[MNT] Fix dependency issues and CI runners: numpy2, optuna, `requ…

…ests`, MacOS MPS

Fixes #1594, fixes #1595, fixes #1596

Added or moved some dependencies to core dependency set.

Fixed some `numpy2` and `optuna-integrations` problems.

`requests` replaced by `urllib.request.urlretrieve`.

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macOS-latest] # add windows-2019 when poetry allows installation with `-f` flag
+        os: [ubuntu-latest, macos-13] # add windows-2019 when poetry allows installation with `-f` flag
         python-version: ["3.8", "3.9", "3.10"]
     defaults:
       run:
@@ -62,7 +62,7 @@ jobs:
         run: poetry run python -m pip install pip -U
 
       - name: Install dependencies
-        run: poetry install -E "github-actions graph mqf2"
+        run: poetry install -E "github-actions graph"
 
       # - name: Install pytorch geometric dependencies
       #   shell: bash

docs/requirements.txt

@@ -7,6 +7,7 @@ lightning >=2.0.0
 cloudpickle
 torch >=2.0,!=2.0.1
 optuna >=3.1.0
+optuna-integration
 scipy
 pandas >=1.3
 scikit-learn >1.2

pyproject.toml

@@ -58,15 +58,18 @@ python = ">=3.8,<3.11"
 torch = "^2.0.0,!=2.0.1"
 lightning = "^2.0.0"
 optuna = "^3.1.0"
+optuna-integration="*"
 scipy = "^1.8"
 pandas = ">=1.3.0,<=3.0.0"
+pyarrow = "*"
 scikit-learn = "^1.2"
 matplotlib = "*"
+tensorboard = "^2.12.1"
+cpflows = "^0.1.2"
 statsmodels = "*"
 
 pytest-github-actions-annotate-failures = { version = "*", optional = true }
 networkx = { version = "^3.0.0", optional = true }
-cpflows = { version = "^0.1.2", optional = true }
 fastapi = ">=0.80"
 pytorch-optimizer = "^2.5.1"
 
@@ -108,7 +111,6 @@ pandoc = "^2.3"
 [tool.poetry.extras] # extras
 github-actions = ["pytest-github-actions-annotate-failures"]
 graph = ["networkx"]
-mqf2 = ["cpflows"]
 
 [tool.poetry-dynamic-versioning]
 enable = true

pytorch_forecasting/data/examples.py

@@ -3,10 +3,10 @@
 """
 
 from pathlib import Path
+from urllib.request import urlretrieve
 
 import numpy as np
 import pandas as pd
-import requests
 
 BASE_URL = "https://github.com/jdb78/pytorch-forecasting/raw/master/examples/data/"
 
@@ -28,9 +28,7 @@ def _get_data_by_filename(fname: str) -> Path:
     # check if file exists - download if necessary
     if not full_fname.exists():
         url = BASE_URL + fname
-        download = requests.get(url, allow_redirects=True)
-        with open(full_fname, "wb") as file:
-            file.write(download.content)
+        urlretrieve(url, full_fname)
 
     return full_fname
 

pytorch_forecasting/models/base_model.py

@@ -18,7 +18,7 @@
 from lightning.pytorch.utilities.parsing import AttributeDict, get_init_args
 import matplotlib.pyplot as plt
 import numpy as np
-from numpy.lib.function_base import iterable
+from numpy import iterable
 import pandas as pd
 import pytorch_optimizer
 from pytorch_optimizer import Ranger21