chore(release): 1.0.5 (#70)

xarray-contrib · Jul 31, 2023 · 1dc9ce6 · 1dc9ce6
2 parents b39bdaf + c95f658
commit 1dc9ce6
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -61,29 +61,14 @@ jobs:
     if: github.ref == 'refs/heads/main'
     runs-on: ubuntu-latest
     concurrency: release
-    permissions:
-      id-token: write
 
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0
-
-      # This action uses Python Semantic Release v8
       - name: Python semantic release
-        id: release
-        uses: python-semantic-release/python-semantic-release@v8.0.0
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        # NOTE: DO NOT wrap the conditional in ${{ }} as it will always evaluate to true.
-        # See https://github.com/actions/runner/issues/1173
-        if: steps.release.outputs.released == 'true'
-
-      - name: Publish package distributions to GitHub Releases
-        uses: python-semantic-release/upload-to-gh-release@main
-        if: steps.release.outputs.released == 'true'
+        uses: python-semantic-release/python-semantic-release@v7.34.6
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          repository_username: __token__
+          repository_password: ${{ secrets.PYPI_TOKEN }}
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,6 +5,13 @@
 # Required
 version: 2
 
+# Use mamba instead of conda
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py

diff --git a/docs/_autosummary/xeofs.models.ComplexMCA.rst b/docs/_autosummary/xeofs.models.ComplexMCA.rst
@@ -21,6 +21,7 @@
       ~ComplexMCA.components_amplitude
       ~ComplexMCA.components_phase
       ~ComplexMCA.compute
+      ~ComplexMCA.covariance_fraction
       ~ComplexMCA.fit
       ~ComplexMCA.get_params
       ~ComplexMCA.heterogeneous_patterns
@@ -29,6 +30,7 @@
       ~ComplexMCA.scores
       ~ComplexMCA.scores_amplitude
       ~ComplexMCA.scores_phase
+      ~ComplexMCA.singular_values
       ~ComplexMCA.squared_covariance
       ~ComplexMCA.squared_covariance_fraction
       ~ComplexMCA.transform

diff --git a/docs/_autosummary/xeofs.models.ComplexMCARotator.rst b/docs/_autosummary/xeofs.models.ComplexMCARotator.rst
@@ -21,6 +21,7 @@
       ~ComplexMCARotator.components_amplitude
       ~ComplexMCARotator.components_phase
       ~ComplexMCARotator.compute
+      ~ComplexMCARotator.covariance_fraction
       ~ComplexMCARotator.fit
       ~ComplexMCARotator.get_params
       ~ComplexMCARotator.heterogeneous_patterns
@@ -29,6 +30,7 @@
       ~ComplexMCARotator.scores
       ~ComplexMCARotator.scores_amplitude
       ~ComplexMCARotator.scores_phase
+      ~ComplexMCARotator.singular_values
       ~ComplexMCARotator.squared_covariance
       ~ComplexMCARotator.squared_covariance_fraction
       ~ComplexMCARotator.transform

diff --git a/docs/_autosummary/xeofs.models.MCA.rst b/docs/_autosummary/xeofs.models.MCA.rst
@@ -19,12 +19,14 @@
       ~MCA.__init__
       ~MCA.components
       ~MCA.compute
+      ~MCA.covariance_fraction
       ~MCA.fit
       ~MCA.get_params
       ~MCA.heterogeneous_patterns
       ~MCA.homogeneous_patterns
       ~MCA.inverse_transform
       ~MCA.scores
+      ~MCA.singular_values
       ~MCA.squared_covariance
       ~MCA.squared_covariance_fraction
       ~MCA.transform

diff --git a/docs/_autosummary/xeofs.models.MCARotator.rst b/docs/_autosummary/xeofs.models.MCARotator.rst
@@ -19,12 +19,14 @@
       ~MCARotator.__init__
       ~MCARotator.components
       ~MCARotator.compute
+      ~MCARotator.covariance_fraction
       ~MCARotator.fit
       ~MCARotator.get_params
       ~MCARotator.heterogeneous_patterns
       ~MCARotator.homogeneous_patterns
       ~MCARotator.inverse_transform
       ~MCARotator.scores
+      ~MCARotator.singular_values
       ~MCARotator.squared_covariance
       ~MCARotator.squared_covariance_fraction
       ~MCARotator.transform

diff --git a/docs/api.rst b/docs/api.rst
@@ -4,41 +4,18 @@
 API
 ==================
 
+.. toctree::
+   :maxdepth: 3
+   :hidden:
 
+   api_core_methods
+   api_rotation
+   api_advanced_techniques
+   api_validation
 
-Models
-==================
-.. autosummary::
-   :toctree: _autosummary
-   :template: custom-class-template.rst
-   :recursive:
-
-   xeofs.models.EOF
-   xeofs.models.ComplexEOF
-   xeofs.models.MCA
-   xeofs.models.ComplexMCA
 
 
-Rotators
-==================
-.. autosummary::
-   :toctree: _autosummary
-   :template: custom-class-template.rst
-   :recursive:
 
-   xeofs.models.EOFRotator
-   xeofs.models.ComplexEOFRotator
-   xeofs.models.MCARotator
-   xeofs.models.ComplexMCARotator
-   xeofs.models.RotatorFactory
 
 
 
-Validation
-==================
-.. autosummary::
-   :toctree: _autosummary
-   :template: custom-class-template.rst
-   :recursive:
-
-   xeofs.validation.EOFBootstrapper
diff --git a/docs/api_advanced_techniques.rst b/docs/api_advanced_techniques.rst
@@ -0,0 +1,11 @@
+Advanced techniques
+==================
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-class-template.rst
+   :recursive:
+
+   xeofs.models.ComplexEOF
+   xeofs.models.ComplexMCA
+   xeofs.models.ComplexEOFRotator
+   xeofs.models.ComplexMCARotator
diff --git a/docs/api_core_methods.rst b/docs/api_core_methods.rst
@@ -0,0 +1,9 @@
+Core methods
+==================
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-class-template.rst
+   :recursive:
+
+   xeofs.models.EOF
+   xeofs.models.MCA
diff --git a/docs/api_rotation.rst b/docs/api_rotation.rst
@@ -0,0 +1,13 @@
+Rotation
+==================
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-class-template.rst
+   :recursive:
+
+   xeofs.models.EOFRotator
+   xeofs.models.MCARotator
+   xeofs.models.ComplexEOFRotator
+   xeofs.models.ComplexMCARotator
+   xeofs.models.RotatorFactory
+
diff --git a/docs/api_validation.rst b/docs/api_validation.rst
@@ -0,0 +1,8 @@
+Validation
+==================
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-class-template.rst
+   :recursive:
+
+   xeofs.validation.EOFBootstrapper
diff --git a/docs/auto_examples/1eof/images/sphx_glr_plot_rotated_eof_001.png b/docs/auto_examples/1eof/images/sphx_glr_plot_rotated_eof_001.png
diff --git a/docs/auto_examples/1eof/images/thumb/sphx_glr_plot_rotated_eof_thumb.png b/docs/auto_examples/1eof/images/thumb/sphx_glr_plot_rotated_eof_thumb.png
diff --git a/docs/auto_examples/1eof/plot_rotated_eof.ipynb b/docs/auto_examples/1eof/plot_rotated_eof.ipynb
@@ -1,5 +1,16 @@
 {
   "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "collapsed": false
+      },
+      "outputs": [],
+      "source": [
+        "%matplotlib inline"
+      ]
+    },
     {
       "cell_type": "markdown",
       "metadata": {},
@@ -15,7 +26,7 @@
       },
       "outputs": [],
       "source": [
-        "import xarray as xr\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom matplotlib.gridspec import GridSpec\nfrom cartopy.crs import Robinson, PlateCarree\n\nfrom xeofs.models import EOF, EOFRotator\n\n\nsns.set_context('paper')\n\nsst = xr.tutorial.open_dataset('ersstv5')['sst']\n\n# There are some grid points with have constant values only.\n# Standardization of these time series cannot work since\n# the standard deviation is zero.\n# Remove these grid points prior to the analysis:\n# minimum_std_dev = 1e-5\n# valid_x = sst.stack(x=['lat', 'lon']).std('time') > minimum_std_dev\n# sst = sst.stack(x=['lat', 'lon']).sel(x=valid_x).unstack()"
+        "import xarray as xr\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nfrom matplotlib.gridspec import GridSpec\nfrom cartopy.crs import Robinson, PlateCarree\n\nfrom xeofs.models import EOF, EOFRotator\n\n\nsns.set_context('paper')\n\nsst = xr.tutorial.open_dataset('ersstv5')['sst']"
       ]
     },
     {

diff --git a/docs/auto_examples/1eof/plot_rotated_eof.py b/docs/auto_examples/1eof/plot_rotated_eof.py
@@ -34,13 +34,6 @@
 
 sst = xr.tutorial.open_dataset('ersstv5')['sst']
 
-# There are some grid points with have constant values only.
-# Standardization of these time series cannot work since
-# the standard deviation is zero.
-# Remove these grid points prior to the analysis:
-# minimum_std_dev = 1e-5
-# valid_x = sst.stack(x=['lat', 'lon']).std('time') > minimum_std_dev
-# sst = sst.stack(x=['lat', 'lon']).sel(x=valid_x).unstack()
 
 #%%
 # Perform the actual analysis

diff --git a/docs/auto_examples/1eof/plot_rotated_eof.py.md5 b/docs/auto_examples/1eof/plot_rotated_eof.py.md5
@@ -1 +1 @@
-0d0961206dea757d52a99005d46ceb42
+77cafc244aaaaff78ba2f3e809fbedf5
diff --git a/docs/auto_examples/1eof/plot_rotated_eof.rst b/docs/auto_examples/1eof/plot_rotated_eof.rst
@@ -10,7 +10,7 @@
     .. note::
         :class: sphx-glr-download-link-note
 
-        :ref:`Go to the end <sphx_glr_download_auto_examples_1eof_plot_rotated_eof.py>`
+        Click :ref:`here <sphx_glr_download_auto_examples_1eof_plot_rotated_eof.py>`
         to download the full example code
 
 .. rst-class:: sphx-glr-example-title
@@ -40,7 +40,7 @@ without regularization, (2) with Varimax rotation, and (3) with Promax rotation.
 
 We'll start by loading the necessary packages and data:
 
-.. GENERATED FROM PYTHON SOURCE LINES 24-45
+.. GENERATED FROM PYTHON SOURCE LINES 24-38
 
 .. code-block:: default
 
@@ -57,13 +57,6 @@ We'll start by loading the necessary packages and data:
 
     sst = xr.tutorial.open_dataset('ersstv5')['sst']
 
-    # There are some grid points with have constant values only.
-    # Standardization of these time series cannot work since
-    # the standard deviation is zero.
-    # Remove these grid points prior to the analysis:
-    # minimum_std_dev = 1e-5
-    # valid_x = sst.stack(x=['lat', 'lon']).std('time') > minimum_std_dev
-    # sst = sst.stack(x=['lat', 'lon']).sel(x=valid_x).unstack()
 
 
 
@@ -72,11 +65,11 @@ We'll start by loading the necessary packages and data:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 46-47
+.. GENERATED FROM PYTHON SOURCE LINES 39-40
 
 Perform the actual analysis
 
-.. GENERATED FROM PYTHON SOURCE LINES 47-67
+.. GENERATED FROM PYTHON SOURCE LINES 40-60
 
 .. code-block:: default
 
@@ -107,15 +100,15 @@ Perform the actual analysis
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 68-73
+.. GENERATED FROM PYTHON SOURCE LINES 61-66
 
 Create figure showing the first 6 modes for all 3 cases. While the first mode
 is very similar in all three cases the subsequent modes of the standard
 solution exhibit dipole and tripole-like patterns. Under Varimax and Promax
 rotation, these structures completely disappear suggesting that these patterns
 were mere artifacts due to the orthogonality.
 
-.. GENERATED FROM PYTHON SOURCE LINES 73-103
+.. GENERATED FROM PYTHON SOURCE LINES 66-96
 
 .. code-block:: default
 
@@ -164,25 +157,28 @@ were mere artifacts due to the orthogonality.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  17.504 seconds)
+   **Total running time of the script:** ( 0 minutes  17.020 seconds)
 
 
 .. _sphx_glr_download_auto_examples_1eof_plot_rotated_eof.py:
 
-.. only:: html
 
-  .. container:: sphx-glr-footer sphx-glr-footer-example
+.. only :: html
+
+ .. container:: sphx-glr-footer
+    :class: sphx-glr-footer-example
+
 
 
+  .. container:: sphx-glr-download sphx-glr-download-python
 
+     :download:`Download Python source code: plot_rotated_eof.py <plot_rotated_eof.py>`
 
-    .. container:: sphx-glr-download sphx-glr-download-python
 
-      :download:`Download Python source code: plot_rotated_eof.py <plot_rotated_eof.py>`
 
-    .. container:: sphx-glr-download sphx-glr-download-jupyter
+  .. container:: sphx-glr-download sphx-glr-download-jupyter
 
-      :download:`Download Jupyter notebook: plot_rotated_eof.ipynb <plot_rotated_eof.ipynb>`
+     :download:`Download Jupyter notebook: plot_rotated_eof.ipynb <plot_rotated_eof.ipynb>`
 
 
 .. only:: html

diff --git a/docs/auto_examples/1eof/plot_rotated_eof_codeobj.pickle b/docs/auto_examples/1eof/plot_rotated_eof_codeobj.pickle
diff --git a/docs/auto_examples/1eof/sg_execution_times.rst b/docs/auto_examples/1eof/sg_execution_times.rst
@@ -3,21 +3,20 @@
 
 .. _sphx_glr_auto_examples_1eof_sg_execution_times:
 
-
 Computation times
 =================
-**00:40.990** total execution time for **auto_examples_1eof** files:
+**00:17.020** total execution time for **auto_examples_1eof** files:
 
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_rotated_eof.py` (``plot_rotated_eof.py``)           | 00:17.504 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_rotated_eof.py` (``plot_rotated_eof.py``)           | 00:17.020 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_mreof.py` (``plot_mreof.py``)                       | 00:06.262 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_eof-smode.py` (``plot_eof-smode.py``)               | 00:00.000 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_eof-smode.py` (``plot_eof-smode.py``)               | 00:05.117 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_eof-tmode.py` (``plot_eof-tmode.py``)               | 00:00.000 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_weighted-eof.py` (``plot_weighted-eof.py``)         | 00:04.978 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_mreof.py` (``plot_mreof.py``)                       | 00:00.000 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_eof-tmode.py` (``plot_eof-tmode.py``)               | 00:04.957 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_multivariate-eof.py` (``plot_multivariate-eof.py``) | 00:00.000 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_1eof_plot_multivariate-eof.py` (``plot_multivariate-eof.py``) | 00:02.172 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_1eof_plot_weighted-eof.py` (``plot_weighted-eof.py``)         | 00:00.000 | 0.0 MB |
 +--------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/docs/auto_examples/2cross/images/sphx_glr_plot_mca_001.png b/docs/auto_examples/2cross/images/sphx_glr_plot_mca_001.png
diff --git a/docs/auto_examples/2cross/images/sphx_glr_plot_rotated_mca_001.png b/docs/auto_examples/2cross/images/sphx_glr_plot_rotated_mca_001.png
diff --git a/docs/auto_examples/2cross/images/thumb/sphx_glr_plot_mca_thumb.png b/docs/auto_examples/2cross/images/thumb/sphx_glr_plot_mca_thumb.png
diff --git a/docs/auto_examples/2cross/images/thumb/sphx_glr_plot_rotated_mca_thumb.png b/docs/auto_examples/2cross/images/thumb/sphx_glr_plot_rotated_mca_thumb.png