pyEQL 1.0.0__tar.gz → 1.0.1__tar.gz

{pyEQL-1.0.0 → 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-1.0.0 → 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-1.0.0 → pyeql-1.0.1}/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).
 
+## [1.0.1] - 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

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-1.0.0/src/pyEQL.egg-info → pyeql-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.0.0
+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"

{pyEQL-1.0.0 → pyeql-1.0.1}/docs/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).
 
+## [1.0.1] - 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

{pyEQL-1.0.0 → pyeql-1.0.1}/pyproject.toml

@@ -47,6 +47,7 @@ select = [
   "UP",   # pyupgrade
   "W",    # pycodestyle warning
   "YTT",  # flake8-2020
+  "NPY201", # Numpy 2.0 migration
 ]
 ignore = [
   "B008",    # Do not perform function call `unit` in argument defaults

{pyEQL-1.0.0 → pyeql-1.0.1}/requirements/macos-latest_py3.10.txt

@@ -6,26 +6,34 @@
 #
 aioitertools==0.11.0
     # via maggma
-annotated-types==0.6.0
+annotated-types==0.7.0
     # via pydantic
-anyio==4.3.0
-    # via starlette
+anyio==4.4.0
+    # via
+    #   httpx
+    #   starlette
+    #   watchfiles
+appdirs==1.4.4
+    # via pint
 attrs==23.2.0
     # via
     #   jsonschema
     #   referencing
-bcrypt==4.1.2
+bcrypt==4.1.3
     # via paramiko
-blinker==1.7.0
+blinker==1.8.2
     # via flask
-boto3==1.34.59
+boto3==1.34.122
     # via maggma
-botocore==1.34.59
+botocore==1.34.122
     # via
     #   boto3
     #   s3transfer
-certifi==2024.2.2
-    # via requests
+certifi==2024.6.2
+    # via
+    #   httpcore
+    #   httpx
+    #   requests
 cffi==1.16.0
     # via
     #   cryptography
@@ -36,46 +44,66 @@ click==8.1.7
     # via
     #   flask
     #   mongogrant
+    #   typer
     #   uvicorn
-contourpy==1.2.0
+contourpy==1.2.1
     # via matplotlib
-cryptography==42.0.5
+cryptography==42.0.8
     # via paramiko
 cycler==0.12.1
     # via matplotlib
 dnspython==2.6.1
     # via
+    #   email-validator
     #   maggma
     #   pymongo
-exceptiongroup==1.2.0
+email-validator==2.1.1
+    # via fastapi
+exceptiongroup==1.2.1
     # via anyio
-fastapi==0.110.0
+fastapi==0.111.0
     # via maggma
-flask==3.0.2
+fastapi-cli==0.0.4
+    # via fastapi
+flask==3.0.3
     # via mongogrant
-fonttools==4.49.0
+flexcache==0.3
+    # via pint
+flexparser==0.3.1
+    # via pint
+fonttools==4.53.0
     # via matplotlib
-future==1.0.0
-    # via uncertainties
 h11==0.14.0
+    # via
+    #   httpcore
+    #   uvicorn
+httpcore==1.0.5
+    # via httpx
+httptools==0.6.1
     # via uvicorn
-iapws==1.5.3
+httpx==0.27.0
+    # via fastapi
+iapws==1.5.4
     # via pyEQL (setup.py)
-idna==3.6
+idna==3.7
     # via
     #   anyio
+    #   email-validator
+    #   httpx
     #   requests
-itsdangerous==2.1.2
-    # via flask
-jinja2==3.1.3
+itsdangerous==2.2.0
     # via flask
+jinja2==3.1.4
+    # via
+    #   fastapi
+    #   flask
 jmespath==1.0.1
     # via
     #   boto3
     #   botocore
-joblib==1.3.2
+joblib==1.4.2
     # via pymatgen
-jsonschema==4.21.1
+jsonschema==4.22.0
     # via maggma
 jsonschema-specifications==2023.12.1
     # via jsonschema
@@ -83,19 +111,23 @@ kiwisolver==1.4.5
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
-maggma==0.63.4
+maggma==0.67.0
     # via pyEQL (setup.py)
+markdown-it-py==3.0.0
+    # via rich
 markupsafe==2.1.5
     # via
     #   jinja2
     #   werkzeug
-matplotlib==3.8.3
+matplotlib==3.9.0
     # via pymatgen
+mdurl==0.1.2
+    # via markdown-it-py
 mongogrant==0.3.3
     # via maggma
 mongomock==4.1.2
     # via maggma
-monty==2024.2.26
+monty==2024.5.24
     # via
     #   maggma
     #   pyEQL (setup.py)
@@ -104,7 +136,7 @@ mpmath==1.3.0
     # via sympy
 msgpack==1.0.8
     # via maggma
-networkx==3.2.1
+networkx==3.3
     # via pymatgen
 numpy==1.26.4
     # via
@@ -117,47 +149,51 @@ numpy==1.26.4
     #   pymatgen
     #   scipy
     #   spglib
-orjson==3.9.15
-    # via maggma
-packaging==23.2
+orjson==3.10.3
+    # via
+    #   fastapi
+    #   maggma
+packaging==24.1
     # via
     #   matplotlib
     #   mongomock
     #   plotly
 palettable==3.3.3
     # via pymatgen
-pandas==2.2.1
+pandas==2.2.2
     # via pymatgen
 paramiko==3.4.0
     # via sshtunnel
-periodictable==1.6.1
+periodictable==1.7.0
     # via phreeqpython
-phreeqpython==1.5.0
+phreeqpython==1.5.2
     # via pyEQL (setup.py)
-pillow==10.2.0
+pillow==10.3.0
     # via matplotlib
-pint==0.23
+pint==0.24
     # via pyEQL (setup.py)
-plotly==5.19.0
+plotly==5.22.0
     # via pymatgen
 pybtex==0.24.0
     # via pymatgen
-pycparser==2.21
+pycparser==2.22
     # via cffi
-pydantic==2.6.3
+pydantic==2.7.3
     # via
     #   fastapi
     #   maggma
     #   pydantic-settings
-pydantic-core==2.16.3
+pydantic-core==2.18.4
     # via pydantic
-pydantic-settings==2.2.1
+pydantic-settings==2.3.1
     # via maggma
-pydash==7.0.7
+pydash==8.0.1
     # via maggma
-pymatgen==2024.3.1
+pygments==2.18.0
+    # via rich
+pymatgen==2024.6.4
     # via pyEQL (setup.py)
-pymongo==4.6.2
+pymongo==4.7.3
     # via
     #   maggma
     #   mongogrant
@@ -174,34 +210,42 @@ python-dateutil==2.9.0.post0
     #   matplotlib
     #   pandas
 python-dotenv==1.0.1
-    # via pydantic-settings
+    # via
+    #   pydantic-settings
+    #   uvicorn
+python-multipart==0.0.9
+    # via fastapi
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1
-    # via pybtex
-pyzmq==25.1.2
+    # via
+    #   pybtex
+    #   uvicorn
+pyzmq==26.0.3
     # via maggma
-referencing==0.33.0
+referencing==0.35.1
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.31.0
+requests==2.32.3
     # via
     #   mongogrant
     #   pymatgen
-rpds-py==0.18.0
+rich==13.7.1
+    # via typer
+rpds-py==0.18.1
     # via
     #   jsonschema
     #   referencing
-ruamel-yaml==0.17.40
+ruamel-yaml==0.18.6
     # via
     #   maggma
     #   pymatgen
 ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
-s3transfer==0.10.0
+s3transfer==0.10.1
     # via boto3
-scipy==1.12.0
+scipy==1.13.1
     # via
     #   iapws
     #   phreeqpython
@@ -209,48 +253,67 @@ scipy==1.12.0
     #   pymatgen
 sentinels==1.0.0
     # via mongomock
+shellingham==1.5.4
+    # via typer
 six==1.16.0
     # via
     #   pybtex
     #   python-dateutil
 sniffio==1.3.1
-    # via anyio
-spglib==2.3.1
+    # via
+    #   anyio
+    #   httpx
+spglib==2.4.0
     # via pymatgen
 sshtunnel==0.4.0
     # via maggma
-starlette==0.36.3
+starlette==0.37.2
     # via fastapi
-sympy==1.12
+sympy==1.12.1
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
-tenacity==8.2.3
+tenacity==8.3.0
     # via plotly
-tqdm==4.66.2
+tqdm==4.66.4
     # via
     #   maggma
     #   pymatgen
-typing-extensions==4.10.0
+typer==0.12.3
+    # via fastapi-cli
+typing-extensions==4.12.2
     # via
     #   anyio
     #   fastapi
+    #   flexcache
+    #   flexparser
     #   pint
     #   pydantic
     #   pydantic-core
     #   pydash
+    #   typer
     #   uvicorn
 tzdata==2024.1
     # via pandas
-uncertainties==3.1.7
+ujson==5.10.0
+    # via fastapi
+uncertainties==3.2.1
     # via pymatgen
-urllib3==2.0.7
+urllib3==2.2.1
     # via
     #   botocore
     #   requests
-uvicorn==0.28.0
-    # via maggma
-werkzeug==3.0.1
+uvicorn[standard]==0.30.1
+    # via
+    #   fastapi
+    #   maggma
+uvloop==0.19.0
+    # via uvicorn
+watchfiles==0.22.0
+    # via uvicorn
+websockets==12.0
+    # via uvicorn
+werkzeug==3.0.3
     # via flask
 
 # The following packages are considered to be unsafe in a requirements file: