deploy: 934d55b

_sources/about.rst.txt

@@ -27,11 +27,12 @@ requirements**:
 #. Minimal documentation is provided (what your code does, how to install it,
    and how to use it)
 #. At least minimal regression tests are present; continuous integration is encouraged
+#. The code is installable as a standard package
 
 It is also highly encouraged that the MDAKit also satisfies:
 
-#. The code is installable as a standard package
 #. Information on bug reporting, user discussions, and community guidelines is made available
+#. The code is made available on a package distribution platform (e.g. PyPi or conda-forge).
 
 Registered MDAKits are then `listed here`_ with the intention of providing a centralised
 place where the community can find out more about them. Where possible, the MDAKits are

_sources/makingakit.rst.txt

@@ -15,11 +15,12 @@ In order to be accepted, there are several :ref:`requirements <requirements>` th
 #. Minimal documentation is provided (what your code does, how to install it,
    and how to use it)
 #. At least minimal regression tests are present; continuous integration is encouraged
+#. The source code is installable as a standard package
 
 It is also highly encouraged that the MDAKit also satisfies:
 
-#. Code is installable as a standard package
 #. Information on bug reporting, user discussions, and community guidelines is made available
+#. The code is made available on a package distribution platform (e.g. PyPi or conda-forge).
 
 These requirements ensure that registered packages are FAIR-compliant and hold up to an ideal scientific standard.
 Without prior experience, some of the requirements listed above can be daunting.
@@ -31,7 +32,7 @@ Building from the cookiecutter
 The MDAKits cookiecutter template (using the `Cookiecutter tool <https://cookiecutter.readthedocs.io/en/stable/>`_) can be used to rapidly develop a FAIR-compliant MDAKit by generating placeholder code for documentation, testing, and installation. 
 While its usage is outlined in detail in the `MDAKit cookiecutter <https://cookiecutter-mdakit.readthedocs.io/en/latest/>`_ documentation, here we provide a full walk-through for creating an RMSF analysis kit, recreating the functionality of the `RMSF analysis class <https://docs.mdanalysis.org/stable/documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.RMSF>`_ in the core library.
 
-Starting from an environment with Python 3.9+ and the `Cookiecutter tool <https://cookiecutter.readthedocs.io/en/stable/>`_, the MDAKit template is generated using
+Starting from an environment with Python 3.10+ and the `Cookiecutter tool <https://cookiecutter.readthedocs.io/en/stable/>`_, the MDAKit template is generated using
 
 .. code-block::
 
@@ -639,13 +640,13 @@ The contents of ``metadata.yaml`` for ``rmsfkit`` are:
 	license: GPL-2.0-or-later
 	project_home: https://github.com/yourusername/rmsfkit
 	documentation_home: https://rmsfkit.readthedocs.io/en/latest/
-	documentation_type: API
+        documentation_type: API
+        src_install:
+          - git clone https://github.com/yourusername/rmsfkit.git
+          - cd rmsfkit/
+          - pip install .
 
 	## Optional entries
-	src_install:
-	  - git clone https://github.com/yourusername/rmsfkit.git
-	  - cd rmsfkit/
-	  - pip install .
 	python_requires: ">=3.9"
 	mdanalysis_requires: ">=2.0.0"
 	run_tests:

_sources/reviewersguide.rst.txt

@@ -190,6 +190,24 @@ is failing
   encourage them to do so!)
 
 
+``src_install``: a list of commands to install the Kit from the source code. This is a *list of strings*
+(*AUTOMATIC CHECK*).
+
+
+``run_tests``: a list of commands to run the Kit’s tests. This is a *list of strings* (*AUTOMATIC CHECK*).
+
+- *note*: while (minimal) tests are one of the requirements of an MDAKit, we recognize that there might
+  be testing frameworks that we do not support yet. In those cases please exercise flexibility when
+  reviewing.
+- **RECOMMEND**: While a MDAKit may be registered with only minimal tests, encourage the contributor
+  to continue improving their tests in the future.
+
+
+``test_dependencies``: a list of commands for installing any dependencies required by the MDAKit’s tests.
+This is a *list of strings* (*AUTOMATIC CHECK*).
+
+
+
 *Optional* entries 
 ~~~~~~~~~~~~~~~~~~
 
@@ -203,10 +221,6 @@ CI is passing.
   encourage the contributor to make a release on conda-forge or PyPI. 
 
 
-``src_install``: a list of commands to install the Kit from the source code. This is a *list of strings*
-(*AUTOMATIC CHECK*).
-
-
 ``import_name``: the package name, used to import the Kit in Python. This is a *string* (*AUTOMATIC CHECK*).
 
 
@@ -224,20 +238,6 @@ is a *string* (*AUTOMATIC CHECK*).
   old version is given, enquire why, and recommend updating the Kit to work with a current version. 
 
 
-``run_tests``: a list of commands to run the Kit’s tests. This is a *list of strings* (*AUTOMATIC CHECK*).
-
-- *note*: while (minimal) tests are one of the requirements of an MDAKit, providing instructions on how to run
-  tests in the metadata file is currently optional, in order to allow greater flexibility in
-  what format tests take and so lower the entry barrier for new contributors. However, it is *highly
-  recommended* here to provide this metadata.
-- **RECOMMEND**: While a MDAKit may be registered with only minimal tests, encourage the contributor 
-  to continue improving their tests in the future.
-
-
-``test_dependencies``: a list of commands for installing any dependencies required by the MDAKit’s tests.
-This is a *list of strings* (*AUTOMATIC CHECK*).
-
-
 ``project_org``: the account under which the code is found - this may be an individual user account, or an
 organisation like MDAnalysis. This is a *string*.
 

about.html

@@ -146,11 +146,12 @@ <h1>About MDAKits<a class="headerlink" href="#about-mdakits" title="Link to this
 <li><p>Minimal documentation is provided (what your code does, how to install it,
 and how to use it)</p></li>
 <li><p>At least minimal regression tests are present; continuous integration is encouraged</p></li>
+<li><p>The code is installable as a standard package</p></li>
 </ol>
 <p>It is also highly encouraged that the MDAKit also satisfies:</p>
 <ol class="arabic simple">
-<li><p>The code is installable as a standard package</p></li>
 <li><p>Information on bug reporting, user discussions, and community guidelines is made available</p></li>
+<li><p>The code is made available on a package distribution platform (e.g. PyPi or conda-forge).</p></li>
 </ol>
 <p>Registered MDAKits are then <a class="reference external" href="mdakits.html">listed here</a> with the intention of providing a centralised
 place where the community can find out more about them. Where possible, the MDAKits are

add.html

@@ -296,18 +296,6 @@ <h2>Process<a class="headerlink" href="#process" title="Link to this heading">
 <span class="c1">## str: the type of documentation available [UserGuide, API, README]</span>
 <span class="nt">documentation_type</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">UserGuide + API</span>
 
-<span class="c1">#------------------------------------------------------------</span>
-<span class="c1"># Optional entries</span>
-<span class="c1">#------------------------------------------------------------   </span>
-<span class="c1">## List(str): a list of commands to use when installing the latest</span>
-<span class="c1">## release of the code. Note: only one installation method can currently</span>
-<span class="c1">## be defined. We suggest using mamba where possible (e.g.</span>
-<span class="c1">##   mamba -c conda-forge install MYPROJECT</span>
-<span class="c1">## for a conda package installation).</span>
-<span class="c1">## Here we use a simple PyPi installation:</span>
-<span class="nt">install</span><span class="p">:</span>
-<span class="w">  </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pip install MYPROJECT</span>
-
 <span class="c1">## List(str): a list of commands to use when installing the mdakit from its</span>
 <span class="c1">## source code.</span>
 <span class="nt">src_install</span><span class="p">:</span>
@@ -346,6 +334,18 @@ <h2>Process<a class="headerlink" href="#process" title="Link to this heading">
 <span class="c1">## str: the organisation name the MDAKit falls under</span>
 <span class="nt">project_org</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">GH_HOST_ACCOUNT</span>
 
+<span class="c1">#------------------------------------------------------------</span>
+<span class="c1"># Optional entries</span>
+<span class="c1">#------------------------------------------------------------   </span>
+<span class="c1">## List(str): a list of commands to use when installing the latest</span>
+<span class="c1">## release of the code. Note: only one installation method can currently</span>
+<span class="c1">## be defined. We suggest using mamba where possible (e.g.</span>
+<span class="c1">##   mamba -c conda-forge install MYPROJECT</span>
+<span class="c1">## for a conda package installation).</span>
+<span class="c1">## Here we use a simple PyPi installation:</span>
+<span class="nt">install</span><span class="p">:</span>
+<span class="w">  </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pip install MYPROJECT</span>
+
 <span class="c1">## str: the development status of the MDAKit</span>
 <span class="c1">## See https://pypi.org/classifiers/ for development status classifiers.</span>
 <span class="nt">development_status</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">Production/Stable</span>

makingakit.html

@@ -159,11 +159,12 @@ <h1>Making an MDAKit<a class="headerlink" href="#making-an-mdakit" title="Link t
 <li><p>Minimal documentation is provided (what your code does, how to install it,
 and how to use it)</p></li>
 <li><p>At least minimal regression tests are present; continuous integration is encouraged</p></li>
+<li><p>The source code is installable as a standard package</p></li>
 </ol>
 <p>It is also highly encouraged that the MDAKit also satisfies:</p>
 <ol class="arabic simple">
-<li><p>Code is installable as a standard package</p></li>
 <li><p>Information on bug reporting, user discussions, and community guidelines is made available</p></li>
+<li><p>The code is made available on a package distribution platform (e.g. PyPi or conda-forge).</p></li>
 </ol>
 <p>These requirements ensure that registered packages are FAIR-compliant and hold up to an ideal scientific standard.
 Without prior experience, some of the requirements listed above can be daunting.
@@ -172,7 +173,7 @@ <h1>Making an MDAKit<a class="headerlink" href="#making-an-mdakit" title="Link t
 <h2>Building from the cookiecutter<a class="headerlink" href="#building-from-the-cookiecutter" title="Link to this heading"></a></h2>
 <p>The MDAKits cookiecutter template (using the <a class="reference external" href="https://cookiecutter.readthedocs.io/en/stable/">Cookiecutter tool</a>) can be used to rapidly develop a FAIR-compliant MDAKit by generating placeholder code for documentation, testing, and installation.
 While its usage is outlined in detail in the <a class="reference external" href="https://cookiecutter-mdakit.readthedocs.io/en/latest/">MDAKit cookiecutter</a> documentation, here we provide a full walk-through for creating an RMSF analysis kit, recreating the functionality of the <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/rms.html#MDAnalysis.analysis.rms.RMSF">RMSF analysis class</a> in the core library.</p>
-<p>Starting from an environment with Python 3.9+ and the <a class="reference external" href="https://cookiecutter.readthedocs.io/en/stable/">Cookiecutter tool</a>, the MDAKit template is generated using</p>
+<p>Starting from an environment with Python 3.10+ and the <a class="reference external" href="https://cookiecutter.readthedocs.io/en/stable/">Cookiecutter tool</a>, the MDAKit template is generated using</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cookiecutter gh:MDAnalysis/cookiecutter-mdakit
 
 project_name [ProjectName]: rmsfkit
@@ -697,12 +698,12 @@ <h3>Testing<a class="headerlink" href="#testing" title="Link to this heading">
 <span class="nt">project_home</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">https://github.com/yourusername/rmsfkit</span>
 <span class="nt">documentation_home</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">https://rmsfkit.readthedocs.io/en/latest/</span>
 <span class="nt">documentation_type</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">API</span>
-
-<span class="c1">## Optional entries</span>
 <span class="nt">src_install</span><span class="p">:</span>
 <span class="w">  </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">git clone https://github.com/yourusername/rmsfkit.git</span>
 <span class="w">  </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">cd rmsfkit/</span>
 <span class="w">  </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">pip install .</span>
+
+<span class="c1">## Optional entries</span>
 <span class="nt">python_requires</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;&gt;=3.9&quot;</span>
 <span class="nt">mdanalysis_requires</span><span class="p">:</span><span class="w"> </span><span class="s">&quot;&gt;=2.0.0&quot;</span>
 <span class="nt">run_tests</span><span class="p">:</span>

reviewersguide.html

@@ -300,6 +300,18 @@ <h4>Entries <em>required</em> for registration<a class="headerlink" href="#entri
 docs. If you judge that it does not, see if the submitter intends to continue working on these (and
 encourage them to do so!)</p></li>
 </ul>
+<p><code class="docutils literal notranslate"><span class="pre">src_install</span></code>: a list of commands to install the Kit from the source code. This is a <em>list of strings</em>
+(<em>AUTOMATIC CHECK</em>).</p>
+<p><code class="docutils literal notranslate"><span class="pre">run_tests</span></code>: a list of commands to run the Kit’s tests. This is a <em>list of strings</em> (<em>AUTOMATIC CHECK</em>).</p>
+<ul class="simple">
+<li><p><em>note</em>: while (minimal) tests are one of the requirements of an MDAKit, we recognize that there might
+be testing frameworks that we do not support yet. In those cases please exercise flexibility when
+reviewing.</p></li>
+<li><p><strong>RECOMMEND</strong>: While a MDAKit may be registered with only minimal tests, encourage the contributor
+to continue improving their tests in the future.</p></li>
+</ul>
+<p><code class="docutils literal notranslate"><span class="pre">test_dependencies</span></code>: a list of commands for installing any dependencies required by the MDAKit’s tests.
+This is a <em>list of strings</em> (<em>AUTOMATIC CHECK</em>).</p>
 </section>
 <section id="optional-entries">
 <h4><em>Optional</em> entries<a class="headerlink" href="#optional-entries" title="Link to this heading"></a></h4>
@@ -311,8 +323,6 @@ <h4><em>Optional</em> entries<a class="headerlink" href="#optional-entries" titl
 <li><p><strong>RECOMMEND</strong>: If the installation uses e.g. github or is otherwise complicated (many steps involved),
 encourage the contributor to make a release on conda-forge or PyPI.</p></li>
 </ul>
-<p><code class="docutils literal notranslate"><span class="pre">src_install</span></code>: a list of commands to install the Kit from the source code. This is a <em>list of strings</em>
-(<em>AUTOMATIC CHECK</em>).</p>
 <p><code class="docutils literal notranslate"><span class="pre">import_name</span></code>: the package name, used to import the Kit in Python. This is a <em>string</em> (<em>AUTOMATIC CHECK</em>).</p>
 <p><code class="docutils literal notranslate"><span class="pre">python_requires</span></code>: range specifications for the versions of Python this Kit supports, e.g. “&gt;=3.9”. This
 is a <em>string</em> (<em>AUTOMATIC CHECK</em>).</p>
@@ -325,17 +335,6 @@ <h4><em>Optional</em> entries<a class="headerlink" href="#optional-entries" titl
 <li><p><strong>RECOMMEND</strong>: Ideally, the Kit works with the current version of MDAnalysis - if an upper bound to an
 old version is given, enquire why, and recommend updating the Kit to work with a current version.</p></li>
 </ul>
-<p><code class="docutils literal notranslate"><span class="pre">run_tests</span></code>: a list of commands to run the Kit’s tests. This is a <em>list of strings</em> (<em>AUTOMATIC CHECK</em>).</p>
-<ul class="simple">
-<li><p><em>note</em>: while (minimal) tests are one of the requirements of an MDAKit, providing instructions on how to run
-tests in the metadata file is currently optional, in order to allow greater flexibility in
-what format tests take and so lower the entry barrier for new contributors. However, it is <em>highly
-recommended</em> here to provide this metadata.</p></li>
-<li><p><strong>RECOMMEND</strong>: While a MDAKit may be registered with only minimal tests, encourage the contributor
-to continue improving their tests in the future.</p></li>
-</ul>
-<p><code class="docutils literal notranslate"><span class="pre">test_dependencies</span></code>: a list of commands for installing any dependencies required by the MDAKit’s tests.
-This is a <em>list of strings</em> (<em>AUTOMATIC CHECK</em>).</p>
 <p><code class="docutils literal notranslate"><span class="pre">project_org</span></code>: the account under which the code is found - this may be an individual user account, or an
 organisation like MDAnalysis. This is a <em>string</em>.</p>
 <p><code class="docutils literal notranslate"><span class="pre">development_status</span></code>: the development status of the MDAKit.</p>