From 9096cea3986191395215597d217a5c3b0f782e41 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 08:02:34 -0600
Subject: [PATCH 01/12] attempt to fix docs build

---
 docs/docs-env.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 3068f652f..0821253c4 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -3,7 +3,8 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
-  - python>=3.8
+  - importlib_resources
+  - python>=3.11
   - pip
   - pip:
     - boltons

From 37466da75f593b2270ed7fa7b64e3435a0568cce Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 08:18:39 -0600
Subject: [PATCH 02/12] check if the issue is what we think it is

---
 docs/docs-env.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 0821253c4..64570f33a 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -3,7 +3,6 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
-  - importlib_resources
   - python>=3.11
   - pip
   - pip:

From 43419dd6475e3b0de92bd6a92a8eb9a768f7d28b Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 12:17:47 -0600
Subject: [PATCH 03/12] add back importlib_resources

---
 docs/docs-env.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 64570f33a..0821253c4 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -3,6 +3,7 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 dependencies:
+  - importlib_resources
   - python>=3.11
   - pip
   - pip:

From 2da8f1b506dc064bd3349b323d70abce2dcd9213 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 12:21:37 -0600
Subject: [PATCH 04/12] update python version

---
 docs/conf.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 8ad87a4cf..d04b1b0e4 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -131,10 +131,10 @@
 numpydoc_show_class_members = False
 numpydoc_show_inherited_class_members = False
 
-_python_doc_base = "https://docs.python.org/3.9"
+_python_doc_base = "https://docs.python.org/3.11"
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3.9", None),
+    "python": ("https://docs.python.org/3.11", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
     "scikit-learn": ("https://scikit-learn.org/stable", None),

From ee02b578b524b03dd8439f13b607be89234dd208 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 13:33:34 -0600
Subject: [PATCH 05/12] change latex source file

---
 docs/conf.py      | 2 +-
 docs/docs-env.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index d04b1b0e4..b5dc288a2 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -332,7 +332,7 @@
 """,
 }
 
-latex_master_doc = "indexlatex"
+latex_master_doc = "index"
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 0821253c4..5584f41e2 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -4,7 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - importlib_resources
-  - python>=3.11
+  - python=3.10
   - pip
   - pip:
     - boltons

From 85d93c59818f46440b545e49c8b85ba00203053e Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 13:42:18 -0600
Subject: [PATCH 06/12] up python version in docs

---
 docs/docs-env.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 5584f41e2..3f4897af5 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -4,7 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - importlib_resources
-  - python=3.10
+  - python=3.11
   - pip
   - pip:
     - boltons

From a71644f59b4a8ab92c41fdb013428defebf9e461 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 14:25:30 -0600
Subject: [PATCH 07/12] try to update entry point syntax

---
 mbuild/recipes/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mbuild/recipes/__init__.py b/mbuild/recipes/__init__.py
index e5970a0d1..fc54d51ff 100644
--- a/mbuild/recipes/__init__.py
+++ b/mbuild/recipes/__init__.py
@@ -10,7 +10,7 @@ class Recipes(object):
 recipes = Recipes()
 from importlib import metadata
 
-entry_points = metadata.entry_points()["mbuild.plugins"]
+entry_points = metadata.entry_points().select(group="mbuild.plugins")
 
 available_methods = []
 for entry_point in entry_points:

From 99adf973fc7cdd64aeffdfdb14823521dd6d8acb Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 14:46:43 -0600
Subject: [PATCH 08/12] check python version for appropriate entry point syntax

---
 mbuild/recipes/__init__.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/mbuild/recipes/__init__.py b/mbuild/recipes/__init__.py
index fc54d51ff..20072f03b 100644
--- a/mbuild/recipes/__init__.py
+++ b/mbuild/recipes/__init__.py
@@ -1,5 +1,7 @@
 """Entrypoints for mBuild recipe plugins."""
 
+import sys
+
 
 class Recipes(object):
     """mBuild recipe object."""
@@ -10,8 +12,12 @@ class Recipes(object):
 recipes = Recipes()
 from importlib import metadata
 
-entry_points = metadata.entry_points().select(group="mbuild.plugins")
+if sys.version_info.minor >= 10:
+    entry_points = metadata.entry_points().select(group="mbuild.plugins")
+else:
+    entry_points = metadata.entry_points()["mbuild.plugins"]
 
 available_methods = []
 for entry_point in entry_points:
     setattr(recipes, entry_point.name, entry_point.load())
+e

From ce1b9682df28195380766f1328f5de602bcd02ac Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 14:54:56 -0600
Subject: [PATCH 09/12] fix typo

---
 mbuild/recipes/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/mbuild/recipes/__init__.py b/mbuild/recipes/__init__.py
index 20072f03b..e5caecc5e 100644
--- a/mbuild/recipes/__init__.py
+++ b/mbuild/recipes/__init__.py
@@ -20,4 +20,3 @@ class Recipes(object):
 available_methods = []
 for entry_point in entry_points:
     setattr(recipes, entry_point.name, entry_point.load())
-e

From 7e6c9633d4d4ea6e92e5a318cefc04d944f970a2 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 15:33:30 -0600
Subject: [PATCH 10/12] chagne ipython3 to just ipython in rst

---
 .../quick_start/Box_example.rst               |  6 ++---
 .../quick_start/fill_box_example.rst          | 12 ++++-----
 .../quick_start/load_files.rst                |  8 +++---
 .../quick_start/polymer_example.rst           |  6 ++---
 .../tutorials/tutorial_ethane.rst             | 24 ++++++++---------
 .../tutorials/tutorial_lattice.rst            | 26 +++++++++----------
 .../tutorials/tutorial_methane.rst            | 12 ++++-----
 .../tutorials/tutorial_monolayer.rst          | 16 ++++++------
 .../tutorials/tutorial_polymers.rst           | 22 ++++++++--------
 .../tutorials/tutorial_simple_LJ.rst          | 18 ++++++-------
 10 files changed, 75 insertions(+), 75 deletions(-)

diff --git a/docs/getting_started/quick_start/Box_example.rst b/docs/getting_started/quick_start/Box_example.rst
index b8cff8e22..7a0157bdc 100644
--- a/docs/getting_started/quick_start/Box_example.rst
+++ b/docs/getting_started/quick_start/Box_example.rst
@@ -4,7 +4,7 @@ Box
 
 Import the required mbuild package.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -18,7 +18,7 @@ Build an empty orthogonal **mBuild** Box (i.e., the angle in degrees are 𝛼 =
     Note: if the angles are not specified, the system will default to an orthogonal box
     (i.e., the angle in degrees are 𝛼 = 90, 𝛽 = 90, 𝛾 = 90).
 
-.. code:: ipython3
+.. code:: ipython
 
     empty_box = mb.Box(lengths=[4.0, 4.0, 4.0], angles=[90, 90, 90])
 
@@ -28,6 +28,6 @@ Non-Orthogonal Box
 
 Build an empty non-orthogonal **mBuild** Box (i.e., the angle in degrees are 𝛼 = 90, 𝛽 = 90, 𝛾 = 120) measuring 4.0 nm in the x and y-dimensions, and 5.0 nm in the z-dimension.
 
-.. code:: ipython3
+.. code:: ipython
 
     empty_box = mb.Box(lengths=[4.0, 4.0, 5.0], angles=[90, 90, 120])
diff --git a/docs/getting_started/quick_start/fill_box_example.rst b/docs/getting_started/quick_start/fill_box_example.rst
index 992e5053d..d44ef3f86 100644
--- a/docs/getting_started/quick_start/fill_box_example.rst
+++ b/docs/getting_started/quick_start/fill_box_example.rst
@@ -12,7 +12,7 @@ All-Atom (AA) Hexane and Ethanol System
 
 Import the required mbuild package.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -26,7 +26,7 @@ Lastly, the hexane and ethanol molecule's configuration will be energy minimized
 .. note::
     The energy minimize step requires the `foyer <https://foyer.mosdef.org/en/stable/>`_ package.
 
-.. code:: ipython3
+.. code:: ipython
 
     hexane = mb.load('CCCCCC', smiles=True)
     hexane.name = 'HEX'
@@ -39,7 +39,7 @@ Lastly, the hexane and ethanol molecule's configuration will be energy minimized
 
 The liquid box is built to a density of 680 kg/m\ :sup:`3`, with a 50/50 mol ratio of hexane and ethanol, and will be in an orthogonal box measuring 5.0 nm in the x, y, and z-dimensions.
 
-.. code:: ipython3
+.. code:: ipython
 
     box_liq = mb.fill_box(compound= [hexane, ethanol],
                           density=680,
@@ -58,7 +58,7 @@ United Atom (UA) Methane System
 
 Import the required mbuild package.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -67,7 +67,7 @@ Construct a pseudo-monatomic molecule (united atom (UA) methane), for use with t
 `TraPPE <http://trappe.oit.umn.edu>`_ FF.  The UA methane, bead type `"_CH4"`, will be built as a child (``mbuild.Compound.children``), so the parent (``mbuild.Compound``) will
 allow a user-selected residue name (``mbuild.Compound.name``). If the methane is built using ``methane = mb.Compound(name="_CH4")``, then the user must keep the residue name `"_CH4"` or `foyer <https://foyer.mosdef.org/en/stable/>`_ will not recognize the bead type when using the standard TraPPE force field XML file.
 
-.. code:: ipython3
+.. code:: ipython
 
     methane = mb.Compound(name="MET")
     methane_child_bead = mb.Compound(name="_CH4")
@@ -79,7 +79,7 @@ allow a user-selected residue name (``mbuild.Compound.name``). If the methane is
 
 The orthogonal liquid box contains 1230 methane molecules and measures 4.5 nm in all the x, y, and z-dimensions.
 
-.. code:: ipython3
+.. code:: ipython
 
     box_liq = mb.fill_box(compound=methane,
                           n_compounds=1230,
diff --git a/docs/getting_started/quick_start/load_files.rst b/docs/getting_started/quick_start/load_files.rst
index 0c9af1019..afd07452f 100644
--- a/docs/getting_started/quick_start/load_files.rst
+++ b/docs/getting_started/quick_start/load_files.rst
@@ -11,14 +11,14 @@ Create an ``mbuild.Compound`` (i.e., the "pentane" variable) by loading a molecu
 
 Import the required mbuild packages.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
 
 Load the "pentane.mol2" file from its directory.
 
-.. code:: ipython3
+.. code:: ipython
 
     pentane = mb.load("path_to_mol2_file/pentane.mol2")
 
@@ -31,7 +31,7 @@ Build an ``mbuild.Compound`` (i.e., the "ETV_triclinic" variable) by loading a `
 
 Import the required mbuild packages.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     from mbuild.lattice import load_cif
@@ -40,7 +40,7 @@ Import the required mbuild packages.
 
 The `CIF <https://www.iucr.org/resources/cif>`_ file is loaded using the ``load_cif`` function. Next, three (3) cell units shall be built for all the x, y, and z-dimensions with the populate function.  Finally, the `CIF <https://www.iucr.org/resources/cif>`_'s residues are named 'ETV'.
 
-.. code:: ipython3
+.. code:: ipython
 
     lattice_cif_ETV_triclinic = load_cif("path_to_cif_file/ETV_triclinic.cif")
     ETV_triclinic = lattice_cif_ETV_triclinic.populate(x=3, y=3, z=3)
diff --git a/docs/getting_started/quick_start/polymer_example.rst b/docs/getting_started/quick_start/polymer_example.rst
index ac567bfc9..02c73d7c6 100644
--- a/docs/getting_started/quick_start/polymer_example.rst
+++ b/docs/getting_started/quick_start/polymer_example.rst
@@ -6,7 +6,7 @@ Use two (2) different monomer units, A and B, to construct a polymer, capping it
 
 Import the required mbuild packages.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     from mbuild.lib.recipes.polymer import Polymer
@@ -20,7 +20,7 @@ Set the `chain` as a ``Polymer`` class, adding `comp_1` and `comp_2` as the mono
     Setting the indices identifies which atoms will be removed and have ports created in their place.
 
 
-.. code:: ipython3
+.. code:: ipython
 
     comp_1 = mb.load('CC', smiles=True) # mBuild compound of the monomer unit
     comp_2 = mb.load('COC', smiles=True) # mBuild compound of the monomer unit
@@ -40,7 +40,7 @@ Select the carboxylic acid and amine end groups that we want to use for the head
 Then, build the polymer with three (3) iterations of the AB sequence, and the selected head and tail end groups.
 
 
-.. code:: ipython3
+.. code:: ipython
 
     chain.add_end_groups(mb.load('C(=O)O',smiles=True),
                          index=3,
diff --git a/docs/getting_started/tutorials/tutorial_ethane.rst b/docs/getting_started/tutorials/tutorial_ethane.rst
index 48c2999b3..a3b6293ec 100644
--- a/docs/getting_started/tutorials/tutorial_ethane.rst
+++ b/docs/getting_started/tutorials/tutorial_ethane.rst
@@ -9,7 +9,7 @@ transforms.
 
 First, we need to import the mbuild package:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -23,7 +23,7 @@ connectivity information).
 
 Let’s start by reading a methyl group from a ``.pdb`` file:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -34,7 +34,7 @@ Let’s start by reading a methyl group from a ``.pdb`` file:
 Now let’s use our first coordinate transform to center the methyl at its
 carbon atom:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -49,7 +49,7 @@ typically points to a particle that the ``Port`` should be associated
 with. In our methyl group, the ``Port`` should be anchored to the carbon
 atom so that we can now form bonds to this carbon:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -66,14 +66,14 @@ By default, ``Ports`` are never output from the mBuild structure.
 However, it can be useful to look at a molecule with the ``Ports`` to
 check your work as you go:
 
-.. code:: ipython3
+.. code:: ipython
 
     ch3.visualize(show_ports=True)
 
 Now we wrap the methyl group into a python class, so that we can reuse
 it as a component to build more complex molecules later.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -111,7 +111,7 @@ automatically chosen.
 
 Now the fun part: stick ’em together to create an ethane:
 
-.. code:: ipython3
+.. code:: ipython
 
     ethane = mb.Compound()
 
@@ -126,18 +126,18 @@ rotates and translates it such that two other ``Compounds`` overlap.
 Typically, as in this case, those two other ``Compounds`` are ``Ports``
 - in our case, ``methyl1['up']`` and ``methyl2['up']``.
 
-.. code:: ipython3
+.. code:: ipython
 
     ethane.visualize()
 
-.. code:: ipython3
+.. code:: ipython
 
     ethane.visualize(show_ports=True)
 
 Similarly, if we want to make ethane a reusable component, we need to
 wrap it into a python class.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -151,12 +151,12 @@ wrap it into a python class.
                              from_positions=self['methyl_1']['up'],
                              to_positions=self['methyl_2']['up'])
 
-.. code:: ipython3
+.. code:: ipython
 
     ethane = Ethane()
     ethane.visualize()
 
-.. code:: ipython3
+.. code:: ipython
 
     # Save to .mol2
     ethane.save('ethane.mol2', overwrite=True)
diff --git a/docs/getting_started/tutorials/tutorial_lattice.rst b/docs/getting_started/tutorials/tutorial_lattice.rst
index 2deba6ccc..1b7bf8510 100644
--- a/docs/getting_started/tutorials/tutorial_lattice.rst
+++ b/docs/getting_started/tutorials/tutorial_lattice.rst
@@ -58,7 +58,7 @@ desired crystal structures.
 To begin, we will call the python ``help()`` method to observe the
 parameters and attributes of the ``Lattice`` class.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild
     help(mbuild.Lattice)
@@ -79,7 +79,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example:
 
-   .. code:: ipython3
+   .. code:: ipython
 
        lattice_spacing = [0.5, 0.5, 0.5]
 
@@ -100,7 +100,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For example: Cubic Cell
 
-   .. code:: ipython3
+   .. code:: ipython
 
        lattice_vectors = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
 
@@ -112,7 +112,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For example: Cubic Cell
 
-   .. code:: ipython3
+   .. code:: ipython
 
        angles = [90, 90, 90]
 
@@ -140,7 +140,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example: FCC All Unique
 
-   .. code:: ipython3
+   .. code:: ipython
 
        lattice_points = {'A' : [[0, 0, 0]],
                          'B' : [[0.5, 0.5, 0]],
@@ -150,7 +150,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example: FCC All Same
 
-   .. code:: ipython3
+   .. code:: ipython
 
        lattice_points = {'A' : [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]] }
 
@@ -179,7 +179,7 @@ replications in the x, y, and z directions.
 
       For Example: FCC All Unique
 
-          .. code:: ipython3
+          .. code:: ipython
 
             lattice_points = {'A' : [[0, 0, 0]],
                               'B' : [[0.5, 0.5, 0]],
@@ -197,7 +197,7 @@ replications in the x, y, and z directions.
 
       For Example: FCC All Same
 
-          .. code:: ipython3
+          .. code:: ipython
 
             lattice_points = {'A' : [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]] }
 
@@ -217,7 +217,7 @@ Simple Cubic (SC)
 
 -  Polonium
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import numpy as np
@@ -250,7 +250,7 @@ Body-centered Cubic (BCC)
 
 -  CsCl
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import numpy as np
@@ -285,7 +285,7 @@ Face-centered Cubic (FCC)
 
 -  Cu
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import numpy as np
@@ -318,7 +318,7 @@ Diamond (Cubic)
 
 -  Si
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import numpy as np
@@ -352,7 +352,7 @@ Graphene (2D)
 
 -  C
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import numpy as np
diff --git a/docs/getting_started/tutorials/tutorial_methane.rst b/docs/getting_started/tutorials/tutorial_methane.rst
index 632ba0401..0ae129b43 100644
--- a/docs/getting_started/tutorials/tutorial_methane.rst
+++ b/docs/getting_started/tutorials/tutorial_methane.rst
@@ -7,7 +7,7 @@ The primary building block in mBuild is a ``Compound``. Anything you
 construct will inherit from this class. Let’s start with some basic
 imports and initialization:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -21,7 +21,7 @@ hierarchy are referred to as ``Particles``. Note however, that this is
 purely semantic in mBuild to help clearly designate the bottom of a
 hierarchy.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -56,7 +56,7 @@ hydrogen. Note that for typical use cases, you will almost never have to
 explicitly define a bond when using mBuild - this is just to show you
 what’s going on under the hood:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -78,7 +78,7 @@ fancy label, it’s also referenceable via ``self['HC'][0]``.
 Alright now that we’ve got the basics, let’s finish building our
 ``Methane`` and take a look at it:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -101,12 +101,12 @@ Alright now that we’ve got the basics, let’s finish building our
             self.add_bond((self[0], self['HC'][2]))
             self.add_bond((self[0], self['HC'][3]))
 
-.. code:: ipython3
+.. code:: ipython
 
     methane = Methane()
     methane.visualize()
 
-.. code:: ipython3
+.. code:: ipython
 
     # Save to .mol2
     methane.save('methane.mol2',overwrite=True)
diff --git a/docs/getting_started/tutorials/tutorial_monolayer.rst b/docs/getting_started/tutorials/tutorial_monolayer.rst
index 0538a7b23..11c9eb5c7 100644
--- a/docs/getting_started/tutorials/tutorial_monolayer.rst
+++ b/docs/getting_started/tutorials/tutorial_monolayer.rst
@@ -28,7 +28,7 @@ consistent! The more components we collect in our library with the same
 labeling conventions, the easier it becomes to build ever more complex
 structures.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -50,13 +50,13 @@ structures.
             # Hoist silane port to AlkylSilane level.
             self.add(silane['down'], 'down', containment=False)
 
-.. code:: ipython3
+.. code:: ipython
 
     AlkylSilane(5).visualize()
 
 Now let’s create a substrate to which we can later attach our monomers:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     from mbuild.lib.surfaces import Betacristobalite
@@ -72,7 +72,7 @@ library. The ``TiledCompound`` tool allows you replicate any
 Next, let’s create our monomer and a hydrogen atom that we’ll place on
 unoccupied surface sites:
 
-.. code:: ipython3
+.. code:: ipython
 
     from mbuild.lib.atoms import H
     alkylsilane = AlkylSilane(chain_length=10)
@@ -87,7 +87,7 @@ figures out what the closest ports are to the pattern points and then
 attaches copies of the guest onto the binding sites identified by the
 pattern:
 
-.. code:: ipython3
+.. code:: ipython
 
     pattern = mb.Grid2DPattern(8, 8)  # Evenly spaced, 2D grid of points.
 
@@ -98,12 +98,12 @@ Also note the ``backfill`` optional argument which allows you to place a
 different compound on any unused ports. In this case we want to backfill
 with hydrogen atoms on every port without a chain.
 
-.. code:: ipython3
+.. code:: ipython
 
     monolayer = mb.Compound([tiled_surface, chains, hydrogens])
     monolayer.visualize() # Warning: may be slow in IPython notebooks
 
-.. code:: ipython3
+.. code:: ipython
 
     # Save as .mol2 file
     monolayer.save('monolayer.mol2', overwrite=True)
@@ -111,7 +111,7 @@ with hydrogen atoms on every port without a chain.
 ``lib.recipes.monolayer.py`` wraps many these functions into a simple,
 general class for generating the monolayers, as shown below:
 
-.. code:: ipython3
+.. code:: ipython
 
     from mbuild.lib.recipes import Monolayer
 
diff --git a/docs/getting_started/tutorials/tutorial_polymers.rst b/docs/getting_started/tutorials/tutorial_polymers.rst
index 179c5c530..7e9069ab4 100644
--- a/docs/getting_started/tutorials/tutorial_polymers.rst
+++ b/docs/getting_started/tutorials/tutorial_polymers.rst
@@ -17,7 +17,7 @@ importing the coordinates from a pdb file, as in the previous example,
 we will instead explicitly define them in the class. Recall that
 distance units are nm in mBuild.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -60,7 +60,7 @@ given in radians. Similarly, the ports should be rotated around the
 x-axis by the same amount so that atoms can be added in a realistic
 orientation.
 
-.. code:: ipython3
+.. code:: ipython
 
     import numpy as np
     import mbuild as mb
@@ -108,7 +108,7 @@ make a copy. The ``force_overlap()`` function is used to connect the
 ``'up'`` port from ``current_monomer`` to the ``'down'`` port of
 ``last_mononer``.
 
-.. code:: ipython3
+.. code:: ipython
 
     class AlkanePolymer(mb.Compound):
         def __init__(self):
@@ -135,7 +135,7 @@ We can also add a variable ``chain_length`` both to the for loop and
 ``init`` that will allow the length of the polymer to be adjusted when
 the class is instantiated.
 
-.. code:: ipython3
+.. code:: ipython
 
     import numpy as np
     import mbuild as mb
@@ -182,7 +182,7 @@ the class is instantiated.
                 self.add(current_monomer)
                 last_monomer=current_monomer
 
-.. code:: ipython3
+.. code:: ipython
 
     polymer = AlkanePolymer(chain_length=10)
     polymer.visualize(show_ports=True)
@@ -211,7 +211,7 @@ A simple hexane molecule is built using ``mBuild``'s packaged polymer builder.
 This is done by loading a methane molecule via a SMILES string.
 The indices are explicitly selected, so the molecule builds out in the proper directions and does not overlap.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     from mbuild.lib.recipes.polymer import Polymer
@@ -235,7 +235,7 @@ The end groups are added via the ``add_end_groups`` attribute, specifying the at
 the location of each end group (``label``), and if the tail end group is duplicated to the head of the polymer (``duplicate``).
 The indices are explicitly selected, so the molecule builds out in the proper directions and does not overlap.
 
-.. code:: ipython3
+.. code:: ipython
 
     from mbuild.lib.recipes.polymer import Polymer
     import mbuild as mb
@@ -275,7 +275,7 @@ constructed above and translating and/or rotating the alkanes in space.
 ``mBuild`` provides many routines that can be used to create different
 patterns, to which the polymers can be shifted.
 
-.. code:: ipython3
+.. code:: ipython
 
     comp = mb.load('C', smiles=True) # mBuild compound of the monomer unit
     polymer = Polymer()
@@ -311,7 +311,7 @@ patterns, to which the polymers can be shifted.
 Other patterns can be used, e.g., the ``Grid3DPattern``. We can also use
 the rotation commands to randomize the orientation.
 
-.. code:: ipython3
+.. code:: ipython
 
     import random
 
@@ -344,7 +344,7 @@ the rotation commands to randomize the orientation.
 ``mBuild`` also provides an interface to ``PACKMOL``, allowing the
 creation of a randomized configuration.
 
-.. code:: ipython3
+.. code:: ipython
 
     comp = mb.load('C', smiles=True) # mBuild compound of the monomer unit
     polymer = Polymer()
@@ -373,7 +373,7 @@ amount of perturbation. Note that large values of ``delta`` may result
 in the chain overlapping itself, as ``mBuild`` does not currently
 include routines to exclude such overlaps.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
diff --git a/docs/getting_started/tutorials/tutorial_simple_LJ.rst b/docs/getting_started/tutorials/tutorial_simple_LJ.rst
index 0afb4f5d1..812085bd2 100644
--- a/docs/getting_started/tutorials/tutorial_simple_LJ.rst
+++ b/docs/getting_started/tutorials/tutorial_simple_LJ.rst
@@ -12,7 +12,7 @@ Note, the color and radius associated with a Particle name can be set
 and passed to the visualize command. Colors are passed in hex format
 (see http://www.color-hex.com/color/bfbfbf).
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -63,7 +63,7 @@ translating to the specified location. Since the lj_proto particle in
 this example starts at the origin, these two commands produce identical
 behavior.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -91,7 +91,7 @@ in pattern, cloning, translating, and adding to the system. Note,
 because Grid3DPattern defines points between 0 and 1, they must be
 scaled based on the desired system size, i.e., pattern.scale(2).
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -115,7 +115,7 @@ Larger systems can therefore be easily generated by toggling the values
 given to Grid3DPattern. Other patterns can also be generated using the
 same basic code, such as a 2D grid pattern:
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -142,7 +142,7 @@ Note to show both simultaneously, we shift the x-coordinate of Particles
 in the sphere by -1 (i.e., pos[0]-=1.0) and +1 for the disk (i.e,
 pos[0]+=1.0).
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -177,7 +177,7 @@ corresponds to the sphere (class SphereLJ), and one that corresponds to
 the disk (class DiskLJ), and then instantiate and shift each of these
 individually in the MonoLJ component.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -229,7 +229,7 @@ Again, since mBuild is hierarchical, the pattern functions can be used
 to generate large systems of any arbitary component. For example, we can
 replicate the SphereLJ component on a regular array.
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
 
@@ -270,7 +270,7 @@ command allows a compound to be rotated, in place, about a specific axis
 (i.e., it considers the origin for the rotation to lie at the compound’s
 center of mass).
 
-.. code:: ipython3
+.. code:: ipython
 
     import mbuild as mb
     import random
@@ -319,7 +319,7 @@ Configurations can be dumped to file using the save command; this takes
 advantage of MDTraj and supports a range of file formats (see
 http://MDTraj.org).
 
-.. code:: ipython3
+.. code:: ipython
 
     #save as xyz file
     monoLJ.save('output.xyz')

From 40ffe97fa8c3e34873e4be2b4e5f063b4282d1dc Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 15:46:51 -0600
Subject: [PATCH 11/12] Revert "chagne ipython3 to just ipython in rst"

This reverts commit 7e6c9633d4d4ea6e92e5a318cefc04d944f970a2.
---
 .../quick_start/Box_example.rst               |  6 ++---
 .../quick_start/fill_box_example.rst          | 12 ++++-----
 .../quick_start/load_files.rst                |  8 +++---
 .../quick_start/polymer_example.rst           |  6 ++---
 .../tutorials/tutorial_ethane.rst             | 24 ++++++++---------
 .../tutorials/tutorial_lattice.rst            | 26 +++++++++----------
 .../tutorials/tutorial_methane.rst            | 12 ++++-----
 .../tutorials/tutorial_monolayer.rst          | 16 ++++++------
 .../tutorials/tutorial_polymers.rst           | 22 ++++++++--------
 .../tutorials/tutorial_simple_LJ.rst          | 18 ++++++-------
 10 files changed, 75 insertions(+), 75 deletions(-)

diff --git a/docs/getting_started/quick_start/Box_example.rst b/docs/getting_started/quick_start/Box_example.rst
index 7a0157bdc..b8cff8e22 100644
--- a/docs/getting_started/quick_start/Box_example.rst
+++ b/docs/getting_started/quick_start/Box_example.rst
@@ -4,7 +4,7 @@ Box
 
 Import the required mbuild package.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -18,7 +18,7 @@ Build an empty orthogonal **mBuild** Box (i.e., the angle in degrees are 𝛼 =
     Note: if the angles are not specified, the system will default to an orthogonal box
     (i.e., the angle in degrees are 𝛼 = 90, 𝛽 = 90, 𝛾 = 90).
 
-.. code:: ipython
+.. code:: ipython3
 
     empty_box = mb.Box(lengths=[4.0, 4.0, 4.0], angles=[90, 90, 90])
 
@@ -28,6 +28,6 @@ Non-Orthogonal Box
 
 Build an empty non-orthogonal **mBuild** Box (i.e., the angle in degrees are 𝛼 = 90, 𝛽 = 90, 𝛾 = 120) measuring 4.0 nm in the x and y-dimensions, and 5.0 nm in the z-dimension.
 
-.. code:: ipython
+.. code:: ipython3
 
     empty_box = mb.Box(lengths=[4.0, 4.0, 5.0], angles=[90, 90, 120])
diff --git a/docs/getting_started/quick_start/fill_box_example.rst b/docs/getting_started/quick_start/fill_box_example.rst
index d44ef3f86..992e5053d 100644
--- a/docs/getting_started/quick_start/fill_box_example.rst
+++ b/docs/getting_started/quick_start/fill_box_example.rst
@@ -12,7 +12,7 @@ All-Atom (AA) Hexane and Ethanol System
 
 Import the required mbuild package.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -26,7 +26,7 @@ Lastly, the hexane and ethanol molecule's configuration will be energy minimized
 .. note::
     The energy minimize step requires the `foyer <https://foyer.mosdef.org/en/stable/>`_ package.
 
-.. code:: ipython
+.. code:: ipython3
 
     hexane = mb.load('CCCCCC', smiles=True)
     hexane.name = 'HEX'
@@ -39,7 +39,7 @@ Lastly, the hexane and ethanol molecule's configuration will be energy minimized
 
 The liquid box is built to a density of 680 kg/m\ :sup:`3`, with a 50/50 mol ratio of hexane and ethanol, and will be in an orthogonal box measuring 5.0 nm in the x, y, and z-dimensions.
 
-.. code:: ipython
+.. code:: ipython3
 
     box_liq = mb.fill_box(compound= [hexane, ethanol],
                           density=680,
@@ -58,7 +58,7 @@ United Atom (UA) Methane System
 
 Import the required mbuild package.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -67,7 +67,7 @@ Construct a pseudo-monatomic molecule (united atom (UA) methane), for use with t
 `TraPPE <http://trappe.oit.umn.edu>`_ FF.  The UA methane, bead type `"_CH4"`, will be built as a child (``mbuild.Compound.children``), so the parent (``mbuild.Compound``) will
 allow a user-selected residue name (``mbuild.Compound.name``). If the methane is built using ``methane = mb.Compound(name="_CH4")``, then the user must keep the residue name `"_CH4"` or `foyer <https://foyer.mosdef.org/en/stable/>`_ will not recognize the bead type when using the standard TraPPE force field XML file.
 
-.. code:: ipython
+.. code:: ipython3
 
     methane = mb.Compound(name="MET")
     methane_child_bead = mb.Compound(name="_CH4")
@@ -79,7 +79,7 @@ allow a user-selected residue name (``mbuild.Compound.name``). If the methane is
 
 The orthogonal liquid box contains 1230 methane molecules and measures 4.5 nm in all the x, y, and z-dimensions.
 
-.. code:: ipython
+.. code:: ipython3
 
     box_liq = mb.fill_box(compound=methane,
                           n_compounds=1230,
diff --git a/docs/getting_started/quick_start/load_files.rst b/docs/getting_started/quick_start/load_files.rst
index afd07452f..0c9af1019 100644
--- a/docs/getting_started/quick_start/load_files.rst
+++ b/docs/getting_started/quick_start/load_files.rst
@@ -11,14 +11,14 @@ Create an ``mbuild.Compound`` (i.e., the "pentane" variable) by loading a molecu
 
 Import the required mbuild packages.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
 
 Load the "pentane.mol2" file from its directory.
 
-.. code:: ipython
+.. code:: ipython3
 
     pentane = mb.load("path_to_mol2_file/pentane.mol2")
 
@@ -31,7 +31,7 @@ Build an ``mbuild.Compound`` (i.e., the "ETV_triclinic" variable) by loading a `
 
 Import the required mbuild packages.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     from mbuild.lattice import load_cif
@@ -40,7 +40,7 @@ Import the required mbuild packages.
 
 The `CIF <https://www.iucr.org/resources/cif>`_ file is loaded using the ``load_cif`` function. Next, three (3) cell units shall be built for all the x, y, and z-dimensions with the populate function.  Finally, the `CIF <https://www.iucr.org/resources/cif>`_'s residues are named 'ETV'.
 
-.. code:: ipython
+.. code:: ipython3
 
     lattice_cif_ETV_triclinic = load_cif("path_to_cif_file/ETV_triclinic.cif")
     ETV_triclinic = lattice_cif_ETV_triclinic.populate(x=3, y=3, z=3)
diff --git a/docs/getting_started/quick_start/polymer_example.rst b/docs/getting_started/quick_start/polymer_example.rst
index 02c73d7c6..ac567bfc9 100644
--- a/docs/getting_started/quick_start/polymer_example.rst
+++ b/docs/getting_started/quick_start/polymer_example.rst
@@ -6,7 +6,7 @@ Use two (2) different monomer units, A and B, to construct a polymer, capping it
 
 Import the required mbuild packages.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     from mbuild.lib.recipes.polymer import Polymer
@@ -20,7 +20,7 @@ Set the `chain` as a ``Polymer`` class, adding `comp_1` and `comp_2` as the mono
     Setting the indices identifies which atoms will be removed and have ports created in their place.
 
 
-.. code:: ipython
+.. code:: ipython3
 
     comp_1 = mb.load('CC', smiles=True) # mBuild compound of the monomer unit
     comp_2 = mb.load('COC', smiles=True) # mBuild compound of the monomer unit
@@ -40,7 +40,7 @@ Select the carboxylic acid and amine end groups that we want to use for the head
 Then, build the polymer with three (3) iterations of the AB sequence, and the selected head and tail end groups.
 
 
-.. code:: ipython
+.. code:: ipython3
 
     chain.add_end_groups(mb.load('C(=O)O',smiles=True),
                          index=3,
diff --git a/docs/getting_started/tutorials/tutorial_ethane.rst b/docs/getting_started/tutorials/tutorial_ethane.rst
index a3b6293ec..48c2999b3 100644
--- a/docs/getting_started/tutorials/tutorial_ethane.rst
+++ b/docs/getting_started/tutorials/tutorial_ethane.rst
@@ -9,7 +9,7 @@ transforms.
 
 First, we need to import the mbuild package:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -23,7 +23,7 @@ connectivity information).
 
 Let’s start by reading a methyl group from a ``.pdb`` file:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -34,7 +34,7 @@ Let’s start by reading a methyl group from a ``.pdb`` file:
 Now let’s use our first coordinate transform to center the methyl at its
 carbon atom:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -49,7 +49,7 @@ typically points to a particle that the ``Port`` should be associated
 with. In our methyl group, the ``Port`` should be anchored to the carbon
 atom so that we can now form bonds to this carbon:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -66,14 +66,14 @@ By default, ``Ports`` are never output from the mBuild structure.
 However, it can be useful to look at a molecule with the ``Ports`` to
 check your work as you go:
 
-.. code:: ipython
+.. code:: ipython3
 
     ch3.visualize(show_ports=True)
 
 Now we wrap the methyl group into a python class, so that we can reuse
 it as a component to build more complex molecules later.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -111,7 +111,7 @@ automatically chosen.
 
 Now the fun part: stick ’em together to create an ethane:
 
-.. code:: ipython
+.. code:: ipython3
 
     ethane = mb.Compound()
 
@@ -126,18 +126,18 @@ rotates and translates it such that two other ``Compounds`` overlap.
 Typically, as in this case, those two other ``Compounds`` are ``Ports``
 - in our case, ``methyl1['up']`` and ``methyl2['up']``.
 
-.. code:: ipython
+.. code:: ipython3
 
     ethane.visualize()
 
-.. code:: ipython
+.. code:: ipython3
 
     ethane.visualize(show_ports=True)
 
 Similarly, if we want to make ethane a reusable component, we need to
 wrap it into a python class.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -151,12 +151,12 @@ wrap it into a python class.
                              from_positions=self['methyl_1']['up'],
                              to_positions=self['methyl_2']['up'])
 
-.. code:: ipython
+.. code:: ipython3
 
     ethane = Ethane()
     ethane.visualize()
 
-.. code:: ipython
+.. code:: ipython3
 
     # Save to .mol2
     ethane.save('ethane.mol2', overwrite=True)
diff --git a/docs/getting_started/tutorials/tutorial_lattice.rst b/docs/getting_started/tutorials/tutorial_lattice.rst
index 1b7bf8510..2deba6ccc 100644
--- a/docs/getting_started/tutorials/tutorial_lattice.rst
+++ b/docs/getting_started/tutorials/tutorial_lattice.rst
@@ -58,7 +58,7 @@ desired crystal structures.
 To begin, we will call the python ``help()`` method to observe the
 parameters and attributes of the ``Lattice`` class.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild
     help(mbuild.Lattice)
@@ -79,7 +79,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example:
 
-   .. code:: ipython
+   .. code:: ipython3
 
        lattice_spacing = [0.5, 0.5, 0.5]
 
@@ -100,7 +100,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For example: Cubic Cell
 
-   .. code:: ipython
+   .. code:: ipython3
 
        lattice_vectors = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
 
@@ -112,7 +112,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For example: Cubic Cell
 
-   .. code:: ipython
+   .. code:: ipython3
 
        angles = [90, 90, 90]
 
@@ -140,7 +140,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example: FCC All Unique
 
-   .. code:: ipython
+   .. code:: ipython3
 
        lattice_points = {'A' : [[0, 0, 0]],
                          'B' : [[0.5, 0.5, 0]],
@@ -150,7 +150,7 @@ ever get stuck, remember to use the python built-in ``help()`` method!
 
    For Example: FCC All Same
 
-   .. code:: ipython
+   .. code:: ipython3
 
        lattice_points = {'A' : [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]] }
 
@@ -179,7 +179,7 @@ replications in the x, y, and z directions.
 
       For Example: FCC All Unique
 
-          .. code:: ipython
+          .. code:: ipython3
 
             lattice_points = {'A' : [[0, 0, 0]],
                               'B' : [[0.5, 0.5, 0]],
@@ -197,7 +197,7 @@ replications in the x, y, and z directions.
 
       For Example: FCC All Same
 
-          .. code:: ipython
+          .. code:: ipython3
 
             lattice_points = {'A' : [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]] }
 
@@ -217,7 +217,7 @@ Simple Cubic (SC)
 
 -  Polonium
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import numpy as np
@@ -250,7 +250,7 @@ Body-centered Cubic (BCC)
 
 -  CsCl
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import numpy as np
@@ -285,7 +285,7 @@ Face-centered Cubic (FCC)
 
 -  Cu
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import numpy as np
@@ -318,7 +318,7 @@ Diamond (Cubic)
 
 -  Si
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import numpy as np
@@ -352,7 +352,7 @@ Graphene (2D)
 
 -  C
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import numpy as np
diff --git a/docs/getting_started/tutorials/tutorial_methane.rst b/docs/getting_started/tutorials/tutorial_methane.rst
index 0ae129b43..632ba0401 100644
--- a/docs/getting_started/tutorials/tutorial_methane.rst
+++ b/docs/getting_started/tutorials/tutorial_methane.rst
@@ -7,7 +7,7 @@ The primary building block in mBuild is a ``Compound``. Anything you
 construct will inherit from this class. Let’s start with some basic
 imports and initialization:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -21,7 +21,7 @@ hierarchy are referred to as ``Particles``. Note however, that this is
 purely semantic in mBuild to help clearly designate the bottom of a
 hierarchy.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -56,7 +56,7 @@ hydrogen. Note that for typical use cases, you will almost never have to
 explicitly define a bond when using mBuild - this is just to show you
 what’s going on under the hood:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -78,7 +78,7 @@ fancy label, it’s also referenceable via ``self['HC'][0]``.
 Alright now that we’ve got the basics, let’s finish building our
 ``Methane`` and take a look at it:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -101,12 +101,12 @@ Alright now that we’ve got the basics, let’s finish building our
             self.add_bond((self[0], self['HC'][2]))
             self.add_bond((self[0], self['HC'][3]))
 
-.. code:: ipython
+.. code:: ipython3
 
     methane = Methane()
     methane.visualize()
 
-.. code:: ipython
+.. code:: ipython3
 
     # Save to .mol2
     methane.save('methane.mol2',overwrite=True)
diff --git a/docs/getting_started/tutorials/tutorial_monolayer.rst b/docs/getting_started/tutorials/tutorial_monolayer.rst
index 11c9eb5c7..0538a7b23 100644
--- a/docs/getting_started/tutorials/tutorial_monolayer.rst
+++ b/docs/getting_started/tutorials/tutorial_monolayer.rst
@@ -28,7 +28,7 @@ consistent! The more components we collect in our library with the same
 labeling conventions, the easier it becomes to build ever more complex
 structures.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -50,13 +50,13 @@ structures.
             # Hoist silane port to AlkylSilane level.
             self.add(silane['down'], 'down', containment=False)
 
-.. code:: ipython
+.. code:: ipython3
 
     AlkylSilane(5).visualize()
 
 Now let’s create a substrate to which we can later attach our monomers:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     from mbuild.lib.surfaces import Betacristobalite
@@ -72,7 +72,7 @@ library. The ``TiledCompound`` tool allows you replicate any
 Next, let’s create our monomer and a hydrogen atom that we’ll place on
 unoccupied surface sites:
 
-.. code:: ipython
+.. code:: ipython3
 
     from mbuild.lib.atoms import H
     alkylsilane = AlkylSilane(chain_length=10)
@@ -87,7 +87,7 @@ figures out what the closest ports are to the pattern points and then
 attaches copies of the guest onto the binding sites identified by the
 pattern:
 
-.. code:: ipython
+.. code:: ipython3
 
     pattern = mb.Grid2DPattern(8, 8)  # Evenly spaced, 2D grid of points.
 
@@ -98,12 +98,12 @@ Also note the ``backfill`` optional argument which allows you to place a
 different compound on any unused ports. In this case we want to backfill
 with hydrogen atoms on every port without a chain.
 
-.. code:: ipython
+.. code:: ipython3
 
     monolayer = mb.Compound([tiled_surface, chains, hydrogens])
     monolayer.visualize() # Warning: may be slow in IPython notebooks
 
-.. code:: ipython
+.. code:: ipython3
 
     # Save as .mol2 file
     monolayer.save('monolayer.mol2', overwrite=True)
@@ -111,7 +111,7 @@ with hydrogen atoms on every port without a chain.
 ``lib.recipes.monolayer.py`` wraps many these functions into a simple,
 general class for generating the monolayers, as shown below:
 
-.. code:: ipython
+.. code:: ipython3
 
     from mbuild.lib.recipes import Monolayer
 
diff --git a/docs/getting_started/tutorials/tutorial_polymers.rst b/docs/getting_started/tutorials/tutorial_polymers.rst
index 7e9069ab4..179c5c530 100644
--- a/docs/getting_started/tutorials/tutorial_polymers.rst
+++ b/docs/getting_started/tutorials/tutorial_polymers.rst
@@ -17,7 +17,7 @@ importing the coordinates from a pdb file, as in the previous example,
 we will instead explicitly define them in the class. Recall that
 distance units are nm in mBuild.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -60,7 +60,7 @@ given in radians. Similarly, the ports should be rotated around the
 x-axis by the same amount so that atoms can be added in a realistic
 orientation.
 
-.. code:: ipython
+.. code:: ipython3
 
     import numpy as np
     import mbuild as mb
@@ -108,7 +108,7 @@ make a copy. The ``force_overlap()`` function is used to connect the
 ``'up'`` port from ``current_monomer`` to the ``'down'`` port of
 ``last_mononer``.
 
-.. code:: ipython
+.. code:: ipython3
 
     class AlkanePolymer(mb.Compound):
         def __init__(self):
@@ -135,7 +135,7 @@ We can also add a variable ``chain_length`` both to the for loop and
 ``init`` that will allow the length of the polymer to be adjusted when
 the class is instantiated.
 
-.. code:: ipython
+.. code:: ipython3
 
     import numpy as np
     import mbuild as mb
@@ -182,7 +182,7 @@ the class is instantiated.
                 self.add(current_monomer)
                 last_monomer=current_monomer
 
-.. code:: ipython
+.. code:: ipython3
 
     polymer = AlkanePolymer(chain_length=10)
     polymer.visualize(show_ports=True)
@@ -211,7 +211,7 @@ A simple hexane molecule is built using ``mBuild``'s packaged polymer builder.
 This is done by loading a methane molecule via a SMILES string.
 The indices are explicitly selected, so the molecule builds out in the proper directions and does not overlap.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     from mbuild.lib.recipes.polymer import Polymer
@@ -235,7 +235,7 @@ The end groups are added via the ``add_end_groups`` attribute, specifying the at
 the location of each end group (``label``), and if the tail end group is duplicated to the head of the polymer (``duplicate``).
 The indices are explicitly selected, so the molecule builds out in the proper directions and does not overlap.
 
-.. code:: ipython
+.. code:: ipython3
 
     from mbuild.lib.recipes.polymer import Polymer
     import mbuild as mb
@@ -275,7 +275,7 @@ constructed above and translating and/or rotating the alkanes in space.
 ``mBuild`` provides many routines that can be used to create different
 patterns, to which the polymers can be shifted.
 
-.. code:: ipython
+.. code:: ipython3
 
     comp = mb.load('C', smiles=True) # mBuild compound of the monomer unit
     polymer = Polymer()
@@ -311,7 +311,7 @@ patterns, to which the polymers can be shifted.
 Other patterns can be used, e.g., the ``Grid3DPattern``. We can also use
 the rotation commands to randomize the orientation.
 
-.. code:: ipython
+.. code:: ipython3
 
     import random
 
@@ -344,7 +344,7 @@ the rotation commands to randomize the orientation.
 ``mBuild`` also provides an interface to ``PACKMOL``, allowing the
 creation of a randomized configuration.
 
-.. code:: ipython
+.. code:: ipython3
 
     comp = mb.load('C', smiles=True) # mBuild compound of the monomer unit
     polymer = Polymer()
@@ -373,7 +373,7 @@ amount of perturbation. Note that large values of ``delta`` may result
 in the chain overlapping itself, as ``mBuild`` does not currently
 include routines to exclude such overlaps.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
diff --git a/docs/getting_started/tutorials/tutorial_simple_LJ.rst b/docs/getting_started/tutorials/tutorial_simple_LJ.rst
index 812085bd2..0afb4f5d1 100644
--- a/docs/getting_started/tutorials/tutorial_simple_LJ.rst
+++ b/docs/getting_started/tutorials/tutorial_simple_LJ.rst
@@ -12,7 +12,7 @@ Note, the color and radius associated with a Particle name can be set
 and passed to the visualize command. Colors are passed in hex format
 (see http://www.color-hex.com/color/bfbfbf).
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -63,7 +63,7 @@ translating to the specified location. Since the lj_proto particle in
 this example starts at the origin, these two commands produce identical
 behavior.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -91,7 +91,7 @@ in pattern, cloning, translating, and adding to the system. Note,
 because Grid3DPattern defines points between 0 and 1, they must be
 scaled based on the desired system size, i.e., pattern.scale(2).
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -115,7 +115,7 @@ Larger systems can therefore be easily generated by toggling the values
 given to Grid3DPattern. Other patterns can also be generated using the
 same basic code, such as a 2D grid pattern:
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -142,7 +142,7 @@ Note to show both simultaneously, we shift the x-coordinate of Particles
 in the sphere by -1 (i.e., pos[0]-=1.0) and +1 for the disk (i.e,
 pos[0]+=1.0).
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -177,7 +177,7 @@ corresponds to the sphere (class SphereLJ), and one that corresponds to
 the disk (class DiskLJ), and then instantiate and shift each of these
 individually in the MonoLJ component.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -229,7 +229,7 @@ Again, since mBuild is hierarchical, the pattern functions can be used
 to generate large systems of any arbitary component. For example, we can
 replicate the SphereLJ component on a regular array.
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
 
@@ -270,7 +270,7 @@ command allows a compound to be rotated, in place, about a specific axis
 (i.e., it considers the origin for the rotation to lie at the compound’s
 center of mass).
 
-.. code:: ipython
+.. code:: ipython3
 
     import mbuild as mb
     import random
@@ -319,7 +319,7 @@ Configurations can be dumped to file using the save command; this takes
 advantage of MDTraj and supports a range of file formats (see
 http://MDTraj.org).
 
-.. code:: ipython
+.. code:: ipython3
 
     #save as xyz file
     monoLJ.save('output.xyz')

From b9f45dede26bc2077e3962fc96757e88788daacb Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Fri, 8 Mar 2024 15:48:16 -0600
Subject: [PATCH 12/12] add ipython to docs env

---
 docs/docs-env.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/docs-env.yml b/docs/docs-env.yml
index 3f4897af5..24ada5ee0 100644
--- a/docs/docs-env.yml
+++ b/docs/docs-env.yml
@@ -5,6 +5,7 @@ channels:
 dependencies:
   - importlib_resources
   - python=3.11
+  - ipython
   - pip
   - pip:
     - boltons