dapper 1.7.0__tar.gz → 1.7.1__tar.gz

dapper-1.7.1/PKG-INFO

@@ -0,0 +1,107 @@
+Metadata-Version: 2.4
+Name: dapper
+Version: 1.7.1
+Summary: DAPPER benchmarks the performance of data assimilation (DA) methods.
+Author: Patrick N. Raanes
+Author-email: patrick.n.raanes@gmail.com
+Project-URL: Documentation, https://nansencenter.github.io/DAPPER/
+Project-URL: Source, https://github.com/nansencenter/DAPPER
+Project-URL: Tracker, https://github.com/nansencenter/DAPPER/issues
+Keywords: data-assimilation enkf kalman-filtering state-estimation particle-filter kalman bayesian-methods bayesian-filter chaos
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENCE.txt
+Requires-Dist: scipy>=1.14
+Requires-Dist: numpy~=2.0
+Requires-Dist: matplotlib>=3.10
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: ipython>=7.34
+Requires-Dist: ipdb
+Requires-Dist: jupyter
+Requires-Dist: notebook<7
+Requires-Dist: mpl-tools==0.4.1
+Requires-Dist: tqdm~=4.67
+Requires-Dist: colorama~=0.4.1
+Requires-Dist: tabulate~=0.8.3
+Requires-Dist: pathos~=0.3
+Requires-Dist: dill==0.3.8
+Requires-Dist: patlib==0.3.7
+Requires-Dist: struct-tools==0.2.5
+Requires-Dist: threadpoolctl<4.0.0,>=3.0.0
+Provides-Extra: qt
+Requires-Dist: PyQt5; extra == "qt"
+Requires-Dist: qtpy; extra == "qt"
+Provides-Extra: debug
+Requires-Dist: line_profiler; extra == "debug"
+Requires-Dist: pre-commit; extra == "debug"
+Provides-Extra: test
+Requires-Dist: tox; extra == "test"
+Requires-Dist: coverage>=5.1; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-sugar; extra == "test"
+Requires-Dist: pytest-benchmark; extra == "test"
+Requires-Dist: pytest-clarity; extra == "test"
+Requires-Dist: pytest-xdist; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Provides-Extra: lint
+Requires-Dist: ruff; extra == "lint"
+Provides-Extra: doc
+Requires-Dist: mkdocs-material; extra == "doc"
+Requires-Dist: mkdocstrings; extra == "doc"
+Requires-Dist: mkdocstrings-python; extra == "doc"
+Requires-Dist: mkdocs-gen-files; extra == "doc"
+Requires-Dist: mkdocs-literate-nav; extra == "doc"
+Requires-Dist: mkdocs-section-index; extra == "doc"
+Requires-Dist: mkdocs-glightbox; extra == "doc"
+Requires-Dist: mkdocs-jupyter; extra == "doc"
+Requires-Dist: pybtex; extra == "doc"
+Provides-Extra: build
+Requires-Dist: twine; extra == "build"
+Requires-Dist: jupytext<=1.15; extra == "build"
+Provides-Extra: dev
+Requires-Dist: line_profiler; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: coverage>=5.1; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-sugar; extra == "dev"
+Requires-Dist: pytest-benchmark; extra == "dev"
+Requires-Dist: pytest-clarity; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: pytest-timeout; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: jupytext<=1.15; extra == "dev"
+Requires-Dist: mkdocs-material; extra == "dev"
+Requires-Dist: mkdocstrings; extra == "dev"
+Requires-Dist: mkdocstrings-python; extra == "dev"
+Requires-Dist: mkdocs-gen-files; extra == "dev"
+Requires-Dist: mkdocs-literate-nav; extra == "dev"
+Requires-Dist: mkdocs-section-index; extra == "dev"
+Requires-Dist: mkdocs-glightbox; extra == "dev"
+Requires-Dist: mkdocs-jupyter; extra == "dev"
+Requires-Dist: pybtex; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+It is usually best to install from source (github),
+so that you the code is readily available to play with.
+See full README on [github](https://github.com/nansencenter/DAPPER).

{dapper-1.7.0 → dapper-1.7.1}/README.md

@@ -8,7 +8,7 @@
 !
 -->
 
-<img src="/docs/imgs/logo_wtxt.png" align="left" width="250"/>
+<img src="https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/logo_wtxt.png" align="left" width="250"/>
 
 DAPPER is a set of templates for **benchmarking** the performance of **data assimilation** (DA) methods.
 The numerical experiments provide support and guidance for new developments in DA.
@@ -26,20 +26,19 @@ and then estimate that truth given the models and noisy observations.
 
 ## Getting started
 
-[Install](#installation), then
-read, run and try to understand `examples/basic_{1,2,3}.py`.
-Some of the examples also exist as Jupyter notebooks, and can be run in the cloud
-*without installation* (but requiring Google login): [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](http://colab.research.google.com/github/nansencenter/DAPPER).
-This [screencast](https://www.youtube.com/watch?v=YtalK0Zkzvg&t=6475s)
-provides an overview to DAPPER.
-The [documentation](https://nansencenter.github.io/DAPPER)
-includes general guidelines and the API reference,
-but most users must expect to read the code as well.
-If used towards a publication, please cite as
-*The experiments used (inspiration from) DAPPER [ref], version 1.6.0*,
-or similar, where [ref] points to [![DOI](https://joss.theoj.org/papers/10.21105/joss.05150/status.svg)](https://doi.org/10.21105/joss.05150).
-Also see the interactive [tutorials on DA theory](https://github.com/nansencenter/DA-tutorials)
-with Python.
+- Read & run [examples](examples)/`basic_1.py` and `basic_2.py`,
+  or their corresponding notebooks [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](http://colab.research.google.com/github/nansencenter/DAPPER)
+  (requires Google login).
+- This [screencast](https://www.youtube.com/watch?v=YtalK0Zkzvg&t=6475s)
+  provides an overview to DAPPER.
+- [Install](#installation).
+- The [documentation](https://nansencenter.github.io/DAPPER)
+  includes general guidelines and the API reference,
+  but most users must expect to read the code as well.
+- If used towards a publication, please cite as
+  *The experiments used (inspiration from) DAPPER [ref], version 1.6.0*,
+  or similar, where [ref] points to [![DOI](https://joss.theoj.org/papers/10.21105/joss.05150/status.svg)](https://doi.org/10.21105/joss.05150).
+- Also see the interactive [tutorials on DA theory](https://github.com/nansencenter/DA-tutorials) with Python.
 
 ## Highlights
 
@@ -49,7 +48,7 @@ through a variety of typical [test cases](#test-cases-models) and statistics. It
 (b) facilitates comparative studies, thus promoting the
 (a) reliability and
 (b) relevance of the results.
-For example, the figure below is generated by `examples/basic_3.py`,
+For example, the figure below is generated by `docs/examples/basic_3.py`,
 reproduces figure 5.7 of [these lecture notes](http://cerea.enpc.fr/HomePages/bocquet/teaching/assim-mb-en.pdf).
 DAPPER is
 (c) open source, written in Python, and
@@ -59,10 +58,10 @@ this promotes the
 (d) dissemination of the underlying science,
 and makes it easy to adapt and extend.
 
-![Comparative benchmarks with Lorenz-96 plotted as a function of the ensemble size (N)](./docs/imgs/ex3.svg)
+![Comparative benchmarks with Lorenz-96 plotted as a function of the ensemble size (N)](https://github.com/nansencenter/DAPPER/raw/master/docs/images/ex3.svg)
 
 DAPPER demonstrates how to parallelise ensemble forecasts (e.g., the QG model),
-local analyses (e.g., the LETKF), and independent experiments (e.g., `examples/basic_3.py`).
+local analyses (e.g., the LETKF), and independent experiments (e.g., `docs/examples/basic_3.py`).
 It includes a battery of diagnostics and statistics,
 which all get averaged over subdomains (e.g., "ocean" and "land") and then in time.
 Confidence intervals are computed, including correction for auto-correlations,
@@ -72,7 +71,7 @@ which may be paused for further interactive inspection.
 In summary, DAPPER is well suited for teaching and fundamental DA research.
 Also see its [drawbacks](#similar-projects).
 
-![EnKF - Lorenz-96](./docs/imgs/ex1.jpg)
+![EnKF - Lorenz-96](https://github.com/nansencenter/DAPPER/raw/master/docs/images/ex1.jpg)
 
 <!-- Non-highlighted features:
 - Time sequences use via `tools.chronos.Chronology` and `tools.chronos.Ticker`.
@@ -132,7 +131,7 @@ You should now be able to do run your script with
 `python path/to/script.py`.  
 For example, if you are in the DAPPER dir,
 
-    python examples/basic_1.py
+    python docs/examples/basic_1.py
 
 **PS**: If you closed the terminal (or shut down your computer),
 you'll first need to run `conda activate dapper-env`
@@ -144,16 +143,16 @@ you'll first need to run `conda activate dapper-env`
 <!-- markdownlint-disable line-length -->
 Method                                                 | Literature reproduced
 ------------------------------------------------------ | ------------------------
-EnKF <sup>1</sup>                                      | [Sakov08](https://nansencenter.github.io/DAPPER/bib.html#bib.sakov2008deterministic), [Hoteit15](https://nansencenter.github.io/DAPPER/bib.html#bib.hoteit2015mitigating), [Grudzien2020](https://nansencenter.github.io/DAPPER/bib.html#bib.grudzien2020numerical)
-EnKF-N                                                 | [Bocquet12](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2012combining), [Bocquet15](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2015expanding)
-EnKS, EnRTS                                            | [Raanes2016](https://nansencenter.github.io/DAPPER/bib.html#bib.raanes2016thesis)
-iEnKS / iEnKF / EnRML / ES-MDA <sup>2</sup>            | [Sakov12](https://nansencenter.github.io/DAPPER/bib.html#bib.sakov2012iterative), [Bocquet12](https://nansencenter.github.io/DAPPER/bib.html#bib.Bocquet12), [Bocquet14](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2014iterative)
-LETKF, local & serial EAKF                             | [Bocquet11](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2011ensemble)
-Sqrt. model noise methods                              | [Raanes2014](https://nansencenter.github.io/DAPPER/bib.html#bib.raanes2014ext)
-Particle filter (bootstrap) <sup>3</sup>               | [Bocquet10](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2010beyond)
-Optimal/implicit Particle filter  <sup>3</sup>         | [Bocquet10](https://nansencenter.github.io/DAPPER/bib.html#bib.bocquet2010beyond)
-NETF                                                   | [Tödter15](https://nansencenter.github.io/DAPPER/bib.html#bib.todter2015second), [Wiljes16](https://nansencenter.github.io/DAPPER/bib.html#bib.wiljes2016second)
-Rank histogram filter (RHF)                            | [Anderson10](https://nansencenter.github.io/DAPPER/bib.html#bib.anderson2010non)
+EnKF <sup>1</sup>                                      | [Sakov08](https://nansencenter.github.io/DAPPER/references/#sakov2008b), [Hoteit15](https://nansencenter.github.io/DAPPER/references/#hoteit2015a), [Grudzien2020](https://nansencenter.github.io/DAPPER/references/#grudzien2020a)
+EnKF-N                                                 | [Bocquet12](https://nansencenter.github.io/DAPPER/references/#bocquet2012a), [Bocquet15](https://nansencenter.github.io/DAPPER/references/#bocquet2015)
+EnKS, EnRTS                                            | [Raanes2016](https://nansencenter.github.io/DAPPER/references/#raanes2016thesis)
+iEnKS / iEnKF / EnRML / ES-MDA <sup>2</sup>            | [Sakov12](https://nansencenter.github.io/DAPPER/references/#sakov2012a), [Bocquet12](https://nansencenter.github.io/DAPPER/references/#Bocquet12), [Bocquet14](https://nansencenter.github.io/DAPPER/references/#bocquet2014)
+LETKF, local & serial EAKF                             | [Bocquet11](https://nansencenter.github.io/DAPPER/references/#bocquet2011)
+Sqrt. model noise methods                              | [Raanes2014](https://nansencenter.github.io/DAPPER/references/#raanes2014)
+Particle filter (bootstrap) <sup>3</sup>               | [Bocquet10](https://nansencenter.github.io/DAPPER/references/#bocquet2010a)
+Optimal/implicit Particle filter  <sup>3</sup>         | [Bocquet10](https://nansencenter.github.io/DAPPER/references/#bocquet2010a)
+NETF                                                   | [Tödter15](https://nansencenter.github.io/DAPPER/references/#todter2015a), [Wiljes16](https://nansencenter.github.io/DAPPER/references/#wiljes2016)
+Rank histogram filter (RHF)                            | [Anderson10](https://nansencenter.github.io/DAPPER/references/#anderson2010)
 4D-Var                                                 |
 3D-Var                                                 |
 Extended KF                                            |
@@ -352,11 +351,11 @@ and the Center for Western Weather and Water Extremes (CW3E).
 
 <!-- markdownlint-capture -->
 <!-- markdownlint-disable line-length -->
-![NORCE](./docs/imgs/norce-logo.png)
-![NERSC](./docs/imgs/nansen-logo.png)
-<img src="https://github.com/nansencenter/DAPPER/blob/master/docs/imgs/UoR-logo.png?raw=true" height="120" />
-<img src="https://github.com/nansencenter/DAPPER/blob/master/docs/imgs/nceologo1000.png?raw=true" height="100">
-<img src="./docs/imgs/CW3E-Logo-Horizontal-FullColor.png?raw=true" width="400">
+![NORCE](https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/norce-logo.png)
+![NERSC](https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/nansen-logo.png)
+<img src="https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/UoR-logo.png?raw=true" height="120" />
+<img src="https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/nceologo1000.png?raw=true" height="100">
+<img src="https://github.com/nansencenter/DAPPER/raw/master/docs/images/logos/CW3E-Logo-Horizontal-FullColor.png?raw=true" width="400">
 <!-- markdownlint-restore -->
 
 ## Publications

dapper-1.7.1/dapper/README.md

@@ -0,0 +1,17 @@
+## Adding your own model/method
+
+If you wish to illustrate and run benchmarks with
+your own **model** or **method**, then
+
+- If it is a complex one, you may be better off using DAPPER
+  merely as *inspiration* (but you can still
+  [cite it](../#getting-started))
+  rather than trying to squeeze everything into its templates.
+- If it is relatively simple, however, you may well want to use DAPPER.
+  In that case, read this:
+    - [`mods`](mods)
+    - [`da_methods`](da_methods)
+
+Since the generality of DAPPER is
+[limited](../#similar-projects)
+it is quite likely you will also need to make changes to the DAPPER code itself.

{dapper-1.7.0 → dapper-1.7.1}/dapper/__init__.py

@@ -1,10 +1,10 @@
 """Root package of **DAPPER**
 (Data Assimilation with Python: a Package for Experimental Research)
 
-.. include:: ./README.md
+--8<-- "dapper/README.md"
 """
 
-__version__ = "1.7.0"
+__version__ = "1.7.1"
 
 # A parsimonious list of imports used in the examples
 from .dpr_config import rc

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/README.md

@@ -1,6 +1,4 @@
-Also see the section on
-[DA Methods](https://github.com/nansencenter/DAPPER#DA-Methods)
-in the main README
+Also see [this section on DA Methods](../../#da-methods)
 for an overview of the methods included with DAPPER.
 
 ## Defining your own method
@@ -8,7 +6,7 @@ for an overview of the methods included with DAPPER.
 Follow the example of one of the methods within one of the
 sub-directories/packages.
 The simplest example is perhaps
-`dapper.da_methods.ensemble.EnKF`.
+[`da_methods.ensemble.EnKF`][].
 
 ## General advice for programming/debugging scientific experiments
 

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/__init__.py

@@ -1,6 +1,6 @@
 """Contains the data assimilation methods included with DAPPER.
 
-.. include:: ./README.md
+--8<-- "dapper/da_methods/README.md"
 """
 
 from pathlib import Path
@@ -16,7 +16,7 @@ def da_method(*default_dataclasses):
     The decorated classes are defined like a `dataclass`,
     but are decorated by `@da_method()` instead of `@dataclass`.
 
-    .. note::
+    !!! note
         The classes must define a method called `assimilate`.
         This method gets slightly enhanced by this wrapper which provides:
 
@@ -25,7 +25,8 @@ def da_method(*default_dataclasses):
         - Duration timing
         - Progressbar naming magic.
 
-    Example:
+    Examples
+    --------
     >>> @da_method()
     ... class Sleeper():
     ...     "Do nothing."
@@ -43,7 +44,6 @@ def da_method(*default_dataclasses):
     which enables defining default parameters which can be inherited,
     similar to subclassing.
 
-    Example:
     >>> class ens_defaults:
     ...     infl : float = 1.0
     ...     rot  : bool  = False
@@ -56,13 +56,13 @@ def da_method(*default_dataclasses):
     ...     def assimilate(self, HMM, xx, yy):
     ...         ...
 
-    .. note::
+    !!! note
         Apart from what's listed in the above `Note`, there is nothing special to the
         resulting `xp`.  That is, just like any Python object, it can serve as a data
         container, and you can write any number of attributes to it (at creation-time,
         or later).  For example, you can set attributes that are not used by the
         `assimilate` method, but are instead used to customize other aspects of the
-        experiments (see `dapper.xp_launch.run_experiment`).
+        experiments (see [`xp_launch.run_experiment`][]).
     """
     import dataclasses
     import functools

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/baseline.py

@@ -1,6 +1,6 @@
 """Unsophisticated" but robust (widely applicable) DA methods.
 
-Many are based on `bib.raanes2016thesis`.
+Many are based on [raanes2016thesis][].
 """
 
 from typing import Callable, Optional
@@ -146,10 +146,15 @@ def fit_sigmoid(Sb, L, kb):
 
     The "normalized" sigmoid, `S1`, is symmetric around 0, and `S1(-∞)=0` and `S1(∞)=1`.
 
-    The sigmoid `S(k) = S1(a*(k-kb) + b)` is fitted (see docs/snippets/sigmoid.jpg) with
+    The sigmoid `S(k) = S1(a*(k-kb) + b)` is fitted with
 
     - `a` corresponding to a given corr. length `L`.
     - `b` to match values of `S(kb)` and `Sb`
+
+    <figure markdown="span">
+        ![](../../images/snippets/sigmoid.jpg){ width="300" }
+        <figcaption>Illustration</figcaption>
+    </figure>
     """
 
     def sigmoid(k):

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/ensemble.py

@@ -28,7 +28,7 @@ class ens_method:
 class EnKF:
     """The ensemble Kalman filter.
 
-    Refs: `bib.evensen2009ensemble`.
+    Refs: [evensen2009a][].
     """
 
     upd_a: str
@@ -67,8 +67,8 @@ def EnKF_analysis(E, Eo, hnoise, y, upd_a, stats=None, ko=None):
     This implementation includes several flavours and forms,
     specified by `upd_a`.
 
-    Main references: `bib.sakov2008deterministic`,
-    `bib.sakov2008implications`, `bib.hoteit2015mitigating`
+    Main references: [sakov2008b][],
+    [sakov2008a][], [hoteit2015a][]
     """
     R = hnoise.C  # Obs noise cov
     N, Nx = E.shape  # Dimensionality
@@ -113,7 +113,7 @@ def EnKF_analysis(E, Eo, hnoise, y, upd_a, stats=None, ko=None):
             d = pad0(s**2, N) + N1
             Pw = (V * d ** (-1.0)) @ V.T
             T = (V * d ** (-0.5)) @ V.T * sqrt(N1)
-            # docs/snippets/trHK.jpg
+            # docs/images/snippets/trHK.jpg
             trHK = np.sum((s**2 + N1) ** (-1.0) * s**2)
         elif "sS" in upd_a:
             # Same as 'svd', but with slightly different notation
@@ -123,7 +123,7 @@ def EnKF_analysis(E, Eo, hnoise, y, upd_a, stats=None, ko=None):
             d = pad0(s**2, N) + 1
             Pw = (V * d ** (-1.0)) @ V.T / N1  # = G/(N1)
             T = (V * d ** (-0.5)) @ V.T
-            # docs/snippets/trHK.jpg
+            # docs/images/snippets/trHK.jpg
             trHK = np.sum((s**2 + 1) ** (-1.0) * s**2)
         else:  # 'eig' in upd_a:
             # Implementation using eig. val. decomp.
@@ -261,7 +261,7 @@ def post_process(E, infl, rot):
 def add_noise(E, dt, noise, method):
     """Treatment of additive noise for ensembles.
 
-    Refs: `bib.raanes2014ext`
+    Refs: [raanes2014][]
     """
     if noise.C == 0:
         return E
@@ -354,7 +354,7 @@ def add_noise(E, dt, noise, method):
 class EnKS:
     """The ensemble Kalman smoother.
 
-    Refs: `bib.evensen2009ensemble`
+    Refs: [evensen2009a][]
 
     The only difference to the EnKF
     is the management of the lag and the reshapings.
@@ -414,7 +414,7 @@ class EnKS:
 class EnRTS:
     """EnRTS (Rauch-Tung-Striebel) smoother.
 
-    Refs: `bib.raanes2016thesis`
+    Refs: [raanes2016thesis][]
     """
 
     upd_a: str
@@ -484,7 +484,7 @@ def serial_inds(upd_a, y, cvR, A):
 class SL_EAKF:
     """Serial, covariance-localized EAKF.
 
-    Refs: `bib.karspeck2007experimental`.
+    Refs: [karspeck2007][].
 
     In contrast with LETKF, this iterates over the observations rather
     than over the state (batches).
@@ -614,10 +614,10 @@ def local_analyses(E, Eo, R, y, state_batches, obs_taperer, mp=map, xN=None, g=0
 class LETKF:
     """Same as EnKF (Sqrt), but with localization.
 
-    Refs: `bib.hunt2007efficient`.
+    Refs: [hunt2007][].
 
-    NB: Multiproc. yields slow-down for `dapper.mods.Lorenz96`,
-    even with `batch_size=(1,)`. But for `dapper.mods.QG`
+    NB: Multiproc. yields slow-down for [`mods.Lorenz96`][],
+    even with `batch_size=(1,)`. But for [`mods.QG`][]
     (`batch_size=(2,2)` or less) it is quicker.
 
     NB: If `len(ii)` is small, analysis may be slowed-down with '-N' infl.
@@ -778,7 +778,7 @@ def hyperprior_coeffs(s, N, xN=1, g=0):
 
     - Reason 1: mode correction.
       These parameters bridge the Jeffreys (`xN=1`) and Dirac (`xN=Inf`) hyperpriors
-      for the prior covariance, B, as discussed in `bib.bocquet2015expanding`.
+      for the prior covariance, B, as discussed in [bocquet2015][].
       Indeed, mode correction becomes necessary when $$ R \rightarrow \infty $$
       because then there should be no ensemble update (and also no inflation!).
       More specifically, the mode of `l1`'s should be adjusted towards 1
@@ -790,7 +790,7 @@ def hyperprior_coeffs(s, N, xN=1, g=0):
     - Reason 2: Boosting the inflation prior's certainty from N to xN*N.
       The aim is to take advantage of the fact that the ensemble may not
       have quite as much sampling error as a fully stochastic sample,
-      as illustrated in section 2.1 of `bib.raanes2019adaptive`.
+      as illustrated in section 2.1 of [raanes2019a][].
 
     - Its damping effect is similar to work done by J. Anderson.
 
@@ -809,7 +809,7 @@ def hyperprior_coeffs(s, N, xN=1, g=0):
     eN = (N + 1) / N
     cL = (N + g) / N1
 
-    # Mode correction (almost) as in eqn 36 of `bib.bocquet2015expanding`
+    # Mode correction (almost) as in eqn 36 of [bocquet2015][]
     prior_mode = eN / cL  # Mode of l1 (before correction)
     diagonal = pad0(s**2, N) + N1  # diag of Y@R.inv@Y + N1*I
     #                                           (Hessian of J)
@@ -834,7 +834,7 @@ def zeta_a(eN, cL, w):
     Returns `zeta_a = (N-1)/pre-inflation^2`.
 
     Using this inside an iterative minimization as in the
-    `dapper.da_methods.variational.iEnKS` effectively blends
+    [`da_methods.variational.iEnKS`][] effectively blends
     the distinction between the primal and dual EnKF-N.
     """
     N = len(w)
@@ -847,12 +847,12 @@ def zeta_a(eN, cL, w):
 class EnKF_N:
     """Finite-size EnKF (EnKF-N).
 
-    Refs: `bib.bocquet2011ensemble`, `bib.bocquet2015expanding`
+    Refs: [bocquet2011][], [bocquet2015][]
 
     This implementation is pedagogical, prioritizing the "dual" form.
     In consequence, the efficiency of the "primal" form suffers a bit.
     The primal form is included for completeness and to demonstrate equivalence.
-    In `dapper.da_methods.variational.iEnKS`, however,
+    In [`da_methods.variational.iEnKS`][], however,
     the primal form is preferred because it
     already does optimization for w (as treatment for nonlinear models).
 
@@ -985,7 +985,7 @@ class EnKF_N:
                 # l1 = 1.0
 
                 # Explicitly inflate prior
-                # => formulae look different from `bib.bocquet2015expanding`.
+                # => formulae look different from [bocquet2015][].
                 A *= l1
                 Y *= l1
 
@@ -1000,7 +1000,7 @@ class EnKF_N:
                 else:
                     # Also include angular-radial co-dependence.
                     # Note: denominator not squared coz
-                    # unlike `bib.bocquet2015expanding` we have inflated Y.
+                    # unlike [bocquet2015][] we have inflated Y.
                     Hw = (
                         Y @ R.inv @ Y.T / N1
                         + eye(N)

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/other.py

@@ -15,7 +15,7 @@ from .ensemble import ens_method
 class RHF:
     """Rank histogram filter.
 
-    Refs: `bib.anderson2010non`.
+    Refs: [anderson2010][].
 
     Quick & dirty implementation without attention to (de)tails.
     """
@@ -86,9 +86,9 @@ class RHF:
 class LNETF:
     """The Nonlinear-Ensemble-Transform-Filter (localized).
 
-    Refs: `bib.wiljes2016second`, `bib.todter2015second`.
+    Refs: [wiljes2016][], [todter2015a][].
 
-    It is (supposedly) a deterministic upgrade of the NLEAF of `bib.lei2011moment`.
+    It is (supposedly) a deterministic upgrade of the NLEAF of [lei2011][].
     """
 
     N: int

{dapper-1.7.0 → dapper-1.7.1}/dapper/da_methods/particle.py

@@ -23,7 +23,7 @@ class particle_method:
 class PartFilt:
     r"""Particle filter ≡ Sequential importance (re)sampling SIS (SIR).
 
-    Refs: `bib.wikle2007bayesian`, `bib.van2009particle`, `bib.chen2003bayesian`
+    Refs: [wikle2007][], [van2009][], [chen2003][]
 
     This is the bootstrap version: the proposal density is just
 
@@ -37,7 +37,7 @@ class PartFilt:
      - qroot: "Inflate" (anneal) the proposal noise kernels
        by this root to increase diversity.
        The weights are updated to maintain un-biased-ness.
-       See `bib.chen2003bayesian`, section VI-M.2
+       See [chen2003][], section VI-M.2
     """
 
     N: int
@@ -92,11 +92,10 @@ class PartFilt:
 class OptPF:
     """'Optimal proposal' particle filter, also known as 'Implicit particle filter'.
 
-    Ref: `bib.bocquet2010beyond`.
+    Ref: [bocquet2010a][].
 
-    .. note:: Regularization (`Qs`) is here added BEFORE Bayes' rule.
-              If `Qs==0`: OptPF should be equal to
-              the bootstrap filter `PartFilt`.
+    !!! note Regularization (`Qs`) is here added BEFORE Bayes' rule.
+        If `Qs==0`: OptPF should be equal to the bootstrap filter `PartFilt`.
     """
 
     N: int
@@ -521,7 +520,7 @@ def mask_unique_of_sorted(idx):
 def auto_bandw(N, M):
     """Optimal bandwidth (not bandwidth^2), as per Scott's rule-of-thumb.
 
-    Refs: `bib.doucet2001sequential` section 12.2.2, [Wik17]_ section "Rule_of_thumb"
+    Refs: [doucet2001sequential][] section 12.2.2, [Wik17]_ section "Rule_of_thumb"
     """
     return N ** (-1 / (M + 4))
 
@@ -535,7 +534,7 @@ def regularize(C12, E, idx, no_uniq_jitter):
     (so-named because Dirac-deltas are approximated  Gaussian kernels),
     which controls the strength of the jitter.
     This causes a bias. But, as N-->∞, the reg. bandwidth-->0, i.e. bias-->0.
-    Ref: `bib.doucet2001sequential`, section 12.2.2.
+    Ref: [doucet2001sequential][], section 12.2.2.
     """
     # Select
     E = E[idx]
@@ -555,7 +554,7 @@ def regularize(C12, E, idx, no_uniq_jitter):
 def resample(w, kind="Systematic", N=None, wroot=1.0):
     """Multinomial resampling.
 
-    Refs: `bib.doucet2009tutorial`, `bib.van2009particle`, `bib.liu2001theoretical`.
+    Refs: [doucet2009][], [van2009][], [liu2001theoretical][].
 
     - kind: 'Systematic', 'Residual' or 'Stochastic'.
       'Stochastic' corresponds to `rng.choice` or `rng.multinomial`.
@@ -564,7 +563,7 @@ def resample(w, kind="Systematic", N=None, wroot=1.0):
       Among the three, 'Systematic' is fastest, introduces the least noise,
       and brings continuity benefits for localized particle filters,
       and is therefore generally prefered.
-      Example: see docs/snippets/ex_resample.py.
+      Example: see `docs/images/snippets/ex_resample.py`.
 
     - N can be different from len(w)
       (e.g. in case some particles have been elimintated).
@@ -572,7 +571,7 @@ def resample(w, kind="Systematic", N=None, wroot=1.0):
     - wroot: Adjust weights before resampling by this root to
       promote particle diversity and mitigate thinning.
       The outcomes of the resampling are then weighted to maintain un-biased-ness.
-      Ref: `bib.liu2001theoretical`, section 3.1
+      Ref: [liu2001theoretical][], section 3.1
 
     Note: (a) resampling methods are beneficial because they discard
     low-weight ("doomed") particles and reduce the variance of the weights.