pyEQL 0.15.1__tar.gz → 1.0.1__tar.gz

{pyEQL-0.15.1 → pyeql-1.0.1}/.github/workflows/post-process.yml

@@ -55,7 +55,7 @@ jobs:
           pip install -e ".[testing]"
       - name: Run tests
         run: |
-          pytest --cov=src/pyEQL --cov-report=xml
+          pytest -n auto --cov=src/pyEQL --cov-report=xml
       - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

{pyEQL-0.15.1 → pyeql-1.0.1}/.github/workflows/testing.yaml

@@ -64,7 +64,7 @@ jobs:
           pip install -e ".[testing]"
       - name: Run tests
         run: |
-          pytest --cov=src/pyEQL --cov-report=xml
+          pytest -n auto --cov=src/pyEQL --cov-report=xml
       - uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

{pyEQL-0.15.1 → pyeql-1.0.1}/.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
-        exclude_types: [html]
+        exclude_types: [html, svg]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -38,7 +38,9 @@ repos:
       - id: destroyed-symlinks
       - id: end-of-file-fixer
       - id: mixed-line-ending
+        exclude_types: [svg]
       - id: trailing-whitespace
+        exclude_types: [svg]
 
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8

{pyEQL-0.15.1 → pyeql-1.0.1}/CHANGELOG.md

@@ -5,7 +5,51 @@ 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).
 
-## Unreleased
+## [1.0.1] - 2024-06-17
+
+### Added
+
+- Added `NPY201` ruleset to `ruff` configuration to check support for `numpy` 2.0
+
+### Fixed
+
+- `NativeEOS` and `PHREEQCEOS` `equilibrate`: Fixed a charge balancing bug that cause repeated calls to `equlibrate` to
+  severely distort the pH and/or the composition. (#141)[https://github.com/KingsburyLab/pyEQL/issues/141]
+- `UnicodeDecodeError` when trying to connect to ion database on non-English platforms ([#122](https://github.com/KingsburyLab/pyEQL/issues/122))
+
+### Changed
+
+- Replace `math` with `numpy` functions throughout. This mainly changed calls to `log` and `exp`.
+- Docs: Fix missing close parentheses in docstring (@Andrew S. Rosen)
+
+## [1.0.0] - 2024-03-17
+
+### Added
+
+- `Solution.__init__`: new keyword argument `log_level` allows user to control the verbosity of log messages by setting
+  the level (e.g., ERROR, WARNING, etc.) that will be shown in stdout.
+- Docs: added a note about a workaround for Apple M1/M2 Macs proposed by @xiaoxiaozhu123
+
+### Changed
+
+- `Solution.__init__`: The deprecated format for specifying solutes (e.g., `[["Na+", "0.5 mol/L]]`)
+  which previously only generated log warning message, now raises a `DeprecationWarning`. Use dict-style input (e.g.,
+  `{"Na+":"0.5 mol/L"}`) instead.
+- New logo! Updated the `pyEQL` logo (for the first time in 9 years!) to address an obsolete font in the .svg
+  and modernize the design.
+
+### Removed
+
+- **BREAKING** All methods and functions (with the exception of `Solution.list_XXX` methods) previously marked with
+  deprecation warnings have been removed.
+
+## [0.15.1] - 2024-03-13
+
+### Fixed
+
+- `Solution.get_total_amount`: Fixed an issue in which `ppm` units would fail.
+
+## [0.15.0] - 2024-03-13
 
 ### Added
 
@@ -19,7 +63,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- `Solution.get_total_amount`: Fixed an issue in which `ppm` units would fail.
 - `Solution`: Fixed an issue in which repeated calls to `equilibrate` when using `NativeEOS` or `PHREEQCEOS` would
   change the mass of the `Solution` slightly. This was attributed to the fact that `pyEQL` and `PHREEQC` use slightly
   different molecular weights for water.

pyeql-1.0.1/CITATION.cff

@@ -0,0 +1,26 @@
+cff-version: "1.2.0"
+authors:
+- 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"
+  date-published: 2024-03-25
+  doi: 10.21105/joss.06295
+  issn: 2475-9066
+  issue: 95
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6295
+  title: "pyEQL: A Python interface for water chemistry"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06295"
+  volume: 9
+title: "pyEQL: A Python interface for water chemistry"

{pyEQL-0.15.1/src/pyEQL.egg-info → pyeql-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 0.15.1
+Version: 1.0.1
 Summary: Python tools for solution chemistry
 Home-page: https://github.com/KingsburyLab/pyEQL
 Author: Ryan Kingsbury
@@ -19,18 +19,19 @@ License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
 Requires-Dist: pint>=0.19
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: scipy
-Requires-Dist: pymatgen>=2023.10.11
+Requires-Dist: pymatgen==2024.5.1
 Requires-Dist: iapws
 Requires-Dist: monty
-Requires-Dist: maggma>=0.57.5
+Requires-Dist: maggma>=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pre-commit; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-xdist; extra == "testing"
 Requires-Dist: black; extra == "testing"
 Requires-Dist: mypy; extra == "testing"
 Requires-Dist: ruff; extra == "testing"
@@ -50,11 +51,9 @@ Requires-Dist: rich; extra == "full"
 [![PyPI version](https://badge.fury.io/py/pyEQL.svg)](https://badge.fury.io/py/pyEQL)
 [![status](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6/status.svg)](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6)
 
+<img src="pyeql-logo.png" alt="pyEQL logo" style="width:600px;"/>
 
-![pyeql logo](pyeql-logo.svg)
-
-A python interface for water chemistry
-
+# A python interface for water chemistry
 
 ## Description
 
@@ -122,8 +121,8 @@ Detailed documentation is available at [https://pyeql.readthedocs.io/](https://p
 - [maggma](https://materialsproject.github.io/maggma/) - interface for accessing the property database
 - [scipy](https://www.scipy.org/) - for certain nonlinear equation solvers
 
-<!-- pyscaffold-notes -->
----
+## <!-- pyscaffold-notes -->
+
 pyEQL is licensed under LGPL.
 
 This project has been set up using PyScaffold 4.5. For details and usage

{pyEQL-0.15.1 → pyeql-1.0.1}/README.md

@@ -6,11 +6,9 @@
 [![PyPI version](https://badge.fury.io/py/pyEQL.svg)](https://badge.fury.io/py/pyEQL)
 [![status](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6/status.svg)](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6)
 
+<img src="pyeql-logo.png" alt="pyEQL logo" style="width:600px;"/>
 
-![pyeql logo](pyeql-logo.svg)
-
-A python interface for water chemistry
-
+# A python interface for water chemistry
 
 ## Description
 
@@ -78,8 +76,8 @@ Detailed documentation is available at [https://pyeql.readthedocs.io/](https://p
 - [maggma](https://materialsproject.github.io/maggma/) - interface for accessing the property database
 - [scipy](https://www.scipy.org/) - for certain nonlinear equation solvers
 
-<!-- pyscaffold-notes -->
----
+## <!-- pyscaffold-notes -->
+
 pyEQL is licensed under LGPL.
 
 This project has been set up using PyScaffold 4.5. For details and usage

{pyEQL-0.15.1 → pyeql-1.0.1}/docs/changelog.md

@@ -5,7 +5,51 @@ 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).
 
-## Unreleased
+## [1.0.1] - 2024-06-17
+
+### Added
+
+- Added `NPY201` ruleset to `ruff` configuration to check support for `numpy` 2.0
+
+### Fixed
+
+- `NativeEOS` and `PHREEQCEOS` `equilibrate`: Fixed a charge balancing bug that cause repeated calls to `equlibrate` to
+  severely distort the pH and/or the composition. (#141)[https://github.com/KingsburyLab/pyEQL/issues/141]
+- `UnicodeDecodeError` when trying to connect to ion database on non-English platforms ([#122](https://github.com/KingsburyLab/pyEQL/issues/122))
+
+### Changed
+
+- Replace `math` with `numpy` functions throughout. This mainly changed calls to `log` and `exp`.
+- Docs: Fix missing close parentheses in docstring (@Andrew S. Rosen)
+
+## [1.0.0] - 2024-03-17
+
+### Added
+
+- `Solution.__init__`: new keyword argument `log_level` allows user to control the verbosity of log messages by setting
+  the level (e.g., ERROR, WARNING, etc.) that will be shown in stdout.
+- Docs: added a note about a workaround for Apple M1/M2 Macs proposed by @xiaoxiaozhu123
+
+### Changed
+
+- `Solution.__init__`: The deprecated format for specifying solutes (e.g., `[["Na+", "0.5 mol/L]]`)
+  which previously only generated log warning message, now raises a `DeprecationWarning`. Use dict-style input (e.g.,
+  `{"Na+":"0.5 mol/L"}`) instead.
+- New logo! Updated the `pyEQL` logo (for the first time in 9 years!) to address an obsolete font in the .svg
+  and modernize the design.
+
+### Removed
+
+- **BREAKING** All methods and functions (with the exception of `Solution.list_XXX` methods) previously marked with
+  deprecation warnings have been removed.
+
+## [0.15.1] - 2024-03-13
+
+### Fixed
+
+- `Solution.get_total_amount`: Fixed an issue in which `ppm` units would fail.
+
+## [0.15.0] - 2024-03-13
 
 ### Added
 
@@ -19,7 +63,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- `Solution.get_total_amount`: Fixed an issue in which `ppm` units would fail.
 - `Solution`: Fixed an issue in which repeated calls to `equilibrate` when using `NativeEOS` or `PHREEQCEOS` would
   change the mass of the `Solution` slightly. This was attributed to the fact that `pyEQL` and `PHREEQC` use slightly
   different molecular weights for water.