refactor: pyproject.toml migration + ruff lint clean-up

.github/workflows/tests.yml

@@ -5,27 +5,24 @@ on: [pull_request, push]
 jobs:
   test:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python: ['3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python }}
-
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1.10'
-
-      - uses: julia-actions/cache@v2
+          environment-file: environment.yml
+          auto-activate-base: false
+          miniforge-version: latest
+          use-mamba: true
 
       - name: Install MAGEMin_C
-        run: julia -e 'using Pkg; Pkg.add("MAGEMin_C")'
+        shell: bash -l {0}
+        run: phasetools-julia-setup --install
 
-      - name: Install phasetools
-        run: python -m pip install -e .
+      - name: Verify environment
+        shell: bash -l {0}
+        run: phasetools-julia-setup --check
 
       - name: Run tests
+        shell: bash -l {0}
         run: python -m unittest discover tests -v

AGENTS.md

@@ -2,10 +2,19 @@
 
 ## Quick start
 
+**Conda / mamba (Linux & CI):**
+```bash
+mamba env create -f environment.yml
+conda activate phasetools
+phasetools-julia-setup --install
+phasetools-julia-setup --check
+```
+
+**pip + juliaup (cross-platform, incl. macOS):**
 ```bash
 python -m pip install -e .
-phasetools-julia-setup --check    # verify Julia + MAGEMin_C
 phasetools-julia-setup --install  # install MAGEMin_C in Julia
+phasetools-julia-setup --check    # verify Julia + MAGEMin_C
 python3 -m unittest discover tests   # run all tests (mock-based, no Julia needed)
 ```
 
@@ -282,9 +291,10 @@ The `ox.count("O")` bug undercounts oxygen, inflating the6-O scale factor by ~60
 - Files: `test_redox_logic.py`, `test_site_occupancy.py`, `test_fe_basis.py`, `test_fractionation.py`, `test_iron_oxide_conversions.py`, `test_solvus_instances.py`, `test_lmo_fix.py`.
 - New public functions must be documented in the **directory's README.md** (e.g., `calculators/README.md`, `core/README.md`) **and** the package structure above must be updated.
 
-## Requirements (from `setup.py`)
+## Requirements (from `pyproject.toml`)
 
 `pandas`, `numpy`, `matplotlib`, `scipy`, `molmass`, `juliacall`. Python ≥ 3.10.
+Extras: `[jupyter]` (jupyterlab, ipykernel, nbconvert), `[dev]` (ruff).
 
 ## Tutorials
 

README.md

@@ -25,24 +25,29 @@
 
 ## 📦 Installation
 
-### 1. Python Package
-Install `phasetools` in editable mode from the repository root:
+### 1. Conda / mamba (Linux & CI)
 
 ```bash
-python -m pip install -e .
+mamba env create -f environment.yml
+conda activate phasetools
+phasetools-julia-setup --install
+phasetools-julia-setup --check
 ```
 
-### 2. Julia Environment Setup
-`phasetools` requires Julia and the `MAGEMin_C` package. Use the built-in helper to check your environment:
+*Note: On macOS (especially Apple Silicon), conda-forge's `julia` package is unavailable — use the pip + juliaup path below instead.*
+
+### 2. pip + juliaup (cross-platform, incl. macOS)
 
 ```bash
+python -m pip install -e .
 phasetools-julia-setup --check
+phasetools-julia-setup --install
 ```
 
-If `MAGEMin_C` is missing, install it automatically:
+To also install Jupyter (for tutorials) and dev tooling (ruff):
 
 ```bash
-phasetools-julia-setup --install
+python -m pip install -e ".[jupyter,dev]"
 ```
 
 *Note: If Julia is not installed on your system, please download it from [julialang.org](https://julialang.org/downloads/).*

Tutorials/Garnet/1-Functionality_overview.ipynb

@@ -26,9 +26,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from phasetools import MAGEMinGarnetCalculator\n",
-    "import juliacall\n",
-    "import matplotlib.pyplot as plt"
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "from phasetools import MAGEMinGarnetCalculator"
    ]
   },
   {
@@ -207,6 +207,7 @@
    "outputs": [],
    "source": [
     "from phasetools.utils import create_PTt_path\n",
+    "\n",
     "P = [5., 6., 7., 8., 9., 10.]  # kbar\n",
     "T = [500., 600., 700., 800., 900., 1000.]  # °C\n",
     "t = [1., 2., 3., 4., 5., 6.]  # Myr\n",
@@ -290,7 +291,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from juliacall import Main as jl, convert as jlconvert\n",
+    "from juliacall import Main as jl\n",
+    "from juliacall import convert as jlconvert\n",
+    "\n",
     "rm_j = jlconvert(jl.Vector[jl.String], ['chl'])\n",
     "rmp_MM = MAGEMin_C.remove_phases(rm_j, 'mp')"
    ]

Tutorials/Garnet/2-Overlapping_isopleths.ipynb

@@ -28,15 +28,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pandas as pd\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "from phasetools import PhasePTEstimator\n",
-    "from phasetools.utils import *\n",
-    "import phasetools\n",
     "import os\n",
     "\n",
-    "from juliacall import Main as jl, convert as jlconvert"
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "\n",
+    "from phasetools import PhasePTEstimator\n",
+    "from phasetools.utils import *"
    ]
   },
   {
@@ -122,6 +121,7 @@
    "outputs": [],
    "source": [
     "from phasetools import MAGEMinGarnetCalculator\n",
+    "\n",
     "garnet_calculator = MAGEMinGarnetCalculator(db=db, dataset=636)\n",
     "garnet_calculator.setup_bulk_composition(Xoxides, X, sys_in=sys_in)\n",
     "\n",

Tutorials/Garnet/3-Garnet_cpx_thermometry.ipynb

@@ -52,13 +52,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
-    "from phasetools import MAGEMinPTGridCalculator\n",
-    "\n",
-    "from phasetools import MAGEMin_C\n",
-    "from juliacall import Main as jl, convert as jlconvert"
+    "from phasetools import MAGEMinPTGridCalculator"
    ]
   },
   {
@@ -569,7 +566,7 @@
    "source": [
     "from phasetools.core.phase_properties import get_phase_fe_split\n",
     "\n",
-    "for i in range(0, 5):\n",
+    "for i in range(5):\n",
     "      i0 = int(np.flatnonzero(valid)[i])  # first valid grid point\n",
     "      o0 = out[i0]\n",
     "      cpx_split = get_phase_fe_split(o0, cpx)\n",

Tutorials/General/1-Getting_started.ipynb

@@ -24,10 +24,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "import juliacall\n",
-    "from juliacall import Main as jl, convert as jlconvert\n",
-    "import phasetools\n",
+    "from juliacall import Main as jl\n",
+    "from juliacall import convert as jlconvert\n",
+    "\n",
     "from phasetools import MAGEMin_C"
    ]
   },

Tutorials/General/2-Determining_fractions.ipynb

@@ -28,8 +28,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import juliacall\n",
-    "from juliacall import Main as jl, convert as jlconvert\n",
+    "\n",
     "import phasetools\n",
     "from phasetools import MAGEMin_C"
    ]
@@ -103,6 +102,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "plt.plot(temp, liq_frac_vals, c='k', ls=':')\n",
     "plt.scatter(liquidus_T, 1, marker='x', c='red', label='Liquidus')\n",
     "plt.scatter(solidus_T, 0, marker='x', c='green', label='Solidus')\n",
@@ -192,6 +192,7 @@
    "source": [
     "from scipy.optimize import root_scalar\n",
     "\n",
+    "\n",
     "def melt_fraction(T):\n",
     "    out = MAGEMin_C.single_point_minimization(P, T, data)\n",
     "    return phasetools.phase_frac(phase=\"liq\", MAGEMinOutput=out, sys_in='mol')\n",
@@ -241,6 +242,7 @@
    "outputs": [],
    "source": [
     "from phasetools import PhaseFunctions\n",
+    "\n",
     "phaseFunctions = PhaseFunctions(db=db, dataset=636)\n",
     "phaseFunctions.setup_bulk_composition(list(out.oxides), list(out.bulk), sys_in='mol')"
    ]

Tutorials/General/3-Lunar_Magma_Ocean.ipynb

@@ -24,10 +24,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "from phasetools.models.magma_ocean import MagmaOcean\n",
-    "import sys"
+    "\n",
+    "from phasetools.models.magma_ocean import MagmaOcean"
    ]
   },
   {

environment.yml

@@ -0,0 +1,10 @@
+name: phasetools
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - python=3.11
+  - julia
+  - pip
+  - pip:
+      - -e ".[jupyter,dev]"

pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phasetools"
+version = "0.1.0"
+description = "A python package to perform MAGEMin calculations in python"
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.10"
+authors = [{ name = "Ben Knight", email = "ben.knight@curtin.edu.au" }]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Scientific/Engineering",
+    "Natural Language :: English",
+]
+dependencies = [
+    "pandas>=1.0.0",
+    "numpy>=1.18.0",
+    "matplotlib>=3.0.0",
+    "scipy>=1.4.0",
+    "molmass>=2024.0.0",
+    "juliacall>=0.9",
+]
+
+[project.optional-dependencies]
+jupyter = ["jupyterlab", "ipykernel", "nbconvert"]
+dev = ["ruff"]
+
+[project.scripts]
+phasetools-julia-setup = "phasetools.julia_setup:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+extend-exclude = ["Tutorials"]