Merge branch 'release/0.3.4' into main

morganjwilliams · Jul 21, 2023 · ac7cd52 · ac7cd52
2 parents a9cf8d0 + 5f0756c
commit ac7cd52
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diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/workflows/unittest.yml b/.github/workflows/unittest.yml
@@ -18,18 +18,6 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         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@v3
       - uses: actions/setup-python@v4
@@ -41,26 +29,24 @@ jobs:
         run: |
           python -m pip install --upgrade pip  # upgrade pip
           pip install wheel
-          pip install -q pytest pytest-runner pytest-cov coverage codacy-coverage
-          pip install coveralls
-          pip install .[skl,stats]
+          pip install .[skl,stats,test] codacy-coverage
       - name: Test Windows
         if: runner.os == 'Windows'
         env:
           MPLBACKEND: Agg
-        run: python setup.py test
+        run: pytest
       - name: Test MacOS
         if: runner.os == 'macOS'
-        run: python setup.py test
+        run: pytest
       - name: Prep Linux
         if: runner.os == 'Linux'
         run: |
-          sudo apt-get install jq curl    # codacy requirement
+          sudo apt-get install jq curl  # codacy requirement
           sudo apt-get install xvfb
       - name: Test Linux
         if: runner.os == 'Linux'
         run: |
-          xvfb-run python setup.py test
+          xvfb-run pytest
       - name: Coveralls
         env:
           COVERALLS_SERVICE_NAME: github

diff --git a/.gitignore b/.gitignore
@@ -106,7 +106,5 @@ venv.bak/
 # classifier model builds
 *.clsf.gz
 
-doc/examples/scratch\.py
-
 # local alphamelts install folder
 pyrolite/data/alphamelts/localinstall/*
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
@@ -21,4 +26,8 @@ formats:
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: docs/docs_require.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - skl # for sklearn-based examples
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -9,4 +9,4 @@ recursive-include pyrolite/data/radii *
 recursive-include pyrolite/data/timescale *
 recursive-include pyrolite/data/testing *
 recursive-include pyrolite/data/_config *
-# global-exclude __pycache__
+global-exclude **/__pycache__/*
diff --git a/README.md b/README.md
@@ -65,9 +65,9 @@ If you use pyrolite extensively for your research, citation of the software woul
 [![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://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**                                                                                   |
+|                                                                                  **main**                                                                                  |                                                                                  **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)                                |
+|                               [![Unit Tests on main](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
@@ -7,8 +7,5 @@ channels:
 dependencies:
   - python=3.10
   - pip
-  - matplotlib
-  - scipy>=1.2
-  - pandas>=0.23
   - pip:
-      - -e git+https://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite[dev,skl]
+      - -e git+https://github.com/morganjwilliams/pyrolite.git@develop#egg=pyrolite[dev,skl,excel]
diff --git a/docs/docs_require.txt b/docs/docs_require.txt
diff --git a/docs/source/.gitignore b/docs/source/.gitignore
@@ -0,0 +1,4 @@
+/examples/*
+/tutorials/*
+/data/*
+/_backreferences/*
diff --git a/docs/source/dev/changelog.rst b/docs/source/dev/changelog.rst
@@ -10,15 +10,23 @@ All notable changes to this project will be documented here.
         If you're keen to check something out before its released, you can use a
         `development install <development.html#development-installation>`__ .
 
+`0.3.4`_
+--------------
+
+* **Bugfix**: `Tom Buckle <https://github.com/bomtuckle>`__ contributed a PR with 
+  some minor bugfixes for the CIPW Norm.
+* Various maintainence updates, including migrating the pacakge to use `pyproject.toml`.
+
 `0.3.3`_
 --------------
 
-*  **New Contributor**: `Sarah Shi <https://github.com/sarahshi>`__
-*  **New Contributor**: `Ondrej Lexa <https://github.com/ondrolexa>`__
+* **New Contributor**: `Sarah Shi <https://github.com/sarahshi>`__
+* **New Contributor**: `Ondrej Lexa <https://github.com/ondrolexa>`__
 * **Bugfix**: Updated docs builds to be compatible with recent versions of `sphinx-gallery`.
 * **Bugfix**: Updated some :mod:`pandas` assignment, aggregation and similar operations
   to be compatible with more recent versions of Pandas.
-* Addedd explict Python 3.10 support.
+* Added explicit Python 3.10 and 3.11 support.
+* Removed Python 3.7 support (now end of life).
 
 
 :mod:`pyrolite.mineral`
@@ -1337,8 +1345,9 @@ All notable changes to this project will be documented here.
     `GitHub <https://github.com/morganjwilliams/pyrolite/releases>`__ for reference,
     but were :code:`alpha` versions which were never considered stable.
 
-.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.3.3...develop
-.. _0.3.3: https://github.com/morganjwilliams/pyrolite/compare/0.3.1...0.3.2
+.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.3.4...develop
+.. _0.3.4: https://github.com/morganjwilliams/pyrolite/compare/0.3.3...0.3.4
+.. _0.3.3: https://github.com/morganjwilliams/pyrolite/compare/0.3.2...0.3.3
 .. _0.3.2: https://github.com/morganjwilliams/pyrolite/compare/0.3.1...0.3.2
 .. _0.3.1: https://github.com/morganjwilliams/pyrolite/compare/0.3.0...0.3.1
 .. _0.3.0: https://github.com/morganjwilliams/pyrolite/compare/0.2.8...0.3.0