modify pre-commit; run on all files

.pre-commit-config.yaml

@@ -14,8 +14,12 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.7
     hooks:
+      # Run the linter. filters are to exclude .ipynb files
       - id: ruff
-        args: [--fix, --ignore, "D,E501", "--show-fixes"]
+        types_or: [ python, pyi ]
+        args: [--fix, --ignore, "D,E501", --show-fixes]
+      # Run the formatter. This WILL run on .ipynb files
+      - id: ruff-format
 
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 24.8.0
@@ -41,8 +45,8 @@ repos:
         exclude_types: [svg]
       - id: trailing-whitespace
         exclude_types: [svg]
+      - id: check-yaml
+      - id: check-json
       - id: pretty-format-json
-        indent: 4
         exclude_types: [jupyter]
-      - id: check-yaml
-      - id: check-toml
+        args: [--autofix, --indent=4]

.zenodo.json

@@ -1,25 +1,25 @@
 {
-  "creators": [
-    {
-      "orcid": "0000-0002-7168-3967",
-      "affiliation": "Princeton University",
-      "name": "Kingsbury, Ryan"
-    }
-  ],
-  "rights": [
-    {
-      "description": {
-        "en": ""
-      },
-      "id": "lgpl-3.0-only",
-      "props": {
-        "scheme": "spdx",
-        "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
-      },
-      "title": {
-        "en": "GNU Lesser General Public License v3.0 only"
-      }
-    }
-  ],
-  "title": "pyEQL: A python library for water chemistry"
+    "creators": [
+        {
+            "affiliation": "Princeton University",
+            "name": "Kingsbury, Ryan",
+            "orcid": "0000-0002-7168-3967"
+        }
+    ],
+    "rights": [
+        {
+            "description": {
+                "en": ""
+            },
+            "id": "lgpl-3.0-only",
+            "props": {
+                "scheme": "spdx",
+                "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
+            },
+            "title": {
+                "en": "GNU Lesser General Public License v3.0 only"
+            }
+        }
+    ],
+    "title": "pyEQL: A python library for water chemistry"
 }

docs/examples/.ipynb_checkpoints/pyEQL_demo_1-checkpoint.ipynb

@@ -36,7 +36,7 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "array = np.array([[1,2,3,4,5], [6,7,8,9,10]])\n",
+    "array = np.array([[1, 2, 3, 4, 5], [6, 7, 8, 9, 10]])\n",
     "array"
    ]
   },
@@ -145,9 +145,7 @@
    "source": [
     "from pyEQL import Solution\n",
     "\n",
-    "s1 = Solution({\"Na+\": \"0.1 mol/L\",\n",
-    "               \"Cl-\": \"0.1 mol/L\"\n",
-    "               })"
+    "s1 = Solution({\"Na+\": \"0.1 mol/L\", \"Cl-\": \"0.1 mol/L\"})"
    ]
   },
   {
@@ -277,7 +275,7 @@
     }
    ],
    "source": [
-    "s1.get_activity('Na+')"
+    "s1.get_activity(\"Na+\")"
    ]
   },
   {
@@ -303,7 +301,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Na+', \"mol/kg\")"
+    "s1.get_amount(\"Na+\", \"mol/kg\")"
    ]
   },
   {
@@ -329,7 +327,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Na+', \"mol/L\")"
+    "s1.get_amount(\"Na+\", \"mol/L\")"
    ]
   },
   {
@@ -355,7 +353,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Na+', \"%\") #weight percent"
+    "s1.get_amount(\"Na+\", \"%\")  # weight percent"
    ]
   },
   {
@@ -381,7 +379,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Na+', \"fraction\") # mole fraction"
+    "s1.get_amount(\"Na+\", \"fraction\")  # mole fraction"
    ]
   },
   {
@@ -422,7 +420,7 @@
    "source": [
     "# native engine\n",
     "s1 = Solution({\"Na+\": \"0.1 mol/L\", \"Cl-\": \"0.1 mol/L\"}, engine=\"native\")\n",
-    "s1.get_activity_coefficient('Na+', scale=\"molar\")"
+    "s1.get_activity_coefficient(\"Na+\", scale=\"molar\")"
    ]
   },
   {
@@ -450,7 +448,7 @@
    "source": [
     "# ideal engine\n",
     "s1 = Solution([[\"Na+\", \"0.1 mol/L\"], [\"Cl-\", \"0.1 mol/L\"]], engine=\"native\")\n",
-    "s1.get_activity_coefficient('Na+', scale=\"molar\")"
+    "s1.get_activity_coefficient(\"Na+\", scale=\"molar\")"
    ]
   },
   {
@@ -479,7 +477,7 @@
     "from pyEQL import Solution\n",
     "\n",
     "s1 = Solution({\"Na+\": \"0.1 mol/L\", \"Cl-\": \"0.1 mol/L\"}, engine=\"ideal\")\n",
-    "s1.get_activity_coefficient('Na+', scale=\"molar\")"
+    "s1.get_activity_coefficient(\"Na+\", scale=\"molar\")"
    ]
   },
   {

docs/examples/.ipynb_checkpoints/pyeql_demo-checkpoint.ipynb

@@ -83,7 +83,7 @@
     }
    ],
    "source": [
-    "s1 = Solution({\"Mg+2\": \"0.2 mol/L\", \"Cl-1\": \"0.4 mol/L\"}, temperature='20 degC')"
+    "s1 = Solution({\"Mg+2\": \"0.2 mol/L\", \"Cl-1\": \"0.4 mol/L\"}, temperature=\"20 degC\")"
    ]
   },
   {
@@ -409,7 +409,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Mg+2', 'M')"
+    "s1.get_amount(\"Mg+2\", \"M\")"
    ]
   },
   {
@@ -436,7 +436,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Cl-', '%')"
+    "s1.get_amount(\"Cl-\", \"%\")"
    ]
   },
   {
@@ -463,7 +463,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Mg+2', 'eq/L')"
+    "s1.get_amount(\"Mg+2\", \"eq/L\")"
    ]
   },
   {
@@ -490,7 +490,7 @@
     }
    ],
    "source": [
-    "s1.get_amount('Mg+2', 'ug/kg')"
+    "s1.get_amount(\"Mg+2\", \"ug/kg\")"
    ]
   },
   {
@@ -525,7 +525,7 @@
     }
    ],
    "source": [
-    "s1.get_transport_number('Na+')"
+    "s1.get_transport_number(\"Na+\")"
    ]
   },
   {
@@ -552,7 +552,7 @@
     }
    ],
    "source": [
-    "s1.get_transport_number('Mg+2')"
+    "s1.get_transport_number(\"Mg+2\")"
    ]
   },
   {
@@ -579,7 +579,7 @@
     }
    ],
    "source": [
-    "s1.get_transport_number('Cl-')"
+    "s1.get_transport_number(\"Cl-\")"
    ]
   },
   {
@@ -637,7 +637,8 @@
    "outputs": [],
    "source": [
     "from monty.serialization import dumpfn\n",
-    "dumpfn(s1, 'test_solution.json')"
+    "\n",
+    "dumpfn(s1, \"test_solution.json\")"
    ]
   },
   {
@@ -727,7 +728,7 @@
     }
    ],
    "source": [
-    "s1.volume.to('mL')"
+    "s1.volume.to(\"mL\")"
    ]
   },
   {
@@ -754,7 +755,7 @@
     }
    ],
    "source": [
-    "s1.volume.to('gal')"
+    "s1.volume.to(\"gal\")"
    ]
   },
   {
@@ -783,7 +784,7 @@
     }
    ],
    "source": [
-    "s1.osmotic_pressure.to('bar').magnitude"
+    "s1.osmotic_pressure.to(\"bar\").magnitude"
    ]
   },
   {

docs/examples/.ipynb_checkpoints/pyeql_tutorial_database-checkpoint.ipynb

@@ -242,7 +242,7 @@
    ],
    "source": [
     "# a document with the formula \"Na[+1]\"\n",
-    "IonDB.query_one({\"formula\":'Na[+1]'})"
+    "IonDB.query_one({\"formula\": \"Na[+1]\"})"
    ]
   },
   {
@@ -277,7 +277,7 @@
    ],
    "source": [
     "# a document with the formula \"Na[+1]\", where we only want the formula, charge, and molecular_weight\n",
-    "IonDB.query_one({\"formula\":'Na[+1]'}, [\"formula\",\"charge\",\"molecular_weight\"])"
+    "IonDB.query_one({\"formula\": \"Na[+1]\"}, [\"formula\", \"charge\", \"molecular_weight\"])"
    ]
   },
   {
@@ -302,7 +302,7 @@
    ],
    "source": [
     "# a document with the charge -1, where we only want the formula, charge, and molecular_weight\n",
-    "IonDB.query_one({\"charge\":-1}, [\"formula\",\"charge\",\"molecular_weight\"])"
+    "IonDB.query_one({\"charge\": -1}, [\"formula\", \"charge\", \"molecular_weight\"])"
    ]
   },
   {
@@ -321,7 +321,7 @@
    "outputs": [],
    "source": [
     "# a document with the charge -1, where we only want the formula, charge, and molecular_weight\n",
-    "IonDB.query_one({\"charge\":\"-1\"}, [\"formula\",\"charge\",\"molecular_weight\"])"
+    "IonDB.query_one({\"charge\": \"-1\"}, [\"formula\", \"charge\", \"molecular_weight\"])"
    ]
   },
   {
@@ -405,6 +405,7 @@
    "source": [
     "# pint Quantity\n",
     "from pyEQL import ureg\n",
+    "\n",
     "print(ureg.Quantity(\"2.27 Å\").magnitude)"
    ]
   },
@@ -437,7 +438,7 @@
    ],
    "source": [
     "# all documents with a charge of +2, returning only the formulas\n",
-    "IonDB.query({\"charge\":2}, [\"formula\",\"molecular_weight\"])"
+    "IonDB.query({\"charge\": 2}, [\"formula\", \"molecular_weight\"])"
    ]
   },
   {
@@ -577,7 +578,7 @@
    ],
    "source": [
     "# using list()\n",
-    "list(IonDB.query({\"charge\":2}, [\"formula\",\"molecular_weight\"]))"
+    "list(IonDB.query({\"charge\": 2}, [\"formula\", \"molecular_weight\"]))"
    ]
   },
   {
@@ -709,7 +710,7 @@
    ],
    "source": [
     "# using a comprehension\n",
-    "[doc for doc in IonDB.query({\"charge\":2}, [\"formula\",\"molecular_weight\"])]"
+    "[doc for doc in IonDB.query({\"charge\": 2}, [\"formula\", \"molecular_weight\"])]"
    ]
   },
   {
@@ -810,10 +811,7 @@
    ],
    "source": [
     "# all alkali cations\n",
-    "IonDB.count({\"formula\":\n",
-    "             {\"$in\": [\"Li[+1]\", \"Na[+1]\", \"K[+1]\", \"Rb[+1]\", \"Cs[+1]\"]}\n",
-    "            }\n",
-    "            )"
+    "IonDB.count({\"formula\": {\"$in\": [\"Li[+1]\", \"Na[+1]\", \"K[+1]\", \"Rb[+1]\", \"Cs[+1]\"]}})"
    ]
   },
   {
@@ -845,10 +843,7 @@
    ],
    "source": [
     "# all solutes with a charge less than 0\n",
-    "IonDB.count({\"charge\":\n",
-    "             {\"$lt\": 0}\n",
-    "            }\n",
-    "            )"
+    "IonDB.count({\"charge\": {\"$lt\": 0}})"
    ]
   },
   {
@@ -870,10 +865,7 @@
    ],
    "source": [
     "# all solutes with a charge greater than or equal to 1\n",
-    "IonDB.count({\"charge\":\n",
-    "             {\"$gte\": 1}\n",
-    "            }\n",
-    "            )"
+    "IonDB.count({\"charge\": {\"$gte\": 1}})"
    ]
   },
   {
@@ -1250,7 +1242,7 @@
    ],
    "source": [
     "# list of all unique `formula`\n",
-    "IonDB.distinct('formula')"
+    "IonDB.distinct(\"formula\")"
    ]
   }
  ],