the uv-plane via direct Fourier transforms.
-
-`Andrea Enia <https://github.com/AndreaEnia>`_: Voronoi source-plane plotting tools.
-
-Conor O'Riordan : Broken Power-Law mass profile.
+.. _credits:
+
+
+Credits
+-------
+
+**Developers**:
+
+`James Nightingale <https://github.com/Jammy2211>`_: Lead developer & PyAutoLens guru.
+
+`Richard Hayes <https://github.com/rhayes777>`_: Lead developer & `PyAutoFit <https://github.com/rhayes777/PyAutoFit>`_ guru.
+
+`Jacob Kegerreis <https://github.com/jkeger>`_: arCTIc
+
+Richard Massey: arCTIc
+