diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 83f07e7ee3a..a2a1f95a38d 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -29,7 +29,7 @@ Thank you for contributing to RMG-Py! Please take a moment to review our guideli
 
 ### **Do you want to contribute to the documentation?**
 
-* Documentation is [hosted here](http://reactionmechanismgenerator.github.io/RMG-Py/) using [Sphinx](https://www.sphinx-doc.org/en/master/). 
+* Documentation is [hosted here](https://reactionmechanismgenerator.github.io/RMG-Py/) using [Sphinx](https://www.sphinx-doc.org/en/master/). 
 
 * The live version of the documentation is hosted on the `gh-pages` branch which is updated upon pushes to the `main` branch of RMG-Py.
 
diff --git a/README.md b/README.md
index a2e46fb81d9..dc29b16fe0a 100644
--- a/README.md
+++ b/README.md
@@ -22,12 +22,12 @@ Gaussian, Q-Chem, Molpro, Orca, Psi4, and TeraChem.
 
 ## How to Install
 You can either download the source from GitHub and compile yourself, or download the binaries from Anaconda.
-Please see the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
+Please see the [Download and Install](https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
 
 ## Documentation
-- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [Arkane Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [RMG API Reference](http://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
+- [RMG Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [Arkane Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [RMG API Reference](https://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
 
 ## How to Contribute
 Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md)
@@ -44,10 +44,10 @@ perform thermodynamics and kinetics searches
 - [Issues Page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/): view current issues and feature requests
 
 ## Credits
-- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the 
-[Massachusetts Institute of Technology](http://web.mit.edu/) 
-- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at 
-[Northeastern University](http://www.northeastern.edu/). 
+- [Professor William H. Green's research group](https://greengroup.mit.edu/) at the 
+[Massachusetts Institute of Technology](https://web.mit.edu/) 
+- [Professor Richard H. West's research group](https://www.northeastern.edu/comocheng/) at 
+[Northeastern University](https://www.northeastern.edu/). 
 
 ## Resources and References
 The resources and relevant publications are listed [here](https://rmg.mit.edu/resources) on the RMG-website. 
diff --git a/arkane/README.md b/arkane/README.md
index 98512510bec..86a87dd6606 100644
--- a/arkane/README.md
+++ b/arkane/README.md
@@ -13,13 +13,13 @@ Arkane is distributed via the [RMG-Py repository](https://github.com/ReactionMec
 as a [root module](https://github.com/ReactionMechanismGenerator/RMG-Py/tree/main/arkane).
 
 ## How to Install
-Please follow the [installation instructions](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)
+Please follow the [installation instructions](https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)
 for RMG-Py.
 
 ## Documentation
-- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [Arkane Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [RMG API Reference](http://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
+- [RMG Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [Arkane Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [RMG API Reference](https://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
 
 ## How to cite
 A. Grinberg Dana, M.S. Johnson, J.W. Allen, S. Sharma, S. Raman, M. Liu, C.W. Gao, C.A. Grambow, M.J. Goldman,
@@ -32,7 +32,7 @@ A statistical mechanics, thermodynamics, transition state theory, and master equ
 DOI: [10.1002/kin.21637](https://doi.org/10.1002/kin.21637)
 
 ## How to Contribute
-Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/RMG-Contributor-Guidelines)
+Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md)
 for details on how to contribute to RMG-Py or RMG-database.
 
 ## How to Give Feedback
diff --git a/arkane/encorr/corr.py b/arkane/encorr/corr.py
index 1f9e8f8f328..bcafaedd6ae 100644
--- a/arkane/encorr/corr.py
+++ b/arkane/encorr/corr.py
@@ -221,7 +221,7 @@ def assign_frequency_scale_factor(level_of_theory: Union[LevelOfTheory, Composit
 
     Sources:
         [1] I.M. Alecu, J. Zheng, Y. Zhao, D.G. Truhlar, J. Chem. Theory Comput. 2010, 6, 2872, DOI: 10.1021/ct100326h
-        [2] http://cccbdb.nist.gov/vibscalejust.asp
+        [2] https://cccbdb.nist.gov/vibscalejustx.asp
         [3] http://comp.chem.umn.edu/freqscale/190107_Database_of_Freq_Scale_Factors_v4.pdf
         [4] Calculated as described in 10.1021/ct100326h
         [5] J.A. Montgomery, M.J. Frisch, J. Chem. Phys. 1999, 110, 2822–2827, DOI: 10.1063/1.477924
diff --git a/arkane/ess/gaussian.py b/arkane/ess/gaussian.py
index b822ae4b98f..19d5ba94455 100644
--- a/arkane/ess/gaussian.py
+++ b/arkane/ess/gaussian.py
@@ -524,7 +524,7 @@ def _load_scan_specs(self, letter_spec, get_after_letter_spec=False):
         parameters after letter_spec is found. If not specified or False, it will
         return the preceeding letters, which are typically the atom numbers.
 
-        More information about the syntax can be found http://gaussian.com/opt/
+        More information about the syntax can be found https://gaussian.com/opt/
         """
         output = []
         reached_input_spec_section = False
diff --git a/arkane/main.py b/arkane/main.py
index b5345f99c03..9526b6e75c0 100644
--- a/arkane/main.py
+++ b/arkane/main.py
@@ -465,7 +465,7 @@ def log_header(level=logging.INFO):
     logging.log(level, '#   Authors: RMG Developers (rmg_dev@mit.edu)                  #')
     logging.log(level, '#   P.I.s:   William H. Green (whgreen@mit.edu)                #')
     logging.log(level, '#            Richard H. West (r.west@neu.edu)                  #')
-    logging.log(level, '#   Website: http://reactionmechanismgenerator.github.io/      #')
+    logging.log(level, '#   Website: https://reactionmechanismgenerator.github.io/      #')
     logging.log(level, '#                                                              #')
     logging.log(level, '################################################################')
     logging.log(level, '')
diff --git a/arkane/statmech.py b/arkane/statmech.py
index a77d75219c7..af82a045bb8 100644
--- a/arkane/statmech.py
+++ b/arkane/statmech.py
@@ -1002,7 +1002,7 @@ def project_rotors(conformer, hessian, rotors, linear, is_ts, get_projected_out_
     constant matrix and use this to determine the vibrational frequencies. The
     list of vibrational frequencies is returned in cm^-1.
 
-    Refer to Gaussian whitepaper (http://gaussian.com/vib/) for procedure to calculate
+    Refer to Gaussian whitepaper (https://gaussian.com/vib/) for procedure to calculate
     harmonic oscillator vibrational frequencies using the force constant matrix.
     """
     n_rotors = 0
diff --git a/documentation/RMG-Py_API_Reference.pdf b/documentation/RMG-Py_API_Reference.pdf
index 377313f82c6..e1750792d0f 100644
Binary files a/documentation/RMG-Py_API_Reference.pdf and b/documentation/RMG-Py_API_Reference.pdf differ
diff --git a/documentation/RMG-Py_and_Arkane_Documentation.pdf b/documentation/RMG-Py_and_Arkane_Documentation.pdf
index 3bd4283016c..674e37f91b4 100644
Binary files a/documentation/RMG-Py_and_Arkane_Documentation.pdf and b/documentation/RMG-Py_and_Arkane_Documentation.pdf differ
diff --git a/documentation/source/latex-rmg.rst b/documentation/source/latex-rmg.rst
index 84d4c459d86..5fdeb4998f3 100644
--- a/documentation/source/latex-rmg.rst
+++ b/documentation/source/latex-rmg.rst
@@ -8,19 +8,19 @@ RMG is an automatic chemical reaction mechanism generator
 that constructs kinetic models composed of elementary chemical reaction 
 steps using a general understanding of how molecules react. This documentation is for the newer Python version of RMG that we call RMG-Py.
 
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| I want to...                                | Resource                                                                               |
-+=============================================+========================================================================================+
-| analyze models & search databases           | `RMG website resources <https://rmg.mit.edu/>`__  (no download needed)                 |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| create mechanisms automatically             | Download RMG with the RMG User's Guide                                                 |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| make transition state theory calculations   | Run Arkane after downloading RMG. See the Arkane User's Guide                          |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| post an issue with RMG                      | `GitHub issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__   |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| contribute to the RMG project               | `RMG developer's wiki <https://github.com/ReactionMechanismGenerator/RMG-Py/wiki>`__   |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| I want to...                                | Resource                                                                                                      |
++=============================================+===============================================================================================================+
+| analyze models & search databases           | `RMG website resources <https://rmg.mit.edu/>`__  (no download needed)                                        |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| create mechanisms automatically             | Download RMG with the RMG User's Guide                                                                        |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| make transition state theory calculations   | Run Arkane after downloading RMG. See the Arkane User's Guide                                                 |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| post an issue with RMG                      | `GitHub issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__                          |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| contribute to the RMG project               | `Contributor guidelines <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md>`__   |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
 
 Arkane is developed and distributed as part of RMG-Py, but can be used as a stand-alone
 application for Thermochemistry, Transition State Theory, and Master Equation chemical kinetics
diff --git a/documentation/source/reference/molecule/graph.rst b/documentation/source/reference/molecule/graph.rst
index 8750b3e161c..c37c78de30f 100644
--- a/documentation/source/reference/molecule/graph.rst
+++ b/documentation/source/reference/molecule/graph.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.graph.Graph:
+
 **************************
 rmgpy.molecule.graph.Graph
 **************************
diff --git a/documentation/source/reference/molecule/group.rst b/documentation/source/reference/molecule/group.rst
index 2654849ec31..3f8e0e691cf 100644
--- a/documentation/source/reference/molecule/group.rst
+++ b/documentation/source/reference/molecule/group.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Group:
+
 ********************
 rmgpy.molecule.Group
 ********************
diff --git a/documentation/source/reference/molecule/molecule.rst b/documentation/source/reference/molecule/molecule.rst
index 7a556771beb..777ad002f88 100644
--- a/documentation/source/reference/molecule/molecule.rst
+++ b/documentation/source/reference/molecule/molecule.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Molecule:
+
 ***********************
 rmgpy.molecule.Molecule
 ***********************
diff --git a/documentation/source/users/arkane/faq.rst b/documentation/source/users/arkane/faq.rst
index dd4c6e6cf04..f4cffc64728 100644
--- a/documentation/source/users/arkane/faq.rst
+++ b/documentation/source/users/arkane/faq.rst
@@ -30,8 +30,8 @@ data and physical quantities.
 
 .. [#f2] No longer distributed
 
-.. _MultiWell: https://clasp-research.engin.umich.edu/multiwell/
-.. _UNIMOL: http://www.ccl.net/cca/software/SOURCES/FORTRAN/unimol/index.shtml
-.. _ChemRate: https://kinetics.nist.gov/ChemRate/
-.. _Variflex: http://web.archive.org/web/20181126234555/http://ftp.tcg.anl.gov/pub/variflex/Summary.vrfx
+.. _MultiWell: https://web.archive.org/web/20220927051103/https://multiwell.engin.umich.edu/about/
+.. _UNIMOL: https://server.ccl.net//cca/software/SOURCES/FORTRAN/unimol/index.shtml
+.. _ChemRate: https://web.archive.org/web/20220621125921/https://kinetics.nist.gov/ChemRate/
+.. _Variflex: https://web.archive.org/web/20181126234555/http://ftp.tcg.anl.gov/pub/variflex/Summary.vrfx
 .. _MESMER: https://sourceforge.net/projects/mesmer/
diff --git a/documentation/source/users/arkane/input.rst b/documentation/source/users/arkane/input.rst
index 002b00b1c77..4e3a53de0a9 100644
--- a/documentation/source/users/arkane/input.rst
+++ b/documentation/source/users/arkane/input.rst
@@ -170,7 +170,7 @@ Frequency Scale Factor
 ======================
 
 Frequency scale factors are empirically fit to experiment for different ``modelChemistry``.
-Refer to NIST website for values (http://cccbdb.nist.gov/vibscalejust.asp).
+Refer to NIST website for values (https://cccbdb.nist.gov/vibscalejustx.asp).
 For CBS-QB3, which is not included in the link above, ``frequencyScaleFactor = 0.99`` according to Montgomery et al.
 (*J. Chem. Phys. 1999, 110, 2822–2827*).
 The frequency scale factor is automatically assigned according to the supplied ``modelChemistry``, if available
@@ -617,7 +617,7 @@ systems in literature. For example, if the user is interested in a pressure-depe
 formula C7H8, the single exponential down parameters for toluene in helium availabe from literature could be used for
 all unimolecular isomers in the network (assuming helium is the bath gas). One helpful literature source for calculated
 exponential down parameters is the following paper:
-http://www.sciencedirect.com/science/article/pii/S1540748914001084#s0060
+http://www.sciencedirect.com/science/article/pii/S1540748914001084
 
 
 Option #2: Directly Enter Molecular Properties
@@ -1056,7 +1056,7 @@ An example of the ``network`` function is given below along with a scheme of the
 
 .. image:: acetyl+O2.jpg
 
-Image source: `J.W. Allen, PhD dissertation, MIT 2013 <http://hdl.handle.net/1721.1/81677>`_,
+Image source: `J.W. Allen, PhD dissertation, MIT 2013 <https://dspace.mit.edu/handle/1721.1/81677>`_,
 calculated at the RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level of theory
 
 Pressure Dependent Rate Calculation
diff --git a/documentation/source/users/arkane/introduction.rst b/documentation/source/users/arkane/introduction.rst
index 22cc0857e95..26ab75fe195 100644
--- a/documentation/source/users/arkane/introduction.rst
+++ b/documentation/source/users/arkane/introduction.rst
@@ -31,7 +31,7 @@ License
 =======
 
 Arkane is provided as free, open source code under the terms of the
-`MIT/X11 License <http://www.opensource.org/licenses/mit-license.php>`_. The
+`MIT/X11 License <https://opensource.org/license/mit>`_. The
 full, official license is reproduced below
 
 
diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
index 26c737ad7d9..0b836246a44 100644
--- a/documentation/source/users/rmg/installation/anacondaDeveloper.rst
+++ b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
@@ -121,7 +121,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
     python replace/with/path/to/rmg.py input.py
 
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
-For more information about using conda, please check out the `conda user guide <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+For more information about using conda, please check out the `conda user guide <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
 
 
 Debugging
diff --git a/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst b/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst
index 22503f32308..81b0eff1190 100644
--- a/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst
+++ b/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst
@@ -10,7 +10,7 @@ Installation by Source Using Anaconda Environment for Windows
     .. image:: images/AnacondaInstallWindows.png
         :align: center
 
-#. Install `Git <http://git-scm.com/download/win>`_, the open source version control package. When asked, append Git tools to your Command Prompt. It is also recommended to commit Unix-style line endings:
+#. Install `Git <https://git-scm.com/download/win>`_, the open source version control package. When asked, append Git tools to your Command Prompt. It is also recommended to commit Unix-style line endings:
 
     .. image:: images/InstallGit.png
         :align: center
@@ -44,7 +44,7 @@ Installation by Source Using Anaconda Environment for Windows
 
 #. If you set any new environment variables, you must now close and reopen the command prompt so that those environment variables can be refreshed and used.
    
-#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <http://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <http://openmopac.net/form.php>`_.  Once you have it, type the following into your command prompt ::
+#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <https://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <https://openmopac.net/form.php>`_.  Once you have it, type the following into your command prompt ::
     
     mopac password_string_here
 
diff --git a/documentation/source/users/rmg/installation/anacondaUser.rst b/documentation/source/users/rmg/installation/anacondaUser.rst
index 0244e7ce7f0..d2da18ecdf8 100644
--- a/documentation/source/users/rmg/installation/anacondaUser.rst
+++ b/documentation/source/users/rmg/installation/anacondaUser.rst
@@ -15,7 +15,7 @@ Binary Installation Using Anaconda for Unix-Based Systems: Linux and Mac OSX
 
     conda activate rmg_env
 
-   For more information about using conda, please check out the `conda user guide <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+   For more information about using conda, please check out the `conda user guide <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
   
    To install a specific version of RMG, add the version to the install command::
 
diff --git a/documentation/source/users/rmg/installation/anacondaUserWindows.rst b/documentation/source/users/rmg/installation/anacondaUserWindows.rst
index 082bb8531cb..ac2fb0f145a 100644
--- a/documentation/source/users/rmg/installation/anacondaUserWindows.rst
+++ b/documentation/source/users/rmg/installation/anacondaUserWindows.rst
@@ -17,7 +17,7 @@ Binary Installation Using Anaconda for Windows
     
     activate rmg_env
     
-#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <http://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <http://openmopac.net/form.php>`_.Once you have it, type the following into your command prompt (while the environment is activated) ::
+#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <https://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <https://openmopac.net/form.php>`_.Once you have it, type the following into your command prompt (while the environment is activated) ::
     
     mopac password_string_here
 
diff --git a/documentation/source/users/rmg/installation/index.rst b/documentation/source/users/rmg/installation/index.rst
index d371c960231..00e6f876b4a 100644
--- a/documentation/source/users/rmg/installation/index.rst
+++ b/documentation/source/users/rmg/installation/index.rst
@@ -14,19 +14,19 @@ Recommended Install: Docker
 
 RMG is primarily distributed using Docker, a software package for delivering applications.
 
-#. Download and install `Docker <https://docs.docker.com/get-docker/>`_.
+#. Download and install `Docker <https://docs.docker.com/get-started/get-docker/>`_.
 
-#. Open a terminal, powershell, or command prompt and run ``docker pull reactionmechanismgenerator/rmg:3.2.0``.
+#. Open a terminal, powershell, or command prompt and run ``docker pull reactionmechanismgenerator/rmg:3.3.0``.
 
    This step may take some time as the image is downloaded.
 
-#. Run ``docker run --name rmgcontainer -v "C:\Users\rmguser\myrmgfiles:/rmg/RMG-Py/myrmgfiles" -it reactionmechanismgenerator/rmg:3.2.0``
+#. Run ``docker run --name rmgcontainer -v "C:\Users\rmguser\myrmgfiles:/rmg/RMG-Py/myrmgfiles" -it reactionmechanismgenerator/rmg:3.3.0``
 
    This command will make the folder ``C:\Users\rmguser\myrmgfiles`` on your computer accessible from inside the container to easily edit and transfer input and output files.
    Change the path to match your individual computer.
    If the folder does not exist when the command is run, it will be created.
 
-   If you want to use jupyter notebook inside the docker container, run ``docker run --name rmgcontainer -v "C:\Users\rmguser\myrmgfiles:/rmg/RMG-Py/myrmgfiles" -it -p 8888:8888 reactionmechanismgenerator/rmg:3.2.0`` instead.
+   If you want to use jupyter notebook inside the docker container, run ``docker run --name rmgcontainer -v "C:\Users\rmguser\myrmgfiles:/rmg/RMG-Py/myrmgfiles" -it -p 8888:8888 reactionmechanismgenerator/rmg:3.3.0`` instead.
    And you can start the jupyter notebook by running ``jupyter notebook --ip 0.0.0.0 --no-browser --allow-root`` inside the container.
    Then you can access the jupyter notebook from your browser by going to ``http://localhost:8888``.
    You may need to copy and paste the token from the terminal into the browser to access the notebook.
@@ -40,7 +40,7 @@ For users unfamiliar with bash or Linux, we recommend looking at
 `Must Know Linux/Unix Commands <https://www.guru99.com/must-know-linux-commands.html>`_.
 
 .. NOTE::
-    The docker instructions above which specify ``rmg:3.2.0`` are for the version 3.2.0 release of RMG-Py (August 2023), the user guide for which is archived in a `4mb PDF here <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/3.2.0/documentation/RMG-Py_and_Arkane_Documentation.pdf?raw=true>`_.
+    The docker instructions above which specify ``rmg:3.3.0`` are for the version 3.3.0 release of RMG-Py (July 2025), the user guide for which is archived in a `4mb PDF here <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/3.3.0/documentation/RMG-Py_and_Arkane_Documentation.pdf?raw=true>`_.
     If you want to use the latest development version, which corresponds to the user guide you are reading online `on the RMG website <https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/>`_, you can replace the version number in the docker pull command with "latest" or omit it entirely.
     For example, you can run ``docker pull reactionmechanismgenerator/rmg:latest`` or ``docker pull reactionmechanismgenerator/rmg`` to get the latest development version corresponding to `the main branch <https://github.com/ReactionMechanismGenerator/RMG-Py/commits/main/>`_.
     Be sure to also change the version number in the docker run commands to match the version you pulled.
diff --git a/documentation/source/users/rmg/installation/linux.rst b/documentation/source/users/rmg/installation/linux.rst
index 47aa8fded10..ba6567b2ef6 100644
--- a/documentation/source/users/rmg/installation/linux.rst
+++ b/documentation/source/users/rmg/installation/linux.rst
@@ -16,7 +16,7 @@ The instructions listed below were written for Ubuntu 12.04 and should generally
 	sudo apt-get install git g++ gfortran python-dev liblapack-dev
 	sudo apt-get install python-openbabel python-setuptools python-pip
 
-* After creating a `Github account <https://github.com/join>`_, generate your public key: ::
+* After creating a `Github account <https://github.com/signup>`_, generate your public key: ::
 
 	cd ~; ssh-keygen		# press enter to save to the default directory
 					# create a password if desired
diff --git a/documentation/source/users/rmg/installation/linuxSubsystem.rst b/documentation/source/users/rmg/installation/linuxSubsystem.rst
index 2f49fdc99d8..118e9bf855c 100644
--- a/documentation/source/users/rmg/installation/linuxSubsystem.rst
+++ b/documentation/source/users/rmg/installation/linuxSubsystem.rst
@@ -14,13 +14,13 @@ Installing the Linux Subsystem
 ===================================
 
 1. Follow the instructions provided by Microsoft to install the Linux subsystem, available `here
-   <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_. The basic steps include enabling the Windows Linux
+   <https://learn.microsoft.com/en-us/windows/wsl/install>`_. The basic steps include enabling the Windows Linux
    subsystem from a powershell **run as an administrator**, and downloading the latest LTS version of Ubuntu
    *from the Windows store*. We recommend Ubuntu (for which these instructions were made) over the other Linux
    distributions.
 
 2. Once the Linux subsystem is installed, open a web browser in Windows and go to the
-   `Anaconda Python Platform Downloads Page <https://www.anaconda.com/products/individual#Downloads>`_. Go to the tab for the
+   `Anaconda Python Platform Downloads Page <https://www.anaconda.com/download#Downloads>`_. Go to the tab for the
    **Linux Installer**, and **right click** on the download icon for Python to copy the link location. Open an Ubuntu
    terminal (type in ``Ubuntu`` into the Windows search bar if you are unsure where to find it) and paste the link
    into the terminal immediately after typing the ``wget`` command, so that your terminal looks like the following: ::
diff --git a/documentation/source/users/rmg/installation/macos.rst b/documentation/source/users/rmg/installation/macos.rst
index 1212f096a92..261dfba0957 100644
--- a/documentation/source/users/rmg/installation/macos.rst
+++ b/documentation/source/users/rmg/installation/macos.rst
@@ -30,7 +30,7 @@ homebrew-python (which used to be at ``https://github.com/Homebrew/homebrew-pyth
 	brew update
 	brew install git
 
-* Optional (but recommended for Nitrogen-chemistry nomenclature): install `OpenBabel <http://www.openbabel.org>`_::
+* Optional (but recommended for Nitrogen-chemistry nomenclature): install `OpenBabel <http://openbabel.org>`_::
 
 	brew install open-babel --with-python --HEAD
 
@@ -102,4 +102,4 @@ homebrew-python (which used to be at ``https://github.com/Homebrew/homebrew-pyth
 	make eg2
 
 To run with on-the-fly Quantum Mechanics calculations, you will also need to install
-`MOPAC <http://openmopac.net/downloads.html>`_ or `Gaussian <https://gaussian.com>`_, then run `make QM`.
+`MOPAC <https://openmopac.net/downloads.html>`_ or `Gaussian <https://gaussian.com>`_, then run `make QM`.
diff --git a/documentation/source/users/rmg/installation/updatingSourceCode.rst b/documentation/source/users/rmg/installation/updatingSourceCode.rst
index 0ac84e08353..0f0cf6ad4fb 100644
--- a/documentation/source/users/rmg/installation/updatingSourceCode.rst
+++ b/documentation/source/users/rmg/installation/updatingSourceCode.rst
@@ -32,8 +32,8 @@ We also recommend that the RMS julia package is updated::
     julia -e 'using Pkg; Pkg.update("ReactionMechanismSimulator")'
 
 For more information about how to use the Git workflow to make changes to the source code, please
-refer to the handy `Git Tutorial <http://git-scm.com/docs/gittutorial>`_
+refer to the handy `Git Tutorial <https://git-scm.com/docs/gittutorial>`_
 
 For information on updating your local repository from ``https`` to ``ssh``,
 please see `Managing remote repositories
-<https://docs.github.com/en/get-started/getting-started-with-git/managing-remote-repositories>`_
+<https://docs.github.com/en/get-started/git-basics/managing-remote-repositories>`_
diff --git a/documentation/source/users/rmg/installation/virtualMachineSetup.rst b/documentation/source/users/rmg/installation/virtualMachineSetup.rst
index 5377ddc5c8c..130b6d47a7a 100644
--- a/documentation/source/users/rmg/installation/virtualMachineSetup.rst
+++ b/documentation/source/users/rmg/installation/virtualMachineSetup.rst
@@ -16,10 +16,7 @@ Windows 8/10. Click on the ``Performance`` tab--from here you can see if virtual
 
 .. image:: images/Virtualization_Enabled.png
     :align: center
-
-For Windows 7 or earlier you can download and run
-`Microsoft's Virtualization Detection Tool <http://www.microsoft.com/en-us/download/details.aspx?id=592>`_.
-
+|
 If enabled, you can continue on with installing a virtual machine on your PC. If virtualization is currently disabled,
 though, you will have to enable this from the BIOS setting on your computer. How to do this varies from PC to PC (we
 recommend doing a quick google search for your make/model, as there are many instructions for this online), but the
@@ -50,7 +47,7 @@ popular Linux distributions out there, with plenty of support available online.
 any other Linux distribution you like (see `Linux DistroWatch`_).
 
 .. _Linux DistroWatch: https://distrowatch.com/
-.. _Ubuntu: https://ubuntu.com/#download
+.. _Ubuntu: https://ubuntu.com/#download-ubuntu
 
 1. Go to the Ubuntu_ website and click on the download link for 18.04 LTS (Desktop, not Server). Note that newer
    versions of Ubuntu might be available, but we recommend downloading only the LTS (long term support) versions. Note that
@@ -71,7 +68,7 @@ and `Oracle VirtualBox`_. VMware Workstation Pro is the recommended choice, thou
 access to it (since it is not free). If not, VirtualBox (which is free) runs well and will work just as fine. Use the
 hyperlinks below to jump ahead to the setup instructions for the virtual machine software of your choice.
 
-.. _VMware Workstation Pro: https://my.vmware.com/en/web/vmware/info/slug/desktop_end_user_computing/vmware_workstation_pro/15_0
+.. _VMware Workstation Pro: https://knowledge.broadcom.com/external/article/315638/download-and-install-vmware-fusion.html
 .. _Oracle VirtualBox: https://www.virtualbox.org/wiki/Downloads
 
 
diff --git a/documentation/source/users/rmg/introduction.rst b/documentation/source/users/rmg/introduction.rst
index fcad088b9f7..9757151da05 100644
--- a/documentation/source/users/rmg/introduction.rst
+++ b/documentation/source/users/rmg/introduction.rst
@@ -11,7 +11,7 @@ This version is written in Python, and called RMG-Py.
 License
 =======
 
-RMG is an open source program, available to the general public free of charge. The primary RMG code is distributed under the terms of the `MIT/X11 License <http://www.opensource.org/licenses/mit-license.php>`_. However, RMG has a number of dependencies of various licenses, some of which may be more restrictive. **It is the user's responsibility to ensure these licenses have been obtained.** 
+RMG is an open source program, available to the general public free of charge. The primary RMG code is distributed under the terms of the `MIT/X11 License <https://opensource.org/license/mit>`_. However, RMG has a number of dependencies of various licenses, some of which may be more restrictive. **It is the user's responsibility to ensure these licenses have been obtained.** 
 
 .. literalinclude:: ../../../../LICENSE.txt
    :language: none
diff --git a/documentation/source/users/rmg/releaseNotes.rst b/documentation/source/users/rmg/releaseNotes.rst
index 82c9fbf24a4..c0702736a96 100644
--- a/documentation/source/users/rmg/releaseNotes.rst
+++ b/documentation/source/users/rmg/releaseNotes.rst
@@ -4,6 +4,52 @@
 Release Notes
 *************
 
+RMG-Py Version 3.3.0
+====================
+Date: July 10, 2025
+
+The below list is a summary. For a complete list of all changes, see the `Official Release Page <https://github.com/ReactionMechanismGenerator/RMG-Py/releases/tag/3.3.0>`_.
+
+- Software Improvements
+    - RMG-Py now uses Python 3.9
+    - RMS and Julia are now optional when running RMG
+    - Avoid using proprietary channels with conda
+    - Deploy RMG on Conda and Docker on a continuing basis
+    - Improved documentation build procedure
+    - Testing system overhauled, including automated regression testing and a new testing framework (pytest)
+    - Deprecated conda packages have been replaced with their official versions
+
+- Bug Fixes
+    - cclib incompatibility fixes
+    - Logical short circuits in object comparisons
+
+- New Features
+    - Electrochemistry with Lithium
+    - Automated Fragment Modeling
+    - Surface Reactions and Catalysis functionality
+    - Parses for new methods and software
+
+RMG-Database Version 3.3.0
+==========================
+Date: July 10, 2025
+
+The below list is a summary. For a complete list of all changes, see the `Official Release Page <https://github.com/ReactionMechanismGenerator/RMG-database/releases/tag/3.3.0>`_.
+
+- Features
+    - Electrochemistry with Lithium
+    - AECs and BACs
+    - New families and update autogenerated families
+    - New and updated data for nitrogen combustion, surface catalysis, and others
+
+- Bugfixes
+    - Duplicates removed
+    - Accidental infinite loops resolved
+    - Critical Pressure Estimation bug resolved
+
+- Miscellaneous
+    - Continuous integration updated to use RMG-Py testing
+    - Conda recipe updated for ease of use
+
 RMG-Py Version 3.2.0
 ====================
 Date: August 2, 2023
diff --git a/documentation/source/users/rmg/species.rst b/documentation/source/users/rmg/species.rst
index 4410d48847b..8ae5e640fa0 100644
--- a/documentation/source/users/rmg/species.rst
+++ b/documentation/source/users/rmg/species.rst
@@ -4,7 +4,7 @@
 Species Representation
 **********************
 
-The base class for chemical structures in RMG is ``Graph`` (see :ref:`rmgpy.molecule.Graph`), 
+The base class for chemical structures in RMG is ``Graph`` (see :ref:`rmgpy.molecule.graph.Graph`), 
 which is a basic implementation of a 2D mathematical graph. 
 A graph is comprised of a set of vertices connected by a set of edges. 
 In RMG, the Graph class does not store any chemical information on its own, 
diff --git a/documentation/source/users/rmg/thermo.rst b/documentation/source/users/rmg/thermo.rst
index 53826b8c15d..b3f45cda8ef 100644
--- a/documentation/source/users/rmg/thermo.rst
+++ b/documentation/source/users/rmg/thermo.rst
@@ -287,7 +287,7 @@ References
 
 .. [Allinger] Allinger, N. L., & Lii, J.-H. (2008). MM4(2008) and MM4(2003).
 
-.. [Patchkovskii] Patchkovskii, S. (2003). SYMMETRY, originally from ``http://www.cobalt.chem.ucalgary.ca/ps/symmetry/`` now mirrored at https://github.com/nquesada/symmetry.
+.. [Patchkovskii] Patchkovskii, S. (2003). SYMMETRY, originally from ``https://www.cobalt.chem.ucalgary.ca/ps/symmetry/`` now mirrored at https://github.com/nquesada/symmetry.
 
 .. [Yu] "Estimation method for the thermochemical properties of polycyclic aromatic molecules" (Ph.D), Joanna Yu, M.I.T (2005)
 
diff --git a/rmgpy/chemkin.pyx b/rmgpy/chemkin.pyx
index 2a6c17cfea9..1f4323d311a 100644
--- a/rmgpy/chemkin.pyx
+++ b/rmgpy/chemkin.pyx
@@ -73,7 +73,7 @@ def read_thermo_entry(entry, Tmin=0, Tint=0, Tmax=0):
     the label of the species and the thermodynamics model as a :class:`NASA`
     object.
     
-    Format specification at http://www2.galcit.caltech.edu/EDL/public/formats/chemkin.html
+    Format specification at https://shepherd.caltech.edu/EDL/PublicResources/sdt/formats/chemkin.html
     """
     lines = entry.splitlines()
     species = str(lines[0][0:18].split()[0].strip())
diff --git a/rmgpy/molecule/converter.py b/rmgpy/molecule/converter.py
index e5e619a2b73..7182b204998 100644
--- a/rmgpy/molecule/converter.py
+++ b/rmgpy/molecule/converter.py
@@ -52,7 +52,7 @@
 def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_order=False):
     """
     Convert a molecular structure to a RDKit rdmol object. Uses
-    `RDKit <http://rdkit.org/>`_ to perform the conversion.
+    `RDKit <https://rdkit.org/>`_ to perform the conversion.
     Perceives aromaticity and, unless remove_h==False, removes Hydrogen atoms.
 
     If return_mapping==True then it also returns a dictionary mapping the
@@ -131,7 +131,7 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
 def from_rdkit_mol(mol, rdkitmol, raise_atomtype_exception=True):
     """
     Convert a RDKit Mol object `rdkitmol` to a molecular structure. Uses
-    `RDKit <http://rdkit.org/>`_ to perform the conversion.
+    `RDKit <https://rdkit.org/>`_ to perform the conversion.
     This Kekulizes everything, removing all aromatic atom types.
     """
     cython.declare(i=cython.int,
@@ -234,7 +234,7 @@ def debug_rdkit_mol(rdmol, level=logging.INFO):
 def to_ob_mol(mol, return_mapping=False, save_order=False):
     """
     Convert a molecular structure to an OpenBabel OBMol object. Uses
-    `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
+    `OpenBabel <https://openbabel.org/>`_ to perform the conversion.
     """
     if openbabel is None:
         raise DependencyError('OpenBabel is not installed. Please install or use RDKit.')
@@ -279,7 +279,7 @@ def to_ob_mol(mol, return_mapping=False, save_order=False):
 def from_ob_mol(mol, obmol, raise_atomtype_exception=True):
     """
     Convert a OpenBabel Mol object `obmol` to a molecular structure. Uses
-    `OpenBabel <http://openbabel.org/>`_ to perform the conversion.
+    `OpenBabel <https://openbabel.org/>`_ to perform the conversion.
 
     It estimates radical placement based on undervalence of atoms,
     and assumes overall spin multiplicity is radical count + 1
diff --git a/rmgpy/molecule/draw.py b/rmgpy/molecule/draw.py
index 37a3b47e25c..ad6f0e60701 100644
--- a/rmgpy/molecule/draw.py
+++ b/rmgpy/molecule/draw.py
@@ -29,14 +29,14 @@
 
 """
 This module provides functionality for automatic two-dimensional drawing of the
-`skeletal formulae <http://en.wikipedia.org/wiki/Skeletal_formula>`_ of a wide
+`skeletal formulae <https://en.wikipedia.org/wiki/Skeletal_formula>`_ of a wide
 variety of organic and inorganic molecules. The general method for creating
 these drawings is to utilize the :meth:`draw()` method of the :class:`Molecule`
 you wish to draw; this wraps a call to :meth:`MoleculeDrawer.draw()`, where the
 molecule drawing algorithm begins. Advanced use may require use of the
 :class:`MoleculeDrawer` class directly.
 
-The `Cairo <http://cairographics.org/>`_ 2D graphics library is used to create
+The `Cairo <https://cairographics.org/>`_ 2D graphics library is used to create
 the drawings. The :class:`MoleculeDrawer` class module will fail gracefully if
 Cairo is not installed.
 
diff --git a/rmgpy/molecule/fragment.py b/rmgpy/molecule/fragment.py
index a4e3e98b643..d4fa0acf4d2 100644
--- a/rmgpy/molecule/fragment.py
+++ b/rmgpy/molecule/fragment.py
@@ -771,7 +771,7 @@ def get_num_atoms(self, element=None):
     def from_rdkit_mol(self, rdkitmol, atom_replace_dict=None):
         """
         Convert a RDKit Mol object `rdkitmol` to a molecular structure. Uses
-        `RDKit <http://rdkit.org/>`_ to perform the conversion.
+        `RDKit <https://rdkit.org/>`_ to perform the conversion.
         This Kekulizes everything, removing all aromatic atom types.
         """
 
diff --git a/rmgpy/molecule/molecule.py b/rmgpy/molecule/molecule.py
index c19d35307d4..1a32f07adde 100644
--- a/rmgpy/molecule/molecule.py
+++ b/rmgpy/molecule/molecule.py
@@ -1873,7 +1873,7 @@ def from_smiles(self, smilesstr, backend='openbabel-first', raise_atomtype_excep
     def from_smarts(self, smartsstr, raise_atomtype_exception=True):
         """
         Convert a SMARTS string `smartsstr` to a molecular structure. Uses
-        `RDKit <http://rdkit.org/>`_ to perform the conversion.
+        `RDKit <https://rdkit.org/>`_ to perform the conversion.
         This Kekulizes everything, removing all aromatic atom types.
         """
         translator.from_smarts(self, smartsstr, raise_atomtype_exception=raise_atomtype_exception)
@@ -1947,7 +1947,7 @@ def to_single_bonds(self, raise_atomtype_exception=True):
     def to_inchi(self, backend='rdkit-first'):
         """
         Convert a molecular structure to an InChI string. Uses
-        `RDKit <http://rdkit.org/>`_ to perform the conversion.
+        `RDKit <https://rdkit.org/>`_ to perform the conversion.
         Perceives aromaticity.
 
         or
@@ -1990,7 +1990,7 @@ def to_inchi_key(self, backend='rdkit-first'):
         or
 
         Convert a molecular structure to an InChI Key string. Uses
-        `RDKit <http://rdkit.org/>`_ to perform the conversion.
+        `RDKit <https://rdkit.org/>`_ to perform the conversion.
 
         It is possible to use a single backend or try different backends in sequence.
         The available options for the ``backend`` argument: 'rdkit-first'(default),
@@ -2023,7 +2023,7 @@ def to_augmented_inchi_key(self, backend='rdkit-first'):
     def to_smarts(self):
         """
         Convert a molecular structure to an SMARTS string. Uses
-        `RDKit <http://rdkit.org/>`_ to perform the conversion.
+        `RDKit <https://rdkit.org/>`_ to perform the conversion.
         Perceives aromaticity and removes Hydrogen atoms.
         """
         return translator.to_smarts(self)
@@ -2036,7 +2036,7 @@ def to_smiles(self):
         `OpenBabel <http://openbabel.org/>`_ to perform the conversion,
         and the SMILES may or may not be canonical.
         
-        Otherwise, it uses `RDKit <http://rdkit.org/>`_ to perform the 
+        Otherwise, it uses `RDKit <https://rdkit.org/>`_ to perform the 
         conversion, so it will be canonical SMILES.
         While converting to an RDMolecule it will perceive aromaticity
         and removes Hydrogen atoms.
diff --git a/rmgpy/molecule/translator.py b/rmgpy/molecule/translator.py
index fece53b041a..2cf27e50b23 100644
--- a/rmgpy/molecule/translator.py
+++ b/rmgpy/molecule/translator.py
@@ -247,7 +247,7 @@ def to_inchi_key(mol, backend='rdkit-first', aug_level=0):
 def to_smarts(mol, backend='rdkit'):
     """
     Convert a molecular structure to an SMARTS string. Uses
-    `RDKit <http://rdkit.org/>`_ to perform the conversion.
+    `RDKit <https://rdkit.org/>`_ to perform the conversion.
     Perceives aromaticity and removes Hydrogen atoms.
     """
     return _write(mol, 'sma', backend)
@@ -258,10 +258,10 @@ def to_smiles(mol, backend='default'):
     Convert a molecular structure to an SMILES string.
 
     If there is a Nitrogen/Sulfur atom present it uses
-    `OpenBabel <http://openbabel.org/>`_ to perform the conversion,
+    `OpenBabel <https://openbabel.org/>`_ to perform the conversion,
     and the SMILES may or may not be canonical.
 
-    Otherwise, it uses `RDKit <http://rdkit.org/>`_ to perform the
+    Otherwise, it uses `RDKit <https://rdkit.org/>`_ to perform the
     conversion, so it will be canonical SMILES.
     While converting to an RDMolecule it will perceive aromaticity
     and removes Hydrogen atoms.
@@ -332,7 +332,7 @@ def from_augmented_inchi(mol, aug_inchi, raise_atomtype_exception=True):
 def from_smarts(mol, smartsstr, backend='rdkit', raise_atomtype_exception=True):
     """
     Convert a SMARTS string `smartsstr` to a molecular structure. Uses
-    `RDKit <http://rdkit.org/>`_ to perform the conversion.
+    `RDKit <https://rdkit.org/>`_ to perform the conversion.
     This Kekulizes everything, removing all aromatic atom types.
     """
     return _read(mol, smartsstr, 'sma', backend, raise_atomtype_exception=raise_atomtype_exception)
diff --git a/rmgpy/rmg/input.py b/rmgpy/rmg/input.py
index c2bebbe9855..05a5569efd0 100644
--- a/rmgpy/rmg/input.py
+++ b/rmgpy/rmg/input.py
@@ -1376,7 +1376,7 @@ def options(name='Seed', generateSeedEachIteration=True, saveSeedToDatabase=Fals
         logging.warning("`saveRestartPeriod` flag was set in the input file, but this feature has been removed. Please "
                         "remove this line from the input file. This will throw an error after RMG-Py 3.1. For "
                         "restarting an RMG job see the documentation for restarting from a seed mechanism at "
-                        "http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#restarting-from-a-seed-mechanism")
+                        "https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#restarting-from-a-seed-mechanism")
 
     rmg.name = name
     rmg.generate_seed_each_iteration = generateSeedEachIteration
@@ -1460,7 +1460,7 @@ def uncertainty(localAnalysis=False, globalAnalysis=False, uncorrelated=True, co
 def restart_from_seed(path=None, coreSeed=None, edgeSeed=None, filters=None, speciesMap=None):
     parent_dir = os.path.dirname(rmg.input_file)
     rmg.restart = True
-    doc_link = 'http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#restarting-from-a-seed-mechanism.'
+    doc_link = 'https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#restarting-from-a-seed-mechanism.'
 
     if path:
         if any((coreSeed, edgeSeed, filters, speciesMap)):
diff --git a/setup.py b/setup.py
index e6b47c66c59..78a8e3eeda5 100644
--- a/setup.py
+++ b/setup.py
@@ -33,13 +33,13 @@
     from Cython.Build import cythonize
     from Cython.Compiler import Options
 except ImportError:
-    print('Cython (http://www.cython.org/) is required to build or install RMG Py.')
+    print('Cython (https://cython.org/) is required to build or install RMG Py.')
     raise
     
 try:
     import numpy
 except ImportError:
-    print('NumPy (http://numpy.scipy.org/) is required to build or install RMG Py.')
+    print('NumPy (https://numpy.scipy.org/) is required to build or install RMG Py.')
     raise
 
 from setuptools import find_packages
@@ -145,7 +145,7 @@
     description='Reaction Mechanism Generator',
     author='William H. Green and the RMG Team',
     author_email='rmg_dev@mit.edu',
-    url='http://reactionmechanismgenerator.github.io',
+    url='https://reactionmechanismgenerator.github.io',
     python_requires='>=3.9,<3.10',
     packages=find_packages(where='.', include=["rmgpy*"]) + find_packages(where='.', include=["arkane*"]),
     scripts=scripts,