Merge branch 'release/0.3.3' into main

morganjwilliams · Jul 4, 2023 · a9cf8d0 · a9cf8d0
2 parents b9d05d7 + 3dd3cbf
commit a9cf8d0
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diff --git a/.github/workflows/docstest.yml b/.github/workflows/docstest.yml
@@ -4,10 +4,10 @@ on:
   push:
   pull_request:
     branches:
-    - develop
-    - feature/**
+      - develop
+      - feature/**
   schedule:
-    - cron: '0 0 * * 0' # weekly
+    - cron: "0 0 * * 0" # weekly
 
 jobs:
   build:
@@ -16,24 +16,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Get pip cache dir
-        id: pip-cache-dir
-        run: |
-          echo "::set-output name=dir::$(pip cache dir)"
-      - name: pip cache
-        id: pip-cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ steps.pip-cache-dir.outputs.dir }}
-          key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: pip
+          cache-dependency-path: "setup.py"
       - name: Python Packages Install
         run: |
           python -m pip install --upgrade pip  # upgrade pip

diff --git a/.github/workflows/unittest.yml b/.github/workflows/unittest.yml
@@ -4,10 +4,10 @@ on:
   push:
   pull_request:
     branches:
-    - develop
-    - feature/**
+      - develop
+      - feature/**
   schedule:
-    - cron: '0 0 * * 0' # weekly
+    - cron: "0 0 * * 0" # weekly
 
 jobs:
   unit_tests:
@@ -17,30 +17,26 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
-        exclude:
-        # excludes py38 on macOS, which seems to stall currently
-        - os: macos-latest
-          python-version: 3.8
-        - os: macos-latest
-          python-version: 3.9
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+        # exclude:
+        #   # excludes py38 on macOS, which seems to stall currently
+        #   - os: macos-latest
+        #     python-version: 3.8
+        #   - os: macos-latest
+        #     python-version: 3.9
+        #   - os: macos-latest
+        #     python-version: "3.10"
+        #   - os: macos-latest
+        #     python-version: "3.11"
+        #   - os: windows-latest
+        #     python-version: "3.11"
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Get pip cache dir
-        id: pip-cache-dir
-        run: |
-          echo "::set-output name=dir::$(pip cache dir)"
-      - name: pip cache
-        id: pip-cache
-        uses: actions/cache@v2
-        with:
-          path: ${{ steps.pip-cache-dir.outputs.dir }}
-          key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: pip
+          cache-dependency-path: "setup.py"
       - name: Python Packages Install
         run: |
           python -m pip install --upgrade pip  # upgrade pip
@@ -72,16 +68,17 @@ jobs:
           COVERALLS_FLAG_NAME: ${{ matrix.test-name }}
           COVERALLS_PARALLEL: true
         run: |
-            coveralls
+          coveralls
   coveralls:
     name: Indicate completion to coveralls.io
     needs: unit_tests
+    if: success() || failure()
     runs-on: ubuntu-latest
     container: python:3-slim
     steps:
-    - name: Finished
-      run: |
-        pip3 install --upgrade coveralls
-        coveralls --finish
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Finished
+        run: |
+          pip3 install --upgrade coveralls
+          coveralls --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/README.md b/README.md
@@ -5,10 +5,11 @@
 [![pyrolite Documentation](https://readthedocs.org/projects/pyrolite/badge/?version=develop)](https://pyrolite.readthedocs.io/)
 [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/20)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02314/status.svg)](https://doi.org/10.21105/joss.02314)
-[![License: CSIRO Modified BSD/MIT License](https://img.shields.io/badge/License-CSIRO_BSD/MIT_License-blue.svg?style=flat)](https://github.com/morganjwilliams/pyrolite/blob/master/LICENSE)
-[![Try pyrolite on Binder](https://img.shields.io/badge/TryItOutWith-Binder-F5A252.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/morganjwilliams/pyrolite/develop?filepath=docs%2Fnotebooks%2F)
+[![License: CSIRO Modified BSD/MIT License](https://img.shields.io/badge/License-CSIRO_BSD/MIT_License-blue.svg?style=flat)](https://github.com/morganjwilliams/pyrolite/blob/main/LICENSE)
+[![Try pyrolite on Binder](https://img.shields.io/badge/TryItOutWith-Binder-F5A252.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/morganjwilliams/pyrolite/develop?labpath=docs%2Fnotebooks%2F)
 [![Chat on Gitter](https://img.shields.io/gitter/room/pyrolite/community.svg)](https://gitter.im/pyrolite/community/)
 
+
 pyrolite is a set of tools for making the most of your geochemical data.
 
 The python package includes functions to work with compositional data, to transform
@@ -62,11 +63,11 @@ If you use pyrolite extensively for your research, citation of the software woul
 ## Development & Build Status
 
 [![Formatted with Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
-[![Code Quality](https://api.codacy.com/project/badge/Grade/fd9912a3faae43bf84a47e3da685d84c)](https://www.codacy.com/manual/morganjwilliams/pyrolite?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=morganjwilliams/pyrolite&amp;utm_campaign=Badge_Grade)
+[![Code Quality](https://api.codacy.com/project/badge/Grade/fd9912a3faae43bf84a47e3da685d84c)](https://app.codacy.com/gh/morganjwilliams/pyrolite/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=morganjwilliams/pyrolite&amp;utm_campaign=Badge_Grade)
 
 |                                                                                  **master**                                                                                  |                                                                                  **develop**                                                                                   |
 |:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|
-|                               [![Unit Tests on Master](https://github.com/morganjwilliams/pyrolite/workflows/Unittest/badge.svg?branch=master)](https://github.com/morganjwilliams/pyrolite/actions?query=workflow:Unittest+branch:master)                                |                               [![Unit Tests on Develop](https://github.com/morganjwilliams/pyrolite/workflows/Unittest/badge.svg?branch=develop)](https://github.com/morganjwilliams/pyrolite/actions?query=workflow:Unittest+branch:develop)                                |
-| [![Coverage Status](https://coveralls.io/repos/github/morganjwilliams/pyrolite/badge.svg?branch=master)](https://coveralls.io/github/morganjwilliams/pyrolite?branch=master) | [![Coverage Status](https://coveralls.io/repos/github/morganjwilliams/pyrolite/badge.svg?branch=develop)](https://coveralls.io/github/morganjwilliams/pyrolite?branch=develop) |
+|                               [![Unit Tests on Master](https://github.com/morganjwilliams/pyrolite/workflows/Unittest/badge.svg?branch=main)](https://github.com/morganjwilliams/pyrolite/actions?query=workflow:Unittest+branch:main)                                |                               [![Unit Tests on Develop](https://github.com/morganjwilliams/pyrolite/workflows/Unittest/badge.svg?branch=develop)](https://github.com/morganjwilliams/pyrolite/actions?query=workflow:Unittest+branch:develop)                                |
+| [![Coverage Status](https://coveralls.io/repos/github/morganjwilliams/pyrolite/badge.svg?branch=main)](https://coveralls.io/github/morganjwilliams/pyrolite?branch=main) | [![Coverage Status](https://coveralls.io/repos/github/morganjwilliams/pyrolite/badge.svg?branch=develop)](https://coveralls.io/github/morganjwilliams/pyrolite?branch=develop) |
 
 **Maintainer**: Morgan Williams (morgan.williams _at_ csiro.au)
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -5,7 +5,7 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.7
+  - python=3.10
   - pip
   - matplotlib
   - scipy>=1.2

diff --git a/docs/source/_patch/_sphinx_gallery_patch.py b/docs/source/_patch/_sphinx_gallery_patch.py
@@ -1,3 +1,30 @@
+from sphinx_gallery import gen_rst
+
 from .sphinx_gallery_binder import alt_gen_binder_rst
-from .sphinx_gallery_gen_rst import _save_rst_example
 from .sphinx_gallery_scrapers import alt_matplotlib_scraper
+
+# modify single image arrangement
+gen_rst.SINGLE_IMAGE = """
+.. image:: /%s
+    :class: sphx-glr-single-img
+    :width: 80 %
+    :align: center
+"""
+# remove the 'go to the end' part of the binder/download note
+gen_rst.EXAMPLE_HEADER = """
+.. DO NOT EDIT.
+.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
+.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
+.. "{0}"
+.. LINE NUMBERS ARE GIVEN BELOW.
+
+.. only:: html
+
+    .. note::
+        :class: sphx-glr-download-link-note
+
+.. rst-class:: sphx-glr-example-title
+
+.. _sphx_glr_{1}:
+
+"""
diff --git a/docs/source/_patch/sphinx_gallery_binder.py b/docs/source/_patch/sphinx_gallery_binder.py
@@ -1,9 +1,12 @@
-from sphinx_gallery import binder
+from sphinx_gallery import interactive_example
+
 
 def alt_gen_binder_rst(
     fpath, binder_conf, gallery_conf, img="https://mybinder.org/badge_logo.svg"
 ):
-    """Generate the RST + link for the Binder badge.
+    """
+    Generate the RST + link for the Binder badge.
+
     Parameters
     ----------
     fpath: str
@@ -25,11 +28,12 @@ def alt_gen_binder_rst(
     rst : str
         The reStructuredText for the Binder badge that links to this file.
     """
-    binder_conf = binder.check_binder_conf(binder_conf)
-    binder_url = binder.gen_binder_url(fpath, binder_conf, gallery_conf)
+    binder_conf = interactive_example.check_binder_conf(binder_conf)
+    binder_url = interactive_example.gen_binder_url(fpath, binder_conf, gallery_conf)
     rst = (
         "\n" ".. image:: {0}\n" "    :target: {1}\n" "    :alt: Launch Binder\n"
     ).format(img, binder_url)
     return rst
 
-binder.gen_binder_rst = alt_gen_binder_rst
+
+interactive_example.gen_binder_rst = alt_gen_binder_rst
diff --git a/docs/source/_patch/sphinx_gallery_gen_rst.py b/docs/source/_patch/sphinx_gallery_gen_rst.py
diff --git a/docs/source/_patch/sphinx_gallery_scrapers.py b/docs/source/_patch/sphinx_gallery_scrapers.py
@@ -1,11 +1,13 @@
 import re
 from pathlib import Path
+
 import matplotlib
 import matplotlib.pyplot as plt
 from matplotlib import _pylab_helpers
+from sphinx_gallery import scrapers
+
 from pyrolite.util.plot import save_figure
 
-from sphinx_gallery import scrapers
 
 def alt_matplotlib_scraper(block, block_vars, gallery_conf, **kwargs):
     """Patched matplotlib scraper which won't close figures.
@@ -49,4 +51,5 @@ def alt_matplotlib_scraper(block, block_vars, gallery_conf, **kwargs):
 
     return scrapers.figure_rst(image_paths, gallery_conf["src_dir"])
 
+
 scrapers._scraper_dict.update(dict(altmatplot=alt_matplotlib_scraper))