Fix broken links for User Guide (#394)

* fix #393
* fix broken links

doc/source/contributing.rst

@@ -75,7 +75,7 @@ Some great resources for learning Git:
 
     * the `GitHub help pages <http://help.github.com/>`_.
     * the `NumPy's documentation <http://docs.scipy.org/doc/numpy/dev/index.html>`_.
-    * Matthew Brett's `Pydagogue <http://matthew-brett.github.com/pydagogue/>`_.
+    * Matthew Brett's `Pydagogue <https://matthew-brett.github.io/pydagogue/>`_.
 
 ------------------------
 Getting started with Git

doc/source/examples/analysis/alignment_and_rms/README.rst

@@ -10,10 +10,10 @@ The :mod:`MDAnalysis.analysis.align` and :mod:`MDAnalysis.analysis.rms`
 modules contain the functions used for aligning structures,
 aligning trajectories, and calculating root mean squared quantities.
 
-Demonstrations of alignment are in `align_structure`_,
-`align_trajectory_first`_, and `align_trajectory`_. Another example of
+Demonstrations of alignment are in `align_structure <aligning_structure_to_another.ipynb>`__,
+`align_trajectory_first <aligning_trajectory_to_frame.ipynb>`__, and `align_trajectory <aligning_trajectory.ipynb>`__. Another example of
 generating an average structure from an alignment is demonstrated in
-`rmsf`_. Typically, trajectories need to be aligned for RMSD and
+`rmsf <rmsf.ipynb>`__. Typically, trajectories need to be aligned for RMSD and
 RMSF values to make sense.
 
 .. note::
@@ -33,10 +33,8 @@ RMSF values to make sense.
    /examples/analysis/alignment_and_rms/pairwise_rmsd
    /examples/analysis/alignment_and_rms/rmsf
 
-
-.. _align_structure: /examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb
-.. _align_trajectory_first: /examples/analysis/alignment_and_rms/aligning_trajectory_to_first_frame.ipynb
-.. _align_trajectory: /examples/analysis/alignment_and_rms/aligning_trajectory.ipynb
 .. _rmsd: /examples/analysis/alignment_and_rms/rmsd.ipynb
 .. _pairwise: /examples/analysis/alignment_and_rms/pairwise_rmsd.ipynb
-.. _rmsf: /examples/analysis/alignment_and_rms/rmsf.ipynb
+.. _align_structure: aligning_structure_to_another.ipynb
+.. _align_trajectory: aligning_trajectory.ipynb
+.. _align_trajectory_frame: aligning_trajectory_to_frame.ipynb

doc/source/examples/analysis/alignment_and_rms/rmsd.ipynb

@@ -289,7 +289,7 @@
    "source": [
     "### Plotting the data\n",
     "\n",
-    "We can easily plot this data using the common data analysis package [pandas](https://pandas.pydata.org). We turn the ``R.rmsd`` array into a [DataFrame](https://pandas.pydata.org/pandas-docs/stable/getting_started/dsintro.html#dataframe) and label each column below."
+    "We can easily plot this data using the common data analysis package [pandas](https://pandas.pydata.org). We turn the ``R.rmsd`` array into a [DataFrame](https://pandas.pydata.org/docs/user_guide/dsintro.html#dataframe) and label each column below."
    ]
   },
   {

doc/source/formats/reference/gsd.rst

@@ -18,7 +18,7 @@ Reading in
 
     A user will only get an error if the number of particles changes from the first time step. MDAnalysis does not currently check for changes in the particle identity or topology, and it does not update these over the trajectory.
 
-.. _HOOMD-blue : http://codeblue.umich.edu/hoomd-blue/index.html
+.. _HOOMD-blue : https://glotzerlab.engin.umich.edu/hoomd-blue/
 
 .. note:: **Residue resnames**
 

doc/source/formats/reference/mmtf.rst

@@ -12,4 +12,4 @@ The Macromolecular Transmission Format format
 
 Individual models within the MMTF file are available via the ``models`` attribute of Universe.
 
-.. _MMTF: https://mmtf.rcsb.org/
+.. _MMTF: https://github.com/rcsb/mmtf

doc/source/formats/reference/xml.rst

@@ -13,7 +13,7 @@ Hoomd XML does not identify molecules or residues, so placeholder values
 are used for residue numbers.
 Bonds and angles are read if present.
 
-.. _HOOMD: http://codeblue.umich.edu/hoomd-blue/index.html
+.. _HOOMD: https://glotzerlab.engin.umich.edu/hoomd-blue/index.html
 .. _XML: http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
 
 Hoomd XML format does not contain a node for names. The parser will

doc/source/releases.md

@@ -1,6 +1,6 @@
-# MDAnalysis Release Notes
-
-
+# MDAnalysis Release Notes
+
+
 ## Release 2.8.0 of MDAnalysis
 
 This a minor release of MDAnalysis.
@@ -33,8 +33,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.8.0/
 * The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` kwargs are deprecated for bond guessing during Universe creation.
   Instead, pass `("bonds", "angles", "dihedrals")` into `to_guess` or `force_guess` during Universe creation, and the associated `vdwradii`, `fudge_factor`, and `lower_bound` kwargs into `Guesser` creation. Alternatively, if `vdwradii`, `fudge_factor`, and `lower_bound` are passed into `Universe.guess_TopologyAttrs`, they will override the previous values of those kwargs.
 * MDAnalysis.topology.guessers and MDAnalysis.topology.tables are deprecated in favour of the new Guessers API and will be removed in MDAnalysis v3.0.
-* Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:`Masses`' no_value_label attribute (np.nan).
-
+* Unknown masses are set to 0.0 for current version, this will be depracated in MDAnalysis v3.0.0 and replaced by :class:`Masses`' no_value_label attribute (np.nan).
+
 ## Release 2.7.0 of MDAnalysis
 
 This a minor release of MDAnalysis.
@@ -85,8 +85,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.7.0/
 * [@Sumit112192](https://github.com/Sumit112192) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4346
 * [@HeetVekariya](https://github.com/HeetVekariya) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4359
 * [@JoStoe](https://github.com/JoStoe) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4292
-* [@ljwoods2](https://github.com/ljwoods2) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366
-
+* [@ljwoods2](https://github.com/ljwoods2) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366
+
 ## Release 2.6.1 of MDAnalysis
 
 This is a bugfix release of the 2.6.x version branch of MDAnalysis, it serves as an amendment to the earlier released version 2.6.0.
@@ -102,8 +102,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.6.1/
 * Clarification of SurvivalProbability function documentation [Issue #4247, PR #4248]1
 
 ### New Contributors
-* [@pillose](https://github.com/pillose) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4168
-
+* [@pillose](https://github.com/pillose) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4168
+
 ## Release 2.6.0 of MDAnalysis
 
 This a minor release of MDAnalysis.
@@ -139,13 +139,13 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.6.0/
 
 #### Deprecations:
 * The misspelt `Boltzman_constant` entry in `MDAnalysis.units` is now deprecated in favour the correctly spelt `Boltzmann_constant`. (https://github.com/MDAnalysis/mdanalysis/pull/4230 and https://github.com/MDAnalysis/mdanalysis/pull/4214)
-* `MDAnalysis.analysis.hole2` is now deprecated in favour of a new [HOLE2 MDAKit](https://www.mdanalysis.org/hole2-mdakit/). (https://github.com/MDAnalysis/mdanalysis/pull/4200)
+* `MDAnalysis.analysis.hole2` is now deprecated in favour of a new [HOLE2 MDAKit](https://mdakits.mdanalysis.org/mdahole2.html). (https://github.com/MDAnalysis/mdanalysis/pull/4200)
 
 ### New Contributors
 * [@MohitKumar020291](https://github.com/MohitKumar020291) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4182
 * [@Shubx10](https://github.com/Shubx10) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4184
-* [@ztimol](https://github.com/ztimol) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4191
-
+* [@ztimol](https://github.com/ztimol) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4191
+
 ## Release 2.5.0 of MDAnalysis
 
 This a minor release of MDAnalysis.
@@ -253,25 +253,25 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.5.0/
 * [@SophiaRuan](https://github.com/SophiaRuan) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4072
 * [@marinegor](https://github.com/marinegor) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4085
 * [@g2707](https://github.com/g2707) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4089
-* [@DanielJamesEvans](https://github.com/DanielJamesEvans) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4109
-
+* [@DanielJamesEvans](https://github.com/DanielJamesEvans) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4109
+
 ## Release 2.4.3 of MDAnalysis
 
 This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.2.
 
 ### Bug fixes
 * Fixed DCD reading for large (>2Gb) files (Issue #4039).  This was broken for versions 2.4.0, 2.4.1 and 2.4.2.
-* Fix element parsing from PSF files tests read via Parmed (Issue #4015)
-
+* Fix element parsing from PSF files tests read via Parmed (Issue #4015)
+
 ## Release 2.4.2 of MDAnalysis
 
 This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.1.
 
 ### Bug fixes
 
 * Fixed an issue where the arguments passed to np.histogramdd in `MDAnalysis.analysis.DensityAnalysis` were not compatible with the 1.24 release of NumPy (PR #3976)
-* Fixed upcoming incompatibilities with NumPy 1.25 in `MDAnalysis.visualization.streamlines_3D` and `MDAnalysis.visualization.streamlines` where incorrect comparison of the truth of arrays would have led to failures (PR #3977)
-
+* Fixed upcoming incompatibilities with NumPy 1.25 in `MDAnalysis.visualization.streamlines_3D` and `MDAnalysis.visualization.streamlines` where incorrect comparison of the truth of arrays would have led to failures (PR #3977)
+
 ## Release 2.4.1 of MDAnalysis
 
 This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.0.
@@ -280,8 +280,8 @@ This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an ame
 
 * The minimum version of biopython has been raised to 1.80 for pip installs
 * pytng has been added as an optional dependency 
-
-
+
+
 ## Release 2.4.0 of MDAnalysis
 
 This a minor release of MDAnalysis, as per our once-every-three-months schedule.
@@ -325,8 +325,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.4.0/
 * [@jfennick](https://github.com/jfennick) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3832
 * [@Hakarishirenai](https://github.com/Hakarishirenai) made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3956
 
-
-
+
+
 ## Release 2.3.0 of MDAnalysis
 
 This a minor release of MDAnalysis, as per our once-every-three-months schedule.
@@ -366,8 +366,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.3.0/
 A series of performance improvements to the MDAnalysis library's backend have been made as per planned work under MDAnalysis' CZI EOSS4 grant. Further details about these will be provided in a future blog post.
 
   - `MDAnalysis.lib.distances` now accepts `AtomGroups` as well as NumPy arrays (PR #3730). 
-  - Timestep has been converted to a Cython Extension type (PR #3683).
-
+  - Timestep has been converted to a Cython Extension type (PR #3683).
+
 ## Release 2.2.0 of MDAnalysis
 
 In line with NEP29, this version of MDAnalysis drops support for Python 3.7 and raises the minimum NumPy version to 1.19.0. Minimum version support has also been changed for the following packages; `networkx>=2.0`, `scipy>=1.5.0`, `gsd>=1.9.3`. Further details on MDAnalysis future support strategy and NEP29 will be released shortly.
@@ -425,8 +425,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.2.0/
 
 ### Known test failures:
  - Windows builds
-    * In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).
-
+    * In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).
+
 ## Release 2.1.0 of MDAnalysis
 
 In line with ongoing attempts to align with NEP29, this version of MDAnalysis drops support for Python 3.6 and raises the minimum NumPy version to 1.18.0.
@@ -467,8 +467,8 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.1.0/
  - `pytest-xdist` and more than 4 workers
    * Under these conditions a test related to logging for HydrogenBondAnalysis can fail. This is not thought to impact the validity of MDAnalysis. See here for more details: https://github.com/MDAnalysis/mdanalysis/issues/3543
  - Windows builds
-    * In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).
-
+    * In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).
+
 ## Release 2.0.0 of MDAnalysis
 
 This is the first version of MDAnalysis to solely support python 3.6+
@@ -534,5 +534,5 @@ See the [CHANGELOG](https://github.com/MDAnalysis/mdanalysis/blob/release-2.0.0/
 
 ### Known issues:
  - Windows builds
-    * For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the `MDAnalysisTests.lib.test_augment` tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.1.0.
-
+    * For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the `MDAnalysisTests.lib.test_augment` tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.1.0.
+