Merge branch 'release/0.3.6' into main

.github/workflows/docstest.yml

@@ -14,9 +14,10 @@ jobs:
     name: Build Docs
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5

.github/workflows/unittest.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.DS_Store
 
 # C extensions
 *.so

CITATION.cff

@@ -0,0 +1,97 @@
+cff-version: 1.2.0
+title: 'morganjwilliams/pyrolite: 0.3.5.post0'
+message: Please cite the following works when using this software.
+type: software
+authors:
+  - family-names: Williams 
+    given-names: Morgan
+    orcid: 'https://orcid.org/0000-0003-4764-9555'
+  - family-names: Buckle
+    given-names: Tom
+  - family-names: Myhill
+    given-names: Bob
+    orcid: 'https://orcid.org/0000-0001-9489-5236'
+  - family-names: Shi
+    given-names: Sarah
+    orcid: 'https://orcid.org/0009-0004-8997-7287'
+  - family-names: Nathwani
+    given-names: Chetan
+    orcid: 'https://orcid.org/0000-0003-1208-9041'
+  - family-names: Piette Lauziere
+    given-names: Nicolas
+    orcid: 'https://orcid.org/0000-0003-2812-0357'
+  - family-names: Lexa
+    given-names: Ondrej
+    orcid: 'https://orcid.org/0000-0003-4616-9154'
+  - family-names: Schoneveld
+    given-names: Louise
+    orcid: 'https://orcid.org/0000-0002-9324-1676'
+  - family-names: Afonso Rodrigues
+    given-names: Angela
+    orcid: 'https://orcid.org/0000-0003-3402-9621'
+  - family-names: Mues
+    given-names: Malte
+    orcid: 'https://orcid.org/0000-0002-6291-9886'
+  - family-names: Bentley
+    given-names: Martin
+  - family-names: Gentilini
+    given-names: Alessandro
+  - family-names: Scott
+    given-names: Richard
+identifiers:
+  - type: doi
+    value: 10.5281/ZENODO.2545106
+  - type: url
+    value: 'https://zenodo.org/doi/10.5281/zenodo.2545106'
+url: 'https://zenodo.org/doi/10.5281/zenodo.2545106'
+version: 0.3.5.post0
+date-released: '2024-02-28'
+doi: 10.5281/ZENODO.2545106
+preferred-citation:
+  authors:
+    - family-names: Williams
+      given-names: Morgan
+      orcid: 'https://orcid.org/0000-0003-4764-9555'
+    - family-names: Schoneveld
+      given-names: Louise
+      orcid: 'https://orcid.org/0000-0002-9324-1676'
+    - family-names: Mao
+      given-names: Ya-Jing
+      orcid: 'https://orcid.org/0000-0002-2725-2158'
+    - family-names: Klump
+      given-names: Jens
+      occid: 'https://orcid.org/0000-0001-5911-6022'
+    - family-names: Gosses
+      given-names: Justin
+      orcid: 'https://orcid.org/0000-0002-5351-7295'
+    - family-names: Dalton
+      given-names: Hayden
+      orcid: 'https://orcid.org/0000-0003-2114-9894'
+    - family-names: Bath
+      given-names: Adam
+      orcid: 'https://orcid.org/0000-0003-0882-0807'
+    - family-names: Barnes
+      given-names: Steve
+      orcid: 'https://orcid.org/0000-0002-4912-9177'
+  doi: 10.21105/joss.02314
+  identifiers:
+    - type: doi
+      value: 10.21105/joss.02314
+    - type: url
+      value: 'http://dx.doi.org/10.21105/joss.02314'
+    - type: other
+      value: 'urn:issn:2475-9066'
+  title: 'pyrolite: Python for geochemistry'
+  url: 'http://dx.doi.org/10.21105/joss.02314'
+  database: Crossref
+  date-published: '2020-06-09'
+  year: 2020
+  month: 6
+  issn: 2475-9066
+  issue: '50'
+  journal: Journal of Open Source Software
+  publisher:
+    name: The Open Journal
+  start: '2314'
+  type: article
+  volume: '5'

docs/source/dev/changelog.rst

@@ -10,6 +10,18 @@ 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>`__ .
 
+`0.3.6`_
+----------
+
+* **PR Merged**: `Sarah Shi <https://github.com/sarashi>`__ contributed a PR to 
+  better handle values below zero during compositional renormalisation (to 1 or 100%; 
+  `#104 <https://github.com/morganjwilliams/pyrolite/pull/104>`__).
+  The functions :func:`pyrolite.comp.codata.close` and :func:`pyrolite.comp.codata.renormalise`
+  will now warn where values below zero exist, and replace these with `numpy.nan`.
+* Added a `CITATION.cff` file to the repository.
+* Various administrative changes (formatting, linting, meta-file management), minor bugfixes 
+  and addressing various deprecation/other warnings.
+
 `0.3.5`_
 ----------
 
@@ -26,8 +38,8 @@ All notable changes to this project will be documented here.
   allow series and dataframes with `Pm` data to be used with the `pyrolite.pyrochem`
   REE accessors (i.e., the column will not be dropped if it exists; 
   `#100 <https://github.com/morganjwilliams/pyrolite/pull/100>`__). 
-  This PR aslo included an update for the `pyrolite.util.lambdas` functions to be more 
-  flexible in terms of access, including as indvidual series (allowing performant 
+  This PR also included an update for the `pyrolite.util.lambdas` functions to be more 
+  flexible in terms of access, including as individual series (allowing performant 
   usage with `pandarallel <https://github.com/nalepae/pandarallel>`__).
 * Updates to `pyrolite.pyrochem` accessors to be more flexible, generally allowing 
   usage with both DataFrame and Series objects (e.g. `df.pyrochem.REE`, 
@@ -41,13 +53,13 @@ All notable changes to this project will be documented here.
   (`#91 <https://github.com/morganjwilliams/pyrolite/pull/91>`__), 
   update the TAS field names in the JSON template 
   (`#92 <https://github.com/morganjwilliams/pyrolite/pull/92>`__), 
-  improve the formatting and scaling of TAS diagrams.
+  improve the formatting and scaling of TAS diagrams
   (`#93 <https://github.com/morganjwilliams/pyrolite/pull/93>`__), 
   add an option to add field labels in the visual centre of polygons (rather than the 
   'centroid'; `#94 <https://github.com/morganjwilliams/pyrolite/pull/94>`__),
   update some usage of :mod:`matplotlib` 
   (`#96 <https://github.com/morganjwilliams/pyrolite/pull/96>`__),
-  and allow selective plotting of indiviudal fields when adding a classification 
+  and allow selective plotting of individual  fields when adding a classification 
   diagram to axes (`#98 <https://github.com/morganjwilliams/pyrolite/pull/98>`__).
 
 
@@ -1398,8 +1410,9 @@ 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/0.3.5...develop
-.. _0.3.5: https://github.com/morganjwilliams/pyrolite/compare/0.3.4...0.3.5
+.. _Development: https://github.com/morganjwilliams/pyrolite/compare/0.3.6...develop
+.. _0.3.6: https://github.com/morganjwilliams/pyrolite/compare/0.3.5.post0...0.3.6
+.. _0.3.5: https://github.com/morganjwilliams/pyrolite/compare/0.3.4...0.3.5.post0
 .. _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

docs/source/dev/development.rst

@@ -5,7 +5,7 @@ Development History and Planning
 --------------------------------
 
 * `Changelog <changelog.html>`__
-* `Future <future.html>`__
+* `Roadmap <roadmap.html>`__
 
 
 Contributing

docs/source/dev/future.rst → docs/source/dev/roadmap.rst

@@ -1,4 +1,4 @@
-Future
+Roadmap
 ========
 
 This page details some of the under-development and planned features for
@@ -63,7 +63,6 @@ planned be integrated over the longer term.
     * assessing uncertainties
 
 
-
 Governance and Documentation
 ------------------------------
 

docs/source/gallery/tutorials/templates.py

@@ -0,0 +1,13 @@
+"""
+Creating Classification Diagrams
+==================================
+
+* Create JSON files
+* Add util.classification
+* Add plot.templates file
+
+"""
+#######################################################################################
+# First let's pull in a simple dataset to use throughout these examples:
+#
+from pyrolite.util.synthetic import normal_frame

docs/source/index.rst

@@ -17,7 +17,7 @@ and numerous auxiliary utilities.
 
 - There's also a quick `installation guide <./installation.html>`__, a list of
   `recent changes <./dev/changelog.html>`__ and some notes on
-  where the project is heading in the near `future <./dev/future.html>`__.
+  where the project is heading in the `roadmap <./dev/roadmap.html>`__.
 
 - If you're interested in `contributing to the project <./dev/contributing.html>`__, there are
   many potential avenues, whether you're experienced with python or not.
@@ -73,7 +73,7 @@ make use of your geochemical data to build and test geological models.
 
     dev/development
     dev/changelog
-    dev/future
+    dev/roadmap
     dev/conduct
     dev/contributing
     dev/contributors

environment.yml

@@ -5,7 +5,7 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.10
+  - python=3.11
   # pandas and scientific python
   - numpy
   - numpydoc

pyproject.toml

@@ -31,25 +31,19 @@ dependencies = [
     "numpydoc",
     "tinydb>4.1",     # >4.1 required for read-only access mode for JSON storage
     "periodictable",
-    "matplotlib",
+    "matplotlib<3.9",
     "mpltern>=0.4.0",
     "scipy>=1.2",     # uses scipy.optimize.Bounds, added around 1.2
     "sympy>=1.7",
     "pandas>=1.0",    # dataframe acccessors, attrs attribute
     "requests",       # used by alphaMELTS utilities,  util.web
 ]
 
-[tool.setuptools.packages]
-find = { exclude = ['test*', "docs*"] } # "**/__pycache__/*"
-#  include = ["Aitchison/*.py"],
-
-[tool.setuptools.dynamic]
-readme = { file = "README.md", content-type = "text/markdown" }
-
 [project.urls]
-"Issue tracker" = "https://github.com/morganjwilliams/pyrolite/issues"
-"Documentation" = "https://pyrolite.readthedocs.io/"
-"Code" = "https://github.com/morganjwilliams/pyrolite"
+Issues = "https://github.com/morganjwilliams/pyrolite/issues"
+Documentation = "https://pyrolite.readthedocs.io/"
+Repository = "https://github.com/morganjwilliams/pyrolite"
+Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
 
 [project.optional-dependencies]
 docs = [
@@ -78,8 +72,12 @@ dev = [
     "build",
 ]
 
-[metadata]
-url = "https://github.com/morganjwilliams/pyrolite"
+[tool.setuptools.packages]
+find = { exclude = ['test*', "docs*"] } # "**/__pycache__/*"
+#  include = ["Aitchison/*.py"],
+
+[tool.setuptools.dynamic]
+readme = { file = "README.md", content-type = "text/markdown" }
 
 [tool.coverage.run]
 relative_files = true
@@ -103,6 +101,6 @@ parentdir_prefix = "pyrolite-"
 
 [tool.pytest.ini_options]
 python_files = "*.py"
-addopts = "--cov=pyrolite --cov-report html --cov-report xml --cov-report term-missing --cov-config .coveragerc"
+addopts = "--cov=pyrolite --cov-report html --cov-report xml --cov-report term-missing"
 testpaths = ["test"]
 pythonpath = ["."]

pyrolite/comp/aggregate.py

@@ -233,7 +233,7 @@ def np_cross_ratios(X: np.ndarray, debug=False):
             diags = ratios[:, np.arange(dims), np.arange(dims)]
             # check all diags are 1.
             assert np.allclose(diags, 1.0)
-        except:
+        except AssertionError:
             # check all diags are 1. or nan
             assert np.allclose(diags[~np.isnan(diags)], 1.0)