Cleanup, python upgrade

.github/workflows/tests.yml

@@ -2,12 +2,12 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 env:
-  MAIN_PYTHON_VERSION: "3.13"
+  MAIN_PYTHON_VERSION: "3.14"
 
 jobs:
   # Build and test
@@ -16,30 +16,29 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.9"
-          - "3.10"
           - "3.11"
           - "3.12"
           - "3.13"
+          - "3.14"
     steps:
-    - uses: actions/checkout@v4
-    - name: Install uv and set the python version
-      uses: astral-sh/setup-uv@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install the project
-      run: uv sync --all-extras --dev
-    - name: Run tests
-      run: uv run pytest
-    - name: Run Lint on one python
-      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
-      run: uv run ruff check
-    - name: Run Pytest with coverage
-      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
-      run: |
-        uv run pytest --cov=pgdtools --cov-report xml
-    - name: Upload coverage reports to Codecov
-      if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION && github.repository_owner == 'NASA-Planetary-Science' }}
-      uses: codecov/codecov-action@v3
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      - uses: actions/checkout@v4
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install the project
+        run: uv sync --all-extras --dev
+      - name: Run tests
+        run: uv run pytest
+      - name: Run Lint on one python
+        if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
+        run: uv run ruff check
+      - name: Run Pytest with coverage
+        if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
+        run: |
+          uv run pytest --cov=pgdtools --cov-report xml
+      - name: Upload coverage reports to Codecov
+        if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION && github.repository_owner == 'NASA-Planetary-Science' }}
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.python-version

@@ -1 +1 @@
-3.13
+3.14

README.md

@@ -3,12 +3,10 @@
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/NASA-Planetary-Science/pgdtools/blob/main/LICENSE)
 [![tests](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/tests.yml/badge.svg)](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/NASA-Planetary-Science/pgdtools/branch/main/graph/badge.svg?token=N0NNVEI8CX)](https://codecov.io/gh/NASA-Planetary-Science/pgdtools)
-[![Rye](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/rye/main/artwork/badge.json)](https://rye.astral.sh)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)
 
 # Presolar grain database tools (pgdTools)
 
-
 This package provides a set of tools to
 easily access and interface with the presolar grain database.
 This package allows users to manage which database(s) they want to use

docs/api/pgdtools.md

@@ -5,6 +5,7 @@ You can either load this class either by importing and defining it:
 
 ```python
 from pgdtools import PresolarGrains
+
 pgd = PresolarGrains()
 ```
 

docs/maintainer/db_addition.md

@@ -56,7 +56,9 @@ from pathlib import Path
 
 import pgdtools.maintainer as mt
 
-excel_file = Path("PGD_SiC_2023-07-22.xlsx", quiet=True)  # assuming the file is in the current directory
+excel_file = Path(
+    "PGD_SiC_2023-07-22.xlsx", quiet=True
+)  # assuming the file is in the current directory
 mt.append_reference_json(excel_file)
 ```
 

docs/users/db.md

@@ -54,6 +54,7 @@ Simply updating to the latest version of the database can be done using the foll
 
 ```python
 from pgdtools import db
+
 db.update()
 ```
 
@@ -76,6 +77,7 @@ To display the currently used database, use the following command:
 
 ```python
 from pgdtools import db
+
 db.current()
 ```
 
@@ -106,6 +108,7 @@ To set the current database use the following command:
 
 ```python
 from pgdtools import db
+
 doi = "10.5281/zenodo.8187446"
 db.set_current("sic", "DOI", doi)
 ```

docs/users/install.md

@@ -27,6 +27,7 @@ Alternatively, you can run the following commands inside your python console:
 
 ```python
 from pgdtools import db
+
 db.update()
 ```
 

docs/users/pgd.md

@@ -3,6 +3,7 @@ There are two ways to get the full database:
 
 ```python
 from pgdtools import PresolarGrains
+
 pgd = PresolarGrains()
 ```
 

examples/ruthenium_example.ipynb

@@ -29,11 +29,11 @@
     }
    ],
    "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "from iniabu import (\n",
     "    inimf,\n",
     ")  # iniabu module with abundances as mass fractions - for models!\n",
-    "import matplotlib.pyplot as plt\n",
-    "import numpy as np\n",
     "\n",
     "import pgdtools\n",
     "\n",

examples/silicon_example.py

@@ -1,8 +1,8 @@
 """For Benoit: Compare some Si isotope ratios."""
 
-from iniabu import inimf  # import as mass_fraction values right away
 import matplotlib.pyplot as plt
 import numpy as np
+from iniabu import inimf  # import as mass_fraction values right away
 
 import pgdtools
 
@@ -65,8 +65,8 @@
 ax.set_ylim(ylim)
 
 # labels for axes
-ax.set_xlabel("$\delta^{30}$Si$_{28}$   (‰)")
-ax.set_ylabel("$\delta^{29}$Si$_{28}$   (‰)")
+ax.set_xlabel(r"$\delta^{30}$Si$_{28}$   (‰)")
+ax.set_ylabel(r"$\delta^{29}$Si$_{28}$   (‰)")
 ax.legend()
 
 # aspect and layout

examples/titanium_example.py

@@ -1,8 +1,8 @@
 """For Benoit: Compare some Ti isotope ratios."""
 
-from iniabu import inimf  # import as mass_fraction values right away
 import matplotlib.pyplot as plt
 import numpy as np
+from iniabu import inimf  # import as mass_fraction values right away
 
 import pgdtools
 
@@ -79,14 +79,14 @@
     a.set_ylim(ylim)
 
     # labels for axes
-    a.set_xlabel("$\delta^{46}$Ti$_{48}$   (‰)")
+    a.set_xlabel(r"$\delta^{46}$Ti$_{48}$   (‰)")
 
     # aspect and layout
     a.set_aspect("equal")
 
 # y label
-ax[0].set_ylabel("$\delta^{47}$Ti$_{48}$   (‰)")
-ax[1].set_ylabel("$\delta^{49}$Ti$_{48}$   (‰)")
+ax[0].set_ylabel(r"$\delta^{47}$Ti$_{48}$   (‰)")
+ax[1].set_ylabel(r"$\delta^{49}$Ti$_{48}$   (‰)")
 
 fig.tight_layout()
 

pyproject.toml

@@ -3,36 +3,33 @@ name = "pgdtools"
 version = "0.2.0"
 description = "Read and interact with the presolar grain database with python."
 authors = [
-    { name = "Reto Trappitsch", email = "reto@galactic-forensics.space" }
+  { name = "Reto Trappitsch", email = "reto@galactic-forensics.space" },
 ]
 dependencies = [
-    "iniabu>=1.1.2",
-    "matplotlib>=3.7.4",
-    "numpy>=1.26.4",
-    "scipy>=1.12.0",
-    "pandas>=2.2.0",
-    "requests>=2.31.0",
+  "iniabu>=1.1.2",
+  "matplotlib>=3.7.4",
+  "numpy>=1.26.4",
+  "scipy>=1.12.0",
+  "pandas>=2.2.0",
+  "requests>=2.31.0",
 ]
 readme = "README.md"
-requires-python = ">= 3.9"
+requires-python = ">= 3.11"
 license = { text = "MIT" }
 
 [project.urls]
 Source = "https://github.com/galactic-forensics/pgdtools"
 Documentation = "https://pgdtools.readthedocs.io"
 
 [project.optional-dependencies]
-maintainer = [
-    "bibtexparser>=1.4.1",
-    "openpyxl>=3.1.2",
-]
+maintainer = ["bibtexparser>=1.4.1", "openpyxl>=3.1.2"]
 docs = [
-    "mkdocs>=1.6.0",
-    "mkdocs-material>=9.5.25",
-    "mkdocs-jupyter>=0.24.8",
-    "notebook>=7.2.1",
-    "ceresfit>=0.3.1",
-    "mkdocstrings[python]>=0.25.1",
+  "mkdocs>=1.6.1",
+  "mkdocs-material>=9.7.7",
+  "mkdocs-jupyter>=0.26.3",
+  "notebook>=7.6.2",
+  "ceresfit>=0.3.1",
+  "mkdocstrings[python]>=0.26.3",
 ]
 
 [build-system]
@@ -42,13 +39,13 @@ build-backend = "hatchling.build"
 [tool.uv]
 managed = true
 dev-dependencies = [
-    "hypothesis>=6.98.2",
-    "pytest>=8.0.0",
-    "pytest-cov>=4.1.0",
-    "pytest-mock>=3.12.0",
-    "requests-mock>=1.11.0",
-    "ruff>=0.11.2",
-    "xdoctest>=1.1.5",
+  "hypothesis>=6.98.2",
+  "pytest>=8.0.0",
+  "pytest-cov>=4.1.0",
+  "pytest-mock>=3.12.0",
+  "requests-mock>=1.11.0",
+  "ruff>=0.16",
+  "xdoctest>=1.1.5",
 ]
 
 [tool.hatch.metadata]
@@ -58,5 +55,8 @@ allow-direct-references = true
 packages = ["src/pgdtools"]
 
 [tool.pytest]
-testpaths = "tests"
-addopts = "--cov=pgdtools -v"
+testpaths = ["tests"]
+addopts = ["--cov=pgdtools", "-v"]
+
+[tool.ruff.lint]
+ignore = ["DTZ007"] # ignore timezone missing errors

src/pgdtools/__init__.py

@@ -11,6 +11,6 @@
     "classify_sic_grain",
     "data",
     "db",
-    "pgd",
     "maintainer",
+    "pgd",
 ]