Re-enable nikola check commands in CI

.github/workflows/ci.yml

@@ -22,8 +22,8 @@ jobs:
         - name: Build website
           nox_session: build
 
-#        - name: Perform Nikola checks
-#          nox_session: check
+        - name: Perform Nikola checks
+          nox_session: check
 
     steps:
 

data/affiliated_pkgs.json

@@ -6,12 +6,12 @@
     },
     "urls": {
       "home": "https://www.plasmapy.org",
-      "repo": "https://github.com/plasmapy/plasmapy",
+      "repo": "https://github.com/PlasmaPy/PlasmaPy",
       "image": "/images/plasmapy-graphic-circular.png"
     },
     "description": {
       "short": "A open-source Python 3 package for plasma physics.",
-      "long": "PlasmaPy is an open-source community developed Python 3 package for plasma physics.  PlasmaPy intends to be a collection of functionality commonly used and shared between plasma physicists and researchers globally."
+      "long": "PlasmaPy is an open-source community developed Python package for plasma research and education."
     },
     "affiliated": false,
     "keywords": [
@@ -37,8 +37,8 @@
       "image": null
     },
     "description": {
-      "short": "tofu is an open-source python library providing a toolbox for synthetic diagnostics and tomography.",
-      "long": "<code>tofu</code> is an open-source python library.  It aims at providing the user with a ready-set toolbox for modelling synthetic diagnostics and performing tomographic inversions on linear or toroidal (quasi-axisymmetric) fusion devices.  It is relevant for diagnostics integrating an emissivity on a set of Lines of Sight or Volumes of Sight corresponding to as many detectors or pixels, and for which the plasma can be considered transparent (i.e. not for radio-frequencies / microwaves)."
+      "short": "tofu is an open source python library providing a toolbox for synthetic diagnostics and tomography.",
+      "long": "tofu is an open source python library. It aims at providing the user with a ready-set toolbox for modelling synthetic diagnostics and performing tomographic inversions on linear or toroidal (quasi-axisymmetric) fusion devices.  It is relevant for diagnostics integrating an emissivity on a set of Lines of Sight or Volumes of Sight corresponding to as many detectors or pixels, and for which the plasma can be considered transparent (i.e. not for radio-frequencies or microwaves)."
     },
     "affiliated": true,
     "keywords": [
@@ -67,14 +67,13 @@
     },
     "description": {
       "short": "A open-source Python 3 package for plasma physics.",
-      "long": "OMFIT - One Modeling Framework for Integrated Tasks - is an integrated modeling  and experimental data analysis framework written in python.  The goal of OMFIT is to enhance existing scientific workflows and enable new integrated modeling capabilities."
+      "long": "OMFIT \u2014 One Modeling Framework for Integrated Tasks \u2014 is an integrated modeling and experimental data analysis framework written in python.  The goal of OMFIT is to enhance existing scientific workflows and enable new integrated modeling capabilities."
     },
     "affiliated": false,
     "keywords": [
       "plasma",
       "physics",
       "Python",
-      "Python 3",
       "fusion",
       "simulation",
       "diagnostics"
@@ -126,8 +125,8 @@
       "image": null
     },
     "description": {
-      "short": "<code>ALOHA</code> is a coupling code for LHCD antennas facing tokamak magnetized fusion plasma.",
-      "long": "<code>ALOHA</code> is a coupling code for Lower Hybrid Current Drive antennas facing tokamak magnetized fusion plasma.  This coupling code is based on the linear coupling theory. It allows one to model the coupling of a 'grill'-like antenna to a cold plasma of the kind one can find in Tokamaks. It allows taking into account advanced antennas (such as multijunctions or passive-active multijunction antennas)."
+      "short": "ALOHA is a coupling code for LHCD antennas facing tokamak magnetized fusion plasma.",
+      "long": "ALOHA is a coupling code for Lower Hybrid Current Drive antennas facing tokamak magnetized fusion plasma. This coupling code is based on the linear coupling theory. It allows one to model the coupling of a 'grill'-like antenna to a cold plasma of the kind one can find in Tokamaks. It allows taking into account advanced antennas (such as multijunctions or passive-active multijunction antennas)."
     },
     "affiliated": false,
     "keywords": [

noxfile.py

@@ -12,17 +12,38 @@ def build(session) -> None:
 
 @nox.session
 def check(session) -> None:
-    """Check links and files in the generated site."""
+    """Perform basic checks on the generated site."""
     session.install("-r", "requirements.txt")
     session.run("nikola", "build")
     session.run(
         "nikola",
         "check",
-        "--check-links",
+        "--check-files",
         "--find-sources",
     )
 
 
+@nox.session
+def check_thoroughly(session) -> None:
+    """
+    Perform extensive checks on the generated site, including remote links.
+
+    This check includes some expected failures. For example, the
+    --check-links option fails due to `url('None')` showing up in the
+    generated output for affiliates/index.html.
+    """
+    session.install("-r", "requirements.txt")
+    session.run("nikola", "build")
+    session.run(
+        "nikola",
+        "check",
+        "--check-files",
+        "--find-sources",
+        "--check-links",
+        "--remote",
+    )
+
+
 @nox.session
 def clean(session) -> None:
     """Remove output files."""

pages/affiliates/index.md

@@ -2,25 +2,17 @@ title: Plasma Packages
 hidetitle: True
 author: Erik T. Everson
 
-PlasmaPy's charter includes promoting open-source software for all of
-the plasma community, and not just `plasmapy`.  We feel the entire community
+PlasmaPy's charter includes promoting open source software for all of
+the plasma community, and not just PlasmaPy. The entire community
 benefits when there are multiple efforts trying to build functionality for all
 aspects of the plasma field.  As such, we want to promote any ongoing effort.  This
 page displays projects that have requested to be shown.  If you want your
-project include, and increase its visibility, then please submit a request.
-
-<div style="width: 100%">
-    <a href=https://docs.google.com/forms/d/e/1FAIpQLSfz2djEihWkODbkr1ZC5splkX7ZKLAh_Kuy-aXOngTELIm3xQ/viewform?usp=sf_link
-            class="feature-card feature-link btn-plasmapy-bluegreen"
-            style="width: 200px">
-        <div>Submit Request</div>
-    </a>
-</div>
-<br>
+project include, and increase its visibility, then please submit a request
+to <team@plasmapy.org>.
 
 All projects/packages are considered **Community Packages**
 <span style="vertical-align: 2px">{{% community_shield %}}</span>, but packages designed with
-`plasmapy` interoperability are marked as **Affiliated Packages**
+PlasmaPy interoperability are marked as **Affiliated Packages**
 <span style="vertical-align: 2px">{{% affiliated_shield %}}</span>.
 
 ----

pages/contribute.md

@@ -1,73 +1,29 @@
-title: Contribute to PlasmaPy
+title: Contributing to PlasmaPy
 slug: contribute
 
 # Contributing to PlasmaPy
 
-There are numerous ways to contribute to PlasmaPy, including by
-providing code and documentation, suggesting and discussing ideas,
-submitting issues and bug reports, and engaging the broader plasma
-physics community.
-
-**Imposter syndrome disclaimer**: We want your help. No, really.
-
-There may be a little voice inside your head that is telling you that you're not
-ready to be an open source contributor; that your skills aren't nearly good
-enough to contribute. What could you possibly offer a project like this one?
-
-We assure you - the little voice in your head is wrong. If you can write code at
-all, you can contribute code to open source. Contributing to open source
-projects is a fantastic way to advance one's coding skills. Writing perfect code
-isn't the measure of a good developer (that would disqualify all of us!); it's
-trying to create something, making mistakes, and learning from those
-mistakes. That's how we all improve, and we are happy to help others learn.
-
-Being an open source contributor doesn't just mean writing code, either. You can
-help out by writing documentation, tests, or even giving feedback about the
-project (and yes - that includes giving feedback about the contribution
-process). Some of these contributions may be the most valuable to the project as
-a whole, because you're coming to the project with fresh eyes, so you can see
-the errors and assumptions that seasoned contributors have glossed over.
-
-*This disclaimer was originally written by
-[Adrienne Lowe](https://github.com/adriennefriend) for a
-[PyCon talk](https://www.youtube.com/watch?v=6Uj746j9Heo), and was adapted by
-[yt](https://github.com/yt-project/yt) in their README file based on its use
-in the README file for the [MetPy project](https://github.com/Unidata/MetPy).
-It was then adapted by PlasmaPy.*
-
-## Sharing ideas
-
-There are several methods of communication that are being used in the
-early stages of PlasmaPy development:
-
-* [Signing up for the PlasmaPy email
-  list](https://groups.google.com/forum/#!forum/plasmapy) will allow
-  you to participate in broader discussions and keep up with the
-  latest developments.
-
-* The [PlasmaPy repository on
-  GitHub](https://github.com/PlasmaPy/plasmapy) is the best place to
-  [submit issues](https://github.com/PlasmaPy/plasmapy/issues) and
-  review [pull requests](https://github.com/PlasmaPy/plasmapy/pulls).
-
-* The PlasmaPy [Matrix](https://app.element.io/#/room/#plasmapy:openastronomy.org) or
-  [Gitter](https://gitter.im/PlasmaPy/Lobby) joint channel
-  is a great place to have informal conversations, coordinate efforts,
-  and share ideas.
-* We have biweekly telecons which are announced on the email list.
-
-## Contributing code or documentation to PlasmaPy
-
-If you see something you'd like to work on amongst our
-[issues](https://github.com/PlasmaPy/PlasmaPy/issues), or if you've got
-a great idea for something to include in the package, start hacking away on
-that! However, please announce your intent first in the relevant issue (or make
-one if necessary) to make sure there is no work duplication.
-
-You can find most of what you should know in the [Contributing Guide](http://docs.plasmapy.org/en/latest/development/index.html).
-
-Please note that PlasmaPy has a [Code of Conduct](/conduct).
-
-Issues marked by the community as *help wanted* mean just that - either they're
-good contributions for outsiders or there's an issue in the ongoing work that
-requires a second opinion. Please consider these first!
+Thank you for your interest in contributing to PlasmaPy! To learn more,
+please check out the [Contributor Guide] in PlasmaPy's online documentation.
+This guide describes:
+
+- The [many ways to contribute]
+- [Getting ready to contribute]
+- The [code contribution workflow]
+- Best practices and common conventions for [writing code]
+- Creating and running [software tests]
+- Writing and building [documentation]
+
+If you would like to learn more, we encourage you to stop by one of
+our [community meetings](/meetings/weekly).
+
+The PlasmaPy community abides by the Contributor Covenant [Code of Conduct].
+
+[code contribution workflow]: https://docs.plasmapy.org/en/latest/contributing/workflow.html
+[code of conduct]: https://docs.plasmapy.org/en/latest/CODE_OF_CONDUCT.html
+[contributor guide]: https://docs.plasmapy.org/en/latest/contributing/index.html
+[documentation]: https://docs.plasmapy.org/en/latest/contributing/doc_guide.html
+[getting ready to contribute]: https://docs.plasmapy.org/en/latest/contributing/getting_ready.html
+[many ways to contribute]: https://docs.plasmapy.org/en/latest/contributing/many_ways.html
+[software tests]: https://docs.plasmapy.org/en/latest/contributing/testing_guide.html
+[writing code]: https://docs.plasmapy.org/en/latest/contributing/coding_guide.html

pages/meetings/aps/62nd_dpp_mini_conf_followups.md

@@ -2,19 +2,12 @@ title: 62nd APS DPP - 11.04 Mini-Conference Followups
 author: Erik T. Everson
 hidetitle: True
 
-[Zoom link]: https://harvard.zoom.us/j/91600794594?pwd=L09iTGtTRUN1RmpsVnNvU05LRnNwQT09
-
 # 62nd APS DPP - 11.04 Mini-Conference | Post-Meeting Discussions
 ### Growing an open-source software ecosystem for plasma science
 
-<div style="height: 12px"><!-- Adding vertical whitespace --></div>
-
-**Where:** [On Zoom][Zoom Link] <br/>
 **Day 1:** Tuesday, November 17th at 21 UTC / 4 pm EST / 1 pm PST <br/>
 **Day 2:** Thursday, November 19th at 19 UTC / 2 pm EST / 11 am PST <br/>
 
-<div style="height: 12px"><!-- Adding vertical whitespace --></div>
-
 In order to capitalize on the opportunities afforded by bringing together the
 diversity of speakers and attendees and perspectives during this year's
 mini-conference, we plan to host two **post-meeting discussions**.  Here

pages/meetings/index.md

@@ -25,7 +25,7 @@ We provided a [PlasmaPy tutorial](./magnetus2023) at the
 [MagNetUS 2023 meeting](https://sites.google.com/view/magnetus2023/home?authuser=0)
 at Auburn University on Thursday, June 15.
 
-#### [62nd APS DPP - 11.04 Mini-Conference](https://engage.aps.org/dpp/meetings/annual-meeting/mini-conferences): Growing an open source software ecosystem for plasma science
+#### [62nd APS DPP - 11.04 Mini-Conference](https://engage.aps.org/dpp/meetings/mini-conferences): Growing an open source software ecosystem for plasma science
 November 11 & 12, 2020
 
 <div style="height: 12px"><!-- Adding vertical whitespace --></div>

posts/plasmapy-v01-release.rst

@@ -13,7 +13,7 @@
 
    We are faced with the very newest of releases.
 
-   GitHub calls this one `PlasmaPy v0.1.0 <http://docs.plasmapy.org/en/v0.1/about/release_notes.html#version-0-1-0>`_, the first of the alphas.
+   GitHub calls this one `PlasmaPy v0.1.0 <https://docs.plasmapy.org/en/stable/changelog/0.1.0.html>`_, the first of the alphas.
 
    And yet, for the first time in the history of this project our team has the
    technology to prevent its own procrastination.
@@ -27,18 +27,18 @@
    <https://github.com/PlasmaPy/PlasmaPy/issues>`_, even the code reviews that
    we performed have provided us with the tools to prevent this exciting event.
 
-   Through all the chaos that is our Git tree, through all of the `PEP8
+   Through all the chaos that is our Git tree, through all of the `PEP 8
    <https://github.com/PlasmaPy/PlasmaPy/search?q=pep8&type=Commits>`_ and
    the `Matrix discussion <https://app.element.io/#/room/#plasmapy:openastronomy.org>`_,
    through all the `pain of learning Sphinx <http://docs.plasmapy.org/>`_ and rebasing,
    through `all of our ~2000 commits <https://github.com/PlasmaPy/PlasmaPy/commits/main>`_,
    there is one thing that has nourished our souls, and pushed us to complete
    this release, and that is our `pretty plots
-   <http://docs.plasmapy.org/en/latest/auto_examples/index.html>`_. Oh, and the
+   <https://docs.plasmapy.org/en/stable/examples.html>`_. Oh, and the
    possibility to
-   `apply <http://docs.plasmapy.org/en/v0.1/atomic/decorators.html#passing-particle-instances-to-functions-and-methods>`_
-   `more <http://docs.plasmapy.org/en/v0.1/api/plasmapy.utils.checks.check_relativistic.html#plasmapy.utils.checks.check_relativistic>`_
-   `decorators <http://docs.plasmapy.org/en/v0.1/api/plasmapy.utils.checks.check_quantity.html#plasmapy.utils.checks.check_quantity>`_.
+   `apply <https://docs.plasmapy.org/en/stable/api/plasmapy.particles.decorators.particle_input.html#particle-input>`_
+   `more <https://docs.plasmapy.org/en/stable/api/plasmapy.utils.decorators.checks.check_relativistic.html#check-relativistic>`_
+   `decorators <https://docs.plasmapy.org/en/stable/api/plasmapy.utils.decorators.validators.validate_quantities.html#validate-quantities>`_.
 
    The dreams of the entire PlasmaPy community are focused tonight on these `31
    brave committers <https://github.com/PlasmaPy/PlasmaPy/graphs/contributors>`_,
@@ -47,7 +47,7 @@
    And may we all, plasma enthusiasts the world over, see this release through.
 
    `Thermal speed
-   <http://docs.plasmapy.org/en/v0.1/api/plasmapy.physics.parameters.thermal_speed.html#plasmapy.physics.parameters.thermal_speed>`_,
+   <https://docs.plasmapy.org/en/stable/api/plasmapy.formulary.speeds.thermal_speed.html#thermal-speed>`_,
    and a :math:`\sqrt{2}` to you,
 
    ~PlasmaPy

posts/plasmapy-v011-bugfix-release.rst

@@ -9,7 +9,7 @@
 
 We have just released PlasmaPy v0.1.1, our first bugfix release which attempts to correct many of the flaws in our code we only noticed while releasing v0.1!
 
-Take a look at the `release notes <http://docs.plasmapy.org/en/latest/whatsnew/0.1.1.html>`_ to see what's changed.
+Take a look at the `release notes <https://docs.plasmapy.org/en/stable/changelog/0.1.1.html>`_ to see what's changed.
 
 As usual (although this is likely the first time you have reason to run this command), you should now be able to update via `pip install --upgrade plasmapy`.