📚 revise docs incl. notebooks (#709)

* myst-nb

* use sphinx_book_theme

* add stars and forks to index

* add edit botton

* adapt xclim refs

* rename workflows for shorter badges

* intake-esm app connect

* ignore np FutureWarning

* binder link

.github/workflows/ci-pre-commit.yml

@@ -1,4 +1,4 @@
-name: linting
+name: Linting
 
 on:
   push:

.github/workflows/climpred_installs.yml

@@ -1,4 +1,4 @@
-name: climpred installs
+name: install
 
 on:
   push:

.github/workflows/climpred_testing.yml

@@ -1,4 +1,4 @@
-name: climpred testing  # based on https://github.com/pydata/xarray/blob/master/.github/workflows/ci.yaml
+name: CI  # based on https://github.com/pydata/xarray/blob/master/.github/workflows/ci.yaml
 
 on:
   push:
@@ -128,7 +128,7 @@ jobs:
         run: |
           python -m pytest --doctest-modules climpred --ignore climpred/tests
 
-  docs_notebooks:  # Checks that pre-compiled notebooks in docs still work.
+  notebooks:  # Checks that pre-compiled notebooks in docs still work.
     runs-on: ubuntu-latest
     defaults:
         run:

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lint
+name: Linting
 
 on: pull_request
 

README.rst

@@ -18,7 +18,7 @@ Verification of weather and climate forecasts.
     * - license
       - |license|
     * - community
-      - |gitter| |contributors|
+      - |gitter| |contributors| |forks| |stars| |issues| |PRs|
     * - tutorials
       - |gallery| |workshop| |cloud|
 
@@ -40,7 +40,7 @@ Verification of weather and climate forecasts.
 
 .. |upstream| image:: https://github.com/pangeo-data/climpred/actions/workflows/upstream-dev-ci.yml/badge.svg
     :target: https://github.com/pangeo-data/climpred/actions/workflows/upstream-dev-ci.yml
-    :alt: upstream
+    :alt: CI upstream
 
 .. |codecov| image:: https://codecov.io/gh/pangeo-data/climpred/branch/main/graph/badge.svg
       :target: https://codecov.io/gh/pangeo-data/climpred
@@ -86,6 +86,22 @@ Verification of weather and climate forecasts.
     :alt: climpred cloud demo
     :target: https://github.com/aaronspring/climpred-cloud-demo
 
+.. |forks| image:: https://img.shields.io/github/forks/pangeo-data/climpred
+    :alt: GitHub forks
+    :target: https://github.com/pangeo-data/climpred/network/members
+
+.. |stars| image:: https://img.shields.io/github/stars/pangeo-data/climpred
+    :alt: GitHub stars
+    :target: https://github.com/pangeo-data/climpred/stargazers
+
+.. |issues| image:: https://img.shields.io/github/issues/pangeo-data/climpred
+    :alt: GitHub issues
+    :target: https://github.com/pangeo-data/climpred/issues
+
+.. |PRs| image:: https://img.shields.io/github/issues-pr/pangeo-data/climpred
+    :alt: GitHub PRs
+    :target: https://github.com/pangeo-data/climpred/pulls
+
 ..
 
 .. note::
@@ -117,7 +133,13 @@ You can install the latest release of ``climpred`` using ``pip`` or ``conda``:
     conda install -c conda-forge climpred
 
 You can also install the bleeding edge (pre-release versions) by cloning this
-repository and running ``pip install . --upgrade`` in the main directory or
+repository or installing directly from GitHub:
+
+.. code-block:: bash
+
+    git clone https://github.com/pangeo-data/climpred.git
+    cd climpred
+    pip install . --upgrade
 
 .. code-block:: bash
 

ci/requirements/climpred-dev.yml

@@ -5,9 +5,8 @@ channels:
 dependencies:
   - python>=3.7
   # Documentation
-  - nbsphinx
+  - myst-nb
   - nbstripout
-  - sphinx_rtd_theme
   - sphinx
   - sphinxcontrib-napoleon
   # IDE
@@ -49,10 +48,12 @@ dependencies:
   - eofs
   - esmtools>=1.1.3
   - xskillscore>=0.0.19
+  - xrft
   # Visualization
   - matplotlib-base
   - nc-time-axis>=1.4.0
   - pip
   - pip:
       - pytest-lazy-fixture
       - nb_black  # notebook linting
+      - sphinx_book_theme

ci/requirements/docs.yml

@@ -4,22 +4,26 @@ channels:
   - nodefaults
 dependencies:
   - python=3.8
-  - importlib_metadata
   - matplotlib-base
-  - nbsphinx
+  - myst-nb
+  - esmpy=*=mpi*  # Ensures MPI works with version of esmpy.
+  - xesmf
+  - esmtools
   - nc-time-axis>=1.4.0
   - netcdf4
   - sphinx
   - sphinxcontrib-napoleon
-  - sphinx_rtd_theme
   - sphinx-copybutton
   - toolz
   - xarray>=0.19.0
   - xskillscore>=0.0.18
   - numba>=0.52
   - xclim
+  - xrft
   - bias_correction
   - pip
   - pip:
-    # Install latest version of climpred.
+    # Install latest version of climpred
     - -e ../..
+    - nb_black
+    - sphinx_book_theme

ci/requirements/docs_notebooks.yml

@@ -4,10 +4,10 @@ channels:
   - nodefaults
 dependencies:
   - python>=3.7
-  - importlib_metadata
+  #- ipykernel
   - jupyterlab
   - matplotlib-base
-  - nbsphinx
+  - myst-nb
   - nbstripout
   - netcdf4
   - numpy
@@ -16,7 +16,6 @@ dependencies:
   - dask-core
   - sphinx
   - sphinxcontrib-napoleon
-  - sphinx_rtd_theme
   - sphinx-copybutton
   - toolz
   - xarray>=0.19.0
@@ -28,9 +27,10 @@ dependencies:
   - esmpy
   - bottleneck
   - nc-time-axis>=1.4.0
-  - xrft  # used for varweighted_mean_period
+  - xrft
   - pip
   - pip:
     # Install latest version of climpred.
     - -e ../..
     - nb_black
+    - sphinx_book_theme

climpred/bias_removal.py

@@ -56,7 +56,9 @@ def leave_one_out_drop(bias, dim):
     """
     bias_nan = []
     for i in range(bias[dim].size):
-        bias_nan.append(bias.drop_isel({dim: i}).rename({dim: "sample"}).drop("sample"))
+        bias_nan.append(
+            bias.drop_isel({dim: i}).rename({dim: "sample"}).drop_vars("sample")
+        )
     bias_nan = xr.concat(bias_nan, dim).assign_coords(
         {dim: bias[dim], "sample": np.arange(bias[dim].size - 1)}
     )
@@ -361,7 +363,7 @@ def gaussian_bias_removal(
             dim="member",
             alignment=alignment,
         )
-    bias = bias.drop("skill")
+    bias = bias.drop_vars("skill")
 
     # how to remove bias
     if "mean" in how:

climpred/bootstrap.py

@@ -297,7 +297,7 @@ def resample_uninitialized_from_initialized(init, resample_dim=["init", "member"
     # take time dim and overwrite with sorted
     resampled_uninit = (
         resampled_uninit.swap_dims({"init": "valid_time"})
-        .drop("init")
+        .drop_vars("init")
         .rename({"valid_time": "time"})
     )
     resampled_uninit = resampled_uninit.assign_coords(