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finalize DFE development docs; closes #1085
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petrelharp committed Dec 21, 2024
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Expand Up @@ -1652,7 +1652,7 @@ Testing your DFE model and submitting a PR

After you finished your implementation, and specified all the
necessary citations,
we recommend that you run some basic local tests to see that
we recommend that you run some basic local checks to see that
the model was successfully loaded to ``stdpopsim``.
You may follow the process outlined for `Testing your demographic model and submitting a PR`_.

Expand All @@ -1664,15 +1664,7 @@ At this point, most of your work is done.
**You have officially joined the** ``stdpopsim`` **development team. Welcome!!**
Your DFE model still needs to undergo review by another member
of the development team before it is fully incorporated into ``stdpopsim``.
This will likely require additional feedback from you,
so, stay tuned for discussion during the review process.

---------------------
Reviewing a DFE model
---------------------

The review process for DFE models is currently being developed.
For now, we suggest that you
To facilitate this, please
`open a new blank issue <https://github.com/popsim-consortium/stdpopsim/issues/new>`__
and specify the following information:

Expand All @@ -1682,9 +1674,28 @@ and specify the following information:
4. **Potential issues:**
5. **QC'er requests:**

A reviewer will be assigned to check your implementation and approve it.
All discussion about the review can be conducted in the **QC issue**
mentioned above.
This will likely require additional feedback from you,
so, stay tuned for discussion during the review process.

---------------------
Reviewing a DFE model
---------------------

The process for reviewing a DFE is essentially the same
as for reviewing a demographic model (see `Overview of the stdpopsim review process`_).
Briefly, you will re-implement the DFE "blind", i.e., without looking at the DFE
implementation already added to the code.
Then, the unit tests check whether the implementations are equivalent.
To do this, you add your implementation to ``stdpopsim/qc/<SPECIES_ID>.py``,
followed by a call like

.. code-block:: python
_species.get_dfe(_MODEL_ID_).register_qc(_your_review_function())
where ``_MODEL_ID_`` is the string specified as the ID for the original DFE,
and ``_your_review_function()`` is the function you've added to the QC file
that returns a DFE object.

****************
Coding standards
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