Merge pull request #384 from Living-with-machines/dev_dependencies

Update dependencies

.github/workflows/dependapot-review.yml

@@ -0,0 +1,14 @@
+name: 'Dependency Review'
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout Repository'
+        uses: actions/checkout@v4
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@v4

.github/workflows/mr_ci.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.8]
+        python-version: [3.9, 3.12]
       fail-fast: false
 
     runs-on: ${{ matrix.os }}

.github/workflows/mr_pip_ci.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.8]
+        python-version: [3.9, 3.12]
       fail-fast: false
 
     runs-on: ${{ matrix.os }}

.github/workflows/publish-to-pypi.yml

@@ -16,10 +16,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/publish-to-test-pypi.yml

@@ -20,10 +20,10 @@ jobs:
     - uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         python3 -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
     rev: "23.9.1"
     hooks:
       - id: black-jupyter
-        language_version: python3.8
+        language_version: python3.9
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.0.290"

.ruff.toml

@@ -16,5 +16,5 @@ unfixable = [
 flake8-unused-arguments.ignore-variadic-names = true
 isort.required-imports = ["from __future__ import annotations"]
 
-# Assume Python 3.8
-target-version = "py38"
+# Assume Python 3.9
+target-version = "py39"

CHANGELOG.md

@@ -0,0 +1,18 @@
+# Changelog
+
+# Python versions
+
+The following table shows which versions of MapReader are compatible with which versions of python:
+
++----------+------------+
+| Python   | MapReader  |
++==========+============+
+| 3.9+     | v1.2.0     |
+| 3.8-3.11 | <= v.1.1.5 |
++----------+------------+
+
+
+## v1.2.0 (2024-04-08)
+
+- Remove support for python 3.8
+- Update dependencies and add cartopy as required dependency

docs/source/Install.rst

@@ -17,7 +17,7 @@ You should choose one method within each step and follow the instructions for th
 Step 1: Set up a virtual python environment
 ----------------------------------------------
 
-MapReader supports python versions 3.8 to 3.10.
+The most recent version of MapReader supports python versions 3.9+.
 
 Method 1: Using conda (recommended)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -31,9 +31,9 @@ Once you have installed either Ananconda or miniconda, open your terminal and us
 
    .. code-block:: bash
 
-      conda create -n mapreader python=3.8
+      conda create -n mapreader
 
-   This will create a conda enviroment which uses python version 3.8.
+   This will create a conda enviroment for you to install MapReader and its dependencies into.
 
 -  Activate your conda environment:
 
@@ -54,7 +54,7 @@ For example, if you would like to use venv, open your terminal and use the follo
 
       python3 --version
 
-   If this returns a version below 3.7, you will need download an updated python version.
+   If this returns a version below 3.9, you will need download an updated python version.
    You can do this by downloading from `here <https://www.python.org/downloads/>`__ (make sure you download the right one for your operating system).
 
    You should then run the above command again to check your python version has updated.
@@ -74,16 +74,6 @@ For example, if you would like to use venv, open your terminal and use the follo
 Step 2: Install MapReader
 --------------------------
 
-Cartopy
-~~~~~~~~
-
-`Cartopy <https://scitools.org.uk/cartopy/docs/latest/>`__ is used by MapReader's download subpackage to plot maps and geospatial data.
-It is not essential to the functioning of MapReader and so is not listed as a required dependancy.
-
-If you would like to use MapReader's plotting functions, you will need to ensure you have installed the `required dependencies <https://scitools.org.uk/cartopy/docs/latest/installing.html#required-dependencies>`__ for cartopy.
-
-Then, to install cartopy with your mapreader installation, you should install mapreader with the `geo` optional dependencies (see notes below).
-
 Method 1: Install from `PyPI <https://pypi.org/project/mapreader/>`_
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -97,8 +87,6 @@ This is probably the easiest way to install MapReader.
       pip install mapreader
 
 
-.. note:: Replace ``pip install mapreader`` with ``pip install "mapreader[geo]"`` if you would like to install cartopy with your mapreader installation.
-
 Method 2: Install from source
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -121,8 +109,6 @@ This method will create a ``MapReader`` directory on your machine which will con
       pip install -v -e .
 
 
-.. note:: Replace ``pip install -v -e .`` with ``pip install -v -e ".[geo]"`` if you would like to install cartopy with your mapreader installation.
-
 ..
    Method 3: Install via conda (**EXPERIMENTAL**)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

mapreader/annotate/utils.py

@@ -95,7 +95,7 @@ def prepare_data(
             ).values
             if random_state in ["random"]:
                 df = df.groupby("pixel_groups").sample(
-                    n=10, random_state=random.randint(0, 1e6)
+                    n=10, random_state=random.randint(0, int(1e6))
                 )
             else:
                 df = df.groupby("pixel_groups").sample(n=10, random_state=random_state)

mapreader/classify/classifier.py

@@ -7,8 +7,9 @@
 import socket
 import sys
 import time
+from collections.abc import Hashable, Iterable
 from datetime import datetime
-from typing import Any, Hashable, Iterable
+from typing import Any
 
 import joblib
 import matplotlib.pyplot as plt
@@ -167,7 +168,7 @@ def __init__(
             if not os.path.exists("./tmp_checkpoints"):
                 os.makedirs("./tmp_checkpoints")
             self.tmp_save_filename = (
-                f"./tmp_checkpoints/tmp_{random.randint(0, 1e10)}_checkpoint.pkl"
+                f"./tmp_checkpoints/tmp_{random.randint(0, int(1e10))}_checkpoint.pkl"
             )
 
             # add colors for printing/logging

setup.py

@@ -26,7 +26,7 @@
     packages=setuptools.find_packages(),
     include_package_data=True,
     platforms="OS Independent",
-    python_requires=">=3.8, <3.11",
+    python_requires=">=3.9",
     install_requires=[
         "matplotlib>=3.5.0,<4.0.0",
         "numpy>=1.21.5,<2.0.0",
@@ -38,14 +38,13 @@
         "nest-asyncio>=1.5.1,<2.0.0",
         "scikit-image>=0.18.3",
         "scikit-learn>=1.0.1,<2.0.0",
-        "torch>=1.10.0,<2.0.0",
-        "torchvision>=0.11.1,<0.12.1",
+        "torch>=1.10.0",
+        "torchvision>=0.11.1,<0.17.3",
         "jupyter>=1.0.0,<2.0.0",
         "ipykernel>=6.5.1,<7.0.0",
         "ipywidgets>=8.0.0,<9.0.0",
         "ipyannotate==0.1.0-beta.0",
         "Cython>=0.29.24,<0.30.0",
-        # "proj>=0.2.0,<0.3.0",
         "PyYAML>=6.0,<7.0",
         "tensorboard>=2.7.0,<3.0.0",
         "parhugin>=0.0.3,<0.0.4",
@@ -58,20 +57,18 @@
         "openpyxl<4.0.0",
         "geopandas<1.0.0",
         "pyogrio>=0.7.2",
+        "cartopy>=0.22.0",
     ],
     extras_require={
         "dev": [
-            "pytest<8.0.0",
-            "pytest-cov>=4.1.0,<5.0.0",
+            "pytest<9.0.0",
+            "pytest-cov>=4.1.0,<6.0.0",
             "timm<1.0.0",
             "transformers<5.0.0",
-            "black>=23.7.0,<24.0.0",
-            "flake8>=6.0.0,<7.0.0",
+            "black>=23.7.0,<25.0.0",
+            "flake8>=6.0.0,<8.0.0",
         ],
-        "geo": [
-            "cartopy>=0.20.0"
-        ],
-    },  
+    },
     classifiers=[
         "Development Status :: 3 - Alpha",
         "License :: OSI Approved :: MIT License",