Merge branch 'main' into dependabot/github_actions/actions-72327b8d01

KingsburyLab · Sep 25, 2024 · bda3cf6 · bda3cf6
2 parents d1b6b5e + e171b9a
commit bda3cf6
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,13 +12,13 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.5
+    rev: v0.6.7
     hooks:
       - id: ruff
         args: [--fix, --ignore, "D,E501", "--show-fixes"]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
 
@@ -41,8 +41,8 @@ repos:
         exclude_types: [svg]
       - id: trailing-whitespace
         exclude_types: [svg]
-
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
-    hooks:
-      - id: prettier
+      - id: pretty-format-json
+        indent: 4
+        exclude_types: [jupyter]
+      - id: check-yaml
+      - id: check-toml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.2.0] - 2024-09-24
+
+### Fixed
+
+- Database: removed several erroneous species (such as `CO32-` which was really `CO3[-2]`),
+  corrected other parsing errors, and updated formula syntax for consistency with recent
+  `standardize_formula` changes (e.g., `H4NCl -> NH4Cl`) (#190, @rkingsbury)
+
+### Changed
+
+- Bump `pymatgen` to `v2024.9.10` for additional upstream formula fixes. (#188, @abhardwaj73)
+
+### Removed
+
+- **BREAKING** - dropped python 3.9 support, in accordance with numpy deprecation policy.
+  (#188, @abhardwaj73)
+
 ## [1.1.6] - 2024-09-01
 
 ### Fixed

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,16 +1,16 @@
 cff-version: "1.2.0"
 authors:
-- family-names: Kingsbury
-  given-names: Ryan
-  orcid: "https://orcid.org/0000-0002-7168-3967"
+  - family-names: Kingsbury
+    given-names: Ryan
+    orcid: "https://orcid.org/0000-0002-7168-3967"
 doi: 10.5281/zenodo.8332915
 message: If you use this software, please cite our article in the
   Journal of Open Source Software.
 preferred-citation:
   authors:
-  - family-names: Kingsbury
-    given-names: Ryan
-    orcid: "https://orcid.org/0000-0002-7168-3967"
+    - family-names: Kingsbury
+      given-names: Ryan
+      orcid: "https://orcid.org/0000-0002-7168-3967"
   date-published: 2024-03-25
   doi: 10.21105/joss.06295
   issn: 2475-9066

diff --git a/docs/creating.md b/docs/creating.md
@@ -2,7 +2,6 @@
 
 The `Solution` class defines a pythonic interface for **creating**, **modifying**, and **estimating properties** of electrolyte solutions. It is the core feature of `pyEQL` and the primary user-facing class. There are several ways to create a `Solution`.
 
-
 ## Empty solution
 
 With no input arguments, you get an empty `Solution` at pH 7 and 1 atm pressure.
@@ -29,7 +28,6 @@ passed as a `dict` with amounts given **as strings** that include units (see [un
 
 You can also specify conditions such as temperature, pressure, pH, and pE (redox potential).
 
-
 Finally, you can manually create a solution with any list of solutes, temperature, pressure, etc. that you need:
 
 ```python

diff --git a/setup.py b/setup.py
@@ -6,6 +6,7 @@
 PyScaffold helps you to put up the scaffold of your new Python project.
 Learn more under: https://pyscaffold.org/
 """
+
 from setuptools import setup
 
 if __name__ == "__main__":