pyEQL 1.1.0__tar.gz → 1.1.2__tar.gz

{pyeql-1.1.0 → pyeql-1.1.2}/.github/dependabot.yml

@@ -1,6 +1,11 @@
 version: 2
 updates:
+  # Maintain dependencies for GitHub Actions
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

{pyeql-1.1.0 → pyeql-1.1.2}/.pre-commit-config.yaml

@@ -12,18 +12,18 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.2
+    rev: v0.5.5
     hooks:
       - id: ruff
         args: [--fix, --ignore, "D,E501", "--show-fixes"]
 
-  - repo: https://github.com/psf/black
-    rev: 24.2.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     hooks:
       - id: black
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -31,7 +31,7 @@ repos:
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-case-conflict
       - id: check-symlinks

{pyeql-1.1.0 → pyeql-1.1.2}/CHANGELOG.md

@@ -5,6 +5,58 @@ 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).
 
+## [1.1.2] - 2024-07-28
+
+### Fixed
+
+- `Solution`: Fix a bug in which setting `balance_charge` to `auto` when the initial
+  composition was electroneutral would cause errors and/or improper charge balancing
+  after `equilibrate` was called.
+
+## [1.1.1] - 2024-07-27
+
+### Fixed
+
+- `equilibrate`: Fixed a bug that could cause an `AttributeError` when pH was used for charge
+  balancing.
+- Database: `size.radius_ionic` was missing units for `Ni[+2]` and `Cr[+3]`. Correct units have been added.
+
+### Added
+
+- `Solution`: New automatic charge balancing method will automatically identify the majority (highest concentration)
+  cation or anion as appropriate (depending on the charge balance) for charge balancing. To use this mode, set
+  `balance_charge='auto'` when instantiating a `Solution`.
+
+### Changed
+
+- `Solution.add_amount`: This method will now add solutes that are absent from the Solution. Previously, calling, e.g.,
+  `add_amount('Na+', '1 mol')` on a `Solution` that did not contain any sodium would result in an error. A warning
+  is logged if the method has to add a new solute.
+- Units: use the upstream chemistry context from `pint` instead of the custom one from 2013.
+- `pre-commit autoupdate`
+- Misc. linting and code quality improvements.
+- Unit tests: update `tmpdir` to `tmp_path` text fixture.
+- CI: Small updates to pre-commit and GitHub actions per scientific python [repo review](https://scientific-python.github.io/repo-review/?repo=kingsburylab%2FpyEQL&branch=main).
+
+## [1.0.3] - 2024-07-20
+
+### Fixed
+
+- `standardize_formula`: Fix incorrect display of additional formulas, including methane which
+  was shown as "H4C(aq)", other tri-anions (N3-, P3-), and a variety of haloacetic acids. For
+  example, tricholoracetic acid was previously shown as `'C2Cl3O2[-1]'` but will now display
+  as `'CCl3COO[-1]'`.
+
+### Added
+
+- `standardize_formula`: `pyEQL` can now parse ion formulas that contain unicode superscript
+  or subscript characters, which makes input even more flexible. For example, `"PO₄³⁻"` and `"Co²⁺"`
+  will now standardize correctly to `"PO4[-3]"` and `"Co[+2]"`, respectively.
+
+### Changed
+
+- Housekeeping: move all project configuration to `pyproject.toml`
+
 ## [1.0.2] - 2024-07-09
 
 ### Fixed

{pyeql-1.1.0 → pyeql-1.1.2}/MANIFEST.in

@@ -2,6 +2,5 @@ include README COPYING CHANGELOG LICENSE README.md README.rst README.txt CHANGES
 recursive-include src/pyEQL/database/ *
 recursive-include src/pyEQL/presets/ *
 recursive-include docs/ *
-include src/pyEQL/pint_custom_units.txt
 prune docs/build
 global-exclude *.pyc *~ .DS_Store *__pycache__* *.pyo

{pyeql-1.1.0/src/pyEQL.egg-info → pyeql-1.1.2}/PKG-INFO

@@ -1,20 +1,22 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.1.0
-Summary: Python tools for solution chemistry
-Home-page: https://github.com/KingsburyLab/pyEQL
-Author: Ryan Kingsbury
-Author-email: kingsbury@princeton.edu
-License: LGPL3
-Project-URL: Documentation, https://pyeql.readthedocs.io/
-Platform: any
+Version: 1.1.2
+Summary: A python interface for solution chemistry
+Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
+Project-URL: Docs, https://pyeql.readthedocs.io/
+Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
+Project-URL: Package, https://pypi.org/project/pyEQL
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Development Status :: 4 - Beta
-Classifier: Programming Language :: Python
 Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Software Development :: Libraries
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
@@ -23,7 +25,7 @@ Requires-Dist: numpy<2
 Requires-Dist: scipy
 Requires-Dist: pymatgen==2024.5.1
 Requires-Dist: iapws
-Requires-Dist: monty
+Requires-Dist: monty>=2024.7.12
 Requires-Dist: maggma>=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: testing

{pyeql-1.1.0 → pyeql-1.1.2}/docs/changelog.md

@@ -5,6 +5,58 @@ 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).
 
+## [1.1.2] - 2024-07-28
+
+### Fixed
+
+- `Solution`: Fix a bug in which setting `balance_charge` to `auto` when the initial
+  composition was electroneutral would cause errors and/or improper charge balancing
+  after `equilibrate` was called.
+
+## [1.1.1] - 2024-07-27
+
+### Fixed
+
+- `equilibrate`: Fixed a bug that could cause an `AttributeError` when pH was used for charge
+  balancing.
+- Database: `size.radius_ionic` was missing units for `Ni[+2]` and `Cr[+3]`. Correct units have been added.
+
+### Added
+
+- `Solution`: New automatic charge balancing method will automatically identify the majority (highest concentration)
+  cation or anion as appropriate (depending on the charge balance) for charge balancing. To use this mode, set
+  `balance_charge='auto'` when instantiating a `Solution`.
+
+### Changed
+
+- `Solution.add_amount`: This method will now add solutes that are absent from the Solution. Previously, calling, e.g.,
+  `add_amount('Na+', '1 mol')` on a `Solution` that did not contain any sodium would result in an error. A warning
+  is logged if the method has to add a new solute.
+- Units: use the upstream chemistry context from `pint` instead of the custom one from 2013.
+- `pre-commit autoupdate`
+- Misc. linting and code quality improvements.
+- Unit tests: update `tmpdir` to `tmp_path` text fixture.
+- CI: Small updates to pre-commit and GitHub actions per scientific python [repo review](https://scientific-python.github.io/repo-review/?repo=kingsburylab%2FpyEQL&branch=main).
+
+## [1.0.3] - 2024-07-20
+
+### Fixed
+
+- `standardize_formula`: Fix incorrect display of additional formulas, including methane which
+  was shown as "H4C(aq)", other tri-anions (N3-, P3-), and a variety of haloacetic acids. For
+  example, tricholoracetic acid was previously shown as `'C2Cl3O2[-1]'` but will now display
+  as `'CCl3COO[-1]'`.
+
+### Added
+
+- `standardize_formula`: `pyEQL` can now parse ion formulas that contain unicode superscript
+  or subscript characters, which makes input even more flexible. For example, `"PO₄³⁻"` and `"Co²⁺"`
+  will now standardize correctly to `"PO4[-3]"` and `"Co[+2]"`, respectively.
+
+### Changed
+
+- Housekeeping: move all project configuration to `pyproject.toml`
+
 ## [1.0.2] - 2024-07-09
 
 ### Fixed

{pyeql-1.1.0 → pyeql-1.1.2}/docs/chemistry.md

@@ -23,7 +23,8 @@ Here are some examples:
 | Sodium Sulfate  |      "Na2(SO4)" or "Na2SO4"       |    "Na(SO4)(aq)"    |
 | Sodium Ion      | "Na+", "Na+1", "Na1+", or "Na[+]" |      "Na[+1]"       |
 | Magnesium Ion   |    "Mg+2", "Mg++", or "Mg[++]"    |      "Mg[+2]"       |
-| Methanol        |          "CH3OH", "CH4O"          |    "'CH3OH(aq)'"    |
+| Methanol        |          "CH3OH", "CH4O"          |     "CH3OH(aq)"     |
+| Phosphate Ion   |         "PO4-3", "PO₄³⁻"          |      "PO4[-3]"      |
 
 Specifically, `standardize_formula` uses `Ion.from_formula(<formula>).reduced_formla` (shown in the right hand column
 of the table) to identify solutes. Notice that for charged species, the charges are always placed inside square brackets
@@ -33,6 +34,11 @@ by `(aq)` to disambiguate them from solids.
 ```{important}
 **When writing multivalent ion formulas, it is strongly recommended that you put the charge number AFTER the + or -
 sign** (e.g., type "Mg+2" NOT "Mg2+"). The latter formula is ambiguous - it could mean $Mg_2^+$ or $Mg^{+2}$ and it will be processed incorrectly into `Mg[+0.5]`
+
+There is **one exception** to the rule above. If you really want to list the charge number
+first , you can use unicode superscript characters (e.g., "Co²⁺"), and `pyEQL` will understand
+these regardless of the order of the `+` and the `2`. So you can write "Co²⁺" and it will be
+correctly standardized to `Co[+2]`
 ```
 
 (manual-testing)=

{pyeql-1.1.0 → pyeql-1.1.2}/pyproject.toml

@@ -1,8 +1,69 @@
+[project]
+name = "pyEQL"
+readme = "README.md"
+dynamic = ["version"]
+description="A python interface for solution chemistry"
+authors =[
+    {name = "Ryan Kingsbury", email = "kingsbury@princeton.edu"}
+]
+classifiers=[
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Science/Research",
+        "Operating System :: OS Independent",
+        "Topic :: Scientific/Engineering",
+    ]
+license = {file = "LICENSE"}
+requires-python = ">=3.9"
+dependencies = [
+        "pint>=0.19",
+        "numpy<2",
+        "scipy",
+        "pymatgen==2024.5.1",
+        "iapws",
+        "monty>=2024.7.12",
+        "maggma>=0.67.0",
+        "phreeqpython",
+    ]
+
+[project.urls]
+Docs = "https://pyeql.readthedocs.io/"
+Repo = "https://github.com/KingsburyLab/pyEQL"
+Package = "https://pypi.org/project/pyEQL"
+
+
+[project.optional-dependencies]
+testing = [
+    "setuptools",
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "black",
+    "mypy",
+    "ruff",
+    "tox<4",
+    ]
+docs = [
+    "sphinx>=3.2.1",
+    "sphinx-rtd-theme",
+    "myst-parser[linkify]",
+    ]
+full = ["rich"]
+
 [build-system]
 # AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
 requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = ["tests"]
+
 [tool.setuptools_scm]
 # See configuration details in https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
@@ -11,7 +72,6 @@ version_scheme = "no-guess-dev"
 line-length = 120
 
 [tool.ruff]
-target-version = "py39"
 line-length = 120
 exclude = [".dat"]
 src = ["src"]
@@ -84,7 +144,13 @@ addopts = [
   "--strict-config",
   "--color=yes",
   "--import-mode=importlib",
-  "--durations=30"
+  "--durations=30",
+  "--verbose",
+]
+norecursedirs = [
+  "dist",
+  "build",
+  ".tox",
 ]
 xfail_strict = true
 filterwarnings = ["error", "ignore::UserWarning", "ignore::DeprecationWarning"]

{pyeql-1.1.0 → pyeql-1.1.2}/requirements/macos-latest_py3.10.txt

@@ -8,44 +8,29 @@ aioitertools==0.11.0
     # via maggma
 annotated-types==0.7.0
     # via pydantic
-anyio==4.4.0
-    # via
-    #   httpx
-    #   starlette
-    #   watchfiles
 appdirs==1.4.4
     # via pint
 attrs==23.2.0
     # via
+    #   jsonlines
     #   jsonschema
     #   referencing
 bcrypt==4.1.3
     # via paramiko
-blinker==1.8.2
-    # via flask
-boto3==1.34.122
+boto3==1.34.142
     # via maggma
-botocore==1.34.122
+botocore==1.34.142
     # via
     #   boto3
     #   s3transfer
-certifi==2024.6.2
-    # via
-    #   httpcore
-    #   httpx
-    #   requests
+certifi==2024.7.4
+    # via requests
 cffi==1.16.0
     # via
     #   cryptography
     #   pynacl
 charset-normalizer==3.3.2
     # via requests
-click==8.1.7
-    # via
-    #   flask
-    #   mongogrant
-    #   typer
-    #   uvicorn
 contourpy==1.2.1
     # via matplotlib
 cryptography==42.0.8
@@ -54,56 +39,27 @@ cycler==0.12.1
     # via matplotlib
 dnspython==2.6.1
     # via
-    #   email-validator
     #   maggma
     #   pymongo
-email-validator==2.1.1
-    # via fastapi
-exceptiongroup==1.2.1
-    # via anyio
-fastapi==0.111.0
-    # via maggma
-fastapi-cli==0.0.4
-    # via fastapi
-flask==3.0.3
-    # via mongogrant
 flexcache==0.3
     # via pint
 flexparser==0.3.1
     # via pint
-fonttools==4.53.0
+fonttools==4.53.1
     # via matplotlib
-h11==0.14.0
-    # via
-    #   httpcore
-    #   uvicorn
-httpcore==1.0.5
-    # via httpx
-httptools==0.6.1
-    # via uvicorn
-httpx==0.27.0
-    # via fastapi
 iapws==1.5.4
     # via pyEQL (setup.py)
 idna==3.7
-    # via
-    #   anyio
-    #   email-validator
-    #   httpx
-    #   requests
-itsdangerous==2.2.0
-    # via flask
-jinja2==3.1.4
-    # via
-    #   fastapi
-    #   flask
+    # via requests
 jmespath==1.0.1
     # via
     #   boto3
     #   botocore
 joblib==1.4.2
     # via pymatgen
-jsonschema==4.22.0
+jsonlines==4.0.0
+    # via maggma
+jsonschema==4.23.0
     # via maggma
 jsonschema-specifications==2023.12.1
     # via jsonschema
@@ -111,20 +67,10 @@ kiwisolver==1.4.5
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
-maggma==0.67.0
+maggma==0.69.0
     # via pyEQL (setup.py)
-markdown-it-py==3.0.0
-    # via rich
-markupsafe==2.1.5
-    # via
-    #   jinja2
-    #   werkzeug
-matplotlib==3.9.0
+matplotlib==3.9.1
     # via pymatgen
-mdurl==0.1.2
-    # via markdown-it-py
-mongogrant==0.3.3
-    # via maggma
 mongomock==4.1.2
     # via maggma
 monty==2024.5.24
@@ -149,10 +95,8 @@ numpy==1.26.4
     #   pymatgen
     #   scipy
     #   spglib
-orjson==3.10.3
-    # via
-    #   fastapi
-    #   maggma
+orjson==3.10.6
+    # via maggma
 packaging==24.1
     # via
     #   matplotlib
@@ -161,16 +105,18 @@ packaging==24.1
 palettable==3.3.3
     # via pymatgen
 pandas==2.2.2
-    # via pymatgen
+    # via
+    #   maggma
+    #   pymatgen
 paramiko==3.4.0
     # via sshtunnel
-periodictable==1.7.0
+periodictable==1.7.1
     # via phreeqpython
 phreeqpython==1.5.2
     # via pyEQL (setup.py)
-pillow==10.3.0
+pillow==10.4.0
     # via matplotlib
-pint==0.24
+pint==0.24.1
     # via pyEQL (setup.py)
 plotly==5.22.0
     # via pymatgen
@@ -178,25 +124,20 @@ pybtex==0.24.0
     # via pymatgen
 pycparser==2.22
     # via cffi
-pydantic==2.7.3
+pydantic==2.8.2
     # via
-    #   fastapi
     #   maggma
     #   pydantic-settings
-pydantic-core==2.18.4
+pydantic-core==2.20.1
     # via pydantic
-pydantic-settings==2.3.1
+pydantic-settings==2.3.4
     # via maggma
 pydash==8.0.1
     # via maggma
-pygments==2.18.0
-    # via rich
-pymatgen==2024.6.4
+pymatgen==2024.5.1
     # via pyEQL (setup.py)
-pymongo==4.7.3
-    # via
-    #   maggma
-    #   mongogrant
+pymongo==4.8.0
+    # via maggma
 pynacl==1.5.0
     # via paramiko
 pyparsing==3.1.2
@@ -210,17 +151,11 @@ python-dateutil==2.9.0.post0
     #   matplotlib
     #   pandas
 python-dotenv==1.0.1
-    # via
-    #   pydantic-settings
-    #   uvicorn
-python-multipart==0.0.9
-    # via fastapi
+    # via pydantic-settings
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1
-    # via
-    #   pybtex
-    #   uvicorn
+    # via pybtex
 pyzmq==26.0.3
     # via maggma
 referencing==0.35.1
@@ -228,12 +163,8 @@ referencing==0.35.1
     #   jsonschema
     #   jsonschema-specifications
 requests==2.32.3
-    # via
-    #   mongogrant
-    #   pymatgen
-rich==13.7.1
-    # via typer
-rpds-py==0.18.1
+    # via pymatgen
+rpds-py==0.19.0
     # via
     #   jsonschema
     #   referencing
@@ -243,9 +174,9 @@ ruamel-yaml==0.18.6
     #   pymatgen
 ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
-s3transfer==0.10.1
+s3transfer==0.10.2
     # via boto3
-scipy==1.13.1
+scipy==1.14.0
     # via
     #   iapws
     #   phreeqpython
@@ -253,68 +184,40 @@ scipy==1.13.1
     #   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
-    #   httpx
 spglib==2.4.0
     # via pymatgen
 sshtunnel==0.4.0
     # via maggma
-starlette==0.37.2
-    # via fastapi
-sympy==1.12.1
+sympy==1.13.0
     # via pymatgen
 tabulate==0.9.0
     # via pymatgen
-tenacity==8.3.0
+tenacity==8.5.0
     # via plotly
 tqdm==4.66.4
     # via
     #   maggma
     #   pymatgen
-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
-ujson==5.10.0
-    # via fastapi
-uncertainties==3.2.1
+uncertainties==3.2.2
     # via pymatgen
-urllib3==2.2.1
+urllib3==2.2.2
     # via
     #   botocore
     #   requests
-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:
 # setuptools