Add changes needed to make tests and src_install non-optional (#159)

Author: IAlibay

README.rst

@@ -37,19 +37,6 @@ this repository and adding a new `metadata`_ file within it's own
 respective directory under `mdakits`.
 
 
-Workflow
-========
-
-Shown below is the MDAKit framework workflow.
-
-
-.. image:: https://github.com/MDAnalysis/MDAKits/blob/main/assets/MDAKitFramework.png
-   :alt: The MDAKit Framework
-   :align: center
-
-
-For more details see the `MDAKit Whitepaper`_.
-
 License
 =======
 

docs/source/about.rst

@@ -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

docs/source/makingakit.rst

@@ -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:

docs/source/reviewersguide.rst

@@ -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*.
 

mdakits/template/metadata.yaml

@@ -52,18 +52,6 @@ documentation_home: https://MYPROJECT.readthedocs.io
 ## str: the type of documentation available [UserGuide, API, README]
 documentation_type: UserGuide + API
 
-#------------------------------------------------------------
-# Optional entries
-#------------------------------------------------------------   
-## List(str): a list of commands to use when installing the latest
-## release of the code. Note: only one installation method can currently
-## be defined. We suggest using mamba where possible (e.g.
-##   mamba -c conda-forge install MYPROJECT
-## for a conda package installation).
-## Here we use a simple PyPi installation:
-install:
-  - pip install MYPROJECT
-
 ## List(str): a list of commands to use when installing the mdakit from its
 ## source code.
 src_install:
@@ -102,6 +90,18 @@ test_dependencies:
 ## str: the organisation name the MDAKit falls under
 project_org: GH_HOST_ACCOUNT
 
+#------------------------------------------------------------
+# Optional entries
+#------------------------------------------------------------   
+## List(str): a list of commands to use when installing the latest
+## release of the code. Note: only one installation method can currently
+## be defined. We suggest using mamba where possible (e.g.
+##   mamba -c conda-forge install MYPROJECT
+## for a conda package installation).
+## Here we use a simple PyPi installation:
+install:
+  - pip install MYPROJECT
+
 ## str: the development status of the MDAKit
 ## See https://pypi.org/classifiers/ for development status classifiers.
 development_status: Production/Stable