feat: Adding initial implementation of AYO input conversion to EXOSIMS and updating to match the new yippy API

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
         platform: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v6

.pre-commit-config.yaml

@@ -4,14 +4,13 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: name-tests-test
+        args: [--pytest-test-first]
       - id: end-of-file-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.0
+    rev: v0.15.4
     hooks:
-      # Run the linter.
-      - id: ruff
-        args: [ --fix ]
-      # Run the formatter.
+      - id: ruff-check
+        args: [--fix]
       - id: ruff-format
   - repo: https://github.com/compilerla/conventional-pre-commit
     rev: v4.3.0

docs/tutorials/yieldplotlib_tutorial.ipynb

@@ -167,7 +167,7 @@
     "\n",
     "def read_markdown_table(filepath):\n",
     "    \"\"\"Parses our markdown table file into a Pandas DataFrame.\"\"\"\n",
-    "    with open(filepath, \"r\") as f:\n",
+    "    with open(filepath) as f:\n",
     "        lines = f.readlines()\n",
     "    clean_lines = [line for line in lines if \"|\" in line and \"---\" not in line]\n",
     "    clean_data = \"\".join(clean_lines)\n",

noxfile.py

@@ -3,7 +3,7 @@
 import nox
 
 
-@nox.session(venv_backend="uv", python=["3.10", "3.11", "3.12", "3.13"])
+@nox.session(venv_backend="uv", python=["3.11", "3.12", "3.13"])
 def tests(session):
     """Run the test suite with pytest."""
     # Install all test dependencies

pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
 ]
 license = { file = "LICENSE" }
 dynamic = ['readme', 'version']
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
   "Programming Language :: Python :: 3",
   "License :: OSI Approved :: MIT License",
@@ -69,7 +69,7 @@ test = ["nox", "pytest", "pytest-cov"]
 exclude = ["src/yieldplotlib/key_map.py"]
 
 [tool.ruff.lint]
-select = ["D", "E", "F", "I"]
+select = ["B", "D", "E", "F", "I", "UP", "RUF"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"

scripts/loader_test.py

@@ -15,7 +15,7 @@
 titles = ["EXOSIMS", "AYO"]
 fig, axs = plt.subplots(1, len(runs), figsize=(15, 5))
 y_range = (0.001, 200)
-for i, (run, title) in enumerate(zip(runs, titles)):
+for i, (run, title) in enumerate(zip(runs, titles, strict=True)):
     star_L = run.get("star_L")
     star_dist = run.get("star_dist")
     star_comp = run.get("star_comp")

src/yieldplotlib/__init__.py

@@ -1,23 +1,23 @@
 """yieldplotlib - A library for plotting yield data."""
 
 __all__ = [
+    "KEY_MAP",
     "__version__",
+    "calculate_axis_limits_and_ticks",
+    "compare",
     "fetch_ayo_data",
     "fetch_exosims_data",
     "fetch_yip_data",
-    "KEY_MAP",
-    "logger",
-    "calculate_axis_limits_and_ticks",
     "get_nice_number",
-    "subplots",
-    "compare",
+    "logger",
     "multi",
     "panel",
+    "subplots",
+    "xy_grid",
     "ypl_cmap",
     "ypl_colors",
     "ypl_cycler",
     "ypl_rainbow",
-    "xy_grid",
 ]
 
 from importlib.resources import as_file, files

src/yieldplotlib/core/__init__.py

@@ -1,12 +1,12 @@
 """Core module of yieldplotlib."""
 
 __all__ = [
-    "DirectoryNode",
     "CSVFile",
+    "DirectoryNode",
     "FileNode",
     "JSONFile",
-    "PickleFile",
     "Node",
+    "PickleFile",
 ]
 
 from .directory_node import DirectoryNode

src/yieldplotlib/core/file_nodes.py

@@ -118,7 +118,7 @@ def __init__(self, file_path: Path):
 
     def load(self):
         """Load the JSON file into memory."""
-        with open(self.file_path, "r") as f:
+        with open(self.file_path) as f:
             self.data = json.load(f)
 
     def _get(self, key: str, **kwargs):
@@ -133,7 +133,7 @@ def json_recur(data, target_key):
                             values[data["name"]] = data.get(key, None)
                         except KeyError:
                             values[data["instName"]] = data.get(key, None)
-                    elif isinstance(v, (dict, list)):
+                    elif isinstance(v, dict | list):
                         json_recur(v, target_key)
             elif isinstance(data, list):
                 for item in data:

src/yieldplotlib/core/single_inputs.py

@@ -13,14 +13,14 @@ class SingleInput(dict):
 
     def __init__(self, *args, **kwargs):
         """Initialise the SingleInput class."""
-        super(SingleInput, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def apply(self, key, func):
         """Apply a function to all values of a given key."""
         try:
             self[key] = func(self.get(key))
-        except TypeError:
-            raise TypeError(f"Could not apply function to {key}")
+        except TypeError as err:
+            raise TypeError(f"Could not apply function to {key}") from err
 
     def check_units(self, key, desired_unit):
         """Checks that all values of key have the appropriate desired unit."""
@@ -30,15 +30,13 @@ def check_units(self, key, desired_unit):
                 for value in iterator:
                     if value.unit != desired_unit:
                         raise AssertionError(
-                            (
-                                f"Value {value} for {key} does not have desired "
-                                f"unit {desired_unit}"
-                            )
+                            f"Value {value} for {key} does not have desired "
+                            f"unit {desired_unit}"
                         )
-            except AttributeError:
+            except AttributeError as err:
                 raise AttributeError(
                     f"{key} does not have a value of type astropy.units.Quantity"
-                )
+                ) from err
 
         except TypeError:
             try:
@@ -47,10 +45,10 @@ def check_units(self, key, desired_unit):
                         f"Value {self.get(key)} for {key} does not have desired "
                         f"unit {desired_unit}"
                     )
-            except AttributeError:
+            except AttributeError as err:
                 raise AttributeError(
                     f"{key} does not have a value of type astropy.units.Quantity"
-                )
+                ) from err
 
         finally:
             logger.info("All unit checks passed.")

src/yieldplotlib/generate_docs.py

@@ -24,7 +24,6 @@
 import io
 import os
 import sys
-from typing import Optional
 
 import pandas as pd
 from google.oauth2 import service_account
@@ -53,7 +52,7 @@ def parse_args():
 
 
 def download_from_google_sheets(
-    sheet_id: str, credentials_json_path: Optional[str] = None
+    sheet_id: str, credentials_json_path: str | None = None
 ) -> str:
     """Download a CSV file from Google Sheets.
 
@@ -128,7 +127,7 @@ def read_csv_file(file_path: str) -> str:
         CSV content as a string.
     """
     try:
-        with open(file_path, "r", encoding="utf-8") as f:
+        with open(file_path, encoding="utf-8") as f:
             return f.read()
     except Exception as e:
         print(f"Error reading CSV file: {e}")

src/yieldplotlib/generate_key_map.py

@@ -78,11 +78,9 @@ def download_from_google_sheets(sheet_id, output_path, credentials_json_path=Non
         from googleapiclient.discovery import build
     except ImportError:
         print(
-            (
-                "Error: Google API libraries not installed. "
-                "Run: pip install google-auth google-auth-oauthlib"
-                " google-api-python-client"
-            )
+            "Error: Google API libraries not installed. "
+            "Run: pip install google-auth google-auth-oauthlib"
+            " google-api-python-client"
         )
         sys.exit(1)
 
@@ -91,7 +89,7 @@ def download_from_google_sheets(sheet_id, output_path, credentials_json_path=Non
     # First check for credentials file path
     if credentials_json_path:
         try:
-            with open(credentials_json_path, "r") as f:
+            with open(credentials_json_path) as f:
                 credentials_info = json.load(f)
             credentials = service_account.Credentials.from_service_account_info(
                 credentials_info,
@@ -106,10 +104,8 @@ def download_from_google_sheets(sheet_id, output_path, credentials_json_path=Non
         credentials_b64 = os.environ.get("GOOGLE_CREDENTIALS_B64")
         if not credentials_b64:
             print(
-                (
-                    "Error: No credentials provided. Either set GOOGLE_CREDENTIALS_B64"
-                    " or provide --credentials"
-                )
+                "Error: No credentials provided. Either set GOOGLE_CREDENTIALS_B64"
+                " or provide --credentials"
             )
             sys.exit(1)
 
@@ -206,10 +202,8 @@ def parse_csv(input_csv):
                     key = exo_name
                 else:
                     print(
-                        (
-                            f"Warning: Row {row_num} has no 'yieldplotlib name'"
-                            " and no clear library names. Skipping."
-                        )
+                        f"Warning: Row {row_num} has no 'yieldplotlib name'"
+                        " and no clear library names. Skipping."
                     )
                     continue  # Skip rows that don't meet criteria
 
@@ -255,10 +249,8 @@ def parse_csv(input_csv):
             else:
                 # If neither library has complete info, skip the row
                 print(
-                    (
-                        f"Warning: Row {row_num} does not have complete "
-                        "information for either library. Skipping."
-                    )
+                    f"Warning: Row {row_num} does not have complete "
+                    "information for either library. Skipping."
                 )
                 continue
 
@@ -303,10 +295,8 @@ def add_to_key_map(entry, context):
 
         if key in key_map:
             print(
-                (
-                    f"Warning: Duplicate key '{key}' found in {context}."
-                    " Overwriting previous entry."
-                )
+                f"Warning: Duplicate key '{key}' found in {context}."
+                " Overwriting previous entry."
             )
 
         key_map[key] = map_entry

src/yieldplotlib/load/__init__.py

@@ -2,11 +2,11 @@
 
 __all__ = [
     "AYODirectory",
-    "YIPDirectory",
     "DRMDirectory",
     "EXOSIMSCSVDirectory",
     "EXOSIMSDirectory",
     "SPCDirectory",
+    "YIPDirectory",
 ]
 
 from .ayo_directory import AYODirectory