RTD badge

CITATIONS.rst

@@ -4,9 +4,9 @@ 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>`_.
+`here <https://github.com/Jammy2211/PyAutoCTI/blob/main/files/citations.bib>`_, with example text for citing **PyAutoCTI**
+in `.tex format here <https://github.com/Jammy2211/PyAutoCTI/blob/main/files/citations.tex>`_ format here and
+`.md format here <https://github.com/Jammy2211/PyAutoCTI/blob/main/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!

CODE_OF_CONDUCT.md

@@ -301,7 +301,7 @@ the situation is not yet resolved.
 
 ## License
 
-This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/master/manual/numfocus-coc.md#the-short-version),
-which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/master/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/master/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
+This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/main/manual/numfocus-coc.md#the-short-version),
+which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
 
 **PyAutoCTI Code of Conduct is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/).**

README.rst

@@ -7,13 +7,17 @@ PyAutoCTI: Charge Transfer Inefficiency Modeling
 .. |binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/Jammy2211/autocti_workspace/HEAD
 
+.. |RTD| image:: https://readthedocs.org/projects/pyautocti/badge/?version=latest
+    :target: https://pyautocti.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
 .. |code-style| image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
 
 .. |arXiv| image:: https://img.shields.io/badge/arXiv-1708.07377-blue
     :target: https://arxiv.org/abs/0909.0507
 
-|binder| |code-style| |arXiv|
+|binder| |RTD| |code-style| |arXiv|
 
 `Installation Guide <https://pyautocti.readthedocs.io/en/latest/installation/overview.html>`_ |
 `readthedocs <https://pyautocti.readthedocs.io/en/latest/index.html>`_ |
@@ -22,11 +26,11 @@ PyAutoCTI: Charge Transfer Inefficiency Modeling
 
 Charge Transfer Inefficiency, or CTI for short, is an effect that occurs when acquiring imaging data from
 Charge Coupled Devices (CCDs). Due to radiation damage to the CCD's silicon lattice electrons are read-out inefficiently,
-creating a characterstic trailing or smearing effect.
+creating a characteristic trailing or smearing effect.
 
 Here is an example of CTI in the Hubble space telescope, after decades of radiation damage:
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png
   :width: 600
   :alt: Alternative text
 

autocti/instruments/acs/array_2d.py

@@ -21,7 +21,7 @@ class Array2DACS(Array2D):
     """
     An ACS array consists of four quadrants ('A', 'B', 'C', 'D') which have the following layout (which are described
     at the following STScI
-    link https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418).
+    link https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418).
 
        <--------S-----------   ---------S----------->
     [] [========= 2 =========] [========= 3 =========] []          /\
@@ -48,7 +48,7 @@ def from_fits(cls, file_path, quadrant_letter):
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
 
         hdu = acs_util.fits_hdu_via_quadrant_letter_from(
@@ -75,7 +75,7 @@ def from_ccd(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
         if quadrant_letter == "A":
 
@@ -146,7 +146,7 @@ def quadrant_a(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
 
         array_electrons = layout_util.rotate_array_via_roe_corner_from(
@@ -192,7 +192,7 @@ def quadrant_b(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
 
         array_electrons = layout_util.rotate_array_via_roe_corner_from(
@@ -236,7 +236,7 @@ def quadrant_c(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
 
         array_electrons = layout_util.rotate_array_via_roe_corner_from(
@@ -276,7 +276,7 @@ def quadrant_d(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
         """
 
         array_electrons = layout_util.rotate_array_via_roe_corner_from(

autocti/instruments/acs/image.py

@@ -41,7 +41,7 @@ def from_fits(
         See the docstring of the `FrameACS` class for a complete description of the HST FPA, quadrants and
         rotations.
 
-        Also see https://github.com/spacetelescope/hstcal/blob/master/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
+        Also see https://github.com/spacetelescope/hstcal/blob/main/pkg/acs/calacs/acscte/dopcte-gen2.c#L418
 
         Parameters
         ----------

docs/general/citations.rst

@@ -4,9 +4,9 @@ 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>`_.
+`here <https://github.com/Jammy2211/PyAutoCTI/blob/main/files/citations.bib>`_, with example text for citing **PyAutoCTI**
+in `.tex format here <https://github.com/Jammy2211/PyAutoCTI/blob/main/files/citations.tex>`_ format here and
+`.md format here <https://github.com/Jammy2211/PyAutoCTI/blob/main/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!

docs/index.rst

@@ -7,9 +7,8 @@ Coupled Devices (CCDs).
 Lets take a look at a extract of data taken from the Advanced Camera for Surveys (ACS) instrument on board the
 Hubble Space Telescope (this figure is taken from Massey et al 2009 ``https://arxiv.org/abs/1009.4335``):
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png
   :width: 600
-  :alt: Alternative text
 
 Trailing
 --------
@@ -48,7 +47,7 @@ massive over simplification, but in order to understand CTI this process can be
 
 The animation below shows this process in action:
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti.gif
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti.gif
   :width: 600
 
 CTI
@@ -66,7 +65,7 @@ electron, one of two things can happen:
 
 The animation below shows the CCD clocking process, but now includes one of these traps:
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd.gif
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd.gif
   :width: 600
 
 Charge Transfer

docs/overview/overview_1_what_is_cti.rst

@@ -9,7 +9,7 @@ Coupled Devices (CCDs).
 Lets take a look at a extract of data taken from the Advanced Camera for Surveys (ACS) instrument on board the
 Hubble Space Telescope (this figure is taken from Massey et al 2009 ``https://arxiv.org/abs/1009.4335``):
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/what_is_cti.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/what_is_cti.png
   :width: 600
   :alt: Alternative text
 
@@ -42,7 +42,7 @@ massive over simplification, but in order to understand CTI this process can be
 
 The animation below shows this process in action:
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti.gif
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti.gif
   :width: 600
 
 CTI
@@ -60,7 +60,7 @@ electron, one of two things can happen:
 
 The animation below shows the CCD clocking process, but now includes one of these traps:
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd.gif
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd.gif
   :width: 600
 
 Charge Transfer
@@ -101,7 +101,7 @@ library has numerous wrappers like this which will crop up throughout the overvi
     array_1d_plotter = aplt.Array1DPlotter(y=pre_cti_data_1d)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d.png
   :width: 600
   :alt: Alternative text
 
@@ -163,7 +163,7 @@ Note that, in 1D, clocking is to the left of the image.
     array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d_with_cti.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d_with_cti.png
   :width: 600
   :alt: Alternative text
 
@@ -194,7 +194,7 @@ above, alongside the CTI model used to create it.
     array_1d_plotter = aplt.Array1DPlotter(y=corrected_cti_data_1d)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_1/array_1d_cti_corrected.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_1/array_1d_cti_corrected.png
   :width: 600
   :alt: Alternative text
 
@@ -224,7 +224,7 @@ traps. The longer our telescope has been in space, the more radiation will have
 have formed. The figure below slows the level of CTI in Hubble over the course of its lifetime -- as a function of
 time, CTI increases.
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/cti_time_evolution.gif
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/cti_time_evolution.gif
   :width: 600
 
 Wrap Up

docs/overview/overview_2_parallel_and_serial.rst

@@ -19,7 +19,7 @@ the image below) interspersed around regions with no charge.
 (It turns out that charge injection images are crucial to calibrating CTI -- a process we have to undertake before
 we can correct CTI in data. We cover this in overviews 4 and 5!).
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/ccd_schematic.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/ccd_schematic.png
   :width: 600
   :alt: Alternative text
 
@@ -97,7 +97,7 @@ with functionality used by **PyAutoCTI** which is expanded upon elsewhere in the
     array_2d_plotter = aplt.Array2DPlotter(array=pre_cti_data_2d)
     array_2d_plotter.figure_2d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/pre_cti_data_2d.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/pre_cti_data_2d.png
   :width: 600
   :alt: Alternative text
 
@@ -148,7 +148,7 @@ block of 10 electrons.
     array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d)
     array_2d_plotter.figure_2d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_parallel.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_parallel.png
   :width: 600
   :alt: Alternative text
 
@@ -191,7 +191,7 @@ block of 10 electrons.
     array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d)
     array_2d_plotter.figure_2d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_serial.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_serial.png
   :width: 600
   :alt: Alternative text
 
@@ -220,7 +220,7 @@ parallel CTI trails then trailed during serial clocking.
     array_2d_plotter = aplt.Array2DPlotter(array=post_cti_data_2d)
     array_2d_plotter.figure_2d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_parallel_serial.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_parallel_serial.png
   :width: 600
   :alt: Alternative text
 
@@ -236,7 +236,7 @@ Correcting CTI in 2D is as easy as it was in 1D, by simply calling the clockers
     array_2d_plotter = aplt.Array2DPlotter(array=corrected_cti_image_2d)
     array_2d_plotter.figure_2d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_2/post_cti_data_2d_corrected.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_2/post_cti_data_2d_corrected.png
   :width: 600
   :alt: Alternative text
 

docs/overview/overview_3_cti_features.rst

@@ -59,11 +59,11 @@ Now lets plot the two datasets and compare their appearance.
     array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/density_1.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/density_1.png
   :width: 600
   :alt: Alternative text
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/density_2.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/density_2.png
   :width: 600
   :alt: Alternative text
 
@@ -121,11 +121,11 @@ Now lets plot the two datasets and compare their appearance.
     array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/timescale_1.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/timescale_1.png
   :width: 600
   :alt: Alternative text
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/timescale_2.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/timescale_2.png
   :width: 600
   :alt: Alternative text
 
@@ -208,10 +208,10 @@ We can illustrate this by comparing the addition of CTI to two 1D datasets with
     array_1d_plotter = aplt.Array1DPlotter(y=post_cti_data_1d_1)
     array_1d_plotter.figure_1d()
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/volume_1.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/volume_1.png
   :width: 600
   :alt: Alternative text
 
-.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/master/docs/overview/images/overview_3/volume_2.png
+.. image:: https://raw.githubusercontent.com/Jammy2211/PyAutoCTI/main/docs/overview/images/overview_3/volume_2.png
   :width: 600
   :alt: Alternative text